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zakv opened this issue May 27, 2020 · 5 comments
Closed

h5py 2.10.0 Deprecation Warning #47

zakv opened this issue May 27, 2020 · 5 comments

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@zakv
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zakv commented May 27, 2020

Hi all, I get the deprecation warning below when using h5py 2.10.0. It appears in runmanager when compiling shots and in lyse when analysis scripts run.

C:\Users\waveguide3\Desktop\labscript_test_install_3\labscript_utils\h5_lock.py:64: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
  _File.__init__(self, name, mode, driver, libver, **kwds)

This was done using labscript-utils mercurial changeset e5a908bdc9cb. In the most recent git commit, this command is now on line 53:

labscript-utils/labscript_utils/h5_lock.py

Line 53 in 6bb2067

_File.__init__(self, name, mode, driver, libver, **kwds)
.

Looks like having mode=None is deprecated now. The h5py code for handling that case is here: https://github.com/h5py/h5py/blob/497d6a8ccbf3519fea2cd10093d0cee5da72358a/h5py/_hl/files.py#L188. I'm not very familiar with h5_lock.py but it may be fine to just use mode='a'. Alternatively the old h5py behavior could be reproduced by recreating those try/except statements from h5py in h5lock.py.

The warning pollutes the terminal outputs in runmanager and lyse but doesn't prevent anything from working, so this is a pretty minor issue. Also, h5py 2.9.0 works fine and doesn't issue this warning.
@chrisjbillington
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Thanks! We need to fix these before h5py 3.0, and to decrease the pollution in the meantime. I'll search the codebase for every time we open a HDF5 file and see how many there are where we're not specifying it.

@philipstarkey
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Related: labscript-suite/lyse#42

@chrisjbillington
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There are 37, and apparently nobody uses double quotes for file modes:

[bilbo:labscript] $ grep -rn --include="*.py" "h5py.File" * | egrep -v "'r'|'a'|'r\+'|'w'"
blacs/blacs/plugins/cycle_time/__init__.py:71:        with h5py.File(h5_filepath) as f:
blacs/blacs/experiment_queue.py:385:            with h5py.File(h5_filepath) as h5_file:
labscript/labscript/labscript.py:2282:    with h5py.File(compiler.hdf5_filename) as hdf5_file:
labscript-devices/labscript_devices/imaqdx_server.py:366:            with h5py.File(h5_filepath) as h5_file:
labscript-devices/labscript_devices/TekScope/blacs_workers.py:20:        with h5py.File(h5file) as hdf5_file:
labscript-devices/labscript_devices/TekScope/blacs_workers.py:56:        with h5py.File(self.h5file) as hdf_file:
labscript-devices/labscript_devices/ZaberStageController/blacs_workers.py:93:        with h5py.File(h5file) as hdf5_file:
labscript-devices/labscript_devices/AlazarTechBoard.py:319:        with h5py.File(h5file) as hdf5_file:
labscript-devices/labscript_devices/AlazarTechBoard.py:382:        with h5py.File(h5file) as hdf5_file:
labscript-devices/labscript_devices/AlazarTechBoard.py:588:        with h5py.File(self.h5file) as hdf5_file:
labscript-devices/labscript_devices/FunctionRunner/labscript_devices.py:53:            with h5py.File(self.h5_file) as f:
labscript-devices/labscript_devices/IMAQdxCamera/blacs_workers.py:432:        with h5py.File(self.h5_filepath) as f:
labscript-devices/labscript_devices/PhaseMatrixQuickSyn.py:336:        with h5py.File(h5file) as hdf5_file:
labscript-devices/labscript_devices/LightCrafterDMD.py:320:        with h5py.File(h5file) as hdf5_file:
labscript-devices/labscript_devices/NovaTechDDS9M.py:460:        with h5py.File(h5file) as hdf5_file:
labscript-utils/labscript_utils/camera_server.py:161:        with h5py.File(h5_filepath) as f:
labscript-utils/labscript_utils/h5_lock.py:39:_File = h5py.File
labscript-utils/labscript_utils/h5_lock.py:68:    # Overriding __exit__ is crucial. Since h5py.File.__exit__() holds h5py's
labscript-utils/labscript_utils/h5_lock.py:70:    # method does not need the lock (h5py.File.close() does, but it acquires it itself
labscript-utils/labscript_utils/h5_lock.py:90:    h5py.File = File
lyse/lyse/__init__.py:109:            with h5py.File(h5_path) as h5_file:
lyse/lyse/__init__.py:121:                with h5py.File(h5_path) as h5_file:
lyse/lyse/__init__.py:135:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:141:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:149:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:155:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:162:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:172:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:291:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:310:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:316:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:325:            with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:329:                with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:336:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:377:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:388:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:393:        with h5py.File(self.h5_path) as h5_file:
lyse/lyse/__init__.py:409:        with h5py.File(h5_path) as h5_file:
lyse/lyse/__init__.py:422:            with h5py.File(h5_path) as h5_file:
runmanager/runmanager/__init__.py:881:    Simple dictionary access as in dict(h5py.File(filepath).attrs) would be fine

