Automated Dihedral Analysis #217

cadeduckworth · 2022-10-20T17:33:40Z

Adding automation functionality for dihedral analysis
Automation function for dihedral analysis includes retrieval of dihedral atom groups and visual representation of data via seaborn-catplot violin plots
close add appropriate error, exception, logging methods for these patterns, throughout #236

* separating functionality for use with _single_universe without iterating frames * retaining functionality for use with _single_frame

* try/except pattern condensed to one run method * single run method implemented for _single_universe and _single_frame * functionality of original run method retained, while removing frame iteration for _single_universe usage * progress bar still active when using _single_universe, but no frame iteration occurs

directory_paths: finds MDPOW project data and returns pandas DataFrame directory_iteration: takes pandas DataFrame or csv and iterates automated_dihedral_analysis over MDPOW project directories automated_dihedral_analysis: group of functions that includes automation scripts for DihedralAnalysis, automatic dihedral atom group selection, seaborn violin plots function, and other required functions Future changes will eliminate redundancies following initial testing

…class to test possible ways to call automation-related functions

orbeckst

Move all automation into a separate module: mdpow/analysis/workflows/base.py.

Add documentation. Need to include it in the html docs.

Add tests.

mdpow/analysis/dihedral.py

orbeckst · 2022-10-20T17:50:54Z

This PR requires PR #216 to be merged, otherwise analysis runs twice.

removed raise added docstrings to describe use of NotImplementedError responded with reason for removing _conclude_universe() next step: updating html documentation following successful testing

fixed expected indent block error removed raise removed _conclude_universe()

…se automation for DihedralAnalysis automated_dihedral_analysis.py directory_iteration.py directory_paths.py

…ained within automated_dihedral_analysis.py

codecov · 2022-10-28T23:06:33Z

Codecov Report

Merging #217 (ac8c8a7) into develop (729a6fb) will increase coverage by 0.90%.
The diff coverage is 93.22%.

@@             Coverage Diff             @@
##           develop     #217      +/-   ##
===========================================
+ Coverage    79.06%   79.96%   +0.90%     
===========================================
  Files           12       13       +1     
  Lines         1729     1847     +118     
  Branches       271      282      +11     
===========================================
+ Hits          1367     1477     +110     
- Misses         277      280       +3     
- Partials        85       90       +5

Impacted Files	Coverage Δ
mdpow/analysis/dihedral.py	`100.00% <ø> (ø)`
mdpow/workflows/dihedrals.py	`93.22% <93.22%> (ø)`

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

…v files in provided parent directory

mdpow/analysis/automation/dihedral/automated_dihedral_analysis.py

orbeckst · 2022-11-14T19:21:30Z

I'll look at this one again when #218 and #216 are addressed.

…alysis

…ted-dihedral-analysis updating with changes for backend and testing from PR #216 ensemble_run_update

orbeckst · 2022-11-23T20:53:53Z

For test files: Create a set of data with XTC files that only contain ~10 frames (evenly spaced along the trajectory). Include only TPR files necessary for the test (eg only Coulomb lambda 0).

orbeckst · 2022-12-12T23:12:04Z

@cadeduckworth please resolve conflicts now that PR #216 has been merged. This should get this PR up-to-date.

orbeckst

TODO

Move all automation into a separate module: mdpow/analysis/workflows ; have a base.py for general stuff and a dihedrals.py for dihedrals specific
Add documentation. Show how one uses your code. Use test files as examples so that someone could directly try it out. These howto-docs also give you an idea how to organize and structure.
Add tests. In particular, create a minimal test set. Automated Dihedral Analysis #217 (comment)

… correct results from atom indices

cadeduckworth · 2023-02-07T06:02:23Z

Some issues need to be unlinked and linked to separate or new PR's after this one is merged

only issue add appropriate error, exception, logging methods for these patterns, throughout #236 should be closed with this PR

… data

cadeduckworth · 2023-02-07T06:31:16Z

@orbeckst
I will double check docs, tests, and modules, and update if I notice anything, but it appears that everything should be ready for final review.

orbeckst

Good changes. I found one incorrect assertion, some formatting issues, and please clean up comments/commented out code and make some of the comments more specific so that people after you (or your future self) has a chance understanding what the problem is.

mdpow/tests/test_automated_dihedral_analysis.py

orbeckst · 2023-02-10T21:03:09Z

mdpow/tests/test_automated_dihedral_analysis.py

+            assert groups[i].all() == self.check_groups[i].all()
+            i+=1
+
+    @pytest.mark.skipif(sys.version_info < (3, 8), reason="scipy circvar gives wrong answers")


Add issue number, add more text to be specific ... whoeever reads this has no clue what "nature of this problem" means.

Read the comments through the eyes of someone who is not an insider.

mdpow/tests/test_automated_dihedral_analysis.py

mdpow/workflows/dihedrals.py

…FacetGrid for test_DataFrame_input

cadeduckworth · 2023-02-11T13:21:10Z

@orbeckst All requested changes have been addressed, and relevant or meaningful inline comments that do not fit the scope of this pull request have been moved to new or existing issues.

