fix psutils import by atravitz · Pull Request #1779 · OpenFreeEnergy/openfe

atravitz · 2026-01-05T22:45:18Z

resolves #1767

We should also do a repodata patch to pin earlier versions of openfe to psutil <7.2.0
(diff here giampaolo/psutil@release-7.1.3...release-7.2.0)

Ideally, we wouldn't use psutils private methods, so it'd be worth checking if we could test this a different way.

Checklist

All new code is appropriately documented (user-facing code must have complete docstrings).
Added a news entry, or the changes are not user-facing.
Ran pre-commit by making a comment with pre-commit.ci autofix before requesting review.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

GPU integration tests
example notebook testing
packaging tests: run this for any large feature PRs or PRs that add test data.

Developers certificate of origin

I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

codecov · 2026-01-05T23:11:34Z

Codecov Report

❌ Patch coverage is 50.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.18%. Comparing base (566d203) to head (afb0740).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
openfe/tests/utils/test_system_probe.py	50.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1779      +/-   ##
==========================================
- Coverage   95.39%   93.18%   -2.22%     
==========================================
  Files         189      190       +1     
  Lines       16646    16802     +156     
==========================================
- Hits        15880    15657     -223     
- Misses        766     1145     +379

Flag	Coverage Δ
fast-tests	`93.18% <50.00%> (?)`
slow-tests	`?`

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IAlibay

Only one failure and it's related to zenodo downloads, this looks great thanks! One thing though!

IAlibay · 2026-01-06T02:46:39Z

openfe/tests/utils/test_system_probe.py

-from psutil._common import sdiskusage
+
+try:
+    from psutil._common import sdiskusage


My understanding is that the new version is the correct one, is that right?
If so, may I suggest inverting these so that the "new" (and hopefully "from now on") import is the one that we try first? That way you don't have to deal with the cost of error checking on import.

agreed, done!

github-actions · 2026-01-06T15:57:29Z

No API break detected ✅

IAlibay

Thanks!

