Merge pull request labscript-suite#109 from dihm/break_runmanager_dep

Break dependency on runmanager by using `labscript_utils.shot_utils.get_shot_globals`

Merge pull request labscript-suite#108 from dihm/tzlocal_hotfix

Update tzlocal call in dataframe_utilities

Squashed commit of the following:

commit 8e60e175edc07024874b5c3dcdd8911eb59ae8d0
Author: David Meyer <[email protected]>
Date:   Wed Apr 19 13:03:50 2023 -0400

    Merge pull request labscript-suite#102 from dihm/lyse_optimization

    Implement optimization described in labscript-suite#92

commit 272e39871e45d6b6dd251abfad3c9478f0fc921a
Author: Chris Billington <[email protected]>
Date:   Wed Apr 19 06:57:13 2023 +1000

    Merge pull request labscript-suite#106 from labscript-suite/group-introspection-simplification

    Resolve issue with Run object choosing group name based on script name

commit 925f0b2551cfebc463e880b1ac7d17258205ed27
Author: David Meyer <[email protected]>
Date:   Mon Apr 17 10:32:31 2023 -0400

    Merge pull request labscript-suite#105 from dihm/hotfix

    Hotfix for lyse figuremanager when in standalone mode

Squashed commit of the following:

commit 82db032
Author: David Meyer <[email protected]>
Date:   Wed Apr 12 19:44:34 2023 -0400

    Update python version support

commit 209071b
Merge: dfbc653 5f05e59
Author: David Meyer <[email protected]>
Date:   Wed Apr 12 16:52:14 2023 -0400

    Merge pull request labscript-suite#104 from dihm/update-workflow

    Sync workflow with latest and greatest

commit 5f05e59
Author: David Meyer <[email protected]>
Date:   Wed Apr 12 16:39:47 2023 -0400

    Sync workflow with latest and greatest

commit dfbc653
Merge: 1f0c876 405331e
Author: David Meyer <[email protected]>
Date:   Wed Apr 12 16:37:40 2023 -0400

    Merge pull request labscript-suite#103 from dihm/figuremanager_hotfix

    Fix signature mis-match when loading custom FigureManager backend

commit 405331e
Author: David Meyer <[email protected]>
Date:   Mon Mar 13 13:11:35 2023 -0400

    Fix signature mis-match when loading custom FigureManager backend.

commit 1f0c876
Merge: e703362 8b03da8
Author: David Meyer <[email protected]>
Date:   Fri Aug 5 16:04:56 2022 -0400

    Merge pull request labscript-suite#100 from dihm/update-workflow

    Bring workflow up to date with sandbox

commit 8b03da8
Author: David Meyer <[email protected]>
Date:   Wed Aug 3 13:19:49 2022 -0400

    Bring workflow up to date with sandbox

commit e703362
Merge: 67a6c8f 6a839f4
Author: David Meyer <[email protected]>
Date:   Thu Jun 2 10:59:07 2022 -0400

    Merge pull request labscript-suite#99 from dihm/fix_docs_build

    Bump sphinx pin and update intersphinx links

commit 6a839f4
Author: David Meyer <[email protected]>
Date:   Thu Jun 2 10:54:25 2022 -0400

    Bump sphinx pin and update intersphinx links

commit 67a6c8f
Merge: 6ade884 ed55aad
Author: David Meyer <[email protected]>
Date:   Tue May 31 12:37:05 2022 -0400

    Merge pull request labscript-suite#97 from ispielma/LyseSimpleData

    Lyse simple data

commit ed55aad
Merge: 1d37c94 6ade884
Author: spielman <[email protected]>
Date:   Tue May 31 08:10:41 2022 -0400

    Merge remote-tracking branch 'origin/master' into LyseSimpleData

commit 6ade884
Merge: 9db7818 981443d
Author: David Meyer <[email protected]>
Date:   Fri May 20 16:46:31 2022 -0400

