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Automated Dihedral Analysis #217

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merged 182 commits into from
Feb 12, 2023
Merged

Automated Dihedral Analysis #217

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e71456d
developing back end run methods
cadeduckworth Sep 15, 2022
6c67ec1
condensed backend run methods
cadeduckworth Sep 15, 2022
9914675
Initial adding of automation functionality to dihedral.py
cadeduckworth Oct 20, 2022
f9b6646
moved directory_paths function to reside within the DihedralAnalysis …
cadeduckworth Oct 20, 2022
7bcdf49
Addressed change requests by Oliver
cadeduckworth Oct 22, 2022
a87cb11
fixed indentation error for _single_frame() block
cadeduckworth Oct 22, 2022
7edde0d
reverting previous tab issue, necessary for normal function
cadeduckworth Oct 22, 2022
48016c5
fixed errors previously reverted for testing
cadeduckworth Oct 23, 2022
59c819c
Merge branch 'develop' into ensemble_run_update
cadeduckworth Oct 23, 2022
6b1be1b
restored original dihedral.py file
cadeduckworth Oct 28, 2022
2ddea0e
created automation/dihedral subdirectory under mdpow/analysis/ to hou…
cadeduckworth Oct 28, 2022
ad6db6e
updated docstrings and added examples for directory_paths.py
cadeduckworth Oct 28, 2022
848dd87
added docstrings and examples for directory_iteration.py
cadeduckworth Oct 28, 2022
6394d7a
added initial draft of docstrings and examples for all functions cont…
cadeduckworth Oct 28, 2022
d8f3ca3
added the option to save the DihedralAnalysis results DataFrame as cs…
cadeduckworth Nov 12, 2022
d8137cb
removed redundant DataFrame saving pattern from automated_dihedral_an…
cadeduckworth Nov 17, 2022
29477ab
Merge remote-tracking branch 'origin/ensemble_run_update' into automa…
cadeduckworth Nov 17, 2022
642e87e
merged updates from PR #216 and PR #218
cadeduckworth Nov 17, 2022
4814376
Merge branch 'develop' into automated-dihedral-analysis
orbeckst Nov 17, 2022
f333ee8
Merge branch 'develop' into automated-dihedral-analysis
orbeckst Nov 18, 2022
6f16b84
resolved conflicts to merge updates in from develop from PR#216
cadeduckworth Dec 14, 2022
ddffbdf
adding data for testing automated dihedral analysis
cadeduckworth Dec 14, 2022
c850448
added starting framework for testing automated dihedral analysis
cadeduckworth Dec 15, 2022
69b0351
reorganized automation directory into workflows directory
cadeduckworth Dec 15, 2022
4cf176d
added preliminary simple core tests for automated dihedral analysis
cadeduckworth Dec 15, 2022
97c4a73
initial reformatting of existing docs for sphinx markup compatibility
cadeduckworth Dec 15, 2022
930d54e
fix errors in docs for workflows
cadeduckworth Dec 15, 2022
84536ff
added imports for automated dihedral analysis tests
cadeduckworth Dec 15, 2022
f01b2a4
added init file for workflows module
cadeduckworth Dec 15, 2022
61ff494
added logging functionality for workflows modules
cadeduckworth Dec 15, 2022
f7b3f53
sphinx markup corrections for workflow modules
cadeduckworth Dec 15, 2022
d16dc7d
redo of reduced testing data for GAFF SM25 from original full dataset…
cadeduckworth Dec 16, 2022
bcfa10f
sphinx docs automodule test
cadeduckworth Dec 16, 2022
b8c309d
sphinx docs test base.txt
cadeduckworth Dec 16, 2022
837f53e
docs
cadeduckworth Dec 16, 2022
44db567
docs
cadeduckworth Dec 16, 2022
e53dfb6
docs
cadeduckworth Dec 16, 2022
5f28b46
edit docs
cadeduckworth Dec 17, 2022
e58703a
edit docs
cadeduckworth Dec 17, 2022
bbcb5de
edit docs
cadeduckworth Dec 17, 2022
