diff --git a/.gitignore b/.gitignore deleted file mode 100644 index 5bd58c1..0000000 --- a/.gitignore +++ /dev/null @@ -1,39 +0,0 @@ - -.idea/workspace.xml - -.idea/vcs.xml - -.idea/python-matlab-bridge.iml - -.idea/modules.xml - -.idea/misc.xml - -.idea/encodings.xml - -.idea/.name - -.DS_Store - - -ADME.markdown - -*.pyc -*~ - -build - -# a nonce file to push this package to our local system. -dpush.sh - -# these are generated by ctags; ignore them -.tags -.mat_tags -.py_tags -rebuildTags.sh - -# binary file in matlab folder -/pymatbridge/matlab/messenger.* - -# caused py setup.py develop -pymatbridge.egg-info diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 72a4326..0000000 --- a/.travis.yml +++ /dev/null @@ -1,49 +0,0 @@ -language: python -deploy: - provider: pypi - user: arokem - password: - secure: AB7BnrkNOTQWXUNiaShedbIEBay+5JbulAxUHY4vEMdiI68bPLYOrIDxuT/lIfWrrgXUuicbJcWUxt6zpdUEQrEfYB6pNhrosZv4+R5HZu1FHY7EfOfsyHxb2wnezKuIEVXdevAmIg5rYNeTPcdl/CFm4xQGfdc4a3eyT5cJT58= - on: - tags: true - repo: arokem/python-matlab-bridge - # until this is fixed: https://github.com/travis-ci/travis-ci/issues/1675 - all_branches: true -env: - - CONDA="python=2.7 numpy=1.7" - - CONDA="python=3.3 numpy" - - CONDA="python=3.4 numpy" -before_install: - - sudo apt-add-repository -y ppa:octave/stable; - - sudo apt-get update; - - sudo apt-get install octave liboctave-dev default-jdk; - - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh; - - bash miniconda.sh -b -p $HOME/miniconda - - export PATH="$HOME/miniconda/bin:$PATH" - - hash -r - - conda config --set always_yes yes - - conda update conda - - conda info -a - - travis_retry conda create -n test $CONDA IPython pip nose pyzmq jsonschema - - source activate test - - if [[ $CONDA == python=3.3* ]]; then - pip install nbformat; - else - travis_retry conda install nbformat; - fi - - travis_retry pip install coveralls - -install: - - export USE_OCTAVE=True - - python setup.py install - -script: - # run coverage on py2.7, regular on others - - if [[ $CONDA == python=2.7* ]]; then - nosetests --exe -v --with-cov --cover-package pymatbridge; - else - nosetests --exe -v pymatbridge; - fi - -after_success: - - coveralls diff --git a/LICENSE b/LICENSE deleted file mode 100644 index d3632fc..0000000 --- a/LICENSE +++ /dev/null @@ -1,10 +0,0 @@ -Copyright (c) 2013. See "Contributors". MATLAB (R) is copyright of the Mathworks. - -All rights reserved. - -Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: - -- Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. - -Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/README.md b/README.md deleted file mode 100644 index 0619ff8..0000000 --- a/README.md +++ /dev/null @@ -1,248 +0,0 @@ -# Python-MATLAB(R) Bridge and IPython `matlab` magic - -[![Build Status](https://travis-ci.org/arokem/python-matlab-bridge.svg?branch=master)](https://travis-ci.org/arokem/python-matlab-bridge) -[![Coverage Status](https://coveralls.io/repos/arokem/python-matlab-bridge/badge.svg?branch=master)](https://coveralls.io/r/arokem/python-matlab-bridge?branch=master) -[![Latest Version](https://pypip.in/version/pymatbridge/badge.svg?style=flat)](https://pypi.python.org/pypi/pymatbridge/) -[![License](https://pypip.in/license/pymatbridge/badge.svg?style=flat)](https://pypi.python.org/pypi/pymatbridge/) -[![Join the chat at https://gitter.im/arokem/python-matlab-bridge](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/arokem/python-matlab-bridge?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) - -A python interface to call out to [Matlab(R)](http://mathworks.com). Original -implementation by [Max Jaderberg](http://www.maxjaderberg.com/). His original -repo of the project can be found [here]( -https://github.com/jaderberg/python-matlab-bridge), but please note that the -development of the two repositories has significantly diverged. - -This implementation also includes an [IPython](http://ipython.org) `matlab_magic` -extension, which provides a simple interface for weaving python and -Matlab code together (requires ipython > 0.13). - - -## Installation - -`pymatbridge` can be installed from [PyPI][1]: - -``` -$ pip install pymatbridge -``` - -If you intend to use the Matlab magic extension, you'll also need -[IPython](http://ipython.org/install.html). - -Finally, if you want to handle sparse arrays, you will need to install -[Scipy](http://scipy.org/). This can also be installed from PyPI, or using -distributions such as [Anaconda](https://store.continuum.io/cshop/anaconda/) or -[Enthought Canopy](https://store.enthought.com/downloads/) - - -## Usage - -To use the pymatbridge you need to connect your python interpreter to a Matlab -session. This is done in the following manner: - - from pymatbridge import Matlab - mlab = Matlab() - -This creates a matlab session class instance, into which you will be able to -inject code and variables, and query for results. By default, when you use -`start`, this will open whatever gets called when you type `matlab` -in your Terminal, but you can also specify the location of your Matlab -application when initializing your matlab session class: - - mlab = Matlab(executable='/Applications/MATLAB_R2011a.app/bin/matlab') - -You can then start the Matlab server, which will kick off your matlab session, -and create the connection between your Python interpreter and this session: - - mlab.start() - -which will return True once connected. - - results = mlab.run_code('a=1') - -Should now run that line of code and return a `results` dict into your Python -namespace. The `results` dict contains the following fields: - - {u'content': {u'code': u'a=1', - u'datadir': u'/private/tmp/MatlabData/', - u'figures': [], - u'stdout': u'\na =\n\n 1\n\n'}, - u'success': u'true'} - -In this case, the variable `a` is available on the Python side, by using -the `get_variable` method: - - mlab.get_variable('a') - -You can run any MATLAB functions contained within a .m file of the -same name. For example, to call the function jk in jk.m: - - %% MATLAB - function lol = jk(args) - arg1 = args.arg1; - arg2 = args.arg2; - lol = arg1 + arg2; - end - -you would call: - - res = mlab.run_func('path/to/jk.m', {'arg1': 3, 'arg2': 5}) - print(res['result']) - -This would print `8`. - -You can shut down the MATLAB server by calling: - - mlab.stop() - -Tip: you can execute MATLAB code at the beginning of each of your matlab -sessions by adding code to the `~/startup.m` file. - -### Octave support & caveats - -A `pymatbridge.Octave` class is provided with exactly the same interface -as `pymatbridge.Matlab`: - - from pymatbridge import Octave - octave = Octave() - -Rather than looking for `matlab` at the shell, this will look for `octave`. -As with `pymatbridge.Matlab`, you can override this by specifying the -`executable` keyword argument. - -Rather than `~/startup.m`, Octave looks for an `~/.octaverc` file for -commands to execute before every session. (This is a good place to manipulate -the runtime path, for example). - -Requires Version 3.8 or higher. Notice: Neither the MXE 3.8.1 nor the Cygwin 3.8.2 version is compatible on Windows. No Windows support will be available -until a working version of Octave 3.8+ with Java support is released. - - -### Matlab magic: - -The Matlab magic allows you to use pymatbridge in the context of the IPython -notebook format. - - %load_ext pymatbridge - -These lines will automatically start the matlab session for you. Then, you can -simply decorate a line/cell with the '%matlab' or '%%matlab' decorator and -write matlab code: - - %%matlab - a = linspace(0.01,6*pi,100); - plot(sin(a)) - grid on - hold on - plot(cos(a),'r') - -If `%load_ext pymatbridge` doesn't work for you use: -``` -import pymatbridge as pymat -pymat.load_ipython_extension(get_ipython(), matlab='/your_matlab_installation_dir/bin/matlab') -``` - -More examples are provided in the `examples` directory - -## Building the pymatbridge messenger from source - -The installation of `pymatbridge` includes a binary of a mex function to communicate between -Python and Matlab using the [0MQ](http://zeromq.org/) messaging library. This should work -without any need for compilation on most computers. However, in some cases, you might want -to build the pymatbridge messenger from source. To do so, you will need to follow the instructions below: - - -### Install zmq library -Please refer to the [official guide](http://zeromq.org/intro:get-the-software) on how to -build and install zmq. On Ubuntu, it is as simple as `sudo apt-get install libzmq3-dev`. -On Windows, suggest using the following method: -- Install [MSYS2](http://sourceforge.net/projects/msys2/) -- Run `$ pacman -S make` -- From the zmq source directory, run: `$ sh configure --prefix=$(pwd) --build=x86_64-w64-mingw32` -- Run `$ make`. - -After zmq is installed, make sure you can find the location where -libzmq is installed. The library extension name and default location on different systems -are listed below. - -| Platform | library name | Default locations | -| ------------- | ------------- | --------------------------------- | -| MacOS | libzmq.dylib | /usr/lib or /usr/local/lib | -| Linux | libzmq.so.3 | /usr/lib or /usr/local/lib | -| Windows | libzmq.dll | C:\Program Files\ZeroMQ 3.2.4\bin | - -If you specified a prefix when installing zmq, the library file should be located at the -same prefix location. - -The pymatbridge MEX extension needs to be able to locate the zmq library. If it's in a -standard location, you may not need to do anything; if not, there are two ways to -accomplish this: - -#### Using the dynamic loader path - -One option is to set an environment variable which will point the loader to the right -directory. - -On MacOS, you can do this by adding the following line to your .bash_profile (or similar -file for your shell): - - export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH: - -On Linux, add the following line to your .bash_profile (or similar file for your shell): - - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH: - -On Windows, add the install location of libzmq.dll to the PATH environment variable. -On Windows 7+, typing "environment variables" into the start menu will bring up the -apporpriate Control Panel links. - -#### Pointing the binary at the right place - -Another option is to modify the MEX binary to point to the right location. This is -preferable in that it doesn't change loader behavior for other libraries than just -the pymatbridge messenger. - -On MacOS, you can do this from the root of the pymatbridge code with: - - install_name_tool -change /usr/local/lib/libzmq.3.dylib /libzmq.3.dylib messenger/maci64/messenger.mexmaci64 - -On Linux, you can add it to the RPATH: - - patchelf --set-rpath messenger/mexa64/messenger.mexa64 - -### Install pyzmq -After step 1 is finished, please grab the latest version of -[pyzmq](http://zeromq.org/bindings:python) and follow the instructions on the official -page. Note that pymatbridge is developed with pyzmq 14.0.0 and older versions might not -be supported. If you have an old version of pyzmq, please update it. - -### Install pymatbridge -After the steps above are done, you can install pymatbridge. Download the zip file of the -latest release. Unzip it somewhere on your machine. - -For Matlab: - - cd messenger - # edit local.cfg in the directory for your platform - python make.py matlab - cd .. - python setup.py install - - -For Octave: - - cd messenger/octave - # edit local_octave.cfg in the directory for your platform - python make.py octave - cd .. - python setup.py - -This should make the python-matlab-bridge import-able. - - -### Warnings - -Python communicates with Matlab via an ad-hoc zmq messenger. This is inherently -insecure, as the Matlab instance may be directed to perform arbitrary system -calls. There is no sandboxing of any kind. Use this code at your own risk. - -[1]: https://pypi.python.org/pypi/pymatbridge diff --git a/images/bg_hr.png b/images/bg_hr.png new file mode 100644 index 0000000..7973bd6 Binary files /dev/null and b/images/bg_hr.png differ diff --git a/images/blacktocat.png b/images/blacktocat.png new file mode 100644 index 0000000..6e264fe Binary files /dev/null and b/images/blacktocat.png differ diff --git a/images/body-bg.jpg b/images/body-bg.jpg new file mode 100644 index 0000000..0e0f861 Binary files /dev/null and b/images/body-bg.jpg differ diff --git a/images/download-button.png b/images/download-button.png new file mode 100644 index 0000000..df3f09a Binary files /dev/null and b/images/download-button.png differ diff --git a/images/github-button.png b/images/github-button.png new file mode 100644 index 0000000..efe07f9 Binary files /dev/null and b/images/github-button.png differ diff --git a/images/header-bg.jpg b/images/header-bg.jpg new file mode 100644 index 0000000..960bff7 Binary files /dev/null and b/images/header-bg.jpg differ diff --git a/images/highlight-bg.jpg b/images/highlight-bg.jpg new file mode 100644 index 0000000..4c4a78e Binary files /dev/null and b/images/highlight-bg.jpg differ diff --git a/images/icon_download.png b/images/icon_download.png new file mode 100644 index 0000000..a2a287f Binary files /dev/null and b/images/icon_download.png differ diff --git a/images/sidebar-bg.jpg b/images/sidebar-bg.jpg new file mode 100644 index 0000000..42890fe Binary files /dev/null and b/images/sidebar-bg.jpg differ diff --git a/images/sprite_download.png b/images/sprite_download.png new file mode 100644 index 0000000..f2babd5 Binary files /dev/null and b/images/sprite_download.png differ diff --git a/index.html b/index.html new file mode 100644 index 0000000..30d9073 --- /dev/null +++ b/index.html @@ -0,0 +1,248 @@ + + + + + + + + + + + Codestin Search App + + + + + +
+
+ View on GitHub + +

Python-matlab-bridge

+

A simple Python => MATLAB(R) interface and a matlab_magic for ipython

+ +
+ Download this project as a .zip file + Download this project as a tar.gz file +
+
+
+ + +
+
+

+Python-MATLAB(R) Bridge and ipython matlab_magic

+ +

A python interface to call out to Matlab(R). Original +implementation by Max Jaderberg.

+ +

This implementation also includes an IPython matlab_magic +extension, which provides a simple interface for weaving python and +Matlab code together (requires ipython > 0.13).

+ +

+Installation

+ +

Pymatbridge communicates with Matlab using zeromq. So before installing +pymatbridge you must have zmq +library and pyzmq installed on your +machine. If you intend to use the Matlab magic extension, you'll also need +IPython. To make pymatbridge work properly, +please follow the following steps.

+ +

+Install zmq library

+ +

Please refer to the official guide on how to +build and install zmq. After zmq is installed, make sure you can find the location where +libzmq is installed. The library extension name and default location on different systems +are listed below.

+ + + + + + + + + + + + + + + + + + + + + + + + +
Platformlibrary nameDefault locations
MacOSlibzmq.dylib/usr/lib or /usr/local/lib
Linuxlibzmq.so.3/usr/lib or /usr/local/lib
Windowslibzmq.dllC:\Program Files\ZeroMQ 3.2.4\bin

If you specified a prefix when installing zmq, the library file should be located at the +same prefix location.

+ +

After the library file is located, you need to add it to dynamic loader path on your +machine. On MacOS, you can do this by adding the following line to your .bash_profile:

+ +
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:<Path to your zmq lib directory>
+
+ +

On Linux, add the following line to your .bash_profile:

+ +
export LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:<Path to your zmq lib directory>
+
+ +

On Windows, add the install location of libzmq.dll to the PATH environment variable. +On Windows 7+, typing "environment variables" into the start menu will bring up the +apporpriate Control Panel links.

+ +

+Install pyzmq

+ +

After step 1 is finished, please grab the latest version of +pyzmq and follow the instructions on the official +page. Note that pymatbridge is developed with pyzmq 14.0.0 and older versions might not +be supported. If you have an old version of pyzmq, please update it.

+ +

+Install pymatbridge

+ +

After the steps above are done, you can install pymatbridge. Download the zip file of the +latest release. Unzip it somewhere on your machine and then issue:

+ +
python setup.py install
+
+ +

This should make the python-matlab-bridge import-able.

+ +

+Usage

+ +

To use the pymatbridge you need to connect your python interperter to a Matlab +session. This is done in the following manner:

+ +
from pymatbridge import Matlab
+mlab = Matlab()
+
+ +

This creates a matlab session class instance, into which you will be able to +inject code and variables, and query for results. By default, when you use +start, this will open whatever gets called when you type matlab +in your Terminal, but you can also specify the location of your Matlab +application when initialzing your matlab session class:

+ +
mlab = Matlab(matlab='/Applications/MATLAB_R2011a.app/bin/matlab')
+
+ +

You can then start the Matlab server, which will kick off your matlab session, +and create the connection between your Python interperter and this session:

+ +
mlab.start()
+
+ +

which will return True once connected.

+ +
results = mlab.run_code('a=1;')
+
+ +

Should now run that line of code and return a results dict into your Python +namespace. The results dict contains the following fields:

+ +
{u'content': {u'code': u'a=1',
+ u'datadir': u'/private/tmp/MatlabData/',
+ u'figures': [],
+ u'stdout': u'\na =\n\n     1\n\n'},
+ u'success': u'true'}
+
+ +

In this case, the variable a is available on the Python side, by using +the get_variable method:

+ +
mlab.get_variable('a')
+
+ +

You can run any MATLAB functions contained within a .m file of the +same name. For example, to call the function jk in jk.m:

+ +
%% MATLAB
+function lol = jk(args)
+    arg1 = args.arg1;
+    arg2 = args.arg2;
+    lol = arg1 + arg2;
+end
+
+ +

you would call:

+ +
res = mlab.run_func('path/to/jk.m', {'arg1': 3, 'arg2': 5})
+print res['result']
+
+ +

This would print 8.

+ +

You can shut down the MATLAB server by calling:

+ +
mlab.stop()
+
+ +

Tip: you can execute MATLAB code at the beginning of each of your matlab +sessions by adding code to the ~/startup.m file.

+ +

+Matlab magic:

+ +

The Matlab magic allows you to use pymatbridge in the context of the IPython +notebook format.

+ +
%load_ext pymatbridge
+
+ +

These lines will automatically start the matlab session for you. Then, you can +simply decorate a line/cell with the '%matlab' or '%%matlab' decorator and +write matlab code:

+ +
%%matlab 
+a = linspace(0.01,6*pi,100);
+plot(sin(a))
+grid on
+hold on
+plot(cos(a),'r')
+
+ +

More examples are provided in the examples directory

+ +

+Warnings

+ +

Python communicates with Matlab via an ad-hoc zmq messenger. This is inherently +insecure, as the Matlab instance may be directed to perform arbitrary system +calls. There is no sandboxing of any kind. Use this code at your own risk.

