CI: Run slow tests on github runner #48
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nscorley
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…f` (#48) * fix: reduce logging level for missing extra fields warnings in `load_atom_array_with_conditions_from_cif` * fix: enable warning suppression in logging --------- Co-authored-by: Rafi Brent <rafi.brent@gmail.com>
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# [1.1.0](v1.0.3...v1.1.0) (2025-11-29) ### Bug Fixes * a couple of Condition updates ([#59](#59)) ([a0f173b](a0f173b)) * add a flag to optionally tolerate the situation of missing or multiple representative/center atoms per token ([#67](#67)) ([896ca38](896ca38)) * add errors for cases where parsing an AtomArrayPlus is problematic ([80d00e3](80d00e3)) * add padding for short residue names in sharding ([94abca1](94abca1)) * add raise_if_not_set to get_msa_dirs_from_env ([0f50eb2](0f50eb2)) * add raise_if_not_set to get_msa_dirs_from_env ([c7bfee6](c7bfee6)) * add within poly res idx on-the-fly option ([c80104b](c80104b)) * address code review issues in performance PR ([9cda94a](9cda94a)) * allow for deleting 2d annotations from AtomArrayPlus ([84e0084](84e0084)) * allow numpy masks in addition to query syntax in SampleSeed ([3468645](3468645)) * allow override in add global token id transform ([381a743](381a743)) * apptainer ([37fe7a2](37fe7a2)) * apptainer ([e3bd135](e3bd135)) * apptainer ([0647b20](0647b20)) * apptainer for CI ([670a82a](670a82a)) * bcif tests ([378d03a](378d03a)) * Be more robust to nulls in a3m files. ([a8552a4](a8552a4)) * better messages and assertions for removing design tasks with 0 frequency ([9b6391d](9b6391d)) * broken tests ([1fcc397](1fcc397)) * bug in default seq cond mask ([00484d4](00484d4)) * change default sequence condition behavior ([981d924](981d924)) * ci for internal ([5096b6c](5096b6c)) * ci workers ([f7da3cd](f7da3cd)) * circular import ([7eafda9](7eafda9)) * claude code review ([885eb53](885eb53)) * condition set mask and terminus conditions changes ([56f661c](56f661c)) * correct cache dir structure and add padding for short IDs ([b8645fc](b8645fc)) * correct sharding path construction for cached residue data ([79d388b](79d388b)) * **databases:** correcting uniontype call bug ([8a3e59e](8a3e59e)) * **databases:** correcting uniontype call bug ([ebc26db](ebc26db)) * datasets documentation, DSSP path ([1565a94](1565a94)) * docstring formatting ([ff296d6](ff296d6)) * documentation ([1e5b0d4](1e5b0d4)) * documentation, formatting ([dcdde14](dcdde14)) * downgrade biotite ([cab5bcf](cab5bcf)) * enable deletion of 2d annotations ([1f88391](1f88391)) * enable spawn multiprocessing ([36ac421](36ac421)) * ensure that parse preserves AtomArrayPlus status, and add a test for this ([681fdeb](681fdeb)) * ensure that the Index condition's default annotation respects its mask ([#50](#50)) ([e57be2a](e57be2a)) * Formatting ([f6fe986](f6fe986)) * general masks in SampleSeed ([53df9a6](53df9a6)) * give more informative error messages for ConditionalRoute or RandomRoute failures ([3b72b18](3b72b18)) * Handle non-uniform shard sizes in AseDBDataset ([e34eb51](e34eb51)) * infer array type of TokenEncoding where possible ([#68](#68)) ([a6a8fb1](a6a8fb1)) * informative Route error messages ([87b1fbc](87b1fbc)) * minor fixes ([f45fafb](f45fafb)) * minor fixes for encodings ([e043104](e043104)) * more informative error messages ([7861023](7861023)) * parse preserves atom array plus ([d1eef92](d1eef92)) * parser defaults ([570f3ce](570f3ce)) * reduce logging level in `load_atom_array_with_conditions_from_cif` ([#48](#48)) ([52f316d](52f316d)) * remove _spoof ([995a260](995a260)) * remove ambiguous Greek characters and improve test assertions ([bad6dff](bad6dff)) * remove ASE import so we dont introduce a dependency ([7e12a8a](7e12a8a)) * remove design tasks with zero frequency during sampling instead of erroring ([4586fa2](4586fa2)) * remove hardcoded environment-specific default path ([24bf03f](24bf03f)) * remove