philipstarkey added a commit to philipstarkey/labscript that referenced this issue Jun 24, 2020
@philipstarkey
Fix h5py deprecation warning
1746399 
Addresses labscript-suite/labscript-utils#47 for the labscript module
@philipstarkey philipstarkey mentioned this issue Jun 24, 2020
Merged
philipstarkey added a commit to philipstarkey/lyse that referenced this issue Jun 24, 2020
@philipstarkey
Run.get_* methods should open the HDF5 file in read-only mode
2d8a80e 
Fixes labscript-suite#42

Also addressed labscript-suite/labscript-utils#47 (removing h5py deprecation warnings) for this module

Also fixed an issue where calling `set_group` on a `Run` inside a `Sequence` could disable the read-only mode of the `Run` object.

Added `no_write` support to `Sequence`.
@philipstarkey philipstarkey mentioned this issue Jun 24, 2020
Merged
philipstarkey added a commit to philipstarkey/labscript-utils that referenced this issue Jun 25, 2020
@philipstarkey
Addresses labscript-suite#47 for this module
bfa6932
philipstarkey added a commit to philipstarkey/blacs that referenced this issue Jun 25, 2020
@philipstarkey
Addresses labscript-suite/labscript-utils#47
cb41ec0
chrisjbillington added a commit to labscript-suite/blacs that referenced this issue Jun 25, 2020
@chrisjbillington
Merge pull request #78 from philipstarkey/fix-h5py-file-mode
f3a5f41 
Addresses labscript-suite/labscript-utils#47
philipstarkey added a commit to philipstarkey/labscript-devices that referenced this issue Jun 25, 2020
@philipstarkey
Fix h5py deprecation warnings
1988032 
Addresses labscript-suite/labscript-utils#47 for this module
chrisjbillington added a commit that referenced this issue Jun 25, 2020
@chrisjbillington
Merge pull request #59 from philipstarkey/fix-h5py-file-mode
d8b8343 
Addresses #47 for this module
This was referenced Jun 25, 2020
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@philipstarkey
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That should be all of them now.

I haven't done the runmanager one you found because it was just in a comment

@philipstarkey
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All PRs are now merged so marking as resolved. Please reopen if anyone finds any others that we missed!

philipstarkey added a commit that referenced this issue Jun 25, 2020
@philipstarkey
Squashed commit of the following:
a953031 
commit d8b8343
Merge: 9bc7a39 bfa6932
Author: Chris Billington <[email protected]>
Date:   Wed Jun 24 20:48:39 2020 -0400

    Merge pull request #59 from philipstarkey/fix-h5py-file-mode

    Addresses #47 for this module

commit 9bc7a39
Merge: 1189334 66d0be4
Author: Chris Billington <[email protected]>
Date:   Wed Jun 24 20:30:42 2020 -0400

    Merge pull request #55 from rpanderson/example_IMAQdx_remote

    Example labscript and analysis scripts for IMAQdxCamera and RemoteBLACS

commit bfa6932
Author: philipstarkey <[email protected]>
Date:   Thu Jun 25 10:25:49 2020 +1000

    Addresses #47 for this module

commit 1189334
Merge: 5025b1b 0b0d07a
Author: Chris Billington <[email protected]>
Date:   Wed Jun 24 19:35:15 2020 -0400

    Merge pull request #54 from rpanderson/example_experiment

    Minimal working connection table and example experiment script

commit 66d0be4
Author: Russell Anderson <[email protected]>
Date:   Mon Jun 15 13:37:23 2020 +1000

    lyse analysis script demonstrating some Run methods for example_IMAQdx_remote

commit a48a9c0
Author: Russell Anderson <[email protected]>
Date:   Mon Jun 15 13:15:48 2020 +1000