+
+
+ + + + + + + + + + diff --git a/javascripts/main.js b/javascripts/main.js new file mode 100644 index 0000000..d8135d3 --- /dev/null +++ b/javascripts/main.js @@ -0,0 +1 @@ +console.log('This would be the main JS file.'); diff --git a/params.json b/params.json new file mode 100644 index 0000000..021affd --- /dev/null +++ b/params.json @@ -0,0 +1 @@ +{"name":"Python-matlab-bridge","tagline":"A simple Python => MATLAB(R) interface and a matlab_magic for ipython","body":"# Python-MATLAB(R) Bridge and ipython matlab_magic\r\n\r\nA python interface to call out to [Matlab(R)](http://mathworks.com). Original\r\nimplementation by [Max Jaderberg](http://www.maxjaderberg.com/).\r\n\r\nThis implementation also includes an [IPython](http://ipython.org) `matlab_magic`\r\nextension, which provides a simple interface for weaving python and\r\nMatlab code together (requires ipython > 0.13). \r\n\r\n\r\n## Installation\r\n\r\nPymatbridge communicates with Matlab using zeromq. So before installing\r\npymatbridge you must have [zmq](http://zeromq.org/intro:get-the-software)\r\nlibrary and [pyzmq](http://zeromq.org/bindings:python) installed on your\r\nmachine. If you intend to use the Matlab magic extension, you'll also need\r\n[IPython](http://ipython.org/install.html). To make pymatbridge work properly,\r\nplease follow the following steps.\r\n\r\n### Install zmq library\r\nPlease refer to the [official guide](http://zeromq.org/intro:get-the-software) on how to\r\nbuild and install zmq. After zmq is installed, make sure you can find the location where\r\nlibzmq is installed. The library extension name and default location on different systems\r\nare listed below.\r\n\r\n| Platform | library name | Default locations |\r\n| ------------- | ------------- | --------------------------------- |\r\n| MacOS | libzmq.dylib\t| /usr/lib or /usr/local/lib |\r\n| Linux | libzmq.so.3\t| /usr/lib or /usr/local/lib |\r\n| Windows | libzmq.dll | C:\\Program Files\\ZeroMQ 3.2.4\\bin |\r\n\r\nIf you specified a prefix when installing zmq, the library file should be located at the\r\nsame prefix location.\r\n\r\nAfter the library file is located, you need to add it to dynamic loader path on your \r\nmachine. On MacOS, you can do this by adding the following line to your .bash_profile:\r\n\r\n\texport DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:\r\n\r\nOn Linux, add the following line to your .bash_profile:\r\n\r\n\texport LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:\r\n\r\nOn Windows, add the install location of libzmq.dll to the PATH environment variable.\r\nOn Windows 7+, typing \"environment variables\" into the start menu will bring up the\r\napporpriate Control Panel links.\r\n\t\r\n### Install pyzmq\r\nAfter step 1 is finished, please grab the latest version of \r\n[pyzmq](http://zeromq.org/bindings:python) and follow the instructions on the official \r\npage. Note that pymatbridge is developed with pyzmq 14.0.0 and older versions might not \r\nbe supported. If you have an old version of pyzmq, please update it. \r\n\r\n### Install pymatbridge\r\nAfter the steps above are done, you can install pymatbridge. Download the zip file of the \r\nlatest release. Unzip it somewhere on your machine and then issue:\r\n\r\n\tpython setup.py install\r\n\t\r\nThis should make the python-matlab-bridge import-able.\r\n\r\n\r\n## Usage\r\n\r\nTo use the pymatbridge you need to connect your python interperter to a Matlab\r\nsession. This is done in the following manner:\r\n\r\n from pymatbridge import Matlab\r\n mlab = Matlab()\r\n\r\nThis creates a matlab session class instance, into which you will be able to\r\ninject code and variables, and query for results. By default, when you use\r\n`start`, this will open whatever gets called when you type `matlab`\r\nin your Terminal, but you can also specify the location of your Matlab\r\napplication when initialzing your matlab session class: \r\n\r\n mlab = Matlab(matlab='/Applications/MATLAB_R2011a.app/bin/matlab')\r\n\t \r\nYou can then start the Matlab server, which will kick off your matlab session,\r\nand create the connection between your Python interperter and this session:\r\n\r\n mlab.start()\r\n\r\nwhich will return True once connected.\r\n\r\n results = mlab.run_code('a=1;')\r\n\r\nShould now run that line of code and return a `results` dict into your Python\r\nnamespace. The `results` dict contains the following fields:\r\n\r\n {u'content': {u'code': u'a=1',\r\n u'datadir': u'/private/tmp/MatlabData/',\r\n u'figures': [],\r\n u'stdout': u'\\na =\\n\\n 1\\n\\n'},\r\n u'success': u'true'}\r\n\r\nIn this case, the variable `a` is available on the Python side, by using\r\nthe `get_variable` method:\r\n\r\n mlab.get_variable('a')\r\n \r\nYou can run any MATLAB functions contained within a .m file of the\r\nsame name. For example, to call the function jk in jk.m:\r\n\r\n %% MATLAB\r\n function lol = jk(args)\r\n arg1 = args.arg1;\r\n arg2 = args.arg2;\r\n lol = arg1 + arg2;\r\n end\r\n\r\nyou would call:\r\n\r\n res = mlab.run_func('path/to/jk.m', {'arg1': 3, 'arg2': 5})\r\n print res['result']\r\n\r\nThis would print `8`.\r\n\r\nYou can shut down the MATLAB server by calling:\r\n\r\n mlab.stop()\r\n\r\nTip: you can execute MATLAB code at the beginning of each of your matlab\r\nsessions by adding code to the `~/startup.m` file.\r\n\r\n\r\n### Matlab magic: \r\n\r\nThe Matlab magic allows you to use pymatbridge in the context of the IPython\r\nnotebook format.\r\n\r\n %load_ext pymatbridge\r\n\r\nThese lines will automatically start the matlab session for you. Then, you can\r\nsimply decorate a line/cell with the '%matlab' or '%%matlab' decorator and\r\nwrite matlab code:\r\n\r\n %%matlab \r\n a = linspace(0.01,6*pi,100);\r\n plot(sin(a))\r\n grid on\r\n hold on\r\n plot(cos(a),'r')\r\n\r\nMore examples are provided in the `examples` directory\r\n \r\n### Warnings\r\n\r\nPython communicates with Matlab via an ad-hoc zmq messenger. This is inherently\r\ninsecure, as the Matlab instance may be directed to perform arbitrary system\r\ncalls. There is no sandboxing of any kind. Use this code at your own risk.\r\n\r\n\r\n","google":"UA-40132410-1","note":"Don't delete this file! It's used internally to help with page regeneration."} \ No newline at end of file diff --git a/pymatbridge/__init__.py b/pymatbridge/__init__.py deleted file mode 100644 index 45d2145..0000000 --- a/pymatbridge/__init__.py +++ /dev/null @@ -1,12 +0,0 @@ -from .pymatbridge import * -from .version import __version__ - -try: - from .publish import * -except ImportError: - pass - -try: - from .matlab_magic import * -except ImportError: - pass diff --git a/pymatbridge/compat.py b/pymatbridge/compat.py deleted file mode 100644 index bca21fc..0000000 --- a/pymatbridge/compat.py +++ /dev/null @@ -1,10 +0,0 @@ -import sys - -PY3 = sys.version_info[0] == 3 - -if PY3: - text_type = str - unichr = chr -else: - text_type = unicode - unichr = unichr diff --git a/pymatbridge/examples/matlab_magic.ipynb b/pymatbridge/examples/matlab_magic.ipynb deleted file mode 100644 index 8b9e1b3..0000000 --- a/pymatbridge/examples/matlab_magic.ipynb +++ /dev/null @@ -1,152 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "import pymatbridge as pymat" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Starting MATLAB on ZMQ socket ipc:///tmp/pymatbridge-13a5236e-5f5a-4b58-a712-84cca5314f75\n", - "Send 'exit' command to kill the server\n", - "..............MATLAB started and connected!\n" - ] - } - ], - "source": [ - "ip = get_ipython()\n", - "pymat.load_ipython_extension(ip)" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "data": { - "image/png": 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JEyCjL0PiHgJWEDRFWeCcBrjDYDEd5L9mYeq+qqYRVy9QLHueKH5/zZXWW8vUuPNQa1Ig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\n4hYvikMZLB2Y0wuJU0Ircl3cun2pWOl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- }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "%%matlab --size 400,350\n", - "t = linspace(0,6*pi,100);\n", - "plot(sin(t))\n", - "grid on\n", - "hold on\n", - "plot(cos(t), 'r')" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "data": { - "image/png": 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rBjEMiFynu0gGRE7NuARhAiHAFDRAVQAsFstf//rXHTt2OB8sLS3Nz88fPHhw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\nAIIgiKSgACAIgkjK/wEH/MzXi5T25AAAAABJRU5ErkJggg==\n" - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "%matlab b = 10*cos(t)+30; plot(b); grid on" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "a = [1,2,3]\n" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "%%matlab -i a -o b\n", - "b = a + 3;" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[[ 4. 5. 6.]]\n" - ] - } - ], - "source": [ - "print(b)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.4.3" - } - }, - "nbformat": 4, - "nbformat_minor": 0 -} diff --git a/pymatbridge/examples/pymatbridge.ipynb b/pymatbridge/examples/pymatbridge.ipynb deleted file mode 100644 index ff116fb..0000000 --- a/pymatbridge/examples/pymatbridge.ipynb +++ /dev/null @@ -1,250 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "import os\n", - "import numpy as np\n", - "import pymatbridge as pymat" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Starting MATLAB on ZMQ socket ipc:///tmp/pymatbridge-051089d9-1f6e-4298-8228-e9e1a8b3f368\n", - "Send 'exit' command to kill the server\n", - ".......MATLAB started and connected!\n" - ] - }, - { - "data": { - "text/plain": [ - "" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "matlab = pymat.Matlab()\n", - "matlab.start()" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "data": { - "text/plain": [ - "11" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "func_file = os.path.dirname(pymat.__file__) + '/matlab/www/demo_func.m'\n", - "res = matlab.run_func(func_file, {'a': 10})\n", - "res['result']" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "data": { - "text/plain": [ - "array([[ 2., 4., 8.]])" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "res_dict = matlab.run_code('a=[1,3,7]')\n", - "res_dict = matlab.run_code('plot(a)')\n", - "res_dict = matlab.run_code('b=a+1')\n", - "matlab.get_variable('b')" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "data": { - "text/plain": [ - "\n", - "b =\n", - "\n", - " 2 4 8\n", - "\n" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "image/png": 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AYtiwYTExMaGhod98882pU6cKCwuLiorefPNN1corAs/zRlLD6+2p4EXV2apV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\npAgAADCp/w/UelOBKsEppQAAAABJRU5ErkJggg==\n" - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "res_dict = matlab.run_code('figure; plot(b); b')\n", - "\n", - "from IPython.core.displaypub import publish_display_data\n", - "imgfiles = res_dict['content']['figures']\n", - "text_output = res_dict['content']['stdout']\n", - "\n", - "display_data = []\n", - "if text_output:\n", - " display_data.append({'text/plain':text_output})\n", - "for imgf in imgfiles:\n", - " try: # python 2\n", - " image = open(imgf, 'rb').read().decode('utf-8') \n", - " except: # python 3\n", - " image = open(imgf, 'rb').read()\n", - " \n", - " display_data.append({'image/png': image})\n", - "\n", - "for d in display_data:\n", - " publish_display_data(d)\n", - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "." - ] - }, - { - "data": { - "text/plain": [ - "True" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "matlab.is_connected()" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "MATLAB closed\n" - ] - }, - { - "data": { - "text/plain": [ - "True" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "matlab.stop()" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "data": { - "text/plain": [ - "False" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "matlab.is_connected()" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.4.2" - } - }, - "nbformat": 4, - "nbformat_minor": 0 -} diff --git a/pymatbridge/matlab/matlabserver.m b/pymatbridge/matlab/matlabserver.m deleted file mode 100644 index e70bc71..0000000 --- a/pymatbridge/matlab/matlabserver.m +++ /dev/null @@ -1,31 +0,0 @@ -function matlabserver(socket_address) -% This function takes a socket address as input and initiates a ZMQ session -% over the socket. I then enters the listen-respond mode until it gets an -% "exit" command - -json_startup -messenger('init', socket_address); - -c=onCleanup(@()exit); - -while(1) - msg_in = messenger('listen'); - req = json_load(msg_in); - - switch(req.cmd) - case {'connect'} - messenger('respond', 'connected'); - - case {'exit'} - messenger('exit'); - break; - - case {'eval'} - resp = pymat_eval(req); - messenger('respond', resp); - - otherwise - messenger('respond', 'i dont know what you want'); - end - -end diff --git a/pymatbridge/matlab/usrprog/array_size.m b/pymatbridge/matlab/usrprog/array_size.m deleted file mode 100644 index 35a300d..0000000 --- a/pymatbridge/matlab/usrprog/array_size.m +++ /dev/null @@ -1,6 +0,0 @@ -function res = array_size(args) -% Simply returns the input array - - res = args.val; - -end %end diff --git a/pymatbridge/matlab/usrprog/demo_func.m b/pymatbridge/matlab/usrprog/demo_func.m deleted file mode 100644 index 394841b..0000000 --- a/pymatbridge/matlab/usrprog/demo_func.m +++ /dev/null @@ -1,9 +0,0 @@ -function res = demo_func(args) - - res = args.a + 1; - figure - plot([1 3 8]) - figure - plot([2,4,9]) - -end %function diff --git a/pymatbridge/matlab/usrprog/demo_sum.m b/pymatbridge/matlab/usrprog/demo_sum.m deleted file mode 100644 index a7e3a6b..0000000 --- a/pymatbridge/matlab/usrprog/demo_sum.m +++ /dev/null @@ -1,5 +0,0 @@ -function res = demo_sum(args) -% This function returns the sum of two arguments val1 and val2 - res = args.val1 + args.val2; - -end %function diff --git a/pymatbridge/matlab/usrprog/precision_divide.m b/pymatbridge/matlab/usrprog/precision_divide.m deleted file mode 100644 index 0e16d5c..0000000 --- a/pymatbridge/matlab/usrprog/precision_divide.m +++ /dev/null @@ -1,5 +0,0 @@ -function res = precision_divide(args) -% This function devides val1 by val2 and returns the result - res = args.val1 / args.val2; - -end %function diff --git a/pymatbridge/matlab/usrprog/precision_multiply.m b/pymatbridge/matlab/usrprog/precision_multiply.m deleted file mode 100644 index 1c12f23..0000000 --- a/pymatbridge/matlab/usrprog/precision_multiply.m +++ /dev/null @@ -1,5 +0,0 @@ -function res = precision_multiply(args) -% This function returns the product of two arguments val1 and val2 - res = args.val1 * args.val2; - -end %function diff --git a/pymatbridge/matlab/usrprog/precision_pass.m b/pymatbridge/matlab/usrprog/precision_pass.m deleted file mode 100644 index 1225c1c..0000000 --- a/pymatbridge/matlab/usrprog/precision_pass.m +++ /dev/null @@ -1,6 +0,0 @@ -function res = precision_pass(args) -% This function takes an argument val and simply return it - - res = args.val; - -end diff --git a/pymatbridge/matlab/usrprog/precision_sqrt.m b/pymatbridge/matlab/usrprog/precision_sqrt.m deleted file mode 100644 index ef87cf0..0000000 --- a/pymatbridge/matlab/usrprog/precision_sqrt.m +++ /dev/null @@ -1,5 +0,0 @@ -function res = precision_sqrt(args) -% This function returns the square root of the value - res = sqrt(args.val); - -end %function diff --git a/pymatbridge/matlab/usrprog/precision_sum.m b/pymatbridge/matlab/usrprog/precision_sum.m deleted file mode 100644 index 6d6bd45..0000000 --- a/pymatbridge/matlab/usrprog/precision_sum.m +++ /dev/null @@ -1,5 +0,0 @@ -function res = precision_sum(args) -% This function returns the sum of two arguments val1 and val2 - res = args.val1 + args.val2; - -end %function diff --git a/pymatbridge/matlab/usrprog/test_sum.m b/pymatbridge/matlab/usrprog/test_sum.m deleted file mode 100644 index 15639d1..0000000 --- a/pymatbridge/matlab/usrprog/test_sum.m +++ /dev/null @@ -1,3 +0,0 @@ -function result = test_sum(args) -result = args.echo; -end diff --git a/pymatbridge/matlab/util/isrow.m b/pymatbridge/matlab/util/isrow.m deleted file mode 100644 index 12848f7..0000000 --- a/pymatbridge/matlab/util/isrow.m +++ /dev/null @@ -1,14 +0,0 @@ -function Y = isrow(X) -% -% ISROW True for row vectors. -% -% Y = ISROW(X) returns logical 1 if X is a row vector, 0 otherwise. -% ISROW returns 1 for scalars also. -% -% - -if ndims(X)==2 && size(X,1)==1 && size(X,2)>=1 - Y = logical(1); -else - Y = logical(0); -end diff --git a/pymatbridge/matlab/util/json_v0.2.2/.gitignore b/pymatbridge/matlab/util/json_v0.2.2/.gitignore deleted file mode 100644 index 93bfd12..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -*~ -.DS_Store diff --git a/pymatbridge/matlab/util/json_v0.2.2/LICENSE b/pymatbridge/matlab/util/json_v0.2.2/LICENSE deleted file mode 100644 index a9eec97..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/LICENSE +++ /dev/null @@ -1,25 +0,0 @@ -Copyright (c) 2013 Kota Yamaguchi -All rights reserved. - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions -are met: - -1. Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. -2. Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. -3. The name of the author may not be used to endorse or promote products - derived from this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR -IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES -OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. -IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, -INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT -NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF -THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/pymatbridge/matlab/util/json_v0.2.2/README.md b/pymatbridge/matlab/util/json_v0.2.2/README.md deleted file mode 100644 index 54a41fb..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/README.md +++ /dev/null @@ -1,102 +0,0 @@ -Matlab JSON v0.2 -================ - -This package contains Matlab class to serialize/decode matlab object in -json format. The software uses org.json java package to convert json to -java object and then translates it into Matlab object. - -API ---- - -All functions are scoped under `json` namespace. - - startup Initialize runtime environment. - dump Encode matlab value into a JSON string. - load Load matlab value from a JSON string. - read Load a matlab value from a JSON file. - write Write a matlab value into a JSON file. - -Usage ------ - -Add path to the directory containing `+json` before use, and call -`json.startup`. - -To serialize matlab object: - - >> X = struct('field1', magic(2), 'field2', 'hello'); - >> S = json.dump(X); - >> disp(S); - {"field2":"hello","field1":[[1,3],[4,2]]} - -To decode json string: - - >> X = json.load(S); - >> disp(X); - field2: 'hello' - field1: [2x2 double] - -To read from or write to a json file. - - >> json.write(X, '/path/to/file.json'); - >> X = json.read('/path/to/file.json'); - -Note ----- - -Due to the multiple ways to represent an array in Matlab (i.e., numeric -array, cell array, or struct array), it is impossible to represent -everything in a compatible format. For example, a json string "[[1,2],[3,4]]" -can be interpreted in different ways in Matlab, such as [1,2;3,4], {1,2;3,4}, -{[1,2],[3,4]}, etc. Because of this, `json.load` does not always yield the -exactly same input to `json.dump`. - -This implementation is designed to maximize the ease of data exchange. For -that purpose, by default, json parser assumes the following. - - * Native arrays precede a cell array. "[1,2]" is [1,2] in matlab. - * Row-major order. e.g., "[[1,2],[3,4]]" is [1,2;3,4] in matlab. - * N-D array is a nested json array. - * Any other ambiguous arrays are treated as cell array. "[]" is {}. - -For example, a nested array with the same sized elements is treated as an N-D -array. - - >> x = json.load('[[[1,2],[3,4]],[[5,6],[7,8]]]') - - x(:,:,1) = - 1 2 - 3 4 - - x(:,:,2) = - 5 6 - 7 8 - - -The `json.load` function can optionally take an option to specify column-major -interpretation or cell-array precedence. Check `help json.load` for details. - -Test ----- - -To run a test, use `test_all` function in the `test` directory. - - >> addpath('test'); - >> test_all; - -License -------- - -You may redistribute this software under BSD license. - - -Version -------- - - * 0.2 API changed to functions from a class. - * 0.1 Initial release. - -Links ------ - -JSON in Java: http://json.org/java/ diff --git a/pymatbridge/matlab/util/json_v0.2.2/json/java/README b/pymatbridge/matlab/util/json_v0.2.2/json/java/README deleted file mode 100644 index 14a1161..