Squashed commit of the following:

commit 8575ff2c
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Tue Dec 7 10:52:15 2021 -0500

    Update setup.cfg to show python 3.9 support

commit e4b57f8d
Merge: 8bf02a2f 915cc1c5
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Tue Dec 7 07:31:45 2021 -0500

    Merge pull request #95 from dihm/msg_replacement

    Msg replacement

commit 8bf02a2f
Merge: 72f82b3c a98a7661
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Tue Dec 7 07:30:06 2021 -0500

    Merge pull request #88 from zakv/move-infer_objects

    Move infer_objects() out of main thread

commit 915cc1c5
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Dec 3 09:01:04 2021 -0500

    Adding the extra bugfixes found in #91.

commit fa9eedb5
Author: David Meyer <dihm@users.noreply.github.com>
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 72f82b3c
Merge: cb606677 26ef7956
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Jul 16 16:09:52 2021 -0400

    Merge pull request #93 from dihm/update_lyse_docs

    Update lyse docs to match autogenerated docs from other modules.

commit 26ef7956
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Thu Jul 15 10:30:09 2021 -0400

    Add docstring coverage to build.

commit 98cac68b
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Thu Jul 15 10:29:57 2021 -0400

    Update sphinx pin.

commit 4671ef69
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Tue Jul 13 17:21:29 2021 -0400

    Add docstrings to the API functions.

    Reasonably sure they are all accurate.

commit 40d207ca
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Jul 12 10:47:31 2021 -0400

    Tweaked docs formatting.

commit 47b60a82
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Jul 12 10:40:42 2021 -0400

    Convert doc generation to recursive autosummary call.

commit 9add58b1
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Jul 12 10:38:50 2021 -0400

    Tweak docstrings.

commit 3873dcc2
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Jul 12 09:26:55 2021 -0400

    Add Qt5 inventory for intersphinx lookup.

commit e7cf19ad
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Jul 12 09:26:31 2021 -0400

    Update sphinx pins to match rest of suite docs.

commit cb606677
Merge: eaca8560 8596deaf
Author: Chris Billington <chrisjbillington@gmail.com>
Date:   Fri Jan 29 14:00:36 2021 +1100

    Merge pull request #89 from chrisjbillington/master

    Do not use deprecated set-env command

commit 8596deaf
Author: chrisjbillington <chrisjbillington@gmail.com>
Date:   Fri Jan 29 13:57:39 2021 +1100

    Do not use deprecated set-env command

commit a98a7661
Author: Zak V <zakven@mit.edu>
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 eaca8560
Merge: fcfda489 bcede155
Author: Phil Starkey <philipstarkey@users.noreply.github.com>
Date:   Sun Nov 8 12:11:30 2020 +1100

    Merge pull request #87 from zakv/fix-86

    Fix 86

commit bcede155
Author: Zak V <zakven@mit.edu>
Date:   Sat Nov 7 17:33:51 2020 -0500

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

commit e56d5fa5
Author: Zak V <zakven@mit.edu>
Date:   Fri Nov 6 20:51:33 2020 -0500

    Added docstring for Run.get_units().

commit 6991aa98
Author: Zak V <zakven@mit.edu>
Date:   Fri Nov 6 20:50:38 2020 -0500

    Run.get_units() now uses its optional group argument

commit fcfda489
Merge: cdef6269 1dac68f6
Author: Phil Starkey <philipstarkey@users.noreply.github.com>
Date:   Thu Nov 5 17:02:14 2020 +1100

    Merge pull request #80 from zakv/fix-78

    Fix 78

commit 1dac68f6
Author: Zak V <zakven@mit.edu>
Date:   Wed Nov 4 12:54:52 2020 -0500

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

commit 7ba70629
Author: Zak V <zakven@mit.edu>
Date:   Wed Nov 4 03:51:30 2020 -0500

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

commit 3d38b3bd
Author: Zak V <zakven@mit.edu>
Date:   Wed Nov 4 03:45:40 2020 -0500

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

commit cdef6269
Merge: 695c2206 86ec2a66
Author: Phil Starkey <philipstarkey@users.noreply.github.com>
Date:   Wed Nov 4 16:39:00 2020 +1100

    Merge pull request #79 from philipstarkey/philipstarkey/issue77

    Fixes #77

commit 695c2206
Merge: 09104471 f80f1829
Author: Phil Starkey <philipstarkey@users.noreply.github.com>
Date:   Wed Nov 4 16:35:54 2020 +1100

    Merge pull request #76 from zakv/dataframe-subset

    Dataframe subset

commit f80f1829
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 20:21:38 2020 -0500

    Corrected formatting in data()'s docstring.

commit ab8e44fc
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 20:07:41 2020 -0500

    Corrected indentation in Run.group's docstring.

commit 005163ed
Author: Zak V <zakven@mit.edu>
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 6a2755b5
Author: Zak V <zakven@mit.edu>
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 c6d8306c
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 15:49:50 2020 -0500