    Example connection table and labscript experiment script for RemoteBLACS and IMAQdxCamera

commit 5025b1b
Merge: f77525f ed76901
Author: Chris Billington <[email protected]>
Date:   Wed Jun 24 02:16:29 2020 -0400

    Merge pull request #58 from philipstarkey/philipstarkey/issue43

    Fixes .pth file has no effect in editable install

commit ed76901
Author: chrisjbillington <[email protected]>
Date:   Wed Jun 24 01:23:44 2020 -0400

    Move copying of .pth file into setup.py

    Use a custom develop command to copy the .pth file into site-packages
    when `python setup.py develop` is run - this is what pip does under the
    hood for `pip install -e`.

    No longer need desktop-app to locate site-packages, as the setuptools
    command class knows it as `self.install_dir`.

    The file is not removed by `pip uninstall`, but due to the `try:
    except:`s in the `.pth` file, leaving it behind is harmless.

    It is removed if the user runs whatever `setup.py` command undoies

commit 894e245
Author: chrisjbillington <[email protected]>
Date:   Wed Jun 24 00:04:13 2020 -0400

    Require desktop-app 0.2.6

    Which renames `_get_install_directory` to not have an underscore,
    and which fixes a bug preventing docs from building on RTD.

commit 271439e
Author: philipstarkey <[email protected]>
Date:   Wed Jun 24 12:53:49 2020 +1000

    Removed support for custom development directories from path

commit dd098a5
Author: philipstarkey <[email protected]>
Date:   Wed Jun 24 12:38:19 2020 +1000

    Fixes .pth file has no effect in editable install
    Fixes #43

    The .pth file is now copied during `labscript-profile-create` if it does not exist in the site-packages dir (where the .egg-info files exist) and if it the .pth file exists in the package structure (aka labscript-utils it is an editable install)

    The labscript-suite.pth file has been updated to not raise an exception if labscript-suite has been uninstalled (so we do not have to worry about cleanup).

    Also updated the `labscript_profile.add_userlib_and_pythonlib` function to use the `site` library for adding userlib and pythonlib to the system path.

commit 0b0d07a
Author: Russell Anderson <[email protected]>
Date:   Mon Jun 22 17:48:00 2020 +1000

    start()/stop() in __main__ block so connection table can be imported

commit 4c19de9
Author: Russell Anderson <[email protected]>
Date:   Mon Jun 15 13:12:52 2020 +1000

    Add AnalogOut with ramp example, rename DigitalOut connection

commit 9b64a0d
Author: Russell Anderson <[email protected]>
Date:   Wed Jun 10 23:09:03 2020 +1000

    Minimal example connection table and labscript using dummy devices

commit f77525f
Author: Phil Starkey <[email protected]>
Date:   Sat Jun 20 18:09:53 2020 +1000

    Removed unnecessary fixed title from main TOC

    This was erroneously added in #57

commit 5e02b01
Merge: 3f78207 8b19766
Author: Phil Starkey <[email protected]>
Date:   Sat Jun 20 18:07:04 2020 +1000

    Merge pull request #57 from philipstarkey/master

    Changed URL for API reference to be shorter
    Fixed bug with readthedocs auto PR build

commit 8b19766
Author: philipstarkey <[email protected]>
Date:   Sat Jun 20 12:02:51 2020 +1000

    Updated method call for stylesheet to remove deprecated warning in build

commit 56fdd63
Author: philipstarkey <[email protected]>
Date:   Sat Jun 20 11:46:33 2020 +1000

    Fixed sphinx conf to detect PR builds and link to 'latest' instead of stable

commit 9889d19
Author: philipstarkey <[email protected]>
Date:   Sat Jun 20 10:44:04 2020 +1000

    Changed URL for API reference to be shorter

commit 3f78207
Merge: bbd928a bf9d10e
Author: Phil Starkey <[email protected]>
Date:   Fri Jun 19 18:58:37 2020 +1000

    Merge pull request #56 from philipstarkey/master

    Added links to other component docs

commit bf9d10e
Author: philipstarkey <[email protected]>
Date:   Fri Jun 19 16:06:09 2020 +1000

    Addressing latest review comments

commit e75b6bc
Author: philipstarkey <[email protected]>
Date:   Fri Jun 19 11:23:49 2020 +1000