45892b6
edit docs
cadeduckworth Dec 17, 2022
eaf767a
edit docs
cadeduckworth Dec 17, 2022
f19f32e
update py.path to pathlib in test_automated_dihedral_analysis
cadeduckworth Dec 17, 2022
41166a4
update reference testing values for new reduced dataset, test_automat…
cadeduckworth Dec 17, 2022
1de662e
change syntax in test_automated_dihedral_analysis to compare objects …
cadeduckworth Dec 17, 2022
4eafa23
update assert_almost_equal to pytest.approx
cadeduckworth Dec 17, 2022
4833a45
bounce redundant function calls to a pytest.fixture for use with mult…
cadeduckworth Dec 17, 2022
5be6684
add bz2 compression for dataframe storage of automated dihedral analy…
cadeduckworth Dec 17, 2022
ef750f1
Update ci.yaml
cadeduckworth Dec 17, 2022
4c9251b
added functionality for user input of alternative SMARTS string selec…
cadeduckworth Jan 5, 2023
187632b
Merge branch 'automated-dihedral-analysis' of github.com:Becksteinlab…
cadeduckworth Jan 5, 2023
7abb0bc
add tests for automated directory iteration of dihedral analysis, wor…
cadeduckworth Jan 5, 2023
372a205
add tests for saving dataframes and saving figures, which covers the …
cadeduckworth Jan 5, 2023
39518c2
add test for directory iteration of fully automated dihedral analysis
cadeduckworth Jan 5, 2023
37eb085
moved location of rdkit install used for testing/pytest
cadeduckworth Jan 7, 2023
85b54f3
remove misplaced hbonds documentation
cadeduckworth Jan 7, 2023
1e5aadc
relocate test data for workflows and change test scripts accordingly
cadeduckworth Jan 7, 2023
edc0a9a
removed unnecessary .ipynb, .lock, and .npz files
cadeduckworth Jan 7, 2023
eb41100
simplified keyword specification for default and user input of SMARTS…
cadeduckworth Jan 7, 2023
b91240e
fixed plotting issue for solvents (name and order)
cadeduckworth Jan 7, 2023
fbca70d
variable name issue in testing module, user_SMARTS -> SMARTS
cadeduckworth Jan 7, 2023
b0081ef
Delete dir.csv
cadeduckworth Jan 8, 2023
0520ffa
import syntax
cadeduckworth Jan 8, 2023
77df0ee
sphinx docs
cadeduckworth Jan 8, 2023
17a0b4a
Merge branch 'automated-dihedral-analysis' of github.com:Becksteinlab…
cadeduckworth Jan 8, 2023
7359319
docs
cadeduckworth Jan 8, 2023
8f8f26c
docs
cadeduckworth Jan 8, 2023
c452475
docs
cadeduckworth Jan 8, 2023
3dd1b31
docs
cadeduckworth Jan 8, 2023
cecd928
docs
cadeduckworth Jan 8, 2023
5b87e83
docs
cadeduckworth Jan 8, 2023
86804d8
docs
cadeduckworth Jan 8, 2023
0ab0299
docs
cadeduckworth Jan 8, 2023
3964a44
docs
cadeduckworth Jan 8, 2023
dfb7e8e
docs
cadeduckworth Jan 8, 2023
be86754
docs
cadeduckworth Jan 8, 2023
f6330cb
docs
cadeduckworth Jan 8, 2023
ab6800e
docs
cadeduckworth Jan 8, 2023
6bdc521
docs
cadeduckworth Jan 8, 2023
0a7963d
docs
cadeduckworth Jan 8, 2023
1866d43
docs
cadeduckworth Jan 8, 2023
495546c
docs
cadeduckworth Jan 8, 2023
956b359
docs
cadeduckworth Jan 8, 2023
0ad73db
docs
cadeduckworth Jan 8, 2023
f6beebb
docs
cadeduckworth Jan 8, 2023
036d939
docs
cadeduckworth Jan 8, 2023
58f33c3
docs
cadeduckworth Jan 8, 2023
d704f95
moving workflows location, subsequent doc changes
cadeduckworth Jan 8, 2023
02e10e5
import changed to reflect moving workflows module
cadeduckworth Jan 8, 2023
891782e
docs
cadeduckworth Jan 8, 2023
148e56f
add requirements for sphinx build
cadeduckworth Jan 8, 2023
a03951c
add requirements for sphinx build
cadeduckworth Jan 8, 2023
31291f1
add requirements for sphinx build
cadeduckworth Jan 8, 2023
652e788
add requirements for sphinx build
cadeduckworth Jan 8, 2023
48c7e88