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/json/java/README +++ /dev/null @@ -1,68 +0,0 @@ -JSON in Java [package org.json] - -Douglas Crockford -douglas@crockford.com - -2011-02-02 - - -JSON is a light-weight, language independent, data interchange format. -See http://www.JSON.org/ - -The files in this package implement JSON encoders/decoders in Java. -It also includes the capability to convert between JSON and XML, HTTP -headers, Cookies, and CDL. - -This is a reference implementation. There is a large number of JSON packages -in Java. Perhaps someday the Java community will standardize on one. Until -then, choose carefully. - -The license includes this restriction: "The software shall be used for good, -not evil." If your conscience cannot live with that, then choose a different -package. - -The package compiles on Java 1.2 thru Java 1.4. - - -JSONObject.java: The JSONObject can parse text from a String or a JSONTokener -to produce a map-like object. The object provides methods for manipulating its -contents, and for producing a JSON compliant object serialization. - -JSONArray.java: The JSONObject can parse text from a String or a JSONTokener -to produce a vector-like object. The object provides methods for manipulating -its contents, and for producing a JSON compliant array serialization. - -JSONTokener.java: The JSONTokener breaks a text into a sequence of individual -tokens. It can be constructed from a String, Reader, or InputStream. - -JSONException.java: The JSONException is the standard exception type thrown -by this package. - - -JSONString.java: The JSONString interface requires a toJSONString method, -allowing an object to provide its own serialization. - -JSONStringer.java: The JSONStringer provides a convenient facility for -building JSON strings. - -JSONWriter.java: The JSONWriter provides a convenient facility for building -JSON text through a writer. - - -CDL.java: CDL provides support for converting between JSON and comma -delimited lists. - -Cookie.java: Cookie provides support for converting between JSON and cookies. - -CookieList.java: CookieList provides support for converting between JSON and -cookie lists. - -HTTP.java: HTTP provides support for converting between JSON and HTTP headers. - -HTTPTokener.java: HTTPTokener extends JSONTokener for parsing HTTP headers. - -XML.java: XML provides support for converting between JSON and XML. - -JSONML.java: JSONML provides support for converting between JSONML and XML. - -XMLTokener.java: XMLTokener extends JSONTokener for parsing XML text. \ No newline at end of file diff --git a/pymatbridge/matlab/util/json_v0.2.2/json/java/json.jar b/pymatbridge/matlab/util/json_v0.2.2/json/java/json.jar deleted file mode 100644 index e15261b..0000000 Binary files a/pymatbridge/matlab/util/json_v0.2.2/json/java/json.jar and /dev/null differ diff --git a/pymatbridge/matlab/util/json_v0.2.2/json/json_dump.m b/pymatbridge/matlab/util/json_v0.2.2/json/json_dump.m deleted file mode 100644 index c085226..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/json/json_dump.m +++ /dev/null @@ -1,331 +0,0 @@ -function str = json_dump(value, varargin) -%DUMP Encode matlab value into a JSON string. -% -% SYNOPSIS -% -% str = json.dump(value) -% str = json.dump(..., optionName, optionValue, ...) -% -% The function converts a matlab value to a JSON string. A value can be any -% of a double array, a logical array, a char array, a cell array, or a -% struct array. Numeric values other than double are converted to double. -% A struct array is mapped to a JSON object. However, since a JSON object -% is unordered, the order of field names are not preserved. -% -% OPTIONS -% -% The function takes following options. -% -% 'ColMajor' Represent matrix in column-major order. Default false. -% 'indent' Pretty-print the output string with indentation. Default -% [] -% -% EXAMPLE -% -% >> X = struct('matrix', magic(2), 'char', 'hello'); -% >> str = json.dump(X) -% str = -% -% {"char":"hello","matrix":[[1,3],[4,2]]} -% -% >> str = json.dump([1,2,3;4,5,6]) -% str = -% -% [[1,2,3],[4,5,6]] -% -% >> str = json.dump([1,2,3;4,5,6], 'ColMajor', true) -% str = -% -% [[1,4],[2,5],[3,6]] -% -% >> str = json.dump([1,2,3;4,5,6], 'indent', 2) -% str = -% -% [ -% [ -% 1, -% 2, -% 3 -% ], -% [ -% 4, -% 5, -% 6 -% ] -% ] -% -% NOTE -% -% Since any matlab values are an array, it is impossible to uniquely map -% all matlab values to JSON primitives. This implementation aims to have -% better interoperability across platforms. Therefore, some matlab values -% are mapped to the same representation. For example, [1,2] and {1,2} are -% mapped to the same json string '[1,2]'. -% -% See also json.load json.write - json_startup('WarnOnAddpath', true); - options = get_options_(varargin{:}); - obj = dump_data_(value, options); - if isempty(options.indent) - str = char(obj.toString()); - else - str = char(obj.toString(options.indent)); - end -end - -function options = get_options_(varargin) -%GET_OPTIONS_ - options = struct(... - 'ColMajor', false,... - 'indent', [] ... - ); - for i = 1:2:numel(varargin) - switch varargin{i} - case 'ColMajor' - options.ColMajor = logical(varargin{i+1}); - case 'indent' - options.indent = varargin{i+1}; - otherwise - error('Unknown option to json.dump') - end - end -end - -function obj = dump_data_(value, options) -%DUMP_DATA_ - if ischar(value) && (isvector(value) || isempty(value)) - obj = javaObject('java.lang.String', value); - elseif isempty(value) && isnumeric(value) - json_object = javaObject('org.json.JSONObject'); - obj = json_object.NULL; - elseif ~isscalar(value) - obj = javaObject('org.json.JSONArray'); - - if isnumeric(value) - % encode arrays as a struct - double_struct = struct; - double_struct.ndarray = 1; - value = double(value); - if isreal(value) - double_struct.data = base64encode(typecast(value(:), 'uint8')); - else - double_struct.real = base64encode(typecast(real(value(:)), 'uint8')); - double_struct.imag = base64encode(typecast(imag(value(:)), 'uint8')); - end - double_struct.shape = base64encode(typecast(size(value), 'uint8')); - obj = dump_data_(double_struct, options); - elseif ndims(value) > 2 - split_value = num2cell(value, 1:ndims(value)-1); - for i = 1:numel(split_value) - obj.put(dump_data_(split_value{i}, options)); - end - else - if options.ColMajor && iscolumn(value) || ... - ~options.ColMajor && isrow(value) - if iscell(value) - for i = 1:numel(value), obj.put(dump_data_(value{i}, options)); end - else - for i = 1:numel(value), obj.put(dump_data_(value(i), options)); end - end - else - value = num2cell(value, 2 - options.ColMajor); - if all(cellfun(@isscalar, value)) - for i = 1:numel(value), obj.put(dump_data_(value(i), options)); end - else - for i = 1:numel(value), obj.put(dump_data_(value{i}, options)); end - end - end - end - elseif iscell(value) - obj = javaObject('org.json.JSONArray'); - for i = 1:numel(value) - obj.put(dump_data_(value{i}, options)); - end - elseif isnumeric(value) - if isreal(value) - obj = value; - % Encode complex number as a struct - else - complex_struct = struct; - complex_struct.real = real(value); - complex_struct.imag = imag(value); - obj = dump_data_(complex_struct, options); - end - elseif islogical(value) - obj = javaObject('java.lang.Boolean', value); - elseif isstruct(value) - obj = javaObject('org.json.JSONObject'); - keys = fieldnames(value); - for i = 1:length(keys) - try - obj.put(keys{i},dump_data_(value.(keys{i}), options)); - catch ME - obj.put(keys{i}, dump_data_(ME.message, options)) - end - end - else - error('json:typeError', 'Unsupported data type: %s', class(value)); - end -end - - -function y = base64encode(x, eol) -%BASE64ENCODE Perform base64 encoding on a string. -% -% BASE64ENCODE(STR, EOL) encode the given string STR. EOL is the line ending -% sequence to use; it is optional and defaults to '\n' (ASCII decimal 10). -% The returned encoded string is broken into lines of no more than 76 -% characters each, and each line will end with EOL unless it is empty. Let -% EOL be empty if you do not want the encoded string broken into lines. -% -% STR and EOL don't have to be strings (i.e., char arrays). The only -% requirement is that they are vectors containing values in the range 0-255. -% -% This function may be used to encode strings into the Base64 encoding -% specified in RFC 2045 - MIME (Multipurpose Internet Mail Extensions). The -% Base64 encoding is designed to represent arbitrary sequences of octets in a -% form that need not be humanly readable. A 65-character subset -% ([A-Za-z0-9+/=]) of US-ASCII is used, enabling 6 bits to be represented per -% printable character. -% -% Examples -% -------- -% -% If you want to encode a large file, you should encode it in chunks that are -% a multiple of 57 bytes. This ensures that the base64 lines line up and -% that you do not end up with padding in the middle. 57 bytes of data fills -% one complete base64 line (76 == 57*4/3): -% -% If ifid and ofid are two file identifiers opened for reading and writing, -% respectively, then you can base64 encode the data with -% -% while ~feof(ifid) -% fwrite(ofid, base64encode(fread(ifid, 60*57))); -% end -% -% or, if you have enough memory, -% -% fwrite(ofid, base64encode(fread(ifid))); -% -% See also BASE64DECODE. - -% Author: Peter J. Acklam -% Time-stamp: 2004-02-03 21:36:56 +0100 -% E-mail: pjacklam@online.no -% URL: http://home.online.no/~pjacklam - - % check number of input arguments - error(nargchk(1, 2, nargin)); - - % make sure we have the EOL value - if nargin < 2 - eol = ''; %sprintf('\n'); - else - if sum(size(eol) > 1) > 1 - error('EOL must be a vector.'); - end - if any(eol(:) > 255) - error('EOL can not contain values larger than 255.'); - end - end - - if sum(size(x) > 1) > 1 - error('STR must be a vector.'); - end - - x = uint8(x); - eol = uint8(eol); - - ndbytes = length(x); % number of decoded bytes - nchunks = ceil(ndbytes / 3); % number of chunks/groups - nebytes = 4 * nchunks; % number of encoded bytes - - % add padding if necessary, to make the length of x a multiple of 3 - if rem(ndbytes, 3) - x(end+1 : 3*nchunks) = 0; - end - - x = reshape(x, [3, nchunks]); % reshape the data - y = repmat(uint8(0), 4, nchunks); % for the encoded data - - %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - % Split up every 3 bytes into 4 pieces - % - % aaaaaabb bbbbcccc ccdddddd - % - % to form - % - % 00aaaaaa 00bbbbbb 00cccccc 00dddddd - % - y(1,:) = bitshift(x(1,:), -2); % 6 highest bits of x(1,:) - - y(2,:) = bitshift(bitand(x(1,:), 3), 4); % 2 lowest bits of x(1,:) - y(2,:) = bitor(y(2,:), bitshift(x(2,:), -4)); % 4 highest bits of x(2,:) - - y(3,:) = bitshift(bitand(x(2,:), 15), 2); % 4 lowest bits of x(2,:) - y(3,:) = bitor(y(3,:), bitshift(x(3,:), -6)); % 2 highest bits of x(3,:) - - y(4,:) = bitand(x(3,:), 63); % 6 lowest bits of x(3,:) - - %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - % Now perform the following mapping - % - % 0 - 25 -> A-Z - % 26 - 51 -> a-z - % 52 - 61 -> 0-9 - % 62 -> + - % 63 -> / - % - % We could use a mapping vector like - % - % ['A':'Z', 'a':'z', '0':'9', '+/'] - % - % but that would require an index vector of class double. - % - z = repmat(uint8(0), size(y)); - i = y <= 25; z(i) = 'A' + double(y(i)); - i = 26 <= y & y <= 51; z(i) = 'a' - 26 + double(y(i)); - i = 52 <= y & y <= 61; z(i) = '0' - 52 + double(y(i)); - i = y == 62; z(i) = '+'; - i = y == 63; z(i) = '/'; - y = z; - - %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - % Add padding if necessary. - % - npbytes = 3 * nchunks - ndbytes; % number of padding bytes - if npbytes - y(end-npbytes+1 : end) = '='; % '=' is used for padding - end - - if isempty(eol) - - % reshape to a row vector - y = reshape(y, [1, nebytes]); - - else - - nlines = ceil(nebytes / 76); % number of lines - neolbytes = length(eol); % number of bytes in eol string - - % pad data so it becomes a multiple of 76 elements - y(nebytes + 1 : 76 * nlines) = 0; - y = reshape(y, 76, nlines); - - % insert eol strings - eol = eol(:); - y(end + 1 : end + neolbytes, :) = eol(:, ones(1, nlines)); - - % remove padding, but keep the last eol string - m = nebytes + neolbytes * (nlines - 1); - n = (76+neolbytes)*nlines - neolbytes; - y(m+1 : n) = ''; - - % extract and reshape to row vector - y = reshape(y, 1, m+neolbytes); - - end - - % output is a character array - y = char(y); -end diff --git a/pymatbridge/matlab/util/json_v0.2.2/json/json_load.m b/pymatbridge/matlab/util/json_v0.2.2/json/json_load.m deleted file mode 100644 index ed2660f..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/json/json_load.m +++ /dev/null @@ -1,298 +0,0 @@ -function value = json_load(str, varargin) -%LOAD Load matlab value from a JSON string. -% -% SYNOPSIS -% -% value = json.load(str) -% value = json.dump(..., optionName, optionValue, ...) -% -% The function parses a JSON string into a matlab value. By default, -% numeric literals are converted to double, string is converted to a char -% array, logical literals are converted to logical. A JSON array is converted -% to either a double array, a logical array, a cell array, or a struct -% array. A JSON object is converted to a struct array. -% -% OPTIONS -% -% The function takes following options. -% -% 'MergeCell' Try to convert a JSON array into a double, a logical, or -% a struct array when possible. Default true. -% -% 'ColMajor' Represent matrix in column-major order. Default false. -% -% EXAMPLE -% -% >> value = json.load('{"char":"hello","matrix":[[1,3],[4,2]]}') -% value = -% -% char: 'hello' -% matrix: [2x2 double] -% -% >> value = json.load('[[1,2,3],[4,5,6]]') -% value = -% -% 1 2 3 -% 4 5 6 -% -% >> value = json.load('[[1,2,3],[4,5,6]]', 'ColMajor', true) -% value = -% 1 4 -% 2 5 -% 3 6 -% -% >> value = json.load('[[1,2,3],[4,5,6]]', 'MergeCell', false) -% value = -% -% {1x3 cell} {1x3 cell} -% -% NOTE -% -% Since any matlab values are an array, it is impossible to uniquely map -% all JSON primitives to matlab values. This implementation aims to have -% better interoperability across platforms. Therefore, some matlab values -% cannot be represented in a JSON string. For example, '[1,2,3]' is mapped to -% either [1, 2, 3] or {{1}, {2}, {3}} depending on 'MergeCell' option, but -% cannot produce {1, 2, 3}. -% -% See also json.dump json.read - - json_startup('WarnOnAddpath', true); - options = get_options_(varargin{:}); - singleton = false; - - str = strtrim(str); - if isempty(str) - error('json:invalidString','Invalid JSON string'); - end - if str(1)=='{' - node = javaObject('org.json.JSONObject', javaObject('java.lang.String', str)); - else - singleton = str(1) ~= '[' && str(end) ~= ']'; - if singleton, str = ['[',str,']']; end - node = javaObject('org.json.JSONArray', javaObject('java.lang.String', str)); - end - value = parse_data_(node, options); - if singleton, value = value{:}; end -end - -function options = get_options_(varargin) -%GET_OPTIONS_ - options = struct(... - 'MergeCell', true,... - 'ColMajor', false... - ); - for i = 1:2:numel(varargin) - switch varargin{i} - case 'MergeCell' - options.MergeCell = logical(varargin{i+1}); - case 'ColMajor' - options.ColMajor = logical(varargin{i+1}); - end - end -end - -function value = parse_data_(node, options) -%LOAD_DATA_ - if isa(node, 'char') - value = char(node); - elseif isa(node, 'double') - value = double(node); - elseif isa(node, 'logical') - value = logical(node); - elseif isa(node, 'org.json.JSONArray') - value = cell(node.length() > 0, node.length()); - for i = 1:node.length() - value{i} = parse_data_(node.get(i-1), options); - end - if options.MergeCell - value = merge_cell_(value, options); - end - elseif isa(node, 'org.json.JSONObject') - value = struct; - itr = node.keys(); - while itr.hasNext() - key = itr.next(); - field = char(key); - safe_field = genvarname(char(key), fieldnames(value)); - if ~strcmp(field, safe_field) - warning('json:fieldNameConflict', ... - 'Field %s renamed to %s', field, safe_field); - end - value.(safe_field) = parse_data_(node.get(javaObject('java.lang.String', key)), ... - options); - end - % Check if the struct just decoded represents an array or complex number - if isfield(value,'ndarray') && isfield(value, 'shape') - if isfield(value, 'data') - arr = typecast(base64decode(value.data), 'double'); - else - r = typecast(base64decode(value.real), 'double'); - im = typecast(base64decode(value.imag), 'double'); - arr = complex(r, im); - end - value = reshape(arr, value.shape); - elseif isfield(value,'real') && isfield(value, 'imag') - complex_value = complex(value.real, value.imag); - value = complex_value; - end - % In MATLAB, nested classes end up with a $ in the name, in Octave it's a . - elseif isa(node, 'org.json.JSONObject$Null') || isa(node, 'org.json.JSONObject.Null') - value = []; - else - error('json:typeError', 'Unknown data type: %s', class(node)); - end -end - -function value = merge_cell_(value, options) -%MERGE_CELL_ - if isempty(value) || all(cellfun(@isempty, value)) - return; - end - if isscalar(value) - return; - end - if ~all(cellfun(@isscalar, value)) && all(cellfun(@ischar, value)) - return; - end - - if is_mergeable_(value); - dim = ndims(value)+1; - mergeable = true; - if options.ColMajor - if all(cellfun(@isscalar, value)) - dim = 1; - if all(cellfun(@iscell, value)) % Singleton row vector [[a],[b]]. - value = cat(2, value{:}); - mergeable = is_mergeable_(value); - dim = 2; - end - elseif all(cellfun(@iscolumn, value)) - dim = 2; - end - else - if all(cellfun(@isscalar, value)) - dim = 2; - if all(cellfun(@iscell, value)) % Singleton col vector [[a],[b]]. - value = cat(1, value{:}); - mergeable = is_mergeable_(value); - dim = 1; - end - elseif all(cellfun(@isrow, value)) - dim = 1; - end - end - if mergeable - value = cat(dim, value{:}); - end - end -end - -function flag = is_mergeable_(value) -%CHECK_MERGEABLE_ Check if the cell array is mergeabhe. - signature = type_info_(value{1}); - flag = true; - for i = 2:numel(value) - vec = type_info_(value{i}); - flag = numel(signature) == numel(vec) && all(signature == vec); - if ~flag, break; end - end -end - -function vec = type_info_(value) -%TYPE_INFO_ Return binary encoding of type information - vec = [uint8(class(value)), typecast(size(value), 'uint8')]; - if isstruct(value) - fields = fieldnames(value); - vec = [vec, uint8([fields{:}])]; - end -end - - - -function y = base64decode(x) - %BASE64DECODE Perform base64 decoding on a string. - % - % BASE64DECODE(STR) decodes the given base64 string STR. - % - % Any character not part of the 65-character base64 subset set is silently - % ignored. - % - % This function is used to decode strings from the Base64 encoding specified - % in RFC 2045 - MIME (Multipurpose Internet Mail Extensions). The Base64 - % encoding is designed to represent arbitrary sequences of octets in a form - % that need not be humanly readable. A 65-character subset ([A-Za-z0-9+/=]) - % of US-ASCII is used, enabling 6 bits to be represented per printable - % character. - % - % See also BASE64ENCODE. - - % Author: Peter J. Acklam - % Time-stamp: 2004-09-20 08:20:50 +0200 - % E-mail: pjacklam@online.no - % URL: http://home.online.no/~pjacklam - - % Modified by Guillaume Flandin, May 2008 - - % check number of input arguments - %-------------------------------------------------------------------------- - - error(nargchk(1, 1, nargin)); - - % Perform the following mapping - %-------------------------------------------------------------------------- - % A-Z -> 0 - 25 a-z -> 26 - 51 0-9 -> 52 - 61 - % + -> 62 / -> 63 = -> 64 - % anything else -> NaN - - base64chars = NaN(1,256); - base64chars('ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/=') = 0:64; - x = base64chars(x); - - % Remove/ignore any characters not in the base64 characters list or '=' - %-------------------------------------------------------------------------- - - x = x(~isnan(x)); - - % Replace any incoming padding ('=' -> 64) with a zero pad - %-------------------------------------------------------------------------- - - if x(end-1) == 64, p = 2; x(end-1:end) = 0; - elseif x(end) == 64, p = 1; x(end) = 0; - else p = 0; - end - - % Allocate decoded data array - %-------------------------------------------------------------------------- - - n = length(x) / 4; % number of groups - x = reshape(uint8(x), 4, n); % input data - y = zeros(3, n, 'uint8'); % decoded data - - % Rearrange every 4 bytes into 3 bytes - %-------------------------------------------------------------------------- - % 00aaaaaa 00bbbbbb 00cccccc 00dddddd - % - % to form - % - % aaaaaabb bbbbcccc ccdddddd - - y(1,:) = bitshift(x(1,:), 2); % 6 highest bits of y(1,:) - y(1,:) = bitor(y(1,:), bitshift(x(2,:), -4)); % 2 lowest bits of y(1,:) - - y(2,:) = bitshift(x(2,:), 4); % 4 highest bits of y(2,:) - y(2,:) = bitor(y(2,:), bitshift(x(3,:), -2)); % 4 lowest bits of y(2,:) - - y(3,:) = bitshift(x(3,:), 6); % 2 highest bits of y(3,:) - y(3,:) = bitor(y(3,:), x(4,:)); % 6 lowest bits of y(3,:) - - % Remove any zero pad that was added to make this a multiple of 24 bits - %-------------------------------------------------------------------------- - - if p, y(end-p+1:end) = []; end - - % Reshape to a row vector - %-------------------------------------------------------------------------- - - y = reshape(y, 1, []); -end diff --git a/pymatbridge/matlab/util/json_v0.2.2/json/json_read.m b/pymatbridge/matlab/util/json_v0.2.2/json/json_read.m deleted file mode 100644 index 213fa47..