commit 8575ff2cc02d4484db8762611e55aa8ed417a4d7
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 e4b57f8d1e0544bae6b728cc534bff56b037cd4c
Merge: 8bf02a2 915cc1c
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 8bf02a2f680d8763c8d3f0c218843a769119990f
Merge: 72f82b3 a98a766
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 915cc1c501cd4c8b37767c369e183e50d6f79c05
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 fa9eedb5676e018946c10917e0ba17e325f6d9b8
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 72f82b3c673182e3dea43ac9976014799c7a627f
Merge: cb60667 26ef795
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 26ef79565d7c1b4ee6c2c865e570a9e363885597
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Thu Jul 15 10:30:09 2021 -0400

    Add docstring coverage to build.

commit 98cac68b8a48deb0bb7949f34fa4ae3e265dddc7
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Thu Jul 15 10:29:57 2021 -0400

    Update sphinx pin.

commit 4671ef699ef69658ac109ebb2d49917e2a204fa2
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 40d207ca253c486eaa9116dc16958f45bd8b2ad0
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Jul 12 10:47:31 2021 -0400

    Tweaked docs formatting.

commit 47b60a828cdbdf8f40dd41a9702c03e37d7e6e47
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Jul 12 10:40:42 2021 -0400

    Convert doc generation to recursive autosummary call.

commit 9add58b171535d07b770bbf8fbb0256c44713ffa
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Jul 12 10:38:50 2021 -0400

    Tweak docstrings.

commit 3873dcc233f527c08bf6408c4622948ba40a598a
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Jul 12 09:26:55 2021 -0400

    Add Qt5 inventory for intersphinx lookup.

commit e7cf19ad41ad4ffe6f9c8e02382858425708100d
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 cb60667744732db1afffee7445e14619a337939e
Merge: eaca856 8596dea
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 8596deaf5e57cab160c47f6c5081ecaebd429920
Author: chrisjbillington <chrisjbillington@gmail.com>
Date:   Fri Jan 29 13:57:39 2021 +1100

    Do not use deprecated set-env command

commit a98a7661d8f110d36265c064711263ebd002ebe3
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 eaca85607520d5b2443e52b63b10a26d06ee776a
Merge: fcfda48 bcede15
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 bcede155a4c997f661ab225144589eb175ff5176
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 e56d5fa5120cd8bf5407422dece0ab0c00f1dbaf
Author: Zak V <zakven@mit.edu>
Date:   Fri Nov 6 20:51:33 2020 -0500

    Added docstring for Run.get_units().

commit 6991aa98c71651123688729e6189606f9b6ffa8a
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 fcfda4899384eefa0182a91010269c0b087d5124
Merge: cdef626 1dac68f
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 1dac68f61cac826303960306ebf28b8b3db7e4cf
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 7ba70629022f06892edb9e20828c39b8ba204221
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 3d38b3bd0626eb2ec11cef3f0cb4abb983a02df0
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 cdef6269cb9e393c9f6fe91968c68710ff9c8ecf
Merge: 695c220 86ec2a6
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 695c2206d7e0229efed68647f902bfaa38ea109a
Merge: 0910447 f80f182
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 f80f182959f874c570a95e62a75c3a8bbb28c53a
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 20:21:38 2020 -0500

    Corrected formatting in data()'s docstring.

commit ab8e44fca555947f95cce80a15f71060fce1c201
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 20:07:41 2020 -0500

    Corrected indentation in Run.group's docstring.

commit 005163ed870d6c1efdd4b3eb54d7410f4075aa11
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 6a2755b5026fc7449f2cdf8388cd53dba06b5e68
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 c6d8306c8b2a4f19d8a0493e686d851571b6c93c
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 15:49:50 2020 -0500

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

commit e7778b543cf64088e3fdab61c1aba9e362276cb4
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 15:49:17 2020 -0500

    Updated docstring for Run.save_result_array().

commit 9a590e566971d7d16d8167f95c86125dd0e16adf
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 15:32:58 2020 -0500

    Removed some trailing whitespace in lyse.Run().

commit cad1435a380ddf11131fc6ae316acb9e2a6d6996
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 9af179cd1236f8237179b3a3fab8bf6d14b578a0
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 60f00a48688bd6a3aa10d1971360e40921fb788d
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 15:04:28 2020 -0500

