`zstandard` import bandaid #1940

mattwthompson · 2024-09-30T19:54:23Z

The plan agreed to on 9/10 is

Import zstandard at the top of openeye_wrapper.py
Make a custom off-label build without zstandard constraint
- Look for noarch/openff-toolkit-0.16.4-pyhc2fc6b4_3.conda
Test locally with custom build (see below)

codecov · 2024-09-30T19:59:07Z

Codecov Report

Attention: Patch coverage is 50.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 93.74%. Comparing base (31e4c4b) to head (a567141).
Report is 2 commits behind head on main.

Additional details and impacted files

mattwthompson · 2024-10-01T14:43:16Z

This seems to work fine if snuck into a conda build as a standalone patch:

$ micromamba create --name with-1940 "openff-toolkit=0.16.4=pyhc2fc6b4_3" openeye-toolkits qcfractal -c conda-forge/label/openff-toolkit_rc -c conda-forge -c openeye -yq
warning  libmamba 'root_prefix' set with default value: /Users/mattthompson/micromamba
warning  libmamba [tk-8.6.13-h5083fa2_1] The following files were already present in the environment:
    - include/X11/DECkeysym.h
    - include/X11/HPkeysym.h
    - include/X11/Sunkeysym.h
    - include/X11/X.h
    - include/X11/XF86keysym.h
    - include/X11/Xatom.h
    - include/X11/Xfuncproto.h
    - include/X11/ap_keysym.h
    - include/X11/keysym.h
    - include/X11/keysymdef.h
warning  libmamba [xorg-libx11-1.8.10-h2321a68_0] The following files were already present in the environment:
    - include/X11/Xlib.h
    - include/X11/Xutil.h
    - include/X11/cursorfont.h
[~]
$ micromamba activate with-1940                                                      9:40:07
warning  libmamba 'root_prefix' set with default value: /Users/mattthompson/micromamba
(with-1940) [~]
$ python -c "from openeye import *; import qcportal"                                 9:40:15
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/qcportal/__init__.py", line 10, in <module>
    from .client import PortalClient
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/qcportal/client.py", line 10, in <module>
    from qcportal.cache import DatasetCache, read_dataset_metadata
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/qcportal/cache.py", line 22, in <module>
    import zstandard
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/zstandard/__init__.py", line 39, in <module>
    from .backend_c import *  # type: ignore
    ^^^^^^^^^^^^^^^^^^^^^^^^
ImportError: zstd C API versions mismatch; Python bindings were not compiled/linked against expected zstd version (10502 returned by the lib, 10506 hardcoded in zstd headers, 10506 hardcoded in the cext)
(with-1940) [~]
$ pytest --pyargs "openff.toolkit" -rf                                               9:40:33
==================================== test session starts =====================================
platform darwin -- Python 3.12.5, pytest-8.3.3, pluggy-1.5.0
rootdir: /Users/mattthompson
plugins: anyio-4.6.0, typeguard-4.3.0
collected 24383 items

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XXXXXXXXXXXXXXXxxXxXXXxXXXXXXXxXXXXXXXXXXXXXXXXxXXXxXXXXXXXXxXXXXXXXXXXXXXxXXXxxXXXXXX [ 70%]
XXXXXxXxXXXxXXxXXxxxXXxXXXxXxXXXXXXxXXXXXXxxXXXXXxXXxXXXxxXXXXXXXXXxXXXxXxXxxXXXXXxXXX [ 71%]
XXXXXXxXXXXXXxxXXXXXXXXXxXxXxXXXxXXXXXXXxXXXXXXXXxXXXXXxxxXXXxXxXXXXXXXXXxXXXXXXXXXxxX [ 71%]
XXxXXxXXXXXXxXXXXXXXXXxXXXXxXXXXxXXXX................................................. [ 71%]
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................................sssssssssss..............ssss.......................Fatal Python error: Aborted

Current thread 0x0000000207678f40 (most recent call first):
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/openff/toolkit/_tests/test_molecule.py", line 3515 in test_visualize_rdkit
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/python.py", line 159 in pytest_pyfunc_call
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/python.py", line 1627 in runtest
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/runner.py", line 174 in pytest_runtest_call
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/runner.py", line 242 in <lambda>
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/runner.py", line 341 in from_call
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/runner.py", line 241 in call_and_report
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/runner.py", line 132 in runtestprotocol
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/runner.py", line 113 in pytest_runtest_protocol
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/main.py", line 362 in pytest_runtestloop
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/main.py", line 337 in _main
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/main.py", line 283 in wrap_session
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/main.py", line 330 in pytest_cmdline_main
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/config/__init__.py", line 175 in main
  File "/Users/mattthompson/micromamba/envs/with-1940/lib/python3.12/site-packages/_pytest/config/__init__.py", line 201 in console_main
  File "/Users/mattthompson/micromamba/envs/with-1940/bin/pytest", line 10 in <module>

