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cli: gather raw option #620

Merged
merged 9 commits into from
Nov 17, 2023
Merged

cli: gather raw option #620

merged 9 commits into from
Nov 17, 2023

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richardjgowers
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@richardjgowers richardjgowers commented Nov 9, 2023 •
edited by IAlibay
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fixes issue #557
fixes issue #618

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pep8speaks commented Nov 9, 2023 •
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Hello @richardjgowers! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

Line 341:80: E501 line too long (93 > 79 characters)

Line 223:80: E501 line too long (84 > 79 characters)

Comment last updated at 2023-11-16 17:27:41 UTC

@richardjgowers richardjgowers force-pushed the issue_557_gather_per_leg branch from 09fe3e2 to c7c251d Compare November 9, 2023 22:44
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I've not added tests for this as the current test files don't have the correct info (see #605 and #595 for ongoing context)

This is what running this patch locally produces:

leg     ligand_i        ligand_j        DG(i->j) (kcal/mol)     uncertainty (kcal/mol)
complex lig_ejm_31      lig_ejm_42      -14.77  0.04
complex lig_ejm_31      lig_ejm_42      -14.74  0.04
complex lig_ejm_31      lig_ejm_42      -14.94  0.04
solvent lig_ejm_31      lig_ejm_42      -15.68  0.03
solvent lig_ejm_31      lig_ejm_42      -15.69  0.03
solvent lig_ejm_31      lig_ejm_42      -15.64  0.03
complex lig_ejm_31      lig_ejm_46      -40.56  0.06
complex lig_ejm_31      lig_ejm_46      -40.76  0.05
complex lig_ejm_31      lig_ejm_46      -40.90  0.04
solvent lig_ejm_31      lig_ejm_46      -39.92  0.04
solvent lig_ejm_31      lig_ejm_46      -39.94  0.04
solvent lig_ejm_31      lig_ejm_46      -39.95  0.04
complex lig_ejm_31      lig_ejm_47      -27.68  0.08
complex lig_ejm_31      lig_ejm_47      -27.80  0.06
complex lig_ejm_31      lig_ejm_47      -27.51  0.07
solvent lig_ejm_31      lig_ejm_47      -27.83  0.05
solvent lig_ejm_31      lig_ejm_47      -27.84  0.05
solvent lig_ejm_31      lig_ejm_47      -27.88  0.05
complex lig_ejm_31      lig_ejm_48      -16.15  0.08
complex lig_ejm_31      lig_ejm_48      -15.96  0.07
complex lig_ejm_31      lig_ejm_48      -16.01  0.08
solvent lig_ejm_31      lig_ejm_48      -16.83  0.06
solvent lig_ejm_31      lig_ejm_48      -16.65  0.07
solvent lig_ejm_31      lig_ejm_48      -16.77  0.06
complex lig_ejm_31      lig_ejm_50      -57.31  0.04
complex lig_ejm_31      lig_ejm_50      -57.45  0.04
complex lig_ejm_31      lig_ejm_50      -57.37  0.04
solvent lig_ejm_31      lig_ejm_50      -58.33  0.04
solvent lig_ejm_31      lig_ejm_50      -58.42  0.04
solvent lig_ejm_31      lig_ejm_50      -58.19  0.04
complex lig_ejm_42      lig_ejm_43      -19.24  0.04
complex lig_ejm_42      lig_ejm_43      -18.72  0.05
complex lig_ejm_42      lig_ejm_43      -18.94  0.04
solvent lig_ejm_42      lig_ejm_43      -20.17  0.03
solvent lig_ejm_42      lig_ejm_43      -20.28  0.03
solvent lig_ejm_42      lig_ejm_43      -20.23  0.03
complex lig_ejm_46      lig_jmc_23      17.31   0.02
complex lig_ejm_46      lig_jmc_23      17.37   0.02
complex lig_ejm_46      lig_jmc_23      17.35   0.02
solvent lig_ejm_46      lig_jmc_23      17.20   0.02
solvent lig_ejm_46      lig_jmc_23      17.40   0.02
solvent lig_ejm_46      lig_jmc_23      17.30   0.02
complex lig_ejm_46      lig_jmc_27      15.84   0.03
complex lig_ejm_46      lig_jmc_27      15.79   0.03
complex lig_ejm_46      lig_jmc_27      15.80   0.03
solvent lig_ejm_46      lig_jmc_27      16.16   0.03
solvent lig_ejm_46      lig_jmc_27      16.01   0.03
solvent lig_ejm_46      lig_jmc_27      16.07   0.03
complex lig_ejm_46      lig_jmc_28      23.43   0.04
complex lig_ejm_46      lig_jmc_28      23.29   0.04
complex lig_ejm_46      lig_jmc_28      23.17   0.04
solvent lig_ejm_46      lig_jmc_28      23.67   0.03
solvent lig_ejm_46      lig_jmc_28      23.61   0.03
solvent lig_ejm_46      lig_jmc_28      23.65   0.03

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codecov bot commented Nov 9, 2023 •
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Codecov Report

Attention: 65 lines in your changes are missing coverage. Please review.

Comparison is base (7a39491) 92.21% compared to head (9a36ad5) 91.37%.
Report is 4 commits behind head on main.

Files Patch % Lines
openfe/tests/protocols/test_openmm_afe_slow.py 25.39% 47 Missing ⚠️
...protocols/openmm_afe/equil_solvation_afe_method.py 60.00% 8 Missing ⚠️
openfe/protocols/openmm_rfe/equil_rfe_methods.py 57.14% 6 Missing ⚠️
openfecli/commands/gather.py 83.33% 3 Missing ⚠️
openfe/protocols/openmm_afe/base.py 0.00% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #620      +/-   ##
==========================================
- Coverage   92.21%   91.37%   -0.84%     
==========================================
  Files         124      125       +1     
  Lines        8594     8491     -103     
==========================================
- Hits         7925     7759     -166     
- Misses        669      732      +63

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

richardjgowers
richardjgowers commented Nov 10, 2023
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openfecli/tests/commands/test_gather.py
return os.path.join(pooch.os_cache('openfe'), 'results.tar.gz.untar', 'results')


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we should probably also add in a pytest plugin that turns tests requiring downloads off by default?

IAlibay
IAlibay reviewed Nov 14, 2023
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I think we need to discuss what "raw" means, or at least how we're not going to confuse users.

I'm not going to ask to write much more, but we should at least consider if we should write better docs?

Pinging @hannahbaumann for thoughts here too.

openfecli/commands/gather.py Show resolved Hide resolved
@richardjgowers richardjgowers force-pushed the issue_557_gather_per_leg branch from 26bb48a to 2529f94 Compare November 15, 2023 09:19
IAlibay
IAlibay approved these changes Nov 15, 2023
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@richardjgowers just the one thing, other LGTM (of course ignoring all the failing tests)

openfecli/commands/gather.py Outdated Show resolved Hide resolved
@richardjgowers richardjgowers merged commit 94929f5 into main Nov 17, 2023
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@richardjgowers richardjgowers deleted the issue_557_gather_per_leg branch November 17, 2023 10:42
@IAlibay IAlibay mentioned this pull request Nov 17, 2023
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@richardjgowers richardjgowers mentioned this pull request Nov 21, 2023
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@IAlibay IAlibay IAlibay approved these changes

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@richardjgowers @pep8speaks @IAlibay