pysto are a few miscellaneous processing python functions.

The name is a play of words on "pisto", a Manchego dish made of tomatoes, onions, courgettes, green and red peppers and olive oil.

1. Install the latest pysto PyPI package

    pip install pysto
   

1. Uninstall the package

    pip uninstall pysto
   

2. If you get the error pip error: Cannot locate installed-files.txt, remove pysto manually. For example, if you are in a conda environment

    rm -rf ${CONDA_PREFIX}/lib/python3.6/site-packages/pysto*
   

We provide scripts install_pysto_environment.sh and build_SimpleElastix.sh to help install necessary software, and a Makefile to simplify testing and releasing.

1. If you want to develop code for pysto, instead of installing the PyPI package, you want to clone the github repository

    git clone https://github.com/rcasero/pysto.git
   

2. Install the development dependencies (this creates local conda environments pysto_2.7 and pysto_3.6, for python 2.7 and 3.6, respectively and installs several Ubuntu and python packages). There are two options, depending on what SimpleITK you want:

   1. If you are happy with the official SimpleITK package, just run (this is very fast)

       cd pysto/tools
       ./install_pysto_environment.sh
      

   2. If you prefer SimpleElastix (an extension of SimpleITK with elastix registration software)

       cd pysto/tools
       ./install_pysto_environment.sh SimpleElastix
      

3. Install the pysto code to one or both of the local environments

    conda activate pysto_2.7
    pip install --upgrade .
    
    conda activate pysto_3.6
    pip install --upgrade .
   

4. You need to have a local file ~/.pypirc (replace <the password> by the password). This will be used by twine to release packages to PyPI

    [distutils]
    index-servers =
      pypi
      pypitest
    
    [pypi]
    username=rcasero
    password=<the password>
    
    [pypitest]
    repository = https://test.pypi.org/legacy/
    username=rcasero
    password=<the password>
   

5. Protect the file so that it can be read only by you

    chmod 600 ~/.pypirc
   

1. Delete the conda local environments (this will delete all the python packages inside the environments)

    source deactivate
    conda remove --name pysto_2.7 --all
    conda remove --name pysto_3.6 --all
   

1. Activate one of the pysto local environments

    cd ~/Software/pysto
    source activate pysto_3.6
   

2. Launch the development IDE, e.g.

    pycharm-community &
   

3. In your code, import the pysto modules/functions in the usual way, e.g.

    import pysto.imgproc as pym
    import pysto.imgprocITK as pymITK
    [...]
    imf = pym.imfuse(im1, im2)
    pymITK.imshow(im3)
   

4. While developing, you can run all tests (both for python 2.7 and 3.6) from the command line with

    make test
   

1. We assume that you have made some changes to the code, and commit/pushed them to the GitHub repository.

2. Update version and download_url in setup.py with new release number. If something else has changed in the project, update other relevant fields in setup.py.

    setup(
        ...
        version='1.0.0',
        download_url='https://github.com/rcasero/pysto/archive/1.0.0.tar.gz',
        ...
    )
   

3. Update ChangeLog.md with the main changes to this release, in markdown format.

4. Commit and push all changes to the repository.

5. Make a test package. (This will also tag the release in github, create the test package/wheel and upload to the test PyPI server), that you can see in https://test.pypi.org/project/pysto/

    make test-package
   

6. If everything has gone well, make the release package, that you can see in https://pypi.org/project/pysto/

    make package
   

7. Go to pysto GitHub release tags, click on "Edit release notes" and copy and paste the new entry from the ChangeLog.md