As a reminder (because I tried, but could not figure out how to do it), issues 232 and 235 need to be unlinked to make sure they are not closed with this PR. Only issue 236 should be closed with this PR.

orbeckst

excellent work, good to go 🎉

I'll squash-merge.

orbeckst · 2023-02-12T03:13:26Z

oops, need entry in CHANGES ... will do that before merge

orbeckst · 2023-02-12T03:43:09Z

Congratulations @cadeduckworth , your big PR is in MDPOW! 🎉 🍾

cadeduckworth added 4 commits September 15, 2022 10:27

developing back end run methods

e71456d

* separating functionality for use with _single_universe without iterating frames * retaining functionality for use with _single_frame

moved directory_paths function to reside within the DihedralAnalysis …

f9b6646

…class to test possible ways to call automation-related functions

orbeckst requested changes Oct 20, 2022

View reviewed changes

cadeduckworth and others added 10 commits October 21, 2022 20:21

Addressed change requests by Oliver

7bcdf49

removed raise added docstrings to describe use of NotImplementedError responded with reason for removing _conclude_universe() next step: updating html documentation following successful testing

fixed indentation error for _single_frame() block

a87cb11

reverting previous tab issue, necessary for normal function

7edde0d

fixed errors previously reverted for testing

48016c5

fixed expected indent block error removed raise removed _conclude_universe()

Merge branch 'develop' into ensemble_run_update

59c819c

restored original dihedral.py file

6b1be1b

created automation/dihedral subdirectory under mdpow/analysis/ to hou…

2ddea0e

…se automation for DihedralAnalysis automated_dihedral_analysis.py directory_iteration.py directory_paths.py

updated docstrings and added examples for directory_paths.py

ad6db6e

added docstrings and examples for directory_iteration.py

848dd87

added initial draft of docstrings and examples for all functions cont…

6394d7a

…ained within automated_dihedral_analysis.py

added the option to save the DihedralAnalysis results DataFrame as cs…

d8f3ca3

…v files in provided parent directory

cadeduckworth commented Nov 12, 2022

View reviewed changes

mdpow/analysis/automation/dihedral/automated_dihedral_analysis.py Outdated Show resolved Hide resolved

cadeduckworth and others added 5 commits November 17, 2022 04:17

removed redundant DataFrame saving pattern from automated_dihedral_an…

d8137cb

…alysis

Merge remote-tracking branch 'origin/ensemble_run_update' into automa…

29477ab

…ted-dihedral-analysis updating with changes for backend and testing from PR #216 ensemble_run_update

merged updates from PR #216 and PR #218

642e87e

Merge branch 'develop' into automated-dihedral-analysis

4814376

Merge branch 'develop' into automated-dihedral-analysis

f333ee8

cadeduckworth added 2 commits December 14, 2022 11:10

resolved conflicts to merge updates in from develop from PR#216

6f16b84

adding data for testing automated dihedral analysis

ddffbdf

orbeckst requested changes Dec 14, 2022

View reviewed changes

cadeduckworth added 8 commits February 6, 2023 19:28

add MDAnalysis, RDKit, Pandas links for intersphinx mapping

cc08976

preliminary changes to docs to test intersphinx links and format changes

32ac646

fix logger.info and associated tests

dfd1098

move or change comments in test module

4ac89a2

add skipif for figure generating and figure saving tests that rely on…

118f4cf

… correct results from atom indices

cleanup and format docs, add seaborn intersphinx mapping

87d0334

doc formatting

9b0e737

fix minor docs format

800d36f

calculate new numerical values for testing from recently reduced test…

ea1b1a8

… data

orbeckst requested changes Feb 10, 2023

View reviewed changes

cadeduckworth added 8 commits February 11, 2023 03:36

clean up new scipy.stats data and associated description

530abf9

cleanup test comments/docs and properly describe fixtures and skipifs

8e3b37f

fix incorrect assertion for test_save_df_info

cf8d562

fix plot assertion to use isinstance() to check for seaborn.axisgrid.…

41258f2

…FacetGrid for test_DataFrame_input

cleanup doc formatting and inline comments

4e2fdb7

test doc indent levels

5053a30

format docs indentations

73aa472

format docs, reST typo

d02da1a

orbeckst self-assigned this Feb 12, 2023

This was unlinked from issues Feb 12, 2023

Finish documentation for workflows/dihedrals automation tutorial notebook (ipynb) #232

Open

change pytest fixture scopes to 'session' and add tmpdir methods if required #235

Open

orbeckst approved these changes Feb 12, 2023

View reviewed changes

update CHANGES

ac8c8a7

orbeckst merged commit 3faba4f into develop Feb 12, 2023

orbeckst deleted the automated-dihedral-analysis branch February 12, 2023 03:42

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Automated Dihedral Analysis #217

Automated Dihedral Analysis #217

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Automated Dihedral Analysis #217

Automated Dihedral Analysis #217

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