    Merge pull request labscript-suite#98 from th0mam/th0mam-patch-1

    Definition of new functions "get_wait" and "get_waits"

commit 981443d
Author: th0mam <[email protected]>
Date:   Fri May 20 09:42:03 2022 +0200

    Update __init__.py

commit 274c6f0
Author: th0mam <[email protected]>
Date:   Mon May 9 13:11:39 2022 +0200

    Definition of new function "get_waits"

    I defined a new function "get_waits".
    Returns a 2D array of times and timeout statuses.
    This may be quite useful to some teams, where timeout signifies faulty experiment, and so unusable data.

commit 1d37c94
Author: spielman <[email protected]>
Date:   Mon May 2 11:22:51 2022 -0400

    Added spaces to be more standard.

commit 9d9d1de
Author: spielman <[email protected]>
Date:   Mon May 2 11:22:00 2022 -0400

    Update for pull request.

commit c3a837f
Author: spielman <[email protected]>
Date:   Fri Apr 22 11:31:49 2022 -0400

    Added method to return a dictionary of images rather than just a list.

commit 263c70f
Merge: 1a3ec8d 9db7818
Author: Ian B. Spielman <[email protected]>
Date:   Wed Feb 16 14:22:27 2022 -0500

    Merge branch 'labscript-suite:master' into LyseSimpleData

commit 1a3ec8d
Author: Ian Spielman <[email protected]>
Date:   Wed Feb 16 14:21:20 2022 -0500

    Changes to allow get trace to return the raw data.  This solves an issue that the TeX scope class does not save timing information, just four traces.

commit 9db7818
Merge: 7b11b71 eb240fd
Author: David Meyer <[email protected]>
Date:   Sat Feb 5 06:09:31 2022 -0500

    Merge pull request labscript-suite#96 from dihm/mock_labscript_utils

    Prevent h5_lock import during docs build

commit eb240fd
Author: David Meyer <[email protected]>
Date:   Sat Feb 5 06:05:04 2022 -0500

    Update docs `conf.py` to get version using importlib_metadata to avoid
    incidental import of labscript_utils.h5_lock.

Update python version support

Squashed commit of the following:

commit 8575ff2
Author: David Meyer <[email protected]>
Date:   Tue Dec 7 10:52:15 2021 -0500

    Update setup.cfg to show python 3.9 support

commit e4b57f8
Merge: 8bf02a2 915cc1c
Author: David Meyer <[email protected]>
Date:   Tue Dec 7 07:31:45 2021 -0500

    Merge pull request labscript-suite#95 from dihm/msg_replacement

    Msg replacement

commit 8bf02a2
Merge: 72f82b3 a98a766
Author: David Meyer <[email protected]>
Date:   Tue Dec 7 07:30:06 2021 -0500

    Merge pull request labscript-suite#88 from zakv/move-infer_objects

    Move infer_objects() out of main thread

commit 915cc1c
Author: David Meyer <[email protected]>
Date:   Fri Dec 3 09:01:04 2021 -0500

    Adding the extra bugfixes found in labscript-suite#91.

commit fa9eedb
Author: David Meyer <[email protected]>
Date:   Fri Dec 3 09:00:29 2021 -0500

    Replace deprecated msgpack with python's pickle for saving dataframes.

    This keeps machinery in place to read msgpack files if the installed
    pandas supports it, but it will always save new dataframes as pickles.

commit 72f82b3
Merge: cb60667 26ef795
Author: David Meyer <[email protected]>
Date:   Fri Jul 16 16:09:52 2021 -0400

    Merge pull request labscript-suite#93 from dihm/update_lyse_docs

    Update lyse docs to match autogenerated docs from other modules.

commit 26ef795
Author: David Meyer <[email protected]>
Date:   Thu Jul 15 10:30:09 2021 -0400

    Add docstring coverage to build.

commit 98cac68
Author: David Meyer <[email protected]>
Date:   Thu Jul 15 10:29:57 2021 -0400

    Update sphinx pin.

commit 4671ef6
Author: David Meyer <[email protected]>
Date:   Tue Jul 13 17:21:29 2021 -0400

    Add docstrings to the API functions.