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/json/json_read.m +++ /dev/null @@ -1,29 +0,0 @@ -function value = json_read(filename, varargin) -%READ Load a matlab value from a JSON file. -% -% SYNOPSIS -% -% value = json.read(filename) -% value = json.read(..., optionName, optionValue, ...) -% -% The function parses a JSON file and load into a matlab value. By default, -% numeric literals are converted to double, string is converted to a char -% array, logical literals are converted to logical. A JSON array is converted -% to either a double array, a logical array, a cell array, or a struct -% array. A JSON object is converted to a struct array. -% -% The function takes the same options as json.load. -% -% See also json.load - - fid = 0; - try - fid = fopen(filename, 'r'); - value = json_load(fscanf(fid, '%c', inf)); - fclose(fid); - catch e - if fid ~= 0, fclose(fid); end - rethrow(e); - end - -end diff --git a/pymatbridge/matlab/util/json_v0.2.2/json/json_startup.m b/pymatbridge/matlab/util/json_v0.2.2/json/json_startup.m deleted file mode 100644 index 77c0853..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/json/json_startup.m +++ /dev/null @@ -1,45 +0,0 @@ -function json_startup(varargin) -%STARTUP Initialize runtime environment. -% -% SYNOPSIS -% -% json.startup(optionName, optionValue, ...) -% -% The function internally adds dynamic java class path. This process clears -% any matlab internal states, such as global/persistent variables or mex -% functions. To avoid unexpected state reset, execute this function once before -% using other json API functions. -% -% OPTIONS -% -% The function takes a following option. -% -% 'WarnOnAddPath' Warn when javaaddpath is internally called. Default false. -% -% EXAMPLE -% -% >> json.startup -% -% See also javaaddpath javaclasspath - - WARN_ON_ADDPATH = false; - for i = 1:2:numel(varargin) - switch varargin{i} - case 'WarnOnAddpath', WARN_ON_ADDPATH = logical(varargin{i+1}); - end - end - - jar_file = fullfile(fileparts(mfilename('fullpath')), 'java', 'json.jar'); - if ~any(strcmp(jar_file, javaclasspath)) - javaaddpath(jar_file); - if WARN_ON_ADDPATH - warning('json:startup', ['Adding json.jar to the dynamic Java class ' ... - 'path. This has cleared matlab internal states, such as global '... - 'variables, persistent variables, or mex functions. To avoid this, '... - 'call json.startup before using other json API functions. See '... - 'javaaddpath for more ' ... - 'information.' ... - ]); - end - end -end diff --git a/pymatbridge/matlab/util/json_v0.2.2/json/json_write.m b/pymatbridge/matlab/util/json_v0.2.2/json/json_write.m deleted file mode 100644 index 8d8862c..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/json/json_write.m +++ /dev/null @@ -1,29 +0,0 @@ -function json_write(value, filename, varargin) -%WRITE Write a matlab value into a JSON file. -% -% SYNOPSIS -% -% json.write(value, filename) -% json.write(..., optionName, optionValue, ...) -% -% The function saves a matlab value in a JSON file. A value can be any -% of a double array, a logical array, a char array, a cell array, or a -% struct array. Numeric values other than double are converted to double. -% A struct array is mapped to a JSON object. However, since a JSON object -% is unordered, the order of field names are not preserved. -% -% The function takes the same options as json.dump. -% -% See also json.dump - - fid = 0; - try - fid = fopen(filename, 'w'); - fprintf(fid, '%s', json_dump(value, varargin{:})); - fclose(fid); - catch e - if fid ~= 0, fclose(fid); end - rethrow(e); - end - -end diff --git a/pymatbridge/matlab/util/json_v0.2.2/test/test_all.m b/pymatbridge/matlab/util/json_v0.2.2/test/test_all.m deleted file mode 100644 index 30a7c9c..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/test/test_all.m +++ /dev/null @@ -1,13 +0,0 @@ -function test_all -%TEST_ALL Run all tests. - - files = dir(fullfile('test', 'test_*.m')); - for i = 1:numel(files) - fname = strrep(files(i).name, '.m', ''); - if ~strcmp(fname, 'test_all') - fprintf('== %s ==\n', fname); - feval(fname); - end - end - -end diff --git a/pymatbridge/matlab/util/json_v0.2.2/test/test_dump.m b/pymatbridge/matlab/util/json_v0.2.2/test/test_dump.m deleted file mode 100644 index 240b7f6..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/test/test_dump.m +++ /dev/null @@ -1,35 +0,0 @@ -function test_dump -%TEST_DUMP Test json.dump. - - fixtures = {... - [], 'null';... - 1, '1.0';... - true, 'true';... - 'foo', 'foo';... - {}, '[]';... - struct(), '{}';... - 1:5, '[1,2,3,4,5]';... - (1:5)', '[[1],[2],[3],[4],[5]]';... - [1,2;3,4], '[[1,2],[3,4]]';... - {1,2;3,4}, '[[1,2],[3,4]]';... - {[1,2],[3,4]}, '[[1,2],[3,4]]';... - cat(3,[1,2;3,4],[5,6;7,8]), '[[[1,2],[3,4]],[[5,6],[7,8]]]';... - {[1,2;3,4],[5,6;7,8]}, '[[[1,2],[3,4]],[[5,6],[7,8]]]';... - {{}}, '[[]]';... - struct('a',[1,2]), '{"a":[1,2]}';... - struct('a',struct('b',{1,2})), '{"a":[{"b":1},{"b":2}]}';... - {'foo','bar','baz'}, '["foo","bar","baz"]';... - ['foo';'bar';'baz'], '["foo","bar","baz"]';... - }; - - for i = 1:size(fixtures, 1) - str = json.dump(fixtures{i,1}); - if strcmp(str, fixtures{i,2}) - fprintf('PASS\n'); - else - fprintf('FAIL: fixture %d: ''%s'', expected ''%s''.\n',... - i, str, fixtures{i,2}); - end - end - -end \ No newline at end of file diff --git a/pymatbridge/matlab/util/json_v0.2.2/test/test_load.m b/pymatbridge/matlab/util/json_v0.2.2/test/test_load.m deleted file mode 100644 index 1b90706..0000000 --- a/pymatbridge/matlab/util/json_v0.2.2/test/test_load.m +++ /dev/null @@ -1,64 +0,0 @@ -function test_load -%TEST_LOAD Test json.load. - - fixtures = {... - [], 'null';... - 1, '1.0';... - true, 'true';... - 'foo', 'foo';... - {}, '[]';... - struct(), '{}';... - 1:5, '[1,2,3,4,5]';... - (1:5)', '[[1],[2],[3],[4],[5]]';... - [1,2;3,4], '[[1,2],[3,4]]';... - cat(3,[1,2;3,4],[5,6;7,8]), '[[[1,2],[3,4]],[[5,6],[7,8]]]';... - {{}}, '[[]]';... - struct('a',[1,2]), '{"a":[1,2]}';... - struct('a',struct('b',{1,2})), '{"a":[{"b":1},{"b":2}]}';... - {'foo','bar','baz'}, '["foo","bar","baz"]';... - }; - - for i = 1:size(fixtures, 1) - value = json.load(fixtures{i,2}); - if equal_(value, fixtures{i,1}) - fprintf('PASS\n'); - else - fprintf('FAIL: fixture %d: ''%s''.\n', i, fixtures{i,2}); - end - end - -end - -function flag = equal_(value1, value2) -%EQUAL_ Check if two values are the same. - t1 = type_info_(value1); - t2 = type_info_(value2); - flag = numel(t1) == numel(t2) && all(t1 == t2); - if ~flag, return; end - - if iscell(value1) - for i = 1:numel(value1) - flag = equal_(value1{i}, value2{i}); - if ~flag, return; end - end - elseif isstruct(value1) - for j = 1:numel(value1) - fields = fieldnames(value1); - for i = 1:numel(fields) - flag = equal_(value1(j).(fields{i}), value2(j).(fields{i})); - if ~flag, return; end - end - end - elseif ~isempty(value1) - flag = all(value1(:) == value2(:)); - end -end - -function vec = type_info_(value) -%TYPE_INFO_ Return binary encoding of type information - vec = [uint8(class(value)), typecast(size(value), 'uint8')]; - if isstruct(value) - fields = fieldnames(value); - vec = [vec, uint8([fields{:}])]; - end -end \ No newline at end of file diff --git a/pymatbridge/matlab/util/make_figs.m b/pymatbridge/matlab/util/make_figs.m deleted file mode 100644 index 94c32ba..0000000 --- a/pymatbridge/matlab/util/make_figs.m +++ /dev/null @@ -1,23 +0,0 @@ -function fig_files = make_figs(figdir) -% Get all the figures that are currently open (presumably from a cell -% that was just executed): -figHandles = get(0, 'children'); - -fig_files = {}; - -for fig=1:length(figHandles) - h = figHandles(fig); - % We will put all of these in the temp dir with an identifying root, so - % that we can grab all of them into the cell (and they will be deleted - % immediately after being rendered). - filename = fullfile(figdir, ['MatlabFig', sprintf('%03d', fig)]); - saveas(h, [filename, '.png']); - % Once you've saved it, close it, so it doesn't get dragged into the - % scope of other cells - if (strcmp(get(h, 'visible'), 'off')) - close(h); - end - fig_files{fig} = [filename '.png']; -end - -end %function diff --git a/pymatbridge/matlab/util/publish_notebook.m b/pymatbridge/matlab/util/publish_notebook.m deleted file mode 100644 index 85657cb..0000000 --- a/pymatbridge/matlab/util/publish_notebook.m +++ /dev/null @@ -1,38 +0,0 @@ -function publish_notebook(mfile, varargin) -% function publish_notebook(mfile, [outputfile]) -% -% Publish a Matlab m file as an interactive notebook in .ipynb format -% -% Parameters -% ---------- -% mfile : str -% Full path to the input m file. -% outputfile -% Full path to the output .ipynb file - -if length(varargin) - outputfile = sprintf('--outfile %s', varargin{1}); -else - outputfile = ''; -end - -% Matlab system path-setting is broken, so we place the -% publish-notebook executable right here, so we can easily find it -libpath = fileparts(which(mfilename)); -prefix = strsplit(libpath, 'lib'); -binpath = strcat(prefix(1), 'bin'); -cmd_str = sprintf('publish-notebook %s %s', mfile, outputfile); - -setenv('PATH', sprintf('%s:%s', binpath{1}, getenv('PATH'))); -[status, result] = system(cmd_str); - -if status == 0 - disp('Conversion completed'); -else - disp(sprintf('There was a problem converting the file %s:', mfile)); - disp(result) -end - - - - diff --git a/pymatbridge/matlab/util/pymat_eval.m b/pymatbridge/matlab/util/pymat_eval.m deleted file mode 100644 index a564be1..0000000 --- a/pymatbridge/matlab/util/pymat_eval.m +++ /dev/null @@ -1,129 +0,0 @@ -function json_response = pymat_eval(req); -% PYMAT_EVAL: Returns a json object of the result of calling the function -% -% json_response = pymat_eval(req); -% -% This allows you to run any matlab code. req should be a struct with the -% following fields: -% dname: The name of a directory to add to the runtime path before attempting to run the code. -% func_name: The name of a function to invoke. -% func_args: An array of arguments to send to the function. -% nargout: An int specifying how many output arguments are expected. -% -% Should return a json object containing the result. -% -% Based on Max Jaderberg's web_feval - -response.success = true; -response.content = ''; -response.result = ''; -response.stack = {}; - -close all hidden; - -try - % tempname is less likely to get bonked by another process. - diary_file = [tempname() '_diary.txt']; - diary(diary_file); - - % Add function path to current path - if req.dname - addpath(req.dname); - end - - % force a rehash of user functions - rehash - - if iscell(req.func_args) - func_args = req.func_args; - else - % If we don't have a cell, the JSON decoder has managed to merge - % everything into an array, which we don't want - func_args = num2cell(req.func_args, 1); - end - [resp{1:req.nargout}] = feval(req.func_name, func_args{:}); - - if req.nargout == 1 - response.result = resp{1}; - else - response.result = resp; - end - - diary('off'); - - datadir = fullfile(tempdir(),'MatlabData'); - response.content.datadir = [datadir, filesep()]; - if ~exist(datadir, 'dir') - mkdir(datadir); - end - - fig_files = make_figs(datadir); - response.content.figures = fig_files; - - % this will not work on Windows: - %[ignore_status, stdout] = system(['cat ' diary_file]); - % cf. http://rosettacode.org/wiki/Read_entire_file#MATLAB_.2F_Octave - FID = fopen(diary_file,'r'); - if (FID > 0) - [stdout,count] = fread(FID, [1,inf], 'uint8=>char'); - fclose(FID); - response.content.stdout = stdout; - else - response.success = false; - response.content.stdout = sprintf('could not open %s for read',diary_file); - end - delete(diary_file) -catch ME - diary('off'); - response.success = false; - response.content.stdout = ME.message; - - % Retrieve the stack trace. - if ~exist('OCTAVE_VERSION', 'builtin'); - % For MATLAB, just grab it off the exception. - response.stack = ME.stack; - else - % Octave exceptions don't seem to have a 'stack' field, so we use lasterror - % instead. lasterror exists in MATLAB too, but it doesn't seem to return - % the correct stack trace in this case. - err = lasterror(); - stack = err.stack; - - % Strip off fields that aren't available on MException. - stack = rmfield(stack, {'column', 'context', 'scope'}); - - % The 'name' fields here look like 'foo>bar' in Octave, where foo is the - % outermost calling function, and bar is the current function. With - % MException there's only 'bar' so let's strip off the 'foo>'. - - % n.b. strsplit doesn't work in Octave when the delimiter is < or >. - % This bug is fixed in Octave 4.0 (http://savannah.gnu.org/bugs/?44641) - % but we support 3.8, so we use the regex mode as a workaround. - for i = 1:numel(stack) - name = stack(i).name; - name = strsplit(name, '>', 'delimitertype', 'regularexpression'); - stack(i).name = name{end}; - end - - response.stack = stack; - end - - % Strip off the last two frames -- these correspond to pymat_eval and - % matlabserver, which we don't want to expose. - response.stack = response.stack(1:end-2, :); - - % FIXME: The stack is returned as a nx1 struct array, and in Octave json_dump - % throws an error trying to serialize it. Let's just transpose it for now. - response.stack = response.stack'; - % FIXME: json_dump loops infinitely if this is a 1x0 struct array, so - % let's just turn it back into an empty array if so. - if ndims(response.stack) == 2 && ... - size(response.stack, 1) == 1 && ... - size(response.stack, 2) == 0 - response.stack = {}; - end -end - -json_response = json_dump(response); - -end %function diff --git a/pymatbridge/matlab_magic.py b/pymatbridge/matlab_magic.py deleted file mode 100644 index fb2c4df..0000000 --- a/pymatbridge/matlab_magic.py +++ /dev/null @@ -1,217 +0,0 @@ -""" - -matlab_magic -============ - -Magic command interface for interactive work with Matlab(R) via the pymatbridge - -""" - -from shutil import rmtree - -import numpy as np -import IPython - -from IPython.core.displaypub import publish_display_data -from IPython.core.magic import (Magics, magics_class, - line_cell_magic, needs_local_scope) -from IPython.core.magic_arguments import (argument, magic_arguments, - parse_argstring) -from IPython.utils.py3compat import unicode_to_str, PY3 - -import pymatbridge as pymat -from .compat import text_type - - -class MatlabInterperterError(RuntimeError): - """ - Some error occurs while matlab is running - """ - def __init__(self, line, err): - self.line = line - self.err = err - - def __unicode__(self): - s = "Failed to parse and evaluate line %r.\n Matlab error message: %r"%\ - (self.line, self.err) - return s - - if PY3: - __str__ = __unicode__ - else: - def __str__(self): - return unicode_to_str(text_type(self), 'utf-8') - - - -@magics_class -class MatlabMagics(Magics): - """ - A set of magics for interactive work with Matlab(R). - """ - def __init__(self, shell, - matlab='matlab', - pyconverter=np.asarray, - **kwargs): - """ - Parameters - ---------- - - shell : IPython shell - - matlab : str - The system call to start a matlab session. Allows you to choose a - particular version of matlab if you want - - pyconverter : callable - To be called on matlab variables returning into the ipython - namespace - - kwargs: additional key-word arguments to pass to initialization of - the Matlab/Octave process - """ - super(MatlabMagics, self).__init__(shell) - - if 'octave' in matlab.lower(): - self.Matlab = pymat.Octave(matlab, **kwargs) - else: - self.Matlab = pymat.Matlab(matlab, **kwargs) - self.Matlab.start() - self.pyconverter = pyconverter - - def eval(self, line): - """ - Parse and evaluate a single line of matlab - """ - run_dict = self.Matlab.run_code(line) - - if not run_dict['success']: - raise MatlabInterperterError(line, run_dict['content']['stdout']) - - # This is the matlab stdout: - return run_dict - - def set_matlab_var(self, name, value): - """ - Set up a variable in Matlab workspace - """ - run_dict = self.Matlab.set_variable(name, value) - - if not run_dict['success']: - raise MatlabInterperterError(line, run_dict['content']['stdout']) - - - @magic_arguments() - @argument( - '-i', '--input', action='append', - help='Names of input variable from shell.user_ns to be assigned to Matlab variables of the same names after calling self.pyconverter. Multiple names can be passed separated only by commas with no whitespace.' - ) - - @argument( - '-o', '--output', action='append', - help='Names of variables to be pushed from matlab to shell.user_ns after executing cell body and applying self.Matlab.get_variable(). Multiple names can be passed separated only by commas with no whitespace.' - ) - - @argument( - '-s', '--silent', action='store_true', - help='Do not display text output of MATLAB command' - ) - - @argument( - '-S', '--size', action='store', default='512,384', - help='Pixel size of plots, "width,height.' - ) - - @argument( - '-g', '--gui', action='store_true', - help='Show plots in a graphical user interface' - ) - - @argument( - 'code', - nargs='*', - ) - - - @needs_local_scope - @line_cell_magic - def matlab(self, line, cell=None, local_ns=None): - "Execute code in matlab." - - args = parse_argstring(self.matlab, line) - code = line if cell is None else ' '.join(args.code) + cell - - if local_ns is None: - local_ns = {} - - width, height = args.size.split(',') - self.Matlab.set_plot_settings(width, height, not args.gui) - - if args.input: - for input in ','.join(args.input).split(','): - try: - val = local_ns[input] - except KeyError: - val = self.shell.user_ns[input] - # The _Session.set_variable function which this calls - # should correctly detect numpy arrays and serialize them - # as json correctly. - self.set_matlab_var(input, val) - - try: - result_dict = self.eval(code) - except MatlabInterperterError: - raise - except: - raise RuntimeError('\n'.join([ - "There was an error running the code:", - code, - "-----------------------", - "Are you sure Matlab is started?", - ])) - - text_output = result_dict['content']['stdout'] - # Figures get saved by matlab in reverse order... - imgfiles = result_dict['content']['figures'][::-1] - data_dir = result_dict['content']['datadir'] - - display_data = [] - if text_output and not args.silent: - display_data.append(('MatlabMagic.matlab', - {'text/plain': text_output})) - - for imgf in imgfiles: - if len(imgf): - # Store the path to the directory so that you can delete it - # later on: - with open(imgf, 'rb') as fid: - image = fid.read() - display_data.append(('MatlabMagic.matlab', - {'image/png': image})) - - for disp_d in display_data: - publish_display_data(source=disp_d[0], data=disp_d[1]) - - # Delete the temporary data files created by matlab: - if len(data_dir): - rmtree(data_dir) - - if args.output: - for output in ','.join(args.output).split(','): - self.shell.push({output:self.Matlab.get_variable(output)}) - - -_loaded = False -def load_ipython_extension(ip, **kwargs): - """Load the extension in IPython.""" - global _loaded - if not _loaded: - ip.register_magics(MatlabMagics(ip, **kwargs)) - _loaded = True - -def unload_ipython_extension(ip): - global _loaded - if _loaded: - magic = ip.magics_manager.registry.pop('MatlabMagics') - magic.Matlab.stop() - _loaded = False diff --git a/pymatbridge/messenger/__init__.py b/pymatbridge/messenger/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/pymatbridge/messenger/make.py b/pymatbridge/messenger/make.py deleted file mode 100755 index 20045bc..0000000 --- a/pymatbridge/messenger/make.py +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/python - -""" -Make : building messenger mex file. - -Some functions have been taken from the pexpect module (https://pexpect.readthedocs.org/en/latest/) - -The license for pexpect is below: - - This license is approved by the OSI and FSF as GPL-compatible. - http://opensource.org/licenses/isc-license.txt - - Copyright (c) 2012, Noah Spurrier - PERMISSION TO USE, COPY, MODIFY, AND/OR DISTRIBUTE THIS SOFTWARE FOR ANY - PURPOSE WITH OR WITHOUT FEE IS HEREBY GRANTED, PROVIDED THAT THE ABOVE - COPYRIGHT NOTICE AND THIS PERMISSION NOTICE APPEAR IN ALL COPIES. - THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF - OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. -""" - -from __future__ import print_function -import os -import platform -import sys -import shlex -import shutil -import subprocess -import stat - -try: - import pty -except ImportError: - pty = None - -def is_executable_file(path): - """Checks that path is an executable regular file (or a symlink to a file). - - This is roughly ``os.path isfile(path) and os.access(path, os.X_OK)``, but - on some platforms :func:`os.access` gives us the wrong answer, so this - checks permission bits directly. - - Note - ---- - This function is taken from the pexpect module, see module doc-string for - license. - """ - # follow symlinks, - fpath = os.path.realpath(path) - - # return False for non-files (directories, fifo, etc.) - if not os.path.isfile(fpath): - return False - - # On Solaris, etc., "If the process has appropriate privileges, an - # implementation may indicate success for X_OK even if none of the - # execute file permission bits are set." - # - # For this reason, it is necessary to explicitly check st_mode - - # get file mode using os.stat, and check if `other', - # that is anybody, may read and execute. - mode = os.stat(fpath).st_mode - if mode & stat.S_IROTH and mode & stat.S_IXOTH: - return True - - # get current user's group ids, and check if `group', - # when matching ours, may read and execute. - user_gids = os.getgroups() + [os.getgid()] - if (os.stat(fpath).st_gid in user_gids and - mode & stat.S_IRGRP and mode & stat.S_IXGRP): - return True - - # finally, if file owner matches our effective userid, - # check if `user', may read and execute. - user_gids = os.getgroups() + [os.getgid()] - if (os.stat(fpath).st_uid == os.geteuid() and - mode & stat.S_IRUSR and mode & stat.S_IXUSR): - return True - - return False - - -def which(filename): - '''This takes a given filename; tries to find it in the environment path; - then checks if it is executable. This returns the full path to the filename - if found and executable. Otherwise this returns None. - - Note - ---- - This function is taken from the pexpect module, see module doc-string for - license. - ''' - - # Special case where filename contains an explicit path. - if os.path.dirname(filename) != '' and is_executable_file(filename): - return filename - if 'PATH' not in os.environ or os.environ['PATH'] == '': - p = os.defpath - else: - p = os.environ['PATH'] - pathlist = p.split(os.pathsep) - for path in pathlist: - ff = os.path.join(path, filename) - if pty: - if is_executable_file(ff): - return ff - else: - pathext = os.environ.get('Pathext', '.exe;.com;.bat;.cmd') - pathext = pathext.split(os.pathsep) + [''] - for ext in pathext: - if os.access(ff + ext, os.X_OK): - return ff + ext - return None - - -use_shell = True if sys.platform.startswith("win32") else False - - -def make_str(byte_or_str): - return byte_or_str if isinstance(byte_or_str, str) \ - else str(byte_or_str.decode("UTF-8")) - - -def esc(path): - if ' ' in path: - return '"' + path + '"' - else: - return path - - -def get_messenger_dir(): - # Check the system platform first - splatform = sys.platform - - if splatform.startswith('linux'): - messenger_dir = 'mexa64' - elif splatform.startswith('darwin'): - messenger_dir = 'mexmaci64' - elif splatform.startswith('win32'): - if splatform == "win32": - # We have a win64 messenger, so we need to figure out if this is 32 - # or 64 bit Windows: - if not platform.machine().endswith('64'): - raise ValueError("pymatbridge does not work on win32") - - # We further need to differentiate 32 from 64 bit: - maxint = sys.maxsize - if maxint == 9223372036854775807: - messenger_dir = 'mexw64' - elif maxint == 2147483647: - messenger_dir = 'mexw32' - return messenger_dir - - -def get_config(): - messenger_dir = get_messenger_dir() - with open(os.path.join(messenger_dir, 'local.cfg')) as fid: - lines = fid.readlines() - - cfg = {} - for line in lines: - if '=' not in line: - continue - name, path = line.split('=') - cfg[name.lower()] = path.strip() or '.' - return cfg - - -def do_build(make_cmd, messenger_exe): - print('Building %s...' % messenger_exe) - print(make_cmd) - messenger_dir = get_messenger_dir() - subprocess.check_output(shlex.split(make_cmd), shell=use_shell) - - messenger_loc = os.path.join(messenger_dir, messenger_exe) - - shutil.move(messenger_exe, messenger_loc) - - if os.path.exists('messenger.o'): - os.remove('messenger.o') - - -def build_octave(): - paths = "-L%(octave_lib)s -I%(octave_inc)s -L%(zmq_lib)s -I%(zmq_inc)s" - paths = paths % get_config() - make_cmd = "mkoctfile --mex %s -lzmq ./src/messenger.c" % paths - do_build(make_cmd, 'messenger.mex') - - -def which_matlab(): - try: - matlab_path = which('matlab').strip() - matlab_path = make_str(matlab_path) - return os.path.dirname(os.path.realpath(matlab_path)) - except (OSError, subprocess.CalledProcessError): - def ensure_path(path, extension=''): - return os.path.isdir(path) and \ - os.path.isfile(os.path.join(path, "matlab" + extension)) - - # need to guess the location of MATLAB - if sys.platform.startswith("darwin"): - MATLABs = [os.path.join("/Applications", i, "bin") - for i in os.listdir("/Applications") - if i.startswith("MATLAB_R")] - # only want ones with MATLAB executables - # sort so we can get the latest - MATLABs = list(sorted(filter(ensure_path, MATLABs))) - return MATLABs[-1] if len(MATLABs) > 0 else None - elif sys.platform.startswith("win32"): - MATLAB_loc = "C:\\Program Files\\MATLAB" - print(MATLAB_loc) - if not os.path.isdir(MATLAB_loc): - return None - MATLABs = [os.path.join(MATLAB_loc, i, "bin") - for i in os.listdir(MATLAB_loc)] - print(MATLABs) - print(i) - # only want ones with MATLAB executables - # sort so we can get the latest - MATLABs = list(sorted(filter(lambda x: ensure_path(x, ".exe"), - MATLABs))) - print(MATLABs) - return MATLABs[-1] if len(MATLABs) > 0 else None - elif sys.platform.startswith("linux"): - MATLAB_loc = "/usr/local/MATLAB/" - if not os.path.isdir(MATLAB_loc): - return None - MATLABs = [os.path.join(MATLAB_loc, i, "bin") - for i in os.listdir(MATLAB_loc) - if i.startswith("R")] - # only want ones with MATLAB executables - # sort so we can get the latest - MATLABs = list(sorted(filter(ensure_path, MATLABs))) - return MATLABs[-1] if len(MATLABs) > 0 else None - - -def build_matlab(static=False): - """build the messenger mex for MATLAB - - static : bool - Determines if the zmq library has been statically linked. - If so, it will append the command line option -DZMQ_STATIC - when compiling the mex so it matches libzmq. - """ - cfg = get_config() - # To deal with spaces, remove quotes now, and add - # to the full commands themselves. - if 'matlab_bin' in cfg and cfg['matlab_bin'] != '.': - matlab_bin = cfg['matlab_bin'].strip('"') - else: # attempt to autodetect MATLAB filepath - matlab_bin = which_matlab() - if matlab_bin is None: - raise ValueError("specify 'matlab_bin' in cfg file") - # Get the extension - extcmd = esc(os.path.join(matlab_bin, "mexext")) - extension = subprocess.check_output(extcmd, shell=use_shell) - extension = extension.decode('utf-8').rstrip('\r\n') - - # Build the mex file - mex = esc(os.path.join(matlab_bin, "mex")) - paths = "-L%(zmq_lib)s -I%(zmq_inc)s" % cfg - make_cmd = '%s -O %s -lzmq ./src/messenger.c' % (mex, paths) - if static: - make_cmd += ' -DZMQ_STATIC' - do_build(make_cmd, 'messenger.%s' % extension) - - -if __name__ == '__main__': - import argparse - parser = argparse.ArgumentParser() - parser.add_argument( - "target", - choices=["matlab", "octave"], - type=str.lower, - help="target to be built") - parser.add_argument("--static", action="store_true", - help="staticly link libzmq") - args = parser.parse_args() - if args.target == "matlab": - build_matlab(static=args.static) - elif args.target == "octave": - if args.static: - raise ValueError("static building not yet supported for octave") - build_octave() - else: - raise ValueError() diff --git a/pymatbridge/messenger/mexa64/local.cfg b/pymatbridge/messenger/mexa64/local.cfg deleted file mode 100644 index a9a742c..0000000 --- a/pymatbridge/messenger/mexa64/local.cfg +++ /dev/null @@ -1,6 +0,0 @@ -MATLAB_BIN= -OCTAVE_INC=/usr/include -OCTAVE_LIB=/usr/lib/x86_64-linux-gnu/ -ZMQ_INC= -ZMQ_LIB= - diff --git a/pymatbridge/messenger/mexa64/messenger.mex b/pymatbridge/messenger/mexa64/messenger.mex deleted file mode 100755 index 85afaa9..0000000 Binary files a/pymatbridge/messenger/mexa64/messenger.mex and /dev/null differ diff --git a/pymatbridge/messenger/mexa64/messenger.mex.zmq4 b/pymatbridge/messenger/mexa64/messenger.mex.zmq4 deleted file mode 100755 index 65e467c..0000000 Binary files a/pymatbridge/messenger/mexa64/messenger.mex.zmq4 and /dev/null differ diff --git a/pymatbridge/messenger/mexa64/messenger.mexa64 b/pymatbridge/messenger/mexa64/messenger.mexa64 deleted file mode 100755 index f585eab..0000000 Binary files a/pymatbridge/messenger/mexa64/messenger.mexa64 and /dev/null differ diff --git a/pymatbridge/messenger/mexmaci64/local.cfg b/pymatbridge/messenger/mexmaci64/local.cfg deleted file mode 100644 index 138795a..0000000 --- a/pymatbridge/messenger/mexmaci64/local.cfg +++ /dev/null @@ -1,5 +0,0 @@ -MATLAB_BIN= -ZMQ_INC= -ZMQ_LIB= -OCTAVE_INC= -OCTAVE_LIB= diff --git a/pymatbridge/messenger/mexmaci64/messenger.mex b/pymatbridge/messenger/mexmaci64/messenger.mex deleted file mode 100755 index 27dbcd6..0000000 Binary files a/pymatbridge/messenger/mexmaci64/messenger.mex and /dev/null differ diff --git a/pymatbridge/messenger/mexmaci64/messenger.mex.zmq3 b/pymatbridge/messenger/mexmaci64/messenger.mex.zmq3 deleted file mode 100755 index c394ada..0000000 Binary files a/pymatbridge/messenger/mexmaci64/messenger.mex.zmq3 and /dev/null differ diff --git a/pymatbridge/messenger/mexmaci64/messenger.mexmaci64 b/pymatbridge/messenger/mexmaci64/messenger.mexmaci64 deleted file mode 100755 index a48edc0..0000000 Binary files a/pymatbridge/messenger/mexmaci64/messenger.mexmaci64 and /dev/null differ diff --git a/pymatbridge/messenger/mexmaci64/messenger.mexmaci64.zmq3 b/pymatbridge/messenger/mexmaci64/messenger.mexmaci64.zmq3 deleted file mode 100755 index dc77206..0000000 Binary files a/pymatbridge/messenger/mexmaci64/messenger.mexmaci64.zmq3 and /dev/null differ diff --git a/pymatbridge/messenger/mexw64/README.md b/pymatbridge/messenger/mexw64/README.md deleted file mode 100644 index 47100e8..0000000 --- a/pymatbridge/messenger/mexw64/README.md +++ /dev/null @@ -1,41 +0,0 @@ -Dynamically linked building instructions ----------------------------------------- - -1) Install zeromq from the website: http://zeromq.org/distro:microsoft-windows - -2) Rename one of the lib/libzmq-*.lib files to libzmq.lib in the ZeroMQ - installation directory - -3) Add the ZeroMQ bin directory to your path. - -4) Edit the messenger/mexw64/local.cfg file in messenger to point to the - zeromq install directory (you will need to update both ZMQ_INC and ZMQ_LIB). - Also ensure the MATLAB directory is correct. - -5) Run ```make.py matlab``` in the messenger directory. This should build - messenger.mexw64 - -Statically linked building instructions ---------------------------------------- - -A statically linked library has the advantage of not requiring libzmq.dll to -be found in the path. For this reason, including it in the installer results -in a simpler and more robust installation process. While building a statically -linked mex is simple in practice, but because zeromq (as of 3/10/15) does not -provide a .lib for static linking with the windows installer, you will need to -compile this yourself. These directions are from zeromq 4.0.5. - -1) Download and unzip the zeromq zip file (listed as Windows sources) from - http://zeromq.org/intro:get-the-software - -2) In the builds/msvc directory open the msvc.sln file in Visual Studio. - -3) Create a new Platform for x64. In the Librarian section of properties, set - the target section to /Machine:X64 - -4) Build libzmq with the "StaticRelease" for x64. - -5) Edit the messenger/mexw64/local.cfg file to point to where you built ZeroMQ - and your MATLAB bin directory. - -6) Build messenger.mexw64 with ```make matlab --static``` diff --git a/pymatbridge/messenger/mexw64/local.cfg b/pymatbridge/messenger/mexw64/local.cfg deleted file mode 100644 index ab61682..0000000 --- a/pymatbridge/messenger/mexw64/local.cfg +++ /dev/null @@ -1,5 +0,0 @@ -MATLAB_BIN="C:\Program Files\MATLAB\2013a\bin" -OCTAVE_INC="C:\Octave\Octave-3.8.2\include\octave-3.8.2\octave" -OCTAVE_LIB="C:\Octave\Octave-3.8.2\lib\octave\3.8.2" -ZMQ_INC="C:\zeromq-4.0.5\include" -ZMQ_LIB="C:\zeromq-4.0.5\lib" diff --git a/pymatbridge/messenger/mexw64/messenger.mex b/pymatbridge/messenger/mexw64/messenger.mex deleted file mode 100644 index 59fb4e0..0000000 Binary files a/pymatbridge/messenger/mexw64/messenger.mex and /dev/null differ diff --git a/pymatbridge/messenger/mexw64/messenger.mexw64 b/pymatbridge/messenger/mexw64/messenger.mexw64 deleted file mode 100644 index 3f0abd5..0000000 Binary files a/pymatbridge/messenger/mexw64/messenger.mexw64 and /dev/null differ diff --git a/pymatbridge/messenger/src/messenger.c b/pymatbridge/messenger/src/messenger.c deleted file mode 100644 index 102999e..0000000 --- a/pymatbridge/messenger/src/messenger.c +++ /dev/null @@ -1,161 +0,0 @@ -#include -#include -#include -#include "mex.h" -#include "zmq.h" - -/* Set a 200MB receiver buffer size */ -#define BUFLEN 200000000 - -/* The variable cannot be named socket on windows */ -void *ctx, *socket_ptr; -static int initialized = 0; - -/* Initialize a ZMQ server */ -int initialize(char *socket_addr) { - int rc; - mexLock(); - ctx = zmq_ctx_new(); - socket_ptr = zmq_socket(ctx, ZMQ_REP); - rc = zmq_bind(socket_ptr, socket_addr); - - if (!rc) { - initialized = 1; - return 0; - } else { - return -1; - } -} - -/* Check if the ZMQ server is intialized and print an error if not */ -int checkInitialized(void) { - if (!initialized) { - mexErrMsgTxt("Error: ZMQ session not initialized"); - return 0; - } - else { - return 1; - } -} - - -/* Cleaning up after session finished */ -void cleanup (void) { - /* Send a confirmation message to the client */ - zmq_send(socket_ptr, "exit", 4, 0); - - zmq_close(socket_ptr); - mexPrintf("Socket closed\n"); - zmq_term(ctx); - mexPrintf("Context terminated\n"); -} - - -/* Gateway function with Matlab */ -void mexFunction(int nlhs, mxArray *plhs[], - int nrhs, const mxArray *prhs[]) { - char *cmd; - /* If no input argument, print out the usage */ - if (nrhs == 0) { - mexErrMsgTxt("Usage: messenger('init|listen|respond', extra1, extra2, ...)"); - } - - /* Get the input command */ - if(!(cmd = mxArrayToString(prhs[0]))) { - mexErrMsgTxt("Cannot read the command"); - } - - /* Initialize a new server session */ - if (strcmp(cmd, "init") == 0) { - char *socket_addr; - mxLogical *p; - - /* Check if the input format is valid */ - if (nrhs != 2) { - mexErrMsgTxt("Missing argument: socket address"); - } - if (!(socket_addr = mxArrayToString(prhs[1]))) { - mexErrMsgTxt("Cannot read socket address"); - } - - plhs[0] = mxCreateLogicalMatrix(1, 1); - p = mxGetLogicals(plhs[0]); - - if (!initialized) { - if (!initialize(socket_addr)) { - p[0] = 1; - mexPrintf("Socket created at: %s\n", socket_addr); - } else { - p[0] = 0; - mexErrMsgTxt("Socket creation failed."); - } - } else { - mexErrMsgTxt("One socket has already been initialized."); - } - - return; - - /* Listen over an existing socket */ - } else if (strcmp(cmd, "listen") == 0) { - int byte_recvd; - char *recv_buffer = mxCalloc(BUFLEN, sizeof(char)); - zmq_pollitem_t polls[] = {{socket_ptr, 0, ZMQ_POLLIN, 0}}; - - if (!checkInitialized()) return; - - /* allow MATLAB to draw its graphics every 20ms */ - while (zmq_poll(polls, 1, 20000) == 0) { - mexEvalString("drawnow"); - } - - byte_recvd = zmq_recv(socket_ptr, recv_buffer, BUFLEN, 0); - - /* Check if the received data is complete and correct */ - if ((byte_recvd > -1) && (byte_recvd <= BUFLEN)) { - plhs[0] = mxCreateString(recv_buffer); - } else if (byte_recvd > BUFLEN){ - mexErrMsgTxt("Receiver buffer overflow. Message truncated"); - } else { - sprintf(recv_buffer, "Failed to receive a message due to ZMQ error %s", strerror(errno)); - mexErrMsgTxt(recv_buffer); - } - - return; - - /* Send a message out */ - } else if (strcmp(cmd, "respond") == 0) { - size_t msglen; - char *msg_out; - mxLogical *p; - - /* Check if the input format is valid */ - if (nrhs != 2) { - mexErrMsgTxt("Please provide the message to send"); - } - - if (!checkInitialized()) return; - - msglen = mxGetNumberOfElements(prhs[1]); - msg_out = mxArrayToString(prhs[1]); - - plhs[0] = mxCreateLogicalMatrix(1, 1); - p = mxGetLogicals(plhs[0]); - - if (msglen == zmq_send(socket_ptr, msg_out, msglen, 0)) { - p[0] = 1; - } else { - p[0] = 0; - mexErrMsgTxt("Failed to send message due to ZMQ error"); - } - - return; - - /* Close the socket and context */ - } else if (strcmp(cmd, "exit") == 0) { - cleanup(); - - return; - } else { - mexErrMsgTxt("Unidentified command"); - } -} diff --git a/pymatbridge/publish.py b/pymatbridge/publish.py deleted file mode 100644 index 213d3cb..0000000 --- a/pymatbridge/publish.py +++ /dev/null @@ -1,135 +0,0 @@ -try: - import nbformat.v4 as nbformat - from nbformat import write as nbwrite -except ImportError: - import IPython.nbformat.v4 as nbformat - from IPython.nbformat import write as nbwrite - -import numpy as np - - -def format_line(line): - """ - Format a line of Matlab into either a markdown line or a code line. - - Parameters - ---------- - line : str - The line of code to be formatted. Formatting occurs according to the - following rules: - - - If the line starts with (at least) two %% signs, a new cell will be - started. - - - If the line doesn't start with a '%' sign, it is assumed to be legit - matlab code. We will continue to add to the same cell until reaching - the next comment line - """ - if line.startswith('%%'): - md = True - new_cell = True - source = line.split('%%')[1] + '\n' # line-breaks in md require a line - # gap! - - elif line.startswith('%'): - md = True - new_cell = False - source = line.split('%')[1] + '\n' - - else: - md = False - new_cell = False - source = line - - - return new_cell, md, source - - -def mfile_to_lines(mfile): - """ - Read the lines from an mfile - - Parameters - ---------- - mfile : string - Full path to an m file - """ - # We should only be able to read this file: - with open(mfile) as fid: - return fid.readlines() - - -def lines_to_notebook(lines, name=None): - """ - Convert the lines of an m file into an IPython notebook - - Parameters - ---------- - lines : list - A list of strings. Each element is a line in the m file - - Returns - ------- - notebook : an IPython NotebookNode class instance, containing the - information required to create a file - - - """ - source = [] - md = np.empty(len(lines), dtype=object) - new_cell = np.empty(len(lines), dtype=object) - for idx, l in enumerate(lines): - new_cell[idx], md[idx], this_source = format_line(l) - # Transitions between markdown and code and vice-versa merit a new - # cell, even if no newline, or "%%" is found. Make sure not to do this - # check for the very first line! - if idx>1 and not new_cell[idx]: - if md[idx] != md[idx-1]: - new_cell[idx] = True - - source.append(this_source) - # This defines the breaking points between cells: - new_cell_idx = np.hstack([np.where(new_cell)[0], -1]) - - # Listify the sources: - cell_source = [source[new_cell_idx[i]:new_cell_idx[i+1]] - for i in range(len(new_cell_idx)-1)] - cell_md = [md[new_cell_idx[i]] for i in range(len(new_cell_idx)-1)] - cells = [] - - # Append the notebook with loading matlab magic extension - notebook_head = "import pymatbridge as pymat\n" + "ip = get_ipython()\n" \ - + "pymat.load_ipython_extension(ip)" - cells.append(nbformat.new_code_cell(notebook_head))#, language='python')) - - for cell_idx, cell_s in enumerate(cell_source): - if cell_md[cell_idx]: - cells.append(nbformat.new_markdown_cell(cell_s)) - else: - cell_s.insert(0, '%%matlab\n') - cells.append(nbformat.new_code_cell(cell_s))#, language='matlab')) - - #ws = nbformat.new_worksheet(cells=cells) - notebook = nbformat.new_notebook(cells=cells) - return notebook - - -def convert_mfile(mfile, outfile=None): - """ - Convert a Matlab m-file into a Matlab notebook in ipynb format - - Parameters - ---------- - mfile : string - Full path to a matlab m file to convert - - outfile : string (optional) - Full path to the output ipynb file - - """ - lines = mfile_to_lines(mfile) - nb = lines_to_notebook(lines) - if outfile is None: - outfile = mfile.split('.m')[0] + '.ipynb' - with open(outfile, 'w') as fid: - nbwrite(nb, fid) diff --git a/pymatbridge/pymatbridge.py