add requirements for sphinx build
cadeduckworth Jan 8, 2023
ba17ceb
docs
cadeduckworth Jan 8, 2023
68cbc9c
docs
cadeduckworth Jan 8, 2023
8c5c2ec
docs structure
cadeduckworth Jan 8, 2023
8d29f91
consistent keyword names in tests
cadeduckworth Jan 8, 2023
24f6c00
imports and docs
cadeduckworth Jan 8, 2023
63e3de4
imports
cadeduckworth Jan 8, 2023
104bf93
imports
cadeduckworth Jan 8, 2023
1ad6b8c
generalizing automation base module for use with other analyses
cadeduckworth Jan 8, 2023
b0585ef
workflows base module cleanup
cadeduckworth Jan 10, 2023
498dfe1
split dihedrals.dihedral_indices and dihedrals.dihedral_groups into s…
cadeduckworth Jan 10, 2023
3f518ba
cleanup imports and naming conventions in workflows base module
cadeduckworth Jan 10, 2023
4b9dd90
new tests for new functions made from splitting dihedrals.dihedral_in…
cadeduckworth Jan 10, 2023
40d4d22
Merge branch 'develop' into automated-dihedral-analysis
orbeckst Jan 12, 2023
75e2614
Merge branch 'develop' into automated-dihedral-analysis
orbeckst Jan 13, 2023
86909d8
added skip for testing pytest=7.2.0, build=py37h89c1867_0
cadeduckworth Jan 15, 2023
e8573c6
Merge branch 'automated-dihedral-analysis' of github.com:Becksteinlab…
cadeduckworth Jan 15, 2023
9672ad1
cleanup unnecessary files and remove workflows base module/move to ne…
cadeduckworth Jan 15, 2023
e8a7c65
remove workflows base import not needed for test
cadeduckworth Jan 15, 2023
76d34b3
Apply suggestions from code review
orbeckst Jan 17, 2023
93cce20
new reduced dataset for testing resources (SM25 & SM26)
cadeduckworth Jan 20, 2023
49478e0
Merge branch 'automated-dihedral-analysis' of github.com:Becksteinlab…
cadeduckworth Jan 20, 2023
a523969
merged add_hydrogens into rdkit_conversion, removed unnecessary tests
cadeduckworth Jan 20, 2023
c1789d2
move default SMARTS string from kwarg to module level, SMARTS_DEFAULT…
cadeduckworth Jan 20, 2023
9fe35ec
fix bz2 compression for results dataframe and added a return of file/…
cadeduckworth Jan 20, 2023
c10369e
bug fixes while building tutorial
cadeduckworth Jan 20, 2023
0d159e5
Merge branch 'develop' into automated-dihedral-analysis
cadeduckworth Jan 20, 2023
87e34be
init workflows-dihedrals tutorial (ipynb) and tutorials subdirectory …
cadeduckworth Jan 20, 2023
458230a
Merge branch 'develop' into automated-dihedral-analysis
cadeduckworth Jan 21, 2023
2f3b3e0
save accurate return of where results csv file is stored (naming conv…
cadeduckworth Jan 31, 2023
5b63fb6
add seaborn to test_env.yaml
cadeduckworth Jan 31, 2023
7dea2d8
add matplotlib, seaborn, rdkit to setup.py (install_requires)
cadeduckworth Jan 31, 2023
2f7e99b
SMARTS string documentation formatting test
cadeduckworth Jan 31, 2023
1076442
Merge branch 'automated-dihedral-analysis' of github.com:Becksteinlab…
cadeduckworth Jan 31, 2023
8189df6
fix unexpected indent in docs for SMARTS
cadeduckworth Jan 31, 2023
78d8877
testing SMARTS docs alternatives
cadeduckworth Jan 31, 2023
5b82ee2
remove the bit about workflows.base, not included in this PR
cadeduckworth Jan 31, 2023
52b3bc5
SMARTS docs
cadeduckworth Jan 31, 2023
e2202c8
SMARTS docs
cadeduckworth Jan 31, 2023
9f44b12
SMARTS docs unexpected indent
cadeduckworth Jan 31, 2023
0aaa993
SMARTS docs unexpected indent
cadeduckworth Jan 31, 2023
5394d6b
SMARTS docs
cadeduckworth Jan 31, 2023
0ad76b8
SMARTS docs
cadeduckworth Jan 31, 2023
d29821b
SMARTS docs
cadeduckworth Jan 31, 2023
89df6dc
final SMARTS docs cleanup
cadeduckworth Jan 31, 2023
1fafe83
:returns: doc tests, MDA Universe class ~link`