    Reasonably sure they are all accurate.

commit 40d207c
Author: David Meyer <[email protected]>
Date:   Mon Jul 12 10:47:31 2021 -0400

    Tweaked docs formatting.

commit 47b60a8
Author: David Meyer <[email protected]>
Date:   Mon Jul 12 10:40:42 2021 -0400

    Convert doc generation to recursive autosummary call.

commit 9add58b
Author: David Meyer <[email protected]>
Date:   Mon Jul 12 10:38:50 2021 -0400

    Tweak docstrings.

commit 3873dcc
Author: David Meyer <[email protected]>
Date:   Mon Jul 12 09:26:55 2021 -0400

    Add Qt5 inventory for intersphinx lookup.

commit e7cf19a
Author: David Meyer <[email protected]>
Date:   Mon Jul 12 09:26:31 2021 -0400

    Update sphinx pins to match rest of suite docs.

commit cb60667
Merge: eaca856 8596dea
Author: Chris Billington <[email protected]>
Date:   Fri Jan 29 14:00:36 2021 +1100

    Merge pull request labscript-suite#89 from chrisjbillington/master

    Do not use deprecated set-env command

commit 8596dea
Author: chrisjbillington <[email protected]>
Date:   Fri Jan 29 13:57:39 2021 +1100

    Do not use deprecated set-env command

commit a98a766
Author: Zak V <[email protected]>
Date:   Thu Nov 19 14:13:34 2020 -0500

    infer_objects() is now run outside of the main thread when data() is called to reduce main thread contention.

commit eaca856
Merge: fcfda48 bcede15
Author: Phil Starkey <[email protected]>
Date:   Sun Nov 8 12:11:30 2020 +1100

    Merge pull request labscript-suite#87 from zakv/fix-86

    Fix 86

commit bcede15
Author: Zak V <[email protected]>
Date:   Sat Nov 7 17:33:51 2020 -0500

    Simplified flow control and append_units() funciton in Run.get_units().

commit e56d5fa
Author: Zak V <[email protected]>
Date:   Fri Nov 6 20:51:33 2020 -0500

    Added docstring for Run.get_units().

commit 6991aa9
Author: Zak V <[email protected]>
Date:   Fri Nov 6 20:50:38 2020 -0500

    Run.get_units() now uses its optional group argument

commit fcfda48
Merge: cdef626 1dac68f
Author: Phil Starkey <[email protected]>
Date:   Thu Nov 5 17:02:14 2020 +1100

    Merge pull request labscript-suite#80 from zakv/fix-78

    Fix 78

commit 1dac68f
Author: Zak V <[email protected]>
Date:   Wed Nov 4 12:54:52 2020 -0500

    Run.__init__() now properly handles when a lyse script is called analysis_subprocess.py.

commit 7ba7062
Author: Zak V <[email protected]>
Date:   Wed Nov 4 03:51:30 2020 -0500

    Changed Run's private attributes from single underscore to double underscore.

commit 3d38b3b
Author: Zak V <[email protected]>
Date:   Wed Nov 4 03:45:40 2020 -0500

    Refactored Sequence.__init__() to use Run.__init__() per Phil's idea in PR labscript-suite#80.

commit cdef626
Merge: 695c220 86ec2a6
Author: Phil Starkey <[email protected]>
Date:   Wed Nov 4 16:39:00 2020 +1100

    Merge pull request labscript-suite#79 from philipstarkey/philipstarkey/issue77

    Fixes labscript-suite#77

commit 695c220
Merge: 0910447 f80f182
Author: Phil Starkey <[email protected]>
Date:   Wed Nov 4 16:35:54 2020 +1100

    Merge pull request labscript-suite#76 from zakv/dataframe-subset

    Dataframe subset

commit f80f182
Author: Zak V <[email protected]>
Date:   Tue Nov 3 20:21:38 2020 -0500

    Corrected formatting in data()'s docstring.

commit ab8e44f
Author: Zak V <[email protected]>
Date:   Tue Nov 3 20:07:41 2020 -0500

    Corrected indentation in Run.group's docstring.

commit 005163e
Author: Zak V <[email protected]>
Date:   Tue Nov 3 20:06:50 2020 -0500

    Fixed issues with Sequence.__init__().