b/pymatbridge/pymatbridge.py deleted file mode 100644 index e107532..0000000 --- a/pymatbridge/pymatbridge.py +++ /dev/null @@ -1,581 +0,0 @@ -""" -pymatbridge -=========== - -This is a module for communicating and running Matlab from within python - -Example -------- - ->>> import pymatbridge ->>> m = pymatbridge.Matlab() ->>> m.start() -Starting MATLAB on ZMQ socket ipc:///tmp/pymatbridge -Send 'exit' command to kill the server -.MATLAB started and connected! -True ->>> m.run_code('a=1;') -{'content': {'stdout': '', 'datadir': '/private/tmp/MatlabData/', 'code': 'a=1;', 'figures': []}, 'success': True} ->>> m.get_variable('a') -1 - -""" - -import atexit -import os -import time -import base64 -import zmq -import subprocess -import sys -import json -import types -import weakref -import random -from uuid import uuid4 - -from numpy import ndarray, generic, float64, frombuffer, asfortranarray - -from pymatbridge.messenger.make import get_messenger_dir - -try: - from scipy.sparse import spmatrix -except ImportError: - class spmatrix: - pass - - -def encode_ndarray(obj): - """Write a numpy array and its shape to base64 buffers""" - shape = obj.shape - if len(shape) == 1: - shape = (1, obj.shape[0]) - if obj.flags.c_contiguous: - obj = obj.T - elif not obj.flags.f_contiguous: - obj = asfortranarray(obj.T) - else: - obj = obj.T - try: - data = obj.astype(float64).tobytes() - except AttributeError: - data = obj.astype(float64).tostring() - - data = base64.b64encode(data).decode('utf-8') - return data, shape - - -# JSON encoder extension to handle complex numbers and numpy arrays -class PymatEncoder(json.JSONEncoder): - - def default(self, obj): - if isinstance(obj, ndarray) and obj.dtype.kind in 'uif': - data, shape = encode_ndarray(obj) - return {'ndarray': True, 'shape': shape, 'data': data} - elif isinstance(obj, ndarray) and obj.dtype.kind == 'c': - real, shape = encode_ndarray(obj.real.copy()) - imag, _ = encode_ndarray(obj.imag.copy()) - return {'ndarray': True, 'shape': shape, - 'real': real, 'imag': imag} - elif isinstance(obj, ndarray): - return obj.tolist() - elif isinstance(obj, complex): - return {'real': obj.real, 'imag': obj.imag} - elif isinstance(obj, generic): - return obj.item() - # Handle the default case - return json.JSONEncoder.default(self, obj) - - -def decode_arr(data): - """Extract a numpy array from a base64 buffer""" - data = data.encode('utf-8') - return frombuffer(base64.b64decode(data), float64) - - -# JSON decoder for arrays and complex numbers -def decode_pymat(dct): - if 'ndarray' in dct and 'data' in dct: - value = decode_arr(dct['data']) - shape = dct['shape'] - if type(dct['shape']) is not list: - shape = decode_arr(dct['shape']).astype(int) - return value.reshape(shape, order='F') - elif 'ndarray' in dct and 'imag' in dct: - real = decode_arr(dct['real']) - imag = decode_arr(dct['imag']) - shape = decode_arr(dct['shape']).astype(int) - data = real + 1j * imag - return data.reshape(shape, order='F') - elif 'real' in dct and 'imag' in dct: - return complex(dct['real'], dct['imag']) - return dct - -MATLAB_FOLDER = '%s/matlab' % os.path.realpath(os.path.dirname(__file__)) -MESSENGER_FOLDER = '%s/messenger/%s' % (os.path.realpath(os.path.dirname(__file__)), get_messenger_dir()) - - -class _Session(object): - """ - A class for communicating with a MATLAB session. It provides the behavior - common across different MATLAB implementations. You shouldn't instantiate - this directly; rather, use the Matlab or Octave subclasses. - """ - - def __init__(self, executable, socket_addr=None, - id='python-matlab-bridge', log=False, maxtime=60, - platform=None, startup_options=None): - """ - Initialize this thing. - - Parameters - ---------- - - executable : str - A string that would start the session at the terminal. - - socket_addr : str - A string that represents a valid ZMQ socket address, such as - "ipc:///tmp/pymatbridge", "tcp://127.0.0.1:55555", etc. Default is - to choose a random IPC file name, or a random socket (for TCP). - - id : str - An identifier for this instance of the pymatbridge. - - log : bool - Whether to save a log file in some known location. - - maxtime : float - The maximal time to wait for a response from the session (optional, - Default is 10 sec) - - platform : string - The OS of the machine on which this is running. Per default this - will be taken from sys.platform. - - startup_options : string - Command line options to include in the executable's invocation. - Optional; sensible defaults are used if this is not provided. - """ - self.started = False - self.executable = executable - self.socket_addr = socket_addr - self.id = id - self.log = log - self.maxtime = maxtime - self.platform = platform if platform is not None else sys.platform - self.startup_options = startup_options - - if socket_addr is None: - self.socket_addr = "tcp://127.0.0.1" if self.platform == "win32" else "ipc:///tmp/pymatbridge-%s"%str(uuid4()) - - if self.log: - startup_options += ' > ./pymatbridge/logs/bashlog_%s.txt' % self.id - - self.context = None - self.socket = None - atexit.register(self.stop) - - def _program_name(self): # pragma: no cover - raise NotImplemented - - def _preamble_code(self): - # suppress warnings while loading the path, in the case of - # overshadowing a built-in function on a newer version of - # Matlab (e.g. isrow) - return ["old_warning_state = warning('off','all');", - "addpath(genpath('%s'));" % MATLAB_FOLDER, - "addpath('%s');" % MESSENGER_FOLDER, - "warning(old_warning_state);", - "clear('old_warning_state');", - "cd('%s');" % os.getcwd()] - - def _execute_flag(self): # pragma: no cover - raise NotImplemented - - def _run_server(self): - code = self._preamble_code() - code.extend([ - "matlabserver('%s')" % self.socket_addr - ]) - command = '%s %s %s "%s"' % (self.executable, self.startup_options, - self._execute_flag(), ','.join(code)) - subprocess.Popen(command, shell=True, stdin=subprocess.PIPE, - stdout=subprocess.PIPE) - - # Start server/client session and make the connection - def start(self): - # Setup socket - self.context = zmq.Context() - self.socket = self.context.socket(zmq.REQ) - if self.platform == "win32": - rndport = random.randrange(49152, 65536) - self.socket_addr = self.socket_addr + ":%s"%rndport - - # Start the MATLAB server in a new process - print("Starting %s on ZMQ socket %s" % (self._program_name(), self.socket_addr)) - print("Send 'exit' command to kill the server") - self._run_server() - - # Start the client - self.socket.connect(self.socket_addr) - - self.started = True - - # Test if connection is established - if self.is_connected(): - print("%s started and connected!" % self._program_name()) - self.set_plot_settings() - return self - else: - raise ValueError("%s failed to start" % self._program_name()) - - def _response(self, **kwargs): - req = json.dumps(kwargs, cls=PymatEncoder) - self.socket.send_string(req) - resp = self.socket.recv_string() - return resp - - # Stop the Matlab server - def stop(self): - if not self.started: - return True - - # Matlab should respond with "exit" if successful - if self._response(cmd='exit') == "exit": - print("%s closed" % self._program_name()) - - self.started = False - return True - - # To test if the client can talk to the server - def is_connected(self): - if not self.started: - time.sleep(2) - return False - - req = json.dumps(dict(cmd="connect"), cls=PymatEncoder) - self.socket.send_string(req) - - start_time = time.time() - while True: - try: - resp = self.socket.recv_string(flags=zmq.NOBLOCK) - return resp == "connected" - except zmq.ZMQError: - sys.stdout.write('.') - time.sleep(1) - if time.time() - start_time > self.maxtime: - print("%s session timed out after %d seconds" % (self._program_name(), self.maxtime)) - return False - - def is_function_processor_working(self): - result = self.run_func('%s/usrprog/test_sum.m' % MATLAB_FOLDER, - {'echo': '%s: Function processor is working!' % self._program_name()}) - return result['success'] - - def _json_response(self, **kwargs): - return json.loads(self._response(**kwargs), object_hook=decode_pymat) - - def run_func(self, func_path, *func_args, **kwargs): - """Run a function in Matlab and return the result. - - Parameters - ---------- - func_path: str - Name of function to run or a path to an m-file. - func_args: object, optional - Function args to send to the function. - nargout: int, optional - Desired number of return arguments. - kwargs: - Keyword arguments are passed to Matlab in the form [key, val] so - that matlab.plot(x, y, '--', LineWidth=2) would be translated into - plot(x, y, '--', 'LineWidth', 2) - - Returns - ------- - Result dictionary with keys: 'message', 'result', and 'success' - """ - if not self.started: - raise ValueError('Session not started, use start()') - - nargout = kwargs.pop('nargout', 1) - func_args += tuple(item for pair in zip(kwargs.keys(), kwargs.values()) - for item in pair) - dname = os.path.dirname(func_path) - fname = os.path.basename(func_path) - func_name, ext = os.path.splitext(fname) - if ext and not ext == '.m': - raise TypeError('Need to give path to .m file') - return self._json_response(cmd='eval', - func_name=func_name, - func_args=func_args or '', - dname=dname, - nargout=nargout) - - def run_code(self, code): - """Run some code in Matlab command line provide by a string - - Parameters - ---------- - code : str - Code to send for evaluation. - """ - return self.run_func('evalin', 'base', code, nargout=0) - - def get_variable(self, varname, default=None): - resp = self.run_func('evalin', 'base', varname) - return resp['result'] if resp['success'] else default - - def set_variable(self, varname, value): - if isinstance(value, spmatrix): - return self._set_sparse_variable(varname, value) - return self.run_func('assignin', 'base', varname, value, nargout=0) - - def set_plot_settings(self, width=512, height=384, inline=True): - if inline: - code = ["set(0, 'defaultfigurevisible', 'off')"] - else: - code = ["set(0, 'defaultfigurevisible', 'on')"] - size = "set(0, 'defaultfigurepaperposition', [0 0 %s %s])" - code += ["set(0, 'defaultfigurepaperunits', 'inches')", - "set(0, 'defaultfigureunits', 'inches')", - size % (int(width) / 150., int(height) / 150.)] - self.run_code(';'.join(code)) - - def _set_sparse_variable(self, varname, value): - value = value.todok() - prefix = 'pymatbridge_temp_sparse_%s_' % uuid4().hex - self.set_variable(prefix + 'keys', list(value.keys())) - # correct for 1-indexing in MATLAB - self.run_code('{0}keys = {0}keys + 1;'.format(prefix)) - self.set_variable(prefix + 'values', list(value.values())) - cmd = "{1} = sparse({0}keys(:, 1), {0}keys(:, 2), {0}values');" - result = self.run_code(cmd.format(prefix, varname)) - self.run_code('clear {0}keys {0}values'.format(prefix)) - return result - - def __getattr__(self, name): - """If an attribute is not found, try to create a bound method""" - return self._bind_method(name) - - def _bind_method(self, name, unconditionally=False): - """Generate a Matlab function and bind it to the instance - - This is where the magic happens. When an unknown attribute of the - Matlab class is requested, it is assumed to be a call to a - Matlab function, and is generated and bound to the instance. - - This works because getattr() falls back to __getattr__ only if no - attributes of the requested name can be found through normal - routes (__getattribute__, __dict__, class tree). - - bind_method first checks whether the requested name is a callable - Matlab function before generating a binding. - - Parameters - ---------- - name : str - The name of the Matlab function to call - e.g. 'sqrt', 'sum', 'svd', etc - unconditionally : bool, optional - Bind the method without performing - checks. Used to bootstrap methods that are required and - know to exist - - Returns - ------- - MatlabFunction - A reference to a newly bound MatlabFunction instance if the - requested name is determined to be a callable function - - Raises - ------ - AttributeError: if the requested name is not a callable - Matlab function - - """ - # TODO: This does not work if the function is a mex function inside a folder of the same name - exists = self.run_func('exist', name)['result'] in [2, 3, 5] - if not unconditionally and not exists: - raise AttributeError("'Matlab' object has no attribute '%s'" % name) - - # create a new method instance - method_instance = MatlabFunction(weakref.ref(self), name) - method_instance.__name__ = name - - # bind to the Matlab instance with a weakref (to avoid circular references) - if sys.version.startswith('3'): - method = types.MethodType(method_instance, weakref.ref(self)) - else: - method = types.MethodType(method_instance, weakref.ref(self), - _Session) - setattr(self, name, method) - return getattr(self, name) - - -class Matlab(_Session): - def __init__(self, executable='matlab', socket_addr=None, - id='python-matlab-bridge', log=False, maxtime=60, - platform=None, startup_options=None): - """ - Initialize this thing. - - Parameters - ---------- - - executable : str - A string that would start Matlab at the terminal. Per default, this - is set to 'matlab', so that you can alias in your bash setup - - socket_addr : str - A string that represents a valid ZMQ socket address, such as - "ipc:///tmp/pymatbridge", "tcp://127.0.0.1:55555", etc. - - id : str - An identifier for this instance of the pymatbridge. - - log : bool - Whether to save a log file in some known location. - - maxtime : float - The maximal time to wait for a response from matlab (optional, - Default is 10 sec) - - platform : string - The OS of the machine on which this is running. Per default this - will be taken from sys.platform. - - startup_options : string - Command line options to pass to MATLAB. Optional; sensible defaults - are used if this is not provided. - """ - if platform is None: - platform = sys.platform - if startup_options is None: - if platform == 'win32': - startup_options = ' -automation -nosplash' - else: - startup_options = ' -nodesktop -nosplash' - if log: - startup_options += ' -logfile ./pymatbridge/logs/matlablog_%s.txt' % id - super(Matlab, self).__init__(executable, socket_addr, id, log, maxtime, - platform, startup_options) - - def _program_name(self): - return 'MATLAB' - - def _execute_flag(self): - return '-r' - - -class Octave(_Session): - def __init__(self, executable='octave', socket_addr=None, - id='python-matlab-bridge', log=False, maxtime=60, - platform=None, startup_options=None): - """ - Initialize this thing. - - Parameters - ---------- - - executable : str - A string that would start Octave at the terminal. Per default, this - is set to 'octave', so that you can alias in your bash setup - - socket_addr : str - A string that represents a valid ZMQ socket address, such as - "ipc:///tmp/pymatbridge", "tcp://127.0.0.1:55555", etc. - - id : str - An identifier for this instance of the pymatbridge. - - log : bool - Whether to save a log file in some known location. - - maxtime : float - The maximal time to wait for a response from octave (optional, - Default is 10 sec) - - platform : string - The OS of the machine on which this is running. Per default this - will be taken from sys.platform. - - startup_options : string - Command line options to pass to Octave. Optional; sensible defaults - are used if this is not provided. - """ - if startup_options is None: - startup_options = '--silent --no-gui' - super(Octave, self).__init__(executable, socket_addr, id, log, maxtime, - platform, startup_options) - - def _program_name(self): - return 'Octave' - - def _preamble_code(self): - code = super(Octave, self)._preamble_code() - if self.log: - code.append("diary('./pymatbridge/logs/octavelog_%s.txt')" % self.id) - code.append("graphics_toolkit('gnuplot')") - return code - - def _execute_flag(self): - return '--eval' - - -class MatlabFunction(object): - - def __init__(self, parent, name): - """An object representing a Matlab function - - Methods are dynamically bound to instances of Matlab objects and - represent a callable function in the Matlab subprocess. - - Parameters - ---------- - parent: Matlab instance - A reference to the parent (Matlab instance) to which the - MatlabFunction is being bound - name: str - The name of the Matlab function this represents - """ - self.name = name - self._parent = parent - self.doc = None - - def __call__(self, unused_parent_weakref, *args, **kwargs): - """Call a function with the supplied arguments in the Matlab subprocess - - Passes parameters to `run_func`. - - """ - return self.parent.run_func(self.name, *args, **kwargs) - - @property - def parent(self): - """Get the actual parent from the stored weakref - - The parent (Matlab instance) is stored as a weak reference - to eliminate circular references from dynamically binding Methods - to Matlab. - - """ - parent = self._parent() - if parent is None: - raise AttributeError('Stale reference to attribute of non-existent Matlab object') - return parent - - @property - def __doc__(self): - """Fetch the docstring from Matlab - - Get the documentation for a Matlab function by calling Matlab's builtin - help() then returning it as the Python docstring. The result is cached - so Matlab is only ever polled on the first request - - """ - if self.doc is None: - self.doc = self.parent.help(self.name)['result'] - return self.doc diff --git a/pymatbridge/tests/test_function_processor.py b/pymatbridge/tests/test_function_processor.py deleted file mode 100644 index 1d1666c..0000000 --- a/pymatbridge/tests/test_function_processor.py +++ /dev/null @@ -1,20 +0,0 @@ -import pymatbridge as pymat -import numpy.testing as npt -import test_utils as tu - - -class TestFunctionProcessor: - - # Start a Matlab session before running any tests - @classmethod - def setup_class(cls): - cls.mlab = tu.connect_to_matlab() - - # Tear down the Matlab session after running all the tests - @classmethod - def teardown_class(cls): - tu.stop_matlab(cls.mlab) - - # Test the "is_function_processor_working()" function - def test_is_function_processor_working(self): - npt.assert_equal(self.mlab.is_function_processor_working(), True) diff --git a/pymatbridge/tests/test_functions.py b/pymatbridge/tests/test_functions.py deleted file mode 100644 index e0367fc..0000000 --- a/pymatbridge/tests/test_functions.py +++ /dev/null @@ -1,59 +0,0 @@ -import numpy as np -import numpy.testing as npt -import test_utils as tu - - -class TestFunctions(object): - - # Start a Matlab session before running any tests - @classmethod - def setup_class(cls): - cls.mlab = tu.connect_to_matlab() - - # Tear down the Matlab session after running all the tests - @classmethod - def teardown_class(cls): - tu.stop_matlab(cls.mlab) - - def test_nargout(self): - res = self.mlab.run_func('svd', np.array([[1,2],[1,3]]), nargout=3) - U, S, V = res['result'] - npt.assert_almost_equal(U, np.array([[-0.57604844, -0.81741556], - [-0.81741556, 0.57604844]])) - - npt.assert_almost_equal(S, np.array([[ 3.86432845, 0.], - [ 0., 0.25877718]])) - - npt.assert_almost_equal(V, np.array([[-0.36059668, -0.93272184], - [-0.93272184, 0.36059668]])) - - res = self.mlab.run_func('svd', np.array([[1,2],[1,3]]), nargout=1) - s = res['result'] - npt.assert_almost_equal(s, [[ 3.86432845], [ 0.25877718]]) - - res = self.mlab.run_func('close', 'all', nargout=0) - assert res['result'] == [] - - def test_tuple_args(self): - res = self.mlab.run_func('ones', (1, 2)) - npt.assert_almost_equal(res['result'], [[1, 1]]) - - res = self.mlab.run_func('chol', - np.array([[2, 2], [1, 1]]), 'lower') - npt.assert_almost_equal(res['result'], - [[1.41421356, 0.], - [0.70710678, 0.70710678]]) - - def test_create_func(self): - test = self.mlab.ones(3) - npt.assert_array_equal(test['result'], np.ones((3, 3))) - doc = self.mlab.zeros.