* fix psutils import * swap import order

* update install instructions (#1744) * update manifest to include all .gz files (#1746) * update manifest to include all .gz files * add min openmmforcefields pin * bump cuda version to 11.8 (#1749) * fix deprecation warning on view_components_3d (#1750) * expose KartografAtomMapper alongside other AtomMappers (#1751) * fix psutils import (#1779) * fix psutils import * swap import order * [pre-commit.ci] pre-commit autoupdate (#1778) updates: - [github.com/tox-dev/pyproject-fmt: v2.8.0 → v2.11.1](tox-dev/pyproject-fmt@v2.8.0...v2.11.1) - [github.com/astral-sh/ruff-pre-commit: v0.13.3 → v0.14.10](astral-sh/ruff-pre-commit@v0.13.3...v0.14.10) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Disable NAGL as a partial charge backend when OEToolkit is installed but not chosen as the registry backend. (#1762) * NAGL can no longer be used with oechem installed if you are using the rdkit backend. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * rename openfecli fixture to avoid duplication with openfe fixture (#1755) Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * openfe gather: add progress bar for loading JSONs (#1786) * all the profiling * make progress bar pretty * revert typing thing * news * all the profiling * make progress bar pretty * revert typing thing * news * update expected outputs * update expected outputs * add dill mock to fix openfe docs build (#1792) * Fix issue 1795 (#1796) * Update method name in CLI YAML documentation * Fix command option case in CLI YAML guide * manually add absolute settings news item to changelog (#1821) * manually add absolute settings news item to changelog * add link * Fixes docstring to clarify argument does not have a default (#1819) * Fixes docstring to clarify argument does not have a default * Modernize typing * fix ligand network cropping bug (#1822) * fix ligand network cropping bug * move to upstream func * whitespace * fix pydantic deprecation of copy method * fix pydantic deprecation of dict method - septop (#1831) * Updated CHANGELOG for 1.8.1 * fix changelog links * add openeye w/ python 3.13 test to CI (#1745) * add openeye w/ python 3.13 test to CI * only run openeye on unbuntu w/ python 3.13 * add explicit openeye no * bump python version for conda cron (#1748) * remove mypy rdkit pin (#1753) * remove mypy rdkit pin * try more explicit import * Revert "try more explicit import" This reverts commit 00cc2a3. * disallow attr-defined error code * try globally disabling attr-defined * try specific override * per-line ignores * Make the multistate hybrid topology samplers not require the HybridTopologyFactory (#1768) * make hybrid samplers not rely on htf but instead on the system & positions. * Migrate validation to Protocol._validate in HybridTopologyProtocol (#1740) * Migrate & add validation to Protocol._validate for hybrid topology Protocol --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk> * Move rfe protocol (#1769) Move RFE protocol files around * HybridTop Unit methods (#1770) * Break down the Hybrid Top protocol unit into various methods. --------- Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> * Have two separate system generators for state A & B in hybrid protocol (#1772) Make it so that the states A and B are generated using two different SystemGenerator objects, allowing for partial charge transformations. * HybridTop structural analysis via API rather than CLI (#1771) * change structural analysis from using CLI to using API * making some language clearer on github-facing things (#1758) * making some language clearer on github-facing things * : * add pre-commit link * clean up * Moving AFE Protocols around a bit (#1775) * move the protocols results to a single file and deduplicate * rename base units file * move units out of method files * move a few things in init * Create setup, run, and analysis units for HybridTop Protocol (#1773) * Turn Hybrid Topology protocol into 3 units. --------- Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * update docs for multiple protocol units (#1793) * Update docstring for hybridtop classes (#1794) * Update docstring for classes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Small improvement in RelativeHybridTopologyProtocol docstring (#1797) Updated class docstring to clarify the use of Hybrid Topology scheme. * turn off zenodo retry (#1802) * turn off zenodo retry * remove retry_if_failed arg * only run CI on macos python 3.12 (#1803) * Turn AFE protocols into multiple units (#1776) * Split the AFE protocol units into setup, simulation, and analysis. * move to src layout (#1805) * Move openfe project layout to `src`. * Temporarily build pooch from main w/ hotfix (#1806) * build with pooch@main to see if hotfix works * add link * make CLI starting guide easier to find from the landing page (#1787) * make CLI starting guide easier to find from the landing page * Python API -> API Docs * bump ci * bump example notebooks pin to 2026.01.26 * change a word * clarifying language * Update pyproject.toml (#1813) * Update pyproject.toml * update classifiers * refactor: clean up test data handling (#1815) * import pooch_cache from conftest * remove unused files from pooch cache * move zenodo cache to conftest * remove duplicate code * min pin pooch to fix data fetching (#1820) * fix ligand network cropping bug (#1822) * fix ligand network cropping bug * move to upstream func * whitespace * fix api break check path (#1825) * fix pydantic deprecation of copy method (#1829) * fix scope mismatch with zenodo data (#1828) * fix scope mismatch with zenodo data * fix session scope --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>

fix psutils import

08fc9f4

atravitz requested a review from mikemhenry January 5, 2026 22:46

IAlibay requested changes Jan 6, 2026

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IAlibay mentioned this pull request Jan 6, 2026

Make the multistate hybrid topology samplers not require the HybridTopologyFactory #1768

Merged

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atravitz and others added 2 commits January 6, 2026 07:56

swap import order

76cd959

Merge branch 'main' into issue_1767

afb0740

atravitz requested a review from IAlibay January 6, 2026 15:57

IAlibay approved these changes Jan 6, 2026

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IAlibay merged commit 8d00389 into main Jan 6, 2026
11 of 12 checks passed

IAlibay deleted the issue_1767 branch January 6, 2026 19:09

atravitz mentioned this pull request Jan 6, 2026

pin psutil conda-forge/openfe-feedstock#114

Merged

5 tasks

atravitz added a commit that referenced this pull request Feb 4, 2026

fix psutils import (#1779)

e5a3c87

* fix psutils import * swap import order

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fix psutils import#1779

fix psutils import#1779
IAlibay merged 3 commits intomainfrom
issue_1767

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