    Updated docs to use jinja template for component doc links

commit 9c61238
Author: philipstarkey <[email protected]>
Date:   Thu Jun 18 17:14:57 2020 +1000

    Removed autogenerated rst file from version control

commit 2303185
Author: philipstarkey <[email protected]>
Date:   Thu Jun 18 16:43:29 2020 +1000

    Updated .gitignore with latest GitHub defaults

commit 87b757e
Author: philipstarkey <[email protected]>
Date:   Thu Jun 18 16:39:52 2020 +1000

    Relocated custom sphinx gitignore rules

commit 75813a5
Author: philipstarkey <[email protected]>
Date:   Thu Jun 18 16:31:01 2020 +1000

    Updated PR as per review in labscript-suite/labscript-suite#48

commit bbd928a
Author: Russell Anderson <[email protected]>
Date:   Wed Jun 17 11:39:17 2020 +1000

    Populated README.md with styling, iconogrpahy, prose, and badges

commit 573c521
Author: philipstarkey <[email protected]>
Date:   Tue Jun 16 18:10:25 2020 +1000

    Added links to other component docs
philipstarkey added a commit to labscript-suite/labscript that referenced this issue Jun 25, 2020
@philipstarkey @chrisjbillington @rpanderson
Squashed commit of the following:
83856d6 
commit c3b7988
Author: Phil Starkey <[email protected]>
Date:   Thu Jun 25 18:27:06 2020 +1000

    Update labscript_utils dependency to `>=3.0.0`

commit 822e5d5
Merge: 2e2785c 39c6f0b
Author: Russell Anderson <[email protected]>
Date:   Thu Jun 25 15:48:15 2020 +1000

    Merge pull request #69 from rpanderson/example_fix

    Make example labscript functional and format using black

commit 39c6f0b
Author: Russell Anderson <[email protected]>
Date:   Thu Jun 25 12:34:08 2020 +1000

    Name all the args

commit 255d74e
Author: Russell Anderson <[email protected]>
Date:   Thu Jun 25 12:11:48 2020 +1000

    Name all arguments in connection table

commit e3d3ece
Author: Russell Anderson <[email protected]>
Date:   Thu Jun 25 11:08:25 2020 +1000

    Omit __init__ import and comply with flake8 F403

commit 6b26f1f
Author: Russell Anderson <[email protected]>
Date:   Sun May 31 17:38:18 2020 +1000

    Make example labscript functional and format using black

commit 2e2785c
Merge: 62b9098 4e77810
Author: Chris Billington <[email protected]>
Date:   Wed Jun 24 21:22:05 2020 -0400

    Merge pull request #70 from rpanderson/is-syntax-warning-bugfix

    Bugfix for ValueError introduced in #68

commit 4e77810
Author: Russell Anderson <[email protected]>
Date:   Thu Jun 25 11:18:56 2020 +1000

    Abbreviated bugfix.

commit a667f7e
Author: Russell Anderson <[email protected]>
Date:   Thu Jun 25 11:17:11 2020 +1000

    Bugfix for ValueError introduced in #68

commit 62b9098
Merge: 0e23ed0 1746399
Author: Chris Billington <[email protected]>
Date:   Wed Jun 24 20:49:32 2020 -0400

    Merge pull request #67 from philipstarkey/fix-h5py-file-mode

    Fix h5py deprecation warning

commit 0e23ed0
Merge: 5b52c20 6373f02
Author: Chris Billington <[email protected]>
Date:   Wed Jun 24 18:47:18 2020 -0400

    Merge pull request #68 from rpanderson/is-syntax-warning

    Do not use 'is' for numeric literal comparisons

commit 6373f02
Author: Russell Anderson <[email protected]>
Date:   Thu Jun 25 08:36:55 2020 +1000

    Omitted 'is' with numeric literal comparisons

commit 1746399
Author: philipstarkey <[email protected]>
Date:   Wed Jun 24 18:29:12 2020 +1000

    Fix h5py deprecation warning

    Addresses labscript-suite/labscript-utils#47 for the labscript module

commit 5b52c20
Merge: 0362fa7 88ce952
Author: Russell Anderson <[email protected]>
Date:   Mon Jun 22 18:09:54 2020 +1000

    Merge pull request #66 from philipstarkey/master

    Doc updates

commit 88ce952
Author: philipstarkey <[email protected]>
Date:   Sat Jun 20 18:17:23 2020 +1000