    First, it was updated to work with recent changes to its parent class. Also it used to error out if the hdf5 file didn't already exist, as first pointed out in PR 73, but that is now resolved..

commit 6a2755b
Author: Zak V <[email protected]>
Date:   Tue Nov 3 16:44:09 2020 -0500

    Replaced double underscores with single for private Run attributes so that child classes, e.g. Sequence, can use them.

commit c6d8306
Author: Zak V <[email protected]>
Date:   Tue Nov 3 15:49:50 2020 -0500

    Corrected typos in lyse.save_result()'s docstring.

commit e7778b5
Author: Zak V <[email protected]>
Date:   Tue Nov 3 15:49:17 2020 -0500

    Updated docstring for Run.save_result_array().

commit 9a590e5
Author: Zak V <[email protected]>
Date:   Tue Nov 3 15:32:58 2020 -0500

    Removed some trailing whitespace in lyse.Run().

commit cad1435
Author: Zak V <[email protected]>
Date:   Tue Nov 3 15:32:31 2020 -0500

    Updated error messages in Run.save_result_array() and replaced Exception with PermissionError to be more specific.

commit 9af179c
Author: Zak V <[email protected]>
Date:   Tue Nov 3 15:22:28 2020 -0500

    Cleaned up error messages in Run.save_result() and changed Exception to PermissionError to be more specific.

commit 60f00a4
Author: Zak V <[email protected]>
Date:   Tue Nov 3 15:04:28 2020 -0500

    Replaced "run" with "shot" in Run's docstring.

commit 575fb4f
Author: Zak V <[email protected]>
Date:   Tue Nov 3 14:56:32 2020 -0500

    Fixed minor typo in comment in Run class.

commit 0bd4a02
Author: Zak V <[email protected]>
Date:   Tue Nov 3 14:54:46 2020 -0500

    Changed Run's h5_path, no_write, and group attributes into properties.

commit d6c6919
Author: Zak V <[email protected]>
Date:   Tue Nov 3 14:29:47 2020 -0500

    Small update to docstring for Run.save_result().

commit c4203f3
Author: Zak V <[email protected]>
Date:   Tue Nov 3 14:25:28 2020 -0500

    Removed print statement from Run.save_results().

commit 5281dea
Author: Zak V <[email protected]>
Date:   Tue Nov 3 14:24:43 2020 -0500

    Updated docstrings for Run.save_result() and Run.save_results().

commit 9132cf3
Author: Zak V <[email protected]>
Date:   Mon Nov 2 16:31:23 2020 -0500

    Run._create_group_if_not_exists() can now handle another thread/process creating the hdf5 group partway through its execution.

commit 997a6c7
Author: Zak V <[email protected]>
Date:   Mon Nov 2 15:50:52 2020 -0500

    Corrected some typos in strings in __init__.py.

commit 565c1b3
Author: Zak V <[email protected]>
Date:   Mon Nov 2 15:45:35 2020 -0500

    Added a docstring for the Run class.

commit 029fdda
Author: Zak V <[email protected]>
Date:   Mon Nov 2 15:08:02 2020 -0500

    Added docstring for Run.set_group().

commit afd9d8f
Author: Zak V <[email protected]>
Date:   Mon Nov 2 14:19:03 2020 -0500

    Simplified Run.group's behavior when initialized outside of a lyse script.