__doc__ - assert 'zeros' in doc - - def test_pass_kwargs(self): - resp = self.mlab.run_func('plot', [1, 2, 3], Linewidth=3) - assert resp['success'] - assert len(resp['content']['figures']) - resp = self.mlab.plot([1, 2, 3], Linewidth=3) - assert resp['result'] is not None - assert len(resp['content']['figures']) diff --git a/pymatbridge/tests/test_get_variable.py b/pymatbridge/tests/test_get_variable.py deleted file mode 100644 index be38ea0..0000000 --- a/pymatbridge/tests/test_get_variable.py +++ /dev/null @@ -1,48 +0,0 @@ -import pymatbridge as pymat -import numpy.testing as npt -import test_utils as tu - - -class TestGetVariable: - - # Start a Matlab session before running any tests - @classmethod - def setup_class(cls): - cls.mlab = tu.connect_to_matlab() - - # Tear down the Matlab session after running all the tests - @classmethod - def teardown_class(cls): - tu.stop_matlab(cls.mlab) - - - # Set up a floating point and get it - def test_get_float(self): - self.mlab.run_code("a = 456345.345345") - self.mlab.run_code("b = 0.39748e3") - - npt.assert_equal(self.mlab.get_variable('a'), 456345.345345) - npt.assert_equal(self.mlab.get_variable('b'), 397.48) - - - # Get some arrays - def test_get_array(self): - self.mlab.run_code("a = [1 2 3 4]") - self.mlab.run_code("b = [1 2; 3 4]") - - npt.assert_equal(self.mlab.get_variable('a'), [[1.,2.,3.,4.]]) - npt.assert_equal(self.mlab.get_variable('b'), [[1.,2.],[3.,4.]]) - - - # Try to get a non-existent variable - def test_nonexistent_var(self): - self.mlab.run_code("clear") - - npt.assert_equal(self.mlab.get_variable('a'), None) - - - # Try to get a non-existent variable with default - def test_nonexistent_var_default(self): - self.mlab.run_code("clear") - - npt.assert_equal(self.mlab.get_variable('a', 'some_val'), 'some_val') diff --git a/pymatbridge/tests/test_json.py b/pymatbridge/tests/test_json.py deleted file mode 100644 index 4028aff..0000000 --- a/pymatbridge/tests/test_json.py +++ /dev/null @@ -1,69 +0,0 @@ -import pymatbridge as pymat -from pymatbridge.compat import unichr -import numpy.testing as npt -import test_utils as tu - -class TestJson: - - # Start a Matlab session before doing any tests - @classmethod - def setup_class(cls): - cls.mlab = tu.connect_to_matlab() - - # Tear down the Matlab session after all the tests are done - @classmethod - def teardown_class(cls): - tu.stop_matlab(cls.mlab) - - - # Add 1 to the argument and return it - def test_demo_func(self): - for i in range(5): - res = self.mlab.run_func('demo_func.m', {'a': i})['result'] - ans = i + 1 - npt.assert_equal(res, ans, err_msg = "demo_func.m test failed") - - # Print some strange characters in Matlab, get them back and compare. - def test_special_character(self): - - # Test 1:"hi"\n - res = self.mlab.run_code('fprintf(1, char([34, 104, 105, 34, 10]));')['content']['stdout'] - ans = unichr(34) + unichr(104) + unichr(105) + unichr(34) + unichr(10) - npt.assert_equal(res, ans, err_msg = "Special Character Test 1 failed") - - # Test 2:\b\n - res = self.mlab.run_code('fprintf(1, char([8,10]));')['content']['stdout'] - ans = unichr(8) + unichr(10) - npt.assert_equal(res, ans, err_msg = "Special Character Test 2 failed") - - # Test 3:\f\n - res = self.mlab.run_code('fprintf(1, char([12,10]));')['content']['stdout'] - ans = unichr(12) + unichr(10) - npt.assert_equal(res, ans, err_msg = "Special Character Test 3 failed") - - # Test 4:\r\n - res = self.mlab.run_code('fprintf(1, char([13,10]));')['content']['stdout'] - ans = unichr(13) + unichr(10) - npt.assert_equal(res, ans, err_msg = "Special Character Test 4 failed") - - # Test 5:\t\n - res = self.mlab.run_code('fprintf(1, char([9,10]));')['content']['stdout'] - ans = unichr(9) + unichr(10) - npt.assert_equal(res, ans, err_msg = "Special Character Test 5 failed") - - # Test 6:\\\n - res = self.mlab.run_code('fprintf(1, char([92,92,10]));')['content']['stdout'] - ans = unichr(92) + unichr(10) # Python already encoded double-slash as 92 - npt.assert_equal(res, ans, err_msg = "Special Character Test 6 failed") - - # Test 7:/\n - res = self.mlab.run_code('fprintf(1, char([47,10]));')['content']['stdout'] - ans = unichr(47) + unichr(10) - npt.assert_equal(res, ans, err_msg = "Special Character Test 7 failed") - - # Test 8: Lots of strange characters - res = self.mlab.run_code('fprintf(1,char([47,92,92,47,8,12,10,13,9,12,8,8,12,47,34,47,10,10,47,34]));')['content']['stdout'] - ans = unichr(47) + unichr(92) + unichr(47) + unichr(8) + unichr(12) + unichr(10) \ - + unichr(13) + unichr(9) + unichr(12) + unichr(8) + unichr(8) + unichr(12) \ - + unichr(47) + unichr(34) + unichr(47) + unichr(10) + unichr(10) + unichr(47) + unichr(34) - npt.assert_equal(res, ans, err_msg = "Special Character Test 8 failed") diff --git a/pymatbridge/tests/test_magic.py b/pymatbridge/tests/test_magic.py deleted file mode 100644 index 4a9d38f..0000000 --- a/pymatbridge/tests/test_magic.py +++ /dev/null @@ -1,110 +0,0 @@ -import sys -import os -from uuid import uuid4 - -import pymatbridge as pymat -from pymatbridge.matlab_magic import MatlabInterperterError -from IPython.testing.globalipapp import get_ipython - -import numpy.testing as npt - - -class TestMagic: - - # Create an IPython shell and load Matlab magic - @classmethod - def setup_class(cls): - cls.ip = get_ipython() - cls.ip.run_cell('import random') - cls.ip.run_cell('import numpy as np') - if 'USE_OCTAVE' in os.environ: - matlab = 'octave' - else: - matlab = 'matlab' - - # We will test the passing of kwargs through to the Matlab or Octave - # objects, by assigning the socket address out here: - socket_addr = "tcp://127.0.0.1" if sys.platform == "win32" else "ipc:///tmp/pymatbridge-%s"%str(uuid4()) - pymat.load_ipython_extension(cls.ip, matlab=matlab, - socket_addr=socket_addr) - - # Unload the magic - @classmethod - def teardown_class(cls): - pymat.unload_ipython_extension(cls.ip) - - # Test single operation on different data structures - def test_cell_magic_number(self): - # A double precision real number - self.ip.run_cell("a = np.float64(random.random())") - self.ip.run_cell_magic('matlab', '-i a -o b', 'b = a*2;') - npt.assert_almost_equal(self.ip.user_ns['b'], - self.ip.user_ns['a']*2, decimal=7) - - def test_cell_magic_number_complex(self): - # A complex number - self.ip.run_cell("x = 3.34+4.56j") - self.ip.run_cell_magic('matlab', '-i x -o y', 'y = x*(11.35 - 23.098j)') - self.ip.run_cell("res = x*(11.35 - 23.098j)") - npt.assert_almost_equal(self.ip.user_ns['y'], - self.ip.user_ns['res'], decimal=7) - - - def test_cell_magic_array(self): - # Random array multiplication - self.ip.run_cell("val1 = np.random.random_sample((3,3))") - self.ip.run_cell("val2 = np.random.random_sample((3,3))") - self.ip.run_cell("respy = np.dot(val1, val2)") - self.ip.run_cell_magic('matlab', '-i val1,val2 -o resmat', - 'resmat = val1 * val2') - npt.assert_almost_equal(self.ip.user_ns['resmat'], - self.ip.user_ns['respy'], decimal=7) - - def test_cell_magic_array_complex(self): - self.ip.run_cell("val1 = np.random.random((3,3)) + np.random.random((3,3))*1j") - self.ip.run_cell("val2 = np.random.random((3,3)) + np.random.random((3,3))*1j") - self.ip.run_cell("respy = np.dot(val1, val2)") - self.ip.run_cell_magic('matlab', '-i val1,val2 -o resmat', - 'resmat = val1 * val2') - npt.assert_almost_equal(self.ip.user_ns['resmat'], - self.ip.user_ns['respy'], decimal=7) - - def test_line_magic(self): - # Some operation in Matlab - self.ip.run_line_magic('matlab', 'a = [1 2 3]') - self.ip.run_line_magic('matlab', 'res = a*2') - # Get the result back to Python - self.ip.run_cell_magic('matlab', '-o actual', 'actual = res') - - self.ip.run_cell("expected = np.array([[2., 4., 6.]])") - npt.assert_almost_equal(self.ip.user_ns['actual'], - self.ip.user_ns['expected'], decimal=7) - - def test_figure(self): - # Just make a plot to get more testing coverage - self.ip.run_line_magic('matlab', 'plot([1 2 3])') - - - def test_matrix(self): - self.ip.run_cell("in_array = np.array([[1,2,3], [4,5,6]])") - self.ip.run_cell_magic('matlab', '-i in_array -o out_array', - 'out_array = in_array;') - npt.assert_almost_equal(self.ip.user_ns['out_array'], - self.ip.user_ns['in_array'], - decimal=7) - - # Matlab struct type should be converted to a Python dict - def test_struct(self): - self.ip.run_cell('num = 2.567') - self.ip.run_cell('num_array = np.array([1.2,3.4,5.6])') - self.ip.run_cell('str = "Hello World"') - self.ip.run_cell_magic('matlab', '-i num,num_array,str -o obj', - 'obj.num = num;obj.num_array = num_array;obj.str = str;') - npt.assert_equal(isinstance(self.ip.user_ns['obj'], dict), True) - npt.assert_equal(self.ip.user_ns['obj']['num'], self.ip.user_ns['num']) - npt.assert_equal(self.ip.user_ns['obj']['num_array'].squeeze(), self.ip.user_ns['num_array']) - npt.assert_equal(self.ip.user_ns['obj']['str'], self.ip.user_ns['str']) - - def test_faulty(self): - npt.assert_raises(MatlabInterperterError, - lambda: self.ip.run_line_magic('matlab', '1 = 2')) diff --git a/pymatbridge/tests/test_precision.py b/pymatbridge/tests/test_precision.py deleted file mode 100644 index 027ea47..0000000 --- a/pymatbridge/tests/test_precision.py +++ /dev/null @@ -1,61 +0,0 @@ -import pymatbridge as pymat -import random as rd -import numpy as np -import numpy.testing as npt -import test_utils as tu - - -class TestPrecision: - - # Start a Matlab session before running any tests - @classmethod - def setup_class(cls): - cls.mlab = tu.connect_to_matlab() - - # Tear down the Matlab session after running all the tests - @classmethod - def teardown_class(cls): - tu.stop_matlab(cls.mlab) - - - # Pass a 64-bit floating number through the signal path - def test_float64_roundtrip(self): - for i in range(0,10): - val = np.float64(rd.random()) - res = self.mlab.run_func('precision_pass.m', {'val':val})['result'] - npt.assert_almost_equal(res, val, decimal=7, err_msg="Float64 roundtrip error") - - # Add two 64-bit floating number in Matlab and return the sum - def test_float64_sum(self): - for i in range(0,10): - val1 = np.float64(rd.random()) - val2 = np.float64(rd.random()) - - res = self.mlab.run_func('precision_sum.m', {'val1':val1, 'val2':val2})['result'] - npt.assert_almost_equal(res, val1 + val2, decimal=7, err_msg="Float64 sum error") - - # Multiply two 64-bit floating number in Matlab and return the product - def test_float64_multiply(self): - for i in range(0,10): - val1 = np.float64(rd.random()) - val2 = np.float64(rd.random()) - - res = self.mlab.run_func('precision_multiply.m', {'val1':val1, 'val2':val2})['result'] - npt.assert_almost_equal(res, val1 * val2, decimal=7, err_msg="Float64 multiply error") - - # Make a division in Matlab and return the results - def test_float64_divide(self): - for i in range(0,10): - val1 = np.float64(rd.random()) - val2 = np.float64(rd.random()) - - res = self.mlab.run_func('precision_divide.m', {'val1':val1, 'val2':val2})['result'] - npt.assert_almost_equal(res, val1 / val2, decimal=7, err_msg="Float64 divide error") - - # Calculate the square root in Matlab and return the result - def test_float64_sqrt(self): - for i in range(0,10): - val = np.float64(rd.random()) - - res = self.mlab.run_func('precision_sqrt.m', {'val':val})['result'] - npt.assert_almost_equal(res, np.sqrt(val), decimal=7, err_msg="Float64 square root error") diff --git a/pymatbridge/tests/test_publish.m b/pymatbridge/tests/test_publish.m deleted file mode 100644 index 2590b0c..0000000 --- a/pymatbridge/tests/test_publish.m +++ /dev/null @@ -1,14 +0,0 @@ -%% Experimenting with conversion from matlab to ipynb -% This is a second comment line within the header block -% Next, I will put in an empty line (new cell?) and then some code - -% This is some code: -t = linspace(1, 6*pi, 100); -a = sin(t); -plot(a) -grid on - -%% A new cell -b = cos(t); -plot(b); -b(1:10) % What happens if you print to the command line? \ No newline at end of file diff --git a/pymatbridge/tests/test_publish.py b/pymatbridge/tests/test_publish.py deleted file mode 100644 index cb3f093..0000000 --- a/pymatbridge/tests/test_publish.py +++ /dev/null @@ -1,59 +0,0 @@ -import numpy.testing as npt -import pymatbridge.publish as publish -import json -import os - - -MFILE = os.path.join(os.path.dirname(__file__), 'test_publish.m') - - -def test_format_line(): - """ - Test that lines get formatted properly - - """ - npt.assert_equal(publish.format_line('%% This begins a new cell'), - (True, True, ' This begins a new cell\n')) - - npt.assert_equal(publish.format_line('% This should be just markdown'), - (False, True, ' This should be just markdown\n')) - - npt.assert_equal(publish.format_line('This is just code'), - (False, False, 'This is just code')) - - -def test_lines_to_notebook(): - """ - Test that conversion of some lines gives you a proper notebook - """ - - lines = ["%% This is a first line\n", - "\n", - "% This should be in another cell\n", - "a = 1; % This is code\n", - "b = 2; % This is also code\n", - "c = 3; % code in another cell\n"] - - nb = publish.lines_to_notebook(lines) - - npt.assert_equal(nb['cells'][1]['source'][0], - ' This is a first line\n\n') - - -def test_convert_mfile(): - publish.convert_mfile(MFILE) - nb_file = MFILE.replace('.m', '.ipynb') - with open(nb_file) as fid: - nb = json.load(fid) - npt.assert_equal(nb['cells'][1]['source'][0], - ' Experimenting with conversion from matlab to ipynb\n\n') - os.remove(nb_file) - - -def test_mfile_to_lines(): - lines = publish.mfile_to_lines(MFILE) - - nb = publish.lines_to_notebook(lines) - - npt.assert_equal(nb['cells'][1]['source'][0], - ' Experimenting with conversion from matlab to ipynb\n\n') diff --git a/pymatbridge/tests/test_run_code.py b/pymatbridge/tests/test_run_code.py deleted file mode 100644 index e4255e7..0000000 --- a/pymatbridge/tests/test_run_code.py +++ /dev/null @@ -1,84 +0,0 @@ -import os - -import pymatbridge as pymat -from pymatbridge.compat import text_type -import numpy as np -import numpy.testing as npt -import test_utils as tu - - -class TestRunCode: - - # Start a Matlab session before running any tests - @classmethod - def setup_class(cls): - cls.mlab = tu.connect_to_matlab() - - # Tear down the Matlab session after running all the tests - @classmethod - def teardown_class(cls): - tu.stop_matlab(cls.mlab) - - # Running 'disp()' in Matlab command window - def test_disp(self): - result1 = self.mlab.run_code("disp('Hello world')")['content']['stdout'] - result2 = self.mlab.run_code("disp(' ')")['content']['stdout'] - result3 = self.mlab.run_code("disp('')")['content']['stdout'] - - npt.assert_equal(result1, "Hello world\n") - npt.assert_equal(result2, " \n") - if tu.on_octave(): - npt.assert_equal(result3, '\n') - else: - npt.assert_equal(result3, "") - - # Make some assignments and run basic operations - def test_basic_operation(self): - result_assignment_a = self.mlab.run_code("a = 21.23452261")['content']['stdout'] - result_assignment_b = self.mlab.run_code("b = 347.745")['content']['stdout'] - result_sum = self.mlab.run_code("a + b")['content']['stdout'] - result_diff = self.mlab.run_code("a - b")['content']['stdout'] - result_product = self.mlab.run_code("a * b")['content']['stdout'] - result_division = self.mlab.run_code("c = a / b")['content']['stdout'] - - if tu.on_octave(): - npt.assert_equal(result_assignment_a, text_type("a = 21.235\n")) - npt.assert_equal(result_assignment_b, text_type("b = 347.75\n")) - npt.assert_equal(result_sum, text_type("ans = 368.98\n")) - npt.assert_equal(result_diff, text_type("ans = -326.51\n")) - npt.assert_equal(result_product, text_type("ans = 7384.2\n")) - npt.assert_equal(result_division, text_type("c = 0.061063\n")) - else: - npt.assert_equal(result_assignment_a, text_type("\na =\n\n 21.2345\n\n")) - npt.assert_equal(result_assignment_b, text_type("\nb =\n\n 347.7450\n\n")) - npt.assert_equal(result_sum, text_type("\nans =\n\n 368.9795\n\n")) - npt.assert_equal(result_diff, text_type("\nans =\n\n -326.5105\n\n")) - npt.assert_equal(result_product, text_type("\nans =\n\n 7.3842e+03\n\n")) - npt.assert_equal(result_division, text_type("\nc =\n\n 0.0611\n\n")) - - # Put in some undefined code - def test_undefined_code(self): - success = self.mlab.run_code("this_is_nonsense")['success'] - message = self.mlab.run_code("this_is_nonsense")['content']['stdout'] - - assert not success - if tu.on_octave(): - npt.assert_equal(message, "'this_is_nonsense' undefined near line 1 column 1") - else: - npt.assert_equal(message, "Undefined function or variable 'this_is_nonsense'.") - - def test_stack_traces(self): - this_dir = os.path.abspath(os.path.dirname(__file__)) - test_file = os.path.join(this_dir, 'test_stack_trace.m') - - self.mlab.run_code("addpath('%s')" % this_dir) - response = self.mlab.run_code('test_stack_trace(10)') - npt.assert_equal(response['stack'], [ - {'name': 'baz', 'line': 14, 'file': test_file}, - {'name': 'bar', 'line': 10, 'file': test_file}, - {'name': 'foo', 'line': 6, 'file': test_file}, - {'name': 'test_stack_trace', 'line': 2, 'file': test_file} - ]) - - response = self.mlab.run_code('x = 2') - npt.assert_equal(response['stack'], []) diff --git a/pymatbridge/tests/test_set_variable.py b/pymatbridge/tests/test_set_variable.py deleted file mode 100644 index fb44624..0000000 --- a/pymatbridge/tests/test_set_variable.py +++ /dev/null @@ -1,49 +0,0 @@ -import pymatbridge as pymat -import random as rd -import numpy as np -import numpy.testing as npt -import test_utils as tu - -class TestArray: - - # Start a Matlab session before any tests - @classmethod - def setup_class(cls): - cls.mlab = tu.connect_to_matlab() - - # Tear down the Matlab session after all the tests are done - @classmethod - def teardown_class(cls): - tu.stop_matlab(cls.mlab) - - - # Pass a 1000*1000 array to Matlab - def test_array_size(self): - array = np.random.random_sample((50,50)) - res = self.mlab.run_func("array_size.m",{'val':array})['result'] - npt.assert_almost_equal(res, array, decimal=8, err_msg = "test_array_size: error") - - - def test_array_content(self): - test_array = np.random.random_integers(2, 20, (5, 10)) - self.mlab.set_variable('test', test_array) - npt.assert_equal(self.mlab.get_variable('test'), test_array) - test_array = np.asfortranarray(test_array) - self.mlab.set_variable('test', test_array) - npt.assert_equal(self.mlab.get_variable('test'), test_array) - # force non-contiguous - test_array = test_array[::-1] - self.mlab.set_variable('test', test_array) - npt.assert_equal(self.mlab.get_variable('test'), test_array) - - def test_object_array(self): - test_array = np.array(['hello', 1]) - self.mlab.set_variable('test', test_array) - npt.assert_equal(self.mlab.get_variable('test'), test_array) - - def test_others(self): - self.mlab.set_variable('test', np.float(1.5)) - npt.assert_equal(self.mlab.get_variable('test'), 1.5) - self.mlab.set_variable('test', 'hello') - npt.assert_equal(self.mlab.get_variable('test'), 'hello') - diff --git a/pymatbridge/tests/test_stack_trace.m b/pymatbridge/tests/test_stack_trace.m deleted file mode 100644 index 0878c2c..0000000 --- a/pymatbridge/tests/test_stack_trace.m +++ /dev/null @@ -1,15 +0,0 @@ -function o = test_stack_trace(input) - o = foo(input); -end - -function o = foo(input) - o = bar(input) -end - -function o = bar(input) - o = baz(input) -end - -function o = baz(input) - o = quux(input) -end diff --git a/pymatbridge/tests/test_utils.py b/pymatbridge/tests/test_utils.py deleted file mode 100644 index ecb7add..0000000 --- a/pymatbridge/tests/test_utils.py +++ /dev/null @@ -1,22 +0,0 @@ -import os -import pymatbridge as pymat -import numpy.testing as npt - -def on_octave(): - return bool(os.environ.get('USE_OCTAVE', False)) - -def connect_to_matlab(): - mlab = pymat.Octave() if on_octave() else pymat.Matlab(log=True) - mlab.start() - npt.assert_(mlab.is_connected(), msg = "connect_to_matlab(): Connection failed") - - return mlab - - -def stop_matlab(mlab): - mlab.stop() - npt.assert_(not mlab.is_connected(), msg = "stop_matlab(): Disconnection failed") - - - - diff --git a/pymatbridge/version.py b/pymatbridge/version.py deleted file mode 100644 index ad5ff15..0000000 --- a/pymatbridge/version.py +++ /dev/null @@ -1,97 +0,0 @@ -"""pymatbridge version/release information""" - -# Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z" -_version_major = 0 -_version_minor = 6 -_version_micro = 0 #'' # use '' for first of series, number for 1 and above -_version_extra = 'dev' -#_version_extra = '' # Uncomment this for full releases - -# Construct full version string from these. -_ver = [_version_major, _version_minor] -if _version_micro: - _ver.append(_version_micro) -if _version_extra: - _ver.append(_version_extra) - -__version__ = '.'