    Doc updates

    Renamed API reference URL to match labscript utils and updated config to fix bugs identified in labscript-suite/labscript-utils#57

commit 0362fa7
Merge: 74869ef 52d3b9f
Author: Phil Starkey <[email protected]>
Date:   Fri Jun 19 18:58:04 2020 +1000

    Merge pull request #65 from philipstarkey/master

    Updated docs to follow our standard conf

commit 52d3b9f
Author: philipstarkey <[email protected]>
Date:   Fri Jun 19 16:04:04 2020 +1000

    Addressing latest review comments

commit 7674a8f
Author: philipstarkey <[email protected]>
Date:   Fri Jun 19 11:19:33 2020 +1000

    Updated docs to use jinja template for component doc links

commit d4474e2
Author: philipstarkey <[email protected]>
Date:   Thu Jun 18 16:43:10 2020 +1000

    Updated .gitignore with latest GitHub defaults

commit a18a0d1
Author: philipstarkey <[email protected]>
Date:   Thu Jun 18 16:39:35 2020 +1000

    Relocated custom sphinx git ignore rules

commit 80aa5a1
Author: philipstarkey <[email protected]>
Date:   Thu Jun 18 16:21:44 2020 +1000

    Restored 64 pixel logo accidentally replaced with 32 pixel logo

commit 42d3bc6
Author: philipstarkey <[email protected]>
Date:   Thu Jun 18 16:17:42 2020 +1000

    Updated install requirement to 3.0.0rc1+

commit 1961a2c
Author: philipstarkey <[email protected]>
Date:   Thu Jun 18 16:13:40 2020 +1000

    testing dependency fix

commit 234753d
Author: philipstarkey <[email protected]>
Date:   Thu Jun 18 16:07:41 2020 +1000

    Updated as per the review in labscript-suite/labscript-suite#48

commit 74869ef
Author: Russell Anderson <[email protected]>
Date:   Wed Jun 17 10:24:43 2020 +1000

    Populated README.md with styling, iconogrpahy, prose, and badges

commit 28dc675
Author: philipstarkey <[email protected]>
Date:   Tue Jun 16 18:24:26 2020 +1000

    Removed unnecessary header and added intersphinx link

commit 35c5466
Author: philipstarkey <[email protected]>
Date:   Tue Jun 16 17:19:33 2020 +1000

    Updated docs to follow our standard conf

    Also added links to other labscript suite docs and standard links.

Co-authored-by: chrisjbillington <[email protected]>
Co-authored-by: Russell Anderson <[email protected]>
philipstarkey added a commit to labscript-suite/lyse that referenced this issue Jun 25, 2020
@philipstarkey @chrisjbillington @rpanderson
Squashed commit of the following:
d9ad984 
commit f7a1427
Author: Phil Starkey <[email protected]>
Date:   Thu Jun 25 19:03:31 2020 +1000

    Update dependencies in setup.cfg

    Bumped runmanager and labscript_utils versions to `>=3.0.0`

commit 20cb9af
Merge: 74dfc19 2d8a80e
Author: Phil Starkey <[email protected]>
Date:   Thu Jun 25 12:56:40 2020 +1000

    Merge pull request #71 from philipstarkey/philipstarkey/issue42

commit 2d8a80e
Author: philipstarkey <[email protected]>
Date:   Wed Jun 24 19:22:04 2020 +1000

    Run.get_* methods should open the HDF5 file in read-only mode
    Fixes #42

    Also addressed labscript-suite/labscript-utils#47 (removing h5py deprecation warnings) for this module

    Also fixed an issue where calling `set_group` on a `Run` inside a `Sequence` could disable the read-only mode of the `Run` object.

    Added `no_write` support to `Sequence`.

commit 74dfc19
Merge: 1fc61cb 6cd5d06
Author: Russell Anderson <[email protected]>
Date:   Mon Jun 22 18:06:38 2020 +1000

    Merge pull request #70 from philipstarkey/master

    fix docs conf bugs identified in labscript-suite/labscript-utils#57

commit 6cd5d06
Author: philipstarkey <[email protected]>
Date:   Sat Jun 20 18:35:29 2020 +1000

    fix docs conf bugs identified in labscript-suite/labscript-utils#57

commit 1fc61cb
Merge: c6c2aa7 eed3f6e
Author: Phil Starkey <[email protected]>
Date:   Fri Jun 19 19:01:03 2020 +1000