lineprofiler stuff ([83fb3c5](83fb3c5)) * remove print statements ([ecd9e5b](ecd9e5b)) * residue starts bug with dependent functions. ([04da354](04da354)) * residue starts bug with dependent functions. ([fc252a8](fc252a8)) * **rf3:** json-level atom selection for bonds argument ([a569a7c](a569a7c)) * ruff formatting after merge with dev ([71ddb86](71ddb86)) * sasa for empty aa ([c2b9302](c2b9302)) * shard cache on structure ID (PDB ID) instead of args hash ([e5c29fd](e5c29fd)) * Support AtomArrayPlus and AtomArrayPlusStack in parse_atom_array, with some restrictions ([#46](#46)) ([c1e3b00](c1e3b00)) * test requirements ([4c4c775](4c4c775)) * tests ([eb10ba6](eb10ba6)) * typing ([8d6e39d](8d6e39d)) * updates for ame ([6530818](6530818)) * use warnings.warn instead of print for missing ase ([b6f9c7a](b6f9c7a)) ### Features * add as_atom_array_plus_stack ([804c854](804c854)) * add Claude Hode GitHub workflow ([0f4e603](0f4e603)) * add customizable annotation names for SSE validity flag ([fd6be37](fd6be37)) * add DSSP secondary structure annotation ([f1cc785](f1cc785)) * add molprobity executable? ([b87f76b](b87f76b)) * add utomatic msa depth and ext determination ([874a1dd](874a1dd)) * adding Conditions, annotator, and io utils ([b08c935](b08c935)) * atom37 with atomization encoding ([d35be40](d35be40)) * atomworks MSA preprocessing (generate, filter, organize) ([ef6ac85](ef6ac85)) * backbone constants and annotators ([de5854c](de5854c)) * **databases:** add experimental data database functionality from datahub ([f69a499](f69a499)) * **databases:** add experimental data database functionality from datahub ([8b71614](8b71614)) * generalize encodings ([c886d09](c886d09)) * generalize encodings ([83c8684](83c8684)) * Make SampleDesignTask handle empty design_tasks gracefully ([c9e5900](c9e5900)) * misc fixes for design ([71decdf](71decdf)) * MSA preprocessing (organizing, generating, filtering) ([89eb73d](89eb73d)) * MSA preprocessing; zst support ([aa3c837](aa3c837)) * paired MSA feature (from Rafi) ([805a27a](805a27a)) * paired MSA feature (from Rafi) ([2df1511](2df1511)) * skip for large structures ([6f2f33c](6f2f33c)) * update to work with transition metals ([6f2a80a](6f2a80a)) ### Performance Improvements * don't actually check symmetry every time on symmetric conditions since there's just too much overhead ([6ae656a](6ae656a)) * improve cache loading and template building performance ([c144ec7](c144ec7)) * performance optimizations for parsing ([e8faf3e](e8faf3e)) * precalculate bond graph for GrowByHoppingAlongBondGraph ([fd85178](fd85178)) * res idx ([22703bf](22703bf)) * res idx optimization ([11b5d0d](11b5d0d)) * speed up 2d symmetrization check and stop actually checking symmetry every time and make some other stuff faster ([5c3127b](5c3127b)) * speed up apply_and_spread ([ac612a4](ac612a4)) * speed up bond_graph creation ([94f0512](94f0512))
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📋 PR Checklist
This PR is tagged as a draft if it is still under development and not ready for review.
I have ensured that all my commits follow angular commit message conventions.
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make formaton the codebase before submitting the PR (this autoformats the code and lints it).I have named the PR in angular PR message format as well (c.f. above), with a sensible tag line that summarizes all the changes in the PR.
ℹ️ PR Description
This PR is to change how pytest submits tests on the github runner so the slow tests are also able to run on the github runner.
What changes were made and why?
This change is for running pytest on the github runner, we run the slow test in tests/ml with 1 processor and the other test with -n auto. The slow test are ran on a single processor to keep from exceeding memory limits of the github runner. This also removes the step that runs tests on digs.
How were the changes tested?
I ran the workflow to see how long this takes compared to before and if it errors out because of memory
Additional Notes