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

commit e7778b54
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 15:49:17 2020 -0500

    Updated docstring for Run.save_result_array().

commit 9a590e56
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 15:32:58 2020 -0500

    Removed some trailing whitespace in lyse.Run().

commit cad1435a
Author: Zak V <zakven@mit.edu>
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 9af179cd
Author: Zak V <zakven@mit.edu>
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 60f00a48
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 15:04:28 2020 -0500

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

commit 575fb4fb
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 14:56:32 2020 -0500

    Fixed minor typo in comment in Run class.

commit 0bd4a020
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 14:54:46 2020 -0500

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

commit d6c6919b
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 14:29:47 2020 -0500

    Small update to docstring for Run.save_result().

commit c4203f37
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 14:25:28 2020 -0500

    Removed print statement from Run.save_results().

commit 5281dea7
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 14:24:43 2020 -0500

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

commit 9132cf35
Author: Zak V <zakven@mit.edu>
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 997a6c70
Author: Zak V <zakven@mit.edu>
Date:   Mon Nov 2 15:50:52 2020 -0500

    Corrected some typos in strings in __init__.py.

commit 565c1b3d
Author: Zak V <zakven@mit.edu>
Date:   Mon Nov 2 15:45:35 2020 -0500

    Added a docstring for the Run class.

commit 029fdda5
Author: Zak V <zakven@mit.edu>
Date:   Mon Nov 2 15:08:02 2020 -0500

    Added docstring for Run.set_group().

commit afd9d8fa
Author: Zak V <zakven@mit.edu>
Date:   Mon Nov 2 14:19:03 2020 -0500

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

commit bff7d19f
Author: Zak V <zakven@mit.edu>
Date:   Mon Nov 2 10:41:33 2020 -0500

    Fixed some formatting in data()'s docstring.

commit 86ec2a66
Author: Phil Starkey <philipstarkey@users.noreply.github.com>
Date:   Mon Nov 2 17:22:49 2020 +1100

    Fixed missing import

commit 9eff3cd4
Author: Phil Starkey <philipstarkey@users.noreply.github.com>
Date:   Mon Nov 2 17:20:07 2020 +1100

    Fixes #77

    We now mock the missing methods in the site module.

commit d79bada4
Author: Zak V <zakven@mit.edu>
Date:   Sat Oct 31 16:47:01 2020 -0400

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

commit 8d2a69ec
Author: Zak V <zakven@mit.edu>
Date:   Fri Oct 30 20:35:03 2020 -0400

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

commit 4c944dd8
Author: Zak V <zakven@mit.edu>
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 f26aba28
Author: Zak V <zakven@mit.edu>
Date:   Fri Oct 30 12:32:55 2020 -0400

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

commit 09104471
Merge: 72fa369c ef03a153
Author: Phil Starkey <philipstarkey@users.noreply.github.com>
Date:   Fri Oct 30 16:56:33 2020 +1100

    Merge pull request #74 from zakv/n_runs

    Add n_runs column to lyse dataframe

commit 72fa369c
Merge: da9de67f 88034479
Author: Phil Starkey <philipstarkey@users.noreply.github.com>
Date:   Fri Oct 30 16:53:22 2020 +1100

    Merge pull request #72 from zakv/set-group

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

commit b344e9ed
Author: Zak V <zakven@mit.edu>
Date:   Thu Oct 29 23:57:09 2020 -0400

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

commit 8c7a456e
Author: Zak V <zakven@mit.edu>
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 b61ab252
Author: Zak V <zakven@mit.edu>
Date:   Thu Oct 29 19:30:50 2020 -0400

    Updated docstring for lyse.data().

commit f1be302d
Author: Zak V <zakven@mit.edu>
Date:   Thu Oct 29 19:14:43 2020 -0400

    Added optional filter_kwargs argument to lyse.data().

commit d134b6ec
Author: Zak V <zakven@mit.edu>
Date:   Thu Oct 29 12:03:23 2020 -0400

    Improved WebServer's thread safety.

commit d1d9897c
Author: Zak V <zakven@mit.edu>
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 c25caef3
Author: Zak V <zakven@mit.edu>
Date:   Wed Oct 28 20:36:02 2020 -0400

    Added a docstring for lyse.data().

commit 9d662eac
Author: Zak V <zakven@mit.edu>
Date:   Wed Oct 28 20:00:43 2020 -0400

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

commit c75b9451
Author: Zak V <zakven@mit.edu>
Date:   Wed Oct 28 19:01:36 2020 -0400

    Added optional n_sequences argument to lyse.data().

commit ef03a153
Author: Zak V <zakven@mit.edu>
Date:   Wed Oct 21 07:54:18 2020 -0400

    Added n_runs column to lyse dataframe.

commit 88034479
Author: Zak V <zakven@mit.edu>
Date:   Thu Jul 16 16:58:30 2020 -0400

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