    Merge pull request #69 from philipstarkey/master

    Empty sphinx project following our template

commit eed3f6e
Author: philipstarkey <[email protected]>
Date:   Fri Jun 19 18:30:22 2020 +1000

    Empty sphinx project following our template

commit c6c2aa7
Author: Russell Anderson <[email protected]>
Date:   Wed Jun 17 11:39:43 2020 +1000

    Populated README.md with styling, iconogrpahy, prose, and badges

commit 5760b8a
Merge: bb2061d 84c6ec7
Author: Russell Anderson <[email protected]>
Date:   Tue Jun 16 12:07:02 2020 +1000

    Merge pull request #68 from rpanderson/master

    experiment_name changed to apparatus_name

commit 84c6ec7
Author: Russell Anderson <[email protected]>
Date:   Wed Jun 10 22:54:44 2020 +1000

    experiment_name changed to apparatus_name

    Per labscript-suite/labscript-utils#53

Co-authored-by: chrisjbillington <[email protected]>
Co-authored-by: Russell Anderson <[email protected]>
philipstarkey added a commit to labscript-suite/labscript-devices that referenced this issue Jun 25, 2020
@philipstarkey @chrisjbillington @rpanderson
Squashed commit of the following:
080e054 
commit c9de425
Author: Phil Starkey <[email protected]>
Date:   Thu Jun 25 19:12:29 2020 +1000

    Update dependencies in setup.cfg

    Bumped blacs, labscript and labscript_utils versions to `>=3.0.0`

commit d43ced1
Merge: 3863607 1988032
Author: Chris Billington <[email protected]>
Date:   Wed Jun 24 22:48:26 2020 -0400

    Merge pull request #58 from philipstarkey/fix-h5py-file-mode

    Fix h5py deprecation warnings

commit 1988032
Author: philipstarkey <[email protected]>
Date:   Thu Jun 25 10:48:10 2020 +1000

    Fix h5py deprecation warnings

    Addresses labscript-suite/labscript-utils#47 for this module

commit 3863607
Merge: 88eeefe cdd34f8
Author: Phil Starkey <[email protected]>
Date:   Wed Jun 24 10:51:04 2020 +1000

    Merge pull request #54 from rpanderson/dummy_pseudoclock_updates

    Save clock instructions and add runviewer parser for DummyPseudoclock

commit 88eeefe
Merge: 55b1bd8 84eb889
Author: Phil Starkey <[email protected]>
Date:   Wed Jun 24 10:50:09 2020 +1000

    Merge pull request #42 from JQIamo/SpinnakerCamera

    Added SpinnakerCamera

commit cdd34f8
Author: philipstarkey <[email protected]>
Date:   Tue Jun 23 18:34:28 2020 +1000

    Implemented review changes

commit d2e5679
Author: Russell Anderson <[email protected]>
Date:   Fri Jun 12 18:47:25 2020 +1000

    Save clock instructions (mock PineBlaster) and add runviewer_parser

commit 84eb889
Author: philipstarkey <[email protected]>
Date:   Tue Jun 23 12:49:00 2020 +1000

    Implemented review changes

commit 55b1bd8
Merge: bb9f6f5 d5fca30
Author: Russell Anderson <[email protected]>
Date:   Mon Jun 22 18:07:08 2020 +1000

    Merge pull request #57 from philipstarkey/master

    fix docs conf bugs identified in labscript-suite/labscript-utils#57

commit d5fca30
Author: philipstarkey <[email protected]>
Date:   Sat Jun 20 18:33:55 2020 +1000

    fix docs conf bugs identified in labscript-suite/labscript-utils#57

commit bb9f6f5
Merge: 0f1cacd 091110b
Author: Russell Anderson <[email protected]>
Date:   Fri Jun 19 17:57:15 2020 +1000

    Merge pull request #56 from philipstarkey/master

    Empty sphinx project following our template

commit 091110b
Author: philipstarkey <[email protected]>
Date:   Fri Jun 19 17:42:46 2020 +1000

    Empty sphinx project following our template

commit 0f1cacd
Author: Russell Anderson <[email protected]>
Date:   Wed Jun 17 16:39:08 2020 +1000

    Added missing devices to README.md

commit 5347098
Author: Russell Anderson <[email protected]>
Date:   Wed Jun 17 11:38:03 2020 +1000

    Populated README.md with styling, iconogrpahy, prose, and badges

commit bd2505e
Author: DSB <[email protected]>
Date:   Mon May 4 14:27:03 2020 -0400

    SpinnakerCamera

    Adding a camera interface that uses FLIR's newer PySpin/Spinnaker API.

