minimum pin for jupyter_client to fix deprecation warnings#1549
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atravitz wants to merge 46 commits intorelease_prep_v1.6.1from
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minimum pin for jupyter_client to fix deprecation warnings#1549atravitz wants to merge 46 commits intorelease_prep_v1.6.1from
atravitz wants to merge 46 commits intorelease_prep_v1.6.1from
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
Update citation file with new ordering.
* use isolated folder for conda cron ci * typo
Evaluate host idxs atoms in DSSP filters after distance evaluation [Issue #1418]
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
Fix minimum distance in host finding [Issue #1422]
Always use atoms in both helices and beta sheets in the DSSP filter
* Update restraint settings (force constant and min/max distance * Change Boresch standard state correction in test after changing the force constant
* Implement single residue boresch host finding strategy
* add pyproject toml formatting * Apply suggestions from code review Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> --------- Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Turn off minimization when we do a dry run --------- Co-authored-by: IAlibay <IAlibay@users.noreply.github.com>
* Change bonded host strategy to use lowest variance restraint * Fix a few things * minimally add the fix * Add some tests * Add bonded anchor strategy trajectory test
* Change default Boresch strategy to bonded * Change default bond strength to 4184.0 kj/mol/nm**2
* add jq code blocks * use tutorial data * news
* don't run CI for rtd changes * dont build env * Revert "dont build env" This reverts commit 03abea5.
* don't build openmm * mambaforge->miniconda for rtd * artifically small build for debugging * dont build env * just build python * add channels * add sphinx packages to env * add all non-openfe-ecosystem deps * remove shim channel * add openfe package * add everything except openmm and toolkit * add openmm * add openff-toolkit * only openff-toolkit * try openff-toolkit-base * try latest openff * everybody back in * build without openmm * build with openff-toolkit-base * bump rtd * add pip build * remove any openff-toolkit * build w/o openmm * add pip install * build everything without pip install * try no deps * try custom build * only python and pip * try openfe-toolkit-base * add temp deps for build with openff-toolkit-base * add temp deps for build with openff-toolkit-base * mock imports * dont mock with toolkit base * bump toolkit version * Revert "bump toolkit version" This reverts commit 6e3108a. * add mocks * try pinnint to toolkit-base 0.13.0, no mocks * back to >= 0.13.0 toolkit to make sure it wasn't a fluke * mock imports
I've seen a few cases in the wild where CI fails because a file failed to download. I think we should try bumping to 5 since with each retry it increases the wait time and I think that ~3s might be too fast so I want to try 5s. Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* deprecate get_alchemical_charge_difference * fix deprecated call within relative alchemical network planner * add test for deprecation * add news item * point env to working gufe branch * fix escape sequence * use warnings.warn instead of decorator * env back to main
…able (#1506) * update tests now that a production NAGL model is available * fix mock * clean up mocking
* add pipe example for jq * pin to docutil 0.20 * try to avoid memory error
* try mambaforge build * Revert "try mambaforge build" This reverts commit 683e07f. * try explicit build * try removing ambertools * use the right env * just add gufe pip install back * add back openfe eco packages * mock py3dmol * add note for pip installs * fix quote * temporarily resort to SettingsBaseModel to get build * specific imports * dont use base settings placeholder
Adds an OpenMM-based SepTop Protocol. --------- Co-authored-by: IAlibay <IAlibay@users.noreply.github.com> Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>
* temporary pin to pre-pydantic v2 gufe commit * pin docs too
* SepTop docs improvements lambda schedule and restraint selection * Remove set_openmm_threads_1 logic from test_septop_slow * change femto acknowledgements * update method docstring limitations * Make sure we fail when we have virtual sites and reassign_velocities is False * clean up usage of openmm imports * clean up equil settings output indices so that it enforces all * generate smc_off_B on the fly * Update enforcement of all output indices * Simulation overview unclear on if the same restraint is used between repeats * Add test for output indices validation --------- Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Removing unnecessary limit on resids indices gathering
* adding new branding assets * remove images * update theme branch * CantinaPurple accent * lowercase convention * updating text * remove dark mode for now * fix sidebars * fix formatting * capitalization * don't break spaces * bump ci * favicon! * whitespace :( * pin to sphinx release
* Ensure PEP-639 Support Eventually (2026-Feb-18) the license field needs to be a SPDX license expression. The table with a "file" or "text" key is deprecated. As of version 77.0.3, setuptools supports this new format. See: https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license-and-license-files * remove license classifier * include license file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * setuptools.errors.InvalidConfigError: 'project.license-files' is defined already. Remove 'tool.setuptools.license-files'. --------- 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>
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No API break detected ✅ |
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closing because #1550 covers this |
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## release_prep_v1.6.1 #1549 +/- ##
=======================================================
- Coverage 95.19% 93.19% -2.00%
=======================================================
Files 165 172 +7
Lines 12433 14467 +2034
=======================================================
+ Hits 11835 13483 +1648
- Misses 598 984 +386
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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draft mode because it's TBD whether this will fix it.
currently seeing
jupyter_client/session.py:203: DeprecationWarning: datetime.datetime.utcnow()in our demo notebook(s).I’m seeing this deprecation warning because, although
jupyter_clientaddressed the deprecation in v8.4.0 in 2023, our env in colab is usingjupyter_client v7.4.9.I tried adding an ignore but it seems flaky, and I think it's our requirements pulling it in in the single file installer.
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