Automated Dihedral Analysis - #217

Merged

orbeckst merged 182 commits into

automated-dihedral-analysis

Feb 12, 2023

Commits on Sep 15, 2022

developing back end run methods
cadeduckworth
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e71456d
condensed backend run methods
cadeduckworth
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6c67ec1

Commits on Oct 20, 2022

Initial adding of automation functionality to dihedral.py
cadeduckworth
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9914675
moved directory_paths function to reside within the DihedralAnalysis class to test possible ways to call automation-related functions
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f9b6646

Commits on Oct 22, 2022

Addressed change requests by Oliver
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7bcdf49
fixed indentation error for _single_frame() block
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a87cb11
reverting previous tab issue, necessary for normal function
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Commits on Oct 23, 2022

fixed errors previously reverted for testing
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Merge branch 'develop' into ensemble_run_update
cadeduckworth
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59c819c

Commits on Oct 28, 2022

Commits on Nov 12, 2022

added the option to save the DihedralAnalysis results DataFrame as csv files in provided parent directory
cadeduckworth
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d8f3ca3

Commits on Nov 18, 2022

Merge branch 'develop' into automated-dihedral-analysis
orbeckst
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f333ee8

Commits on Dec 14, 2022

Commits on Dec 15, 2022

added starting framework for testing automated dihedral analysis
cadeduckworth
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c850448
reorganized automation directory into workflows directory
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added preliminary simple core tests for automated dihedral analysis
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initial reformatting of existing docs for sphinx markup compatibility
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97c4a73
fix errors in docs for workflows
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930d54e
added imports for automated dihedral analysis tests
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added init file for workflows module
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added logging functionality for workflows modules
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sphinx markup corrections for workflow modules
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f7b3f53

Commits on Dec 16, 2022

redo of reduced testing data for GAFF SM25 from original full dataset, reduced original by factor of 100 this time, timestep is now 50ps, amount of frames and total length of simulation preserved
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sphinx docs automodule test
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sphinx docs test base.txt
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docs
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docs
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docs
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Commits on Dec 17, 2022

edit docs
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edit docs
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edit docs
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edit docs
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edit docs
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update py.path to pathlib in test_automated_dihedral_analysis
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f19f32e
update reference testing values for new reduced dataset, test_automated_dihedral_analysis
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41166a4
change syntax in test_automated_dihedral_analysis to compare objects instead of strings
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1de662e
update assert_almost_equal to pytest.approx
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4eafa23
bounce redundant function calls to a pytest.fixture for use with multiple tests
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4833a45
add bz2 compression for dataframe storage of automated dihedral analysis data
cadeduckworth
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5be6684
Update ci.yaml
cadeduckworth
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ef750f1

Commits on Jan 5, 2023

Commits on Jan 7, 2023

Commits on Jan 8, 2023

Delete dir.csv
cadeduckworth
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import syntax
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sphinx docs
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Merge branch 'automated-dihedral-analysis' of github.com:Becksteinlab/MDPOW into automated-dihedral-analysis
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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docs
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moving workflows location, subsequent doc changes
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import changed to reflect moving workflows module
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docs
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add requirements for sphinx build
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add requirements for sphinx build
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add requirements for sphinx build
cadeduckworth
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31291f1
add requirements for sphinx build
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652e788
add requirements for sphinx build
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48c7e88
docs
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ba17ceb
docs
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docs structure
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consistent keyword names in tests
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imports and docs
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imports
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imports
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generalizing automation base module for use with other analyses
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1ad6b8c

Commits on Jan 12, 2023

Merge branch 'develop' into automated-dihedral-analysis
orbeckst
authored
40d4d22

Commits on Jan 13, 2023

Merge branch 'develop' into automated-dihedral-analysis
orbeckst
authored
75e2614

Commits on Jan 17, 2023

Apply suggestions from code review
orbeckst
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76d34b3

Commits on Jan 20, 2023

Commits on Jan 21, 2023

Merge branch 'develop' into automated-dihedral-analysis
cadeduckworth
authored
458230a

Commits on Jan 31, 2023

save accurate return of where results csv file is stored (naming convention - .csv.bz2)
cadeduckworth
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add seaborn to test_env.yaml
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add matplotlib, seaborn, rdkit to setup.py (install_requires)
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7dea2d8
SMARTS string documentation formatting test
cadeduckworth
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2f7e99b
Merge branch 'automated-dihedral-analysis' of github.com:Becksteinlab/MDPOW into automated-dihedral-analysis
cadeduckworth
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1076442
fix unexpected indent in docs for SMARTS
cadeduckworth
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8189df6
testing SMARTS docs alternatives
cadeduckworth
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78d8877
remove the bit about workflows.base, not included in this PR
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SMARTS docs
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SMARTS docs
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SMARTS docs unexpected indent
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SMARTS docs unexpected indent
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SMARTS docs
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SMARTS docs
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SMARTS docs
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final SMARTS docs cleanup
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:returns: doc tests, MDA Universe class ~link`
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more :returns: docs attempts
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docs, :returns:, :rubric:, formatting
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:rubric: workflow examples formatting
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width and padding kwarg docs, accuracy and consistency
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full module review and adding in-line # comments for reminders and to-dos
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remove unnecessary tests and add in-line comments as reminders/questions
cadeduckworth
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7da781b

Commits on Feb 1, 2023

Commits on Feb 2, 2023

Commits on Feb 4, 2023

Commits on Feb 6, 2023

Update test_automated_dihedral_analysis.py
cadeduckworth
authored
525f2cf

Commits on Feb 7, 2023

Commits on Feb 11, 2023

clean up new scipy.stats data and associated description
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530abf9
cleanup test comments/docs and properly describe fixtures and skipifs
cadeduckworth
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fix incorrect assertion for test_save_df_info
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cf8d562
fix plot assertion to use isinstance() to check for seaborn.axisgrid.FacetGrid for test_DataFrame_input
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41258f2
cleanup doc formatting and inline comments
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test doc indent levels
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format docs indentations
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format docs, reST typo
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d02da1a

Commits on Feb 12, 2023

update CHANGES
orbeckst
authored
ac8c8a7