    DSB

Co-authored-by: chrisjbillington <[email protected]>
Co-authored-by: Russell Anderson <[email protected]>
philipstarkey added a commit to labscript-suite/blacs that referenced this issue Jun 25, 2020
@philipstarkey @chrisjbillington @rpanderson
Squashed commit of the following:
6ea046b 
commit 348bbeb
Author: Phil Starkey <[email protected]>
Date:   Thu Jun 25 19:47:34 2020 +1000

    Update dependencies in setup.cfg

    Bumped labscript_devices and labscript_utils versions to `>=3.0.0`

commit 24b3728
Merge: f3a5f41 0a3df34
Author: Phil Starkey <[email protected]>
Date:   Thu Jun 25 12:55:47 2020 +1000

    Merge pull request #77 from chrisjbillington/anywhere-unit-conversions

    Allow BLACS to use conversion classes defined outside labscript_utils

commit 0a3df34
Author: chrisjbillington <[email protected]>
Date:   Wed Jun 24 22:50:15 2020 -0400

    Fix error message formatting args being the wrong way around

commit 9ed2890
Author: chrisjbillington <[email protected]>
Date:   Wed Jun 24 19:26:10 2020 -0400

    Allow BLACS to use conversion classes defined outside labscript_utils

    Labscript has long-since saved unit conversions with their full import
    path instead of just a class name, and
    `labscript_utils.unitconversisons` has provided a function
    `get_unit_conversion_class()` to look them up.

    Here we just use that function to look up unit calibration classes.
    `get_unit_conversion_class()` falls back to the old behaviour of
    importing all unit conversion modules in
    `labscript_utils.unitconversisons` and looking for the given class if it
    encounters an unqualified class name.

commit f3a5f41
Merge: 88eb635 cb41ec0
Author: Chris Billington <[email protected]>
Date:   Wed Jun 24 20:47:58 2020 -0400

    Merge pull request #78 from philipstarkey/fix-h5py-file-mode

    Addresses labscript-suite/labscript-utils#47

commit cb41ec0
Author: philipstarkey <[email protected]>
Date:   Thu Jun 25 10:32:57 2020 +1000

    Addresses labscript-suite/labscript-utils#47

commit 88eb635
Merge: 968afbc 6439a26
Author: Russell Anderson <[email protected]>
Date:   Mon Jun 22 18:07:29 2020 +1000

    Merge pull request #76 from philipstarkey/master

    fix docs conf bugs identified in labscript-suite/labscript-utils#57

commit 6439a26
Author: philipstarkey <[email protected]>
Date:   Sat Jun 20 18:32:02 2020 +1000

    fix docs conf bugs identified in labscript-suite/labscript-utils#57

commit 968afbc
Merge: 51a47c1 de2d967
Author: Phil Starkey <[email protected]>
Date:   Fri Jun 19 19:00:41 2020 +1000

    Merge pull request #75 from philipstarkey/master

    Empty sphinx project following our template

commit de2d967
Author: philipstarkey <[email protected]>
Date:   Fri Jun 19 17:18:04 2020 +1000

    Empty sphinx project following our template

commit 51a47c1
Author: Russell Anderson <[email protected]>
Date:   Wed Jun 17 10:24:16 2020 +1000

    Abbreviate installation instructions in README.md

commit fe40066
Author: Russell Anderson <[email protected]>
Date:   Tue Jun 16 22:19:12 2020 +1000

    Populated README.md with styling, iconogrpahy, prose, and badges

commit 06e430b
Merge: e739553 1d1e9c4
Author: Russell Anderson <[email protected]>
Date:   Tue Jun 16 12:07:07 2020 +1000

    Merge pull request #73 from rpanderson/master

    experiment_name changed to apparatus_name

commit 1d1e9c4
Author: Russell Anderson <[email protected]>
Date:   Wed Jun 10 22:50:36 2020 +1000

    experiment_name changed to apparatus_name

    Per labscript-suite/labscript-utils#53

Co-authored-by: chrisjbillington <[email protected]>
Co-authored-by: Russell Anderson <[email protected]>
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