Extension modules: apsw, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, msgpack._cmsgpack, zstandard.backend_c, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, numexpr.interpreter, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, _cffi_backend, _brotli, yaml._yaml, openmm._openmm, _oechem4101, _oequacpac2241, _oeiupac2911, _oeomega5101, rdkit.rdBase, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, mdtraj.formats.dcd, mdtraj.formats.dtr, mdtraj.formats.trr, mdtraj.formats.xtc, mdtraj.geometry._geometry, mdtraj.geometry.drid, mdtraj.geometry.neighborlist, mdtraj.geometry.neighbors, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, mdtraj._lprmsd, mdtraj._rmsd, rdkit.DataStructs.cDataStructs, rdkit.Chem.rdchem, rdkit.Geometry.rdGeometry, rdkit.Chem.rdinchi, rdkit.Chem.rdCIPLabeler, rdkit.Chem.rdmolfiles, rdkit.Chem.rdmolops, rdkit.Chem.rdMolInterchange, rdkit.Chem.rdCoordGen, rdkit.Chem.MolStandardize.rdMolStandardize, rdkit.Chem.rdDistGeom, rdkit.ForceField.rdForceField, rdkit.Chem.rdChemicalFeatures, rdkit.Chem.rdMolChemicalFeatures, rdkit.Chem.rdChemReactions, rdkit.Chem.rdDepictor, rdkit.Chem.rdFingerprintGenerator, rdkit.Chem.rdForceFieldHelpers, rdkit.Chem.rdMolAlign, rdkit.Chem.rdMolDescriptors, rdkit.Chem.rdMolEnumerator, rdkit.Chem.rdMolTransforms, rdkit.Chem.rdPartialCharges, rdkit.Chem.rdqueries, rdkit.Chem.rdReducedGraphs, rdkit.Chem.rdShapeHelpers, scipy.io.matlab._mio_utils, scipy.io.matlab._streams, scipy.io.matlab._mio5_utils, rdkit.Chem.Draw.rdMolDraw2D (total: 148)
[1]    37710 abort      pytest --pyargs "openff.toolkit" -rf

The crash stems from something with RDKit's drawing functionality, which I doubt is related

Here's the environment: https://gist.github.com/mattwthompson/23b24455f6a64fc9581270b62e01e0fe

mattwthompson · 2024-10-01T16:57:21Z

I suspect the issue is genuine and upstream openforcefield/openff-fragmenter#183

openff/toolkit/utils/openeye_wrapper.py

Co-authored-by: Jeff Wagner <[email protected]>

j-wags

Thanks @mattwthompson! Approved pending releasenotes update. Could you also make the release?

Update top releasenotes version to 0.16.5
Cut the 0.16.5 release and make conda package (using standard checklist)
Update the conda-forge package metadata to not constrain zstandard, and add rdkit !=2024.03.6 (to head off RDKit depiction tests failing on macOS openff-fragmenter#183)

mattwthompson · 2024-10-02T19:55:08Z

+ local tests with and without QCPortal installed

openff/toolkit/utils/openeye_wrapper.py

…ndaid

mattwthompson · 2024-10-03T15:35:48Z

I'm going to defer a large collection of RDKit-related updates (#1942) to a subsequent release. Every issue I've run into has either been something that is upstream's (and not our) responsibility to address or something that requires changes in test/automation code, not source code.

zstandard import bandaid

0e28133

mattwthompson mentioned this pull request Oct 1, 2024

Test with patched zstandard import openforcefield/status#87

Closed

mattwthompson marked this pull request as ready for review October 1, 2024 14:54

j-wags reviewed Oct 2, 2024

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openff/toolkit/utils/openeye_wrapper.py Outdated Show resolved Hide resolved

Update openff/toolkit/utils/openeye_wrapper.py

a567141

Co-authored-by: Jeff Wagner <[email protected]>

j-wags approved these changes Oct 2, 2024

View reviewed changes

j-wags reviewed Oct 2, 2024

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openff/toolkit/utils/openeye_wrapper.py Show resolved Hide resolved

j-wags and others added 3 commits October 2, 2024 12:56

Update openff/toolkit/utils/openeye_wrapper.py

4430c18

Update release history

8ba95f4

Merge remote-tracking branch 'upstream/main' into better-zstandard-ba…

8d2d926

…ndaid

mattwthompson merged commit 21536cc into main Oct 3, 2024
3 checks passed

mattwthompson deleted the better-zstandard-bandaid branch October 3, 2024 15:36

This was referenced Oct 3, 2024

Minimal CI fixes #1943

Merged

Release 0.16.5 conda-forge/openff-toolkit-feedstock#94

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`zstandard` import bandaid #1940

`zstandard` import bandaid #1940

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zstandard import bandaid #1940

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`zstandard` import bandaid #1940

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