.join(map(str, _ver)) - -CLASSIFIERS = ["Development Status :: 3 - Alpha", - "Environment :: Console", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: BSD License", - "Operating System :: OS Independent", - "Programming Language :: Python", - "Topic :: Scientific/Engineering"] - -description = "pymatbridge is a set of python and matlab functions to allow these two systems to talk to each other" - -long_description = """ - -Pymatbridge -=========== - -A python interface to call out to Matlab(R). - - -License information -=================== - -Copyright (c) 2012 -- , Max Jaderberg, Ariel Rokem, Haoxing Zhao -All rights reserved. - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: - -Redistributions of source code must retain the above copyright notice, this -list of conditions and the following disclaimer. - -Redistributions in binary form must reproduce the above copyright notice, this -list of conditions and the following disclaimer in the documentation and/or -other materials provided with the distribution. - -Neither the name of the Oxford University, Stanford University nor the names of -its contributors may be used to endorse or promote products derived from this -software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 'AS IS' AND -ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -""" - -NAME = "pymatbridge" -MAINTAINER = "Ariel Rokem" -MAINTAINER_EMAIL = "arokem@gmail.com" -DESCRIPTION = description -LONG_DESCRIPTION = long_description -URL = "https://github.com/arokem/python-matlab-bridge" -DOWNLOAD_URL = "https://github.com/arokem/python-matlab-bridge/archive/master.tar.gz" -LICENSE = "BSD" -AUTHOR = "https://github.com/arokem/python-matlab-bridge/contributors" -AUTHOR_EMAIL = "arokem@gmail.com" -PLATFORMS = "OS Independent" -MAJOR = _version_major -MINOR = _version_minor -MICRO = _version_micro -VERSION = __version__ -PACKAGES = ['pymatbridge', - 'pymatbridge.messenger'] -PACKAGE_DATA = {"pymatbridge": ["matlab/matlabserver.m", "matlab/messenger.*", - "matlab/usrprog/*", "matlab/util/*.m", - "matlab/util/json_v0.2.2/LICENSE", - "matlab/util/json_v0.2.2/README.md", - "matlab/util/json_v0.2.2/test/*", - "matlab/util/json_v0.2.2/json/*.m", - "matlab/util/json_v0.2.2/json/java/*", - "tests/*.py", "tests/*.m", "examples/*.ipynb"], - "pymatbridge.messenger": ["mexmaci64/*", - "mexw64/*", - "mexa64/*"]} - -REQUIRES = ['pyzmq'] -EXTRAS_REQUIRE = { - 'sparse arrays': ["scipy>=0.13.0"], - 'ipython': ["ipython>=3.0"], -} - -BIN=['scripts/publish-notebook'] diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index ae3bcc7..0000000 --- a/requirements.txt +++ /dev/null @@ -1,2 +0,0 @@ -pyzmq -numpy>=1.7 diff --git a/scripts/publish-notebook b/scripts/publish-notebook deleted file mode 100755 index 14e57c5..0000000 --- a/scripts/publish-notebook +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env python -import argparse as arg -import pymatbridge.publish as publish - -parser = arg.ArgumentParser(description='Publish a matlab file (.m) as an interactive notebook (.ipynb)') - -parser.add_argument('mfile', action='store', metavar='File', - help='Matlab m-file (.m)') - -parser.add_argument('--outfile', action='store', metavar='File', - help='Output notebook (.ipynb). Default: same name and location as the input file ', default=None) - -params = parser.parse_args() - - -if __name__ == "__main__": - publish.convert_mfile(params.mfile, params.outfile) diff --git a/setup.py b/setup.py deleted file mode 100755 index 766aaae..0000000 --- a/setup.py +++ /dev/null @@ -1,39 +0,0 @@ -#!/usr/bin/env python -"""Setup file for python-matlab-bridge""" - -import os - -try: - from setuptools import setup -except ImportError: - from distutils.core import setup - -# Get version and release info, which is all stored in pymatbridge/version.py -ver_file = os.path.join('pymatbridge', 'version.py') -exec(open(ver_file).read()) - -opts = dict(name=NAME, - maintainer=MAINTAINER, - maintainer_email=MAINTAINER_EMAIL, - description=DESCRIPTION, - long_description=LONG_DESCRIPTION, - url=URL, - download_url=DOWNLOAD_URL, - license=LICENSE, - classifiers=CLASSIFIERS, - author=AUTHOR, - author_email=AUTHOR_EMAIL, - platforms=PLATFORMS, - version=VERSION, - packages=PACKAGES, - package_data=PACKAGE_DATA, - requires=REQUIRES, - extras_require=EXTRAS_REQUIRE, - scripts=BIN, - install_requires=['pyzmq', 'numpy'] - ) - - -# Now call the actual setup function -if __name__ == '__main__': - setup(**opts) diff --git a/stylesheets/print.css b/stylesheets/print.css new file mode 100644 index 0000000..541695b --- /dev/null +++ b/stylesheets/print.css @@ -0,0 +1,226 @@ +html, body, div, span, applet, object, iframe, +h1, h2, h3, h4, h5, h6, p, blockquote, pre, +a, abbr, acronym, address, big, cite, code, +del, dfn, em, img, ins, kbd, q, s, samp, +small, strike, strong, sub, sup, tt, var, +b, u, i, center, +dl, dt, dd, ol, ul, li, +fieldset, form, label, legend, +table, caption, tbody, tfoot, thead, tr, th, td, +article, aside, canvas, details, embed, +figure, figcaption, footer, header, hgroup, +menu, nav, output, ruby, section, summary, +time, mark, audio, video { + margin: 0; 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+ max-width: 480px; + font-size: 11px; + } + +} diff --git a/tools/gh_api.py b/tools/gh_api.py deleted file mode 100644 index 8c62098..0000000 --- a/tools/gh_api.py +++ /dev/null @@ -1,292 +0,0 @@ -"""Functions for Github API requests.""" -from __future__ import print_function - -try: - input = raw_input -except NameError: - pass - -import os -import re -import sys - -import requests -import getpass -import json - -try: - import requests_cache -except ImportError: - print("no cache", file=sys.stderr) -else: - requests_cache.install_cache("gh_api", expire_after=3600) - -# Keyring stores passwords by a 'username', but we're not storing a username and -# password -fake_username = 'ipython_tools' - -class Obj(dict): - """Dictionary with attribute access to names.""" - def __getattr__(self, name): - try: - return self[name] - except KeyError: - raise AttributeError(name) - - def __setattr__(self, name, val): - self[name] = val - -token = None -def get_auth_token(): - global token - - if token is not None: - return token - - import keyring - token = keyring.get_password('github', fake_username) - if token is not None: - return token - - print("Please enter your github username and password. These are not " - "stored, only used to get an oAuth token. You can revoke this at " - "any time on Github.") - user = input("Username: ") - pw = getpass.getpass("Password: ") - - auth_request = { - "scopes": [ - "public_repo", - "gist" - ], - "note": "IPython tools", - "note_url": "https://github.com/ipython/ipython/tree/master/tools", - } - response = requests.post('https://api.github.com/authorizations', - auth=(user, pw), data=json.dumps(auth_request)) - response.raise_for_status() - token = json.loads(response.text)['token'] - keyring.set_password('github', fake_username, token) - return token - -def make_auth_header(): - return {'Authorization': 'token ' + get_auth_token()} - -def post_issue_comment(project, num, body): - url = 'https://api.github.com/repos/{project}/issues/{num}/comments'.format(project=project, num=num) - payload = json.dumps({'body': body}) - requests.post(url, data=payload, headers=make_auth_header()) - -def post_gist(content, description='', filename='file', auth=False): - """Post some text to a Gist, and return the URL.""" - post_data = json.dumps({ - "description": description, - "public": True, - "files": { - filename: { - "content": content - } - } - }).encode('utf-8') - - headers = make_auth_header() if auth else {} - response = requests.post("https://api.github.com/gists", data=post_data, headers=headers) - response.raise_for_status() - response_data = json.loads(response.text) - return response_data['html_url'] - -def get_pull_request(project, num, auth=False): - """get pull request info by number - """ - url = "https://api.github.com/repos/{project}/pulls/{num}".format(project=project, num=num) - if auth: - header = make_auth_header() - else: - header = None - response = requests.get(url, headers=header) - response.raise_for_status() - return json.loads(response.text, object_hook=Obj) - -def get_pull_request_files(project, num, auth=False): - """get list of files in a pull request""" - url = "https://api.github.com/repos/{project}/pulls/{num}/files".format(project=project, num=num) - if auth: - header = make_auth_header() - else: - header = None - return get_paged_request(url, headers=header) - -element_pat = re.compile(r'<(.+?)>') -rel_pat = re.compile(r'rel=[\'"](\w+)[\'"]') - -def get_paged_request(url, headers=None, **params): - """get a full list, handling APIv3's paging""" - results = [] - params.setdefault("per_page", 100) - while True: - if '?' in url: - params = None - print("fetching %s" % url, file=sys.stderr) - else: - print("fetching %s with %s" % (url, params), file=sys.stderr) - response = requests.get(url, headers=headers, params=params) - response.raise_for_status() - results.extend(response.json()) - if 'next' in response.links: - url = response.links['next']['url'] - else: - break - return results - -def get_pulls_list(project, auth=False, **params): - """get pull request list""" - params.setdefault("state", "closed") - url = "https://api.github.com/repos/{project}/pulls".format(project=project) - if auth: - headers = make_auth_header() - else: - headers = None - pages = get_paged_request(url, headers=headers, **params) - return pages - -def get_issues_list(project, auth=False, **params): - """get issues list""" - params.setdefault("state", "closed") - url = "https://api.github.com/repos/{project}/issues".format(project=project) - if auth: - headers = make_auth_header() - else: - headers = None - pages = get_paged_request(url, headers=headers, **params) - return pages - -def get_milestones(project, auth=False, **params): - url = "https://api.github.com/repos/{project}/milestones".format(project=project) - if auth: - headers = make_auth_header() - else: - headers = None - milestones = get_paged_request(url, headers=headers, **params) - return milestones - -def get_milestone_id(project, milestone, auth=False, **params): - milestones = get_milestones(project, auth=auth, **params) - for mstone in milestones: - if mstone['title'] == milestone: - return mstone['number'] - else: - raise ValueError("milestone %s not found" % milestone) - -def is_pull_request(issue): - """Return True if the given issue is a pull request.""" - return bool(issue.get('pull_request', {}).get('html_url', None)) - -def get_authors(pr): - print("getting authors for #%i" % pr['number'], file=sys.stderr) - h = make_auth_header() - r = requests.get(pr['commits_url'], headers=h) - r.raise_for_status() - commits = r.json() - authors = [] - for commit in commits: - author = commit['commit']['author'] - authors.append("%s <%s>" % (author['name'], author['email'])) - return authors - -# encode_multipart_formdata is from urllib3.filepost -# The only change is to iter_fields, to enforce S3's required key ordering - -def iter_fields(fields): - fields = fields.copy() - for key in ('key', 'acl', 'Filename', 'success_action_status', 'AWSAccessKeyId', - 'Policy', 'Signature', 'Content-Type', 'file'): - yield (key, fields.pop(key)) - for (k,v) in fields.items(): - yield k,v - -def encode_multipart_formdata(fields, boundary=None): - """ - Encode a dictionary of ``fields`` using the multipart/form-data mime format. - - :param fields: - Dictionary of fields or list of (key, value) field tuples. The key is - treated as the field name, and the value as the body of the form-data - bytes. If the value is a tuple of two elements, then the first element - is treated as the filename of the form-data section. - - Field names and filenames must be unicode. - - :param boundary: - If not specified, then a random boundary will be generated using - :func:`mimetools.choose_boundary`. - """ - # copy requests imports in here: - from io import BytesIO - from requests.packages.urllib3.filepost import ( - choose_boundary, six, writer, b, get_content_type - ) - body = BytesIO() - if boundary is None: - boundary = choose_boundary() - - for fieldname, value in iter_fields(fields): - body.write(b('--%s\r\n' % (boundary))) - - if isinstance(value, tuple): - filename, data = value - writer(body).write('Content-Disposition: form-data; name="%s"; ' - 'filename="%s"\r\n' % (fieldname, filename)) - body.write(b('Content-Type: %s\r\n\r\n' % - (get_content_type(filename)))) - else: - data = value - writer(body).write('Content-Disposition: form-data; name="%s"\r\n' - % (fieldname)) - body.write(b'Content-Type: text/plain\r\n\r\n') - - if isinstance(data, int): - data = str(data) # Backwards compatibility - if isinstance(data, six.text_type): - writer(body).write(data) - else: - body.write(data) - - body.write(b'\r\n') - - body.write(b('--%s--\r\n' % (boundary))) - - content_type = b('multipart/form-data; boundary=%s' % boundary) - - return body.getvalue(), content_type - - -def post_download(project, filename, name=None, description=""): - """Upload a file to the GitHub downloads area""" - if name is None: - name = os.path.basename(filename) - with open(filename, 'rb') as f: - filedata = f.read() - - url = "https://api.github.com/repos/{project}/downloads".format(project=project) - - payload = json.dumps(dict(name=name, size=len(filedata), - description=description)) - response = requests.post(url, data=payload, headers=make_auth_header()) - response.raise_for_status() - reply = json.loads(response.content) - s3_url = reply['s3_url'] - - fields = dict( - key=reply['path'], - acl=reply['acl'], - success_action_status=201, - Filename=reply['name'], - AWSAccessKeyId=reply['accesskeyid'], - Policy=reply['policy'], - Signature=reply['signature'], - file=(reply['name'], filedata), - ) - fields['Content-Type'] = reply['mime_type'] - data, content_type = encode_multipart_formdata(fields) - s3r = requests.post(s3_url, data=data, headers={'Content-Type': content_type}) - return s3r diff --git a/tools/github_stats.py b/tools/github_stats.py deleted file mode 100755 index 572043d..0000000 --- a/tools/github_stats.py +++ /dev/null @@ -1,223 +0,0 @@ -#!/usr/bin/env python -"""Simple tools to query github.com and gather stats about issues. - -Thanks to the IPython team for developing this! - - python github_stats.py --milestone 2.0 --since-tag rel-1.0.0 -""" -#----------------------------------------------------------------------------- -# Imports -#----------------------------------------------------------------------------- - -from __future__ import print_function - -import codecs -import sys - -from argparse import ArgumentParser -from datetime import datetime, timedelta -from subprocess import check_output - -from gh_api import ( - get_paged_request, make_auth_header, get_pull_request, is_pull_request, - get_milestone_id, get_issues_list, get_authors, -) -#----------------------------------------------------------------------------- -# Globals -#----------------------------------------------------------------------------- - -ISO8601 = "%Y-%m-%dT%H:%M:%SZ" -PER_PAGE = 100 - -#----------------------------------------------------------------------------- -# Functions -#----------------------------------------------------------------------------- - -def round_hour(dt): - return dt.replace(minute=0,second=0,microsecond=0) - -def _parse_datetime(s): - """Parse dates in the format returned by the Github API.""" - if s: - return datetime.strptime(s, ISO8601) - else: - return datetime.fromtimestamp(0) - -def issues2dict(issues): - """Convert a list of issues to a dict, keyed by issue number.""" - idict = {} - for i in issues: - idict[i['number']] = i - return idict - -def split_pulls(all_issues, project="arokem/python-matlab-bridge"): - """split a list of closed issues into non-PR Issues and Pull Requests""" - pulls = [] - issues = [] - for i in all_issues: - if is_pull_request(i): - pull = get_pull_request(project, i['number'], auth=True) - pulls.append(pull) - else: - issues.append(i) - return issues, pulls - - -def issues_closed_since(period=timedelta(days=365), project="arokem/python-matlab-bridge", pulls=False): - """Get all issues closed since a particular point in time. period - can either be a datetime object, or a timedelta object. In the - latter case, it is used as a time before the present. - """ - - which = 'pulls' if pulls else 'issues' - - if isinstance(period, timedelta): - since = round_hour(datetime.utcnow() - period) - else: - since = period - url = "https://api.github.com/repos/%s/%s?state=closed&sort=updated&since=%s&per_page=%i" % (project, which, since.strftime(ISO8601), PER_PAGE) - allclosed = get_paged_request(url, headers=make_auth_header()) - - filtered = [ i for i in allclosed if _parse_datetime(i['closed_at']) > since ] - if pulls: - filtered = [ i for i in filtered if _parse_datetime(i['merged_at']) > since ] - # filter out PRs not against master (backports) - filtered = [ i for i in filtered if i['base']['ref'] == 'master' ] - else: - filtered = [ i for i in filtered if not is_pull_request(i) ] - - return filtered - - -def sorted_by_field(issues, field='closed_at', reverse=False): - """Return a list of issues sorted by closing date date.""" - return sorted(issues, key = lambda i:i[field], reverse=reverse) - - -def report(issues, show_urls=False): - """Summary report about a list of issues, printing number and title. - """ - # titles may have unicode in them, so we must encode everything below - if show_urls: - for i in issues: - print(u'#%d: %s' % (i['number'], - i['title'].replace(u'`', u'``'))) - else: - for i in issues: - print(u'* %d: %s' % (i['number'], i['title'].replace(u'`', u'``'))) - -#----------------------------------------------------------------------------- -# Main script -#----------------------------------------------------------------------------- - -if __name__ == "__main__": - # deal with unicode - sys.stdout = codecs.getwriter('utf8')(sys.stdout) - - # Whether to add reST urls for all issues in printout. - show_urls = True - - parser = ArgumentParser() - parser.add_argument('--since-tag', type=str, - help="The git tag to use for the starting point (typically the last major release)." - ) - parser.add_argument('--milestone', type=str, - help="The GitHub milestone to use for filtering issues [optional]." - ) - parser.add_argument('--days', type=int, - help="The number of days of data to summarize (use this or --since-tag)." - ) - parser.add_argument('--project', type=str, default="arokem/python-matlab-bridge", - help="The project to summarize." - ) - - opts = parser.parse_args() - tag = opts.since_tag - - # set `since` from days or git tag - if opts.days: - since = datetime.utcnow() - timedelta(days=opts.days) - else: - if not tag: - tag = check_output(['git', 'describe', '--abbrev=0']).strip() - cmd = ['git', 'log', '-1', '--format=%ai', tag] - tagday, tz = check_output(cmd).strip().rsplit(' ', 1) - since = datetime.strptime(tagday, "%Y-%m-%d %H:%M:%S") - h = int(tz[1:3]) - m = int(tz[3:]) - td = timedelta(hours=h, minutes=m) - if tz[0] == '-': - since += td - else: - since -= td - - since = round_hour(since) - - milestone = opts.milestone - project = opts.project - - print("fetching GitHub stats since %s (tag: %s, milestone: %s)" % (since, tag, milestone), file=sys.stderr) - if milestone: - milestone_id = get_milestone_id(project=project, milestone=milestone, - auth=True) - issues_and_pulls = get_issues_list(project=project, - milestone=milestone_id, - state='closed', - auth=True, - ) - issues, pulls = split_pulls(issues_and_pulls) - else: - issues = issues_closed_since(since, project=project, pulls=False) - pulls = issues_closed_since(since, project=project, pulls=True) - - # For regular reports, it's nice to show them in reverse chronological order - issues = sorted_by_field(issues, reverse=True) - pulls = sorted_by_field(pulls, reverse=True) - - n_issues, n_pulls = map(len, (issues, pulls)) - n_total = n_issues + n_pulls - - # Print summary report we can directly include into release notes. - - print() - since_day = since.strftime("%Y/%m/%d") - today = datetime.today().strftime("%Y/%m/%d") - print("GitHub stats for %s - %s (tag: %s)" % (since_day, today, tag)) - print() - print("These lists are automatically generated, and may be incomplete or contain duplicates.") - print() - - ncommits = 0 - all_authors = [] - if tag: - # print git info, in addition to GitHub info: - since_tag = tag+'..' - cmd = ['git', 'log', '--oneline', since_tag] - ncommits += len(check_output(cmd).splitlines()) - - author_cmd = ['git', 'log', '--use-mailmap', "--format=* %aN", since_tag] - all_authors.extend(check_output(author_cmd).decode('utf-8', 'replace').splitlines()) - - pr_authors = [] - for pr in pulls: - pr_authors.extend(get_authors(pr)) - ncommits = len(pr_authors) + ncommits - len(pulls) - author_cmd = ['git', 'check-mailmap'] + pr_authors - with_email = check_output(author_cmd).decode('utf-8', 'replace').splitlines() - all_authors.extend([ u'* ' + a.split(' <')[0] for a in with_email ]) - unique_authors = sorted(set(all_authors), key=lambda s: s.lower()) - - print("The following %i authors contributed %i commits." % (len(unique_authors), ncommits)) - print() - print('\n'.join(unique_authors)) - - print() - print("We closed %d issues and merged %d pull requests;\n" - "this is the full list (generated with the script \n" - ":file:`tools/github_stats.py`):" % (n_pulls, n_issues)) - print() - print('Pull Requests (%d):\n' % n_pulls) - report(pulls, show_urls) - print() - print('Issues (%d):\n' % n_issues) - report(issues, show_urls)