commit bff7d19
Author: Zak V <[email protected]>
Date:   Mon Nov 2 10:41:33 2020 -0500

    Fixed some formatting in data()'s docstring.

commit 86ec2a6
Author: Phil Starkey <[email protected]>
Date:   Mon Nov 2 17:22:49 2020 +1100

    Fixed missing import

commit 9eff3cd
Author: Phil Starkey <[email protected]>
Date:   Mon Nov 2 17:20:07 2020 +1100

    Fixes labscript-suite#77

    We now mock the missing methods in the site module.

commit d79bada
Author: Zak V <[email protected]>
Date:   Sat Oct 31 16:47:01 2020 -0400

    Reduced the amount of code run with @inmain_decorator() in WebServer.handler().

commit 8d2a69e
Author: Zak V <[email protected]>
Date:   Fri Oct 30 20:35:03 2020 -0400

    Added intersphinx link for Dataframe.filter() in data()'s docstring.

commit 4c944dd
Author: Zak V <[email protected]>
Date:   Fri Oct 30 12:43:37 2020 -0400

    Updated the error message raised in data() when the server is running an outdated version of lyse.

commit f26aba2
Author: Zak V <[email protected]>
Date:   Fri Oct 30 12:32:55 2020 -0400

    Moved df.sort_index() from data() to _rangeindex_to_multiindex().

commit 0910447
Merge: 72fa369 ef03a15
Author: Phil Starkey <[email protected]>
Date:   Fri Oct 30 16:56:33 2020 +1100

    Merge pull request labscript-suite#74 from zakv/n_runs

    Add n_runs column to lyse dataframe

commit 72fa369
Merge: da9de67 8803447
Author: Phil Starkey <[email protected]>
Date:   Fri Oct 30 16:53:22 2020 +1100

    Merge pull request labscript-suite#72 from zakv/set-group

    Make Run.set_group() create the group if necessary.

commit b344e9e
Author: Zak V <[email protected]>
Date:   Thu Oct 29 23:57:09 2020 -0400

    Simplified lyse.data() communication and made it backwards compatible.

commit 8c7a456
Author: Zak V <[email protected]>
Date:   Thu Oct 29 22:21:57 2020 -0400

    Fixed an issue where the conversion to multiindex in lyse.data() could fail when using its filter_kwargs argument.

commit b61ab25
Author: Zak V <[email protected]>
Date:   Thu Oct 29 19:30:50 2020 -0400

    Updated docstring for lyse.data().

commit f1be302
Author: Zak V <[email protected]>
Date:   Thu Oct 29 19:14:43 2020 -0400

    Added optional filter_kwargs argument to lyse.data().

commit d134b6e
Author: Zak V <[email protected]>
Date:   Thu Oct 29 12:03:23 2020 -0400

    Improved WebServer's thread safety.

commit d1d9897
Author: Zak V <[email protected]>
Date:   Wed Oct 28 21:42:03 2020 -0400

    Clarified lyse.data()'s docstring about behavior when n_sequences is greater than number of sequences available.

commit c25caef
Author: Zak V <[email protected]>
Date:   Wed Oct 28 20:36:02 2020 -0400

    Added a docstring for lyse.data().

commit 9d662ea
Author: Zak V <[email protected]>
Date:   Wed Oct 28 20:00:43 2020 -0400

    lyse.data() now correctly handles when n_sequences=0.

commit c75b945
Author: Zak V <[email protected]>
Date:   Wed Oct 28 19:01:36 2020 -0400

    Added optional n_sequences argument to lyse.data().

commit ef03a15
Author: Zak V <[email protected]>
Date:   Wed Oct 21 07:54:18 2020 -0400

    Added n_runs column to lyse dataframe.

commit 8803447
Author: Zak V <[email protected]>
Date:   Thu Jul 16 16:58:30 2020 -0400

    Run.set_group() now creates the group if necessary.

Merge pull request labscript-suite#75 from dihm/lyse-docs

Initial Pass at Lyse docs