cadeduckworth Jan 31, 2023
4dcf023
more :returns: docs attempts
cadeduckworth Jan 31, 2023
9319531
docs, :returns:, :rubric:, formatting
cadeduckworth Jan 31, 2023
9c33e3c
:rubric: workflow examples formatting
cadeduckworth Jan 31, 2023
5578646
width and padding kwarg docs, accuracy and consistency
cadeduckworth Jan 31, 2023
f039bbe
full module review and adding in-line # comments for reminders and to…
cadeduckworth Jan 31, 2023
7da781b
remove unnecessary tests and add in-line comments as reminders/questions
cadeduckworth Jan 31, 2023
8ac9549
docs, :class: method for referencing MDA Universe
cadeduckworth Feb 1, 2023
a340053
docs and kwargs
cadeduckworth Feb 1, 2023
af14ad7
remove incorrect continue pattern
cadeduckworth Feb 1, 2023
bad175f
rearrange top level automated_dihedral_analysis function for datafram…
cadeduckworth Feb 1, 2023
18b33fb
new tests for dataframe input and logger.info/.warning
cadeduckworth Feb 1, 2023
c085cdf
docs test reference for MDA Universe class
cadeduckworth Feb 2, 2023
824a110
docs: some tests with cross-refs for external packages
cadeduckworth Feb 2, 2023
7d6250e
docs: some tests with cross-refs for external packages
cadeduckworth Feb 2, 2023
22ef778
remove broken test
cadeduckworth Feb 2, 2023
b9a1363
fixed string check method for logger info in tests and dihedrals module
cadeduckworth Feb 2, 2023
2d1f3da
update docs for workflows dihedrals
cadeduckworth Feb 4, 2023
403154a
nearly completed docs for workflows.dihedrals
cadeduckworth Feb 4, 2023
d009abe
changed method for testing logger INFO/WARNING
cadeduckworth Feb 4, 2023
153ea71
use caplog pytest fixture for logger.INFO and logger.WARNING
cadeduckworth Feb 4, 2023
525f2cf
Update test_automated_dihedral_analysis.py
cadeduckworth Feb 6, 2023
1b13feb
removed unnecessary components from save_df and made df_save_dir kwar…
cadeduckworth Feb 7, 2023
998d5b0
changed global kwargs to all caps formatting
cadeduckworth Feb 7, 2023
ad2ed7a
removed another unnecessary logger.info for save_df
cadeduckworth Feb 7, 2023
cc08976
add MDAnalysis, RDKit, Pandas links for intersphinx mapping
cadeduckworth Feb 7, 2023
32ac646
preliminary changes to docs to test intersphinx links and format changes
cadeduckworth Feb 7, 2023
dfd1098
fix logger.info and associated tests
cadeduckworth Feb 7, 2023
4ac89a2
move or change comments in test module
cadeduckworth Feb 7, 2023
118f4cf
add skipif for figure generating and figure saving tests that rely on…
cadeduckworth Feb 7, 2023
87d0334
cleanup and format docs, add seaborn intersphinx mapping
cadeduckworth Feb 7, 2023
9b0e737
doc formatting
cadeduckworth Feb 7, 2023
800d36f
fix minor docs format
cadeduckworth Feb 7, 2023
ea1b1a8
calculate new numerical values for testing from recently reduced test…
cadeduckworth Feb 7, 2023
530abf9
clean up new scipy.stats data and associated description
cadeduckworth Feb 11, 2023
8e3b37f
cleanup test comments/docs and properly describe fixtures and skipifs
cadeduckworth Feb 11, 2023
cf8d562
fix incorrect assertion for test_save_df_info
cadeduckworth Feb 11, 2023
41258f2
fix plot assertion to use isinstance() to check for seaborn.axisgrid.…
cadeduckworth Feb 11, 2023
4e2fdb7
cleanup doc formatting and inline comments
cadeduckworth Feb 11, 2023
5053a30
test doc indent levels
cadeduckworth Feb 11, 2023
73aa472
format docs indentations
cadeduckworth Feb 11, 2023
d02da1a
format docs, reST typo
cadeduckworth Feb 11, 2023
ac8c8a7
update CHANGES
orbeckst Feb 12, 2023
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