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

commit 575fb4fbb6303314da00167da78bde3f1e2f82e0
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 14:56:32 2020 -0500

    Fixed minor typo in comment in Run class.

commit 0bd4a020743ad967cad145ac4fc4a9e6193b5e87
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 d6c6919b74ec3ea8752b12682b0eba195fb9e41a
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 14:29:47 2020 -0500

    Small update to docstring for Run.save_result().

commit c4203f3741c972c0a3c4b96643d4cfc5e687bd44
Author: Zak V <zakven@mit.edu>
Date:   Tue Nov 3 14:25:28 2020 -0500

    Removed print statement from Run.save_results().

commit 5281dea7405b038b5740c88df983bdcb666339fd
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 9132cf3506ab0e8b82ac0069adea5a9242c756f2
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 997a6c70ea409e4252447bbb4c598f06421fb021
Author: Zak V <zakven@mit.edu>
Date:   Mon Nov 2 15:50:52 2020 -0500

    Corrected some typos in strings in __init__.py.

commit 565c1b3da4eb2b4bd35041f49220e12aef2d486b
Author: Zak V <zakven@mit.edu>
Date:   Mon Nov 2 15:45:35 2020 -0500

    Added a docstring for the Run class.

commit 029fdda57e27c019e36b5131736d0daceb768ff7
Author: Zak V <zakven@mit.edu>
Date:   Mon Nov 2 15:08:02 2020 -0500

    Added docstring for Run.set_group().

commit afd9d8fa25e2524bbc723050baa5451b06e7a7fc
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 bff7d19f58b70b83417503241619f527e4ddbb9d
Author: Zak V <zakven@mit.edu>
Date:   Mon Nov 2 10:41:33 2020 -0500

    Fixed some formatting in data()'s docstring.

commit 86ec2a662d9806f3c734ed78426de6055f796165
Author: Phil Starkey <philipstarkey@users.noreply.github.com>
Date:   Mon Nov 2 17:22:49 2020 +1100

    Fixed missing import

commit 9eff3cd432f9c2d7cad1ca1a02b9e677a4f15410
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 d79bada47b64279defdb928f039e556c10bd31a8
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 8d2a69ecc7455f4635172426d9df1441a4e349f1
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 4c944dd85715d80ab66f651c927db932d61b4d43
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 f26aba2871d4f0de6e6ee830cefd3005136fc806
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 091044719c801972f62a78fc43e9ae22bd5d0461
Merge: 72fa369 ef03a15
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 72fa369c2fd3681b372358a838ac5d3e35ddaa60
Merge: da9de67 8803447
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 b344e9ed3ba45798d6ecfab0839183546742fb01
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 8c7a456e30bd065dec165752313a2be6856a94a2
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 b61ab2522d4c764353e207d6c4087bf104417738
Author: Zak V <zakven@mit.edu>
Date:   Thu Oct 29 19:30:50 2020 -0400

    Updated docstring for lyse.data().

commit f1be302dafdac9ef1736f62164630ffd3224ba53
Author: Zak V <zakven@mit.edu>
Date:   Thu Oct 29 19:14:43 2020 -0400

    Added optional filter_kwargs argument to lyse.data().

commit d134b6ecf6a2c5f7d9ddf985145f5fbac04cfd31
Author: Zak V <zakven@mit.edu>
Date:   Thu Oct 29 12:03:23 2020 -0400

    Improved WebServer's thread safety.

commit d1d9897c987d0e2d45991e9ac335db19dd527a66
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 c25caef3fff8dbd33078676a8eb396d7cb65c9e9
Author: Zak V <zakven@mit.edu>
Date:   Wed Oct 28 20:36:02 2020 -0400

    Added a docstring for lyse.data().

commit 9d662eac920c744df1bb225c3592653b826b6f03
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 c75b9451ba9e62216880312d74d8496daea78d90
Author: Zak V <zakven@mit.edu>
Date:   Wed Oct 28 19:01:36 2020 -0400

    Added optional n_sequences argument to lyse.data().

commit ef03a153cf62cd546c144efc9067436014b2f447
Author: Zak V <zakven@mit.edu>
Date:   Wed Oct 21 07:54:18 2020 -0400

    Added n_runs column to lyse dataframe.

commit 88034479e3f9d5e841daf786bc79668e7eafac7d
Author: Zak V <zakven@mit.edu>
Date:   Thu Jul 16 16:58:30 2020 -0400

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