deps: track pyiron_workflow_atomistics 0.0.7 pin set#41
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Bump the runtime pin block to match the versions that pyiron-workflow-atomistics==0.0.6 (already pinned here) actually requires, so installs stop conflicting with the upstream resolver. Verbatim from pwa 0.0.6's METADATA: - pandas 2.3.1 -> 3.0.2 - ase 3.26.0 -> 3.28.0 - scipy 1.16.1 -> 1.17.1 - pymatgen 2025.6.14 -> 2026.5.4 - scikit-learn 1.7.2 -> 1.8.0 Numpy / matplotlib / pyiron-workflow / pyiron-snippets / tqdm / lz-GB-code already match upstream; pyiron_lammps stays at 0.4.6 (its own bump to 0.5.4 is being tracked separately in #36 and needs a parser-API review before merging). Updated in lockstep: - pyproject.toml - .ci_support/environment.yml - .ci_support/lower-bound.yml - .binder/environment.yml Closes the coordinated-bump scope flagged in the open-PR triage: supersedes #19 (pymatgen), #30 (ase), #33 (pandas), #37 (numpy); those should be closed once this lands. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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0.0.7 (released 2026-05-14) replaces pwa's exact == pins with bounded ranges (e.g. numpy <1.27.0,>=1.22.0, ase <3.29.0,>=3.21.0, pymatgen <2026.6.0,>=2024.8.8). Every version this branch already chose for the runtime block sits inside those ranges, so the only file edit needed is the pwa pin itself across: - pyproject.toml - .ci_support/environment.yml - .ci_support/lower-bound.yml - .binder/environment.yml Side benefit: with pwa 0.0.7's looser ranges, the future Dependabot PRs against pandas / ase / pymatgen / scikit-learn become resolvable without a second coordinated bump on the pwa side. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Was missed in the previous commit; the CI's [dependabot skip] runner had auto-mirrored the runtime-block bumps into docs/environment.yml but did not touch the pwa pin itself, leaving docs out of sync with the rest of the env files. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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PR #41 bumped ase to 3.28.0 and pandas to 3.0.2 to match what pwa 0.0.7 *allows*, but pyiron_lammps (any released version, including 0.5.4) caps ase at <=3.27.0 and pandas at <=3.0.0 -- both on PyPI and on conda-forge. Likewise pysqa 0.3.0 caps pandas at <=2.3.1. Result: every CI job that creates a conda env (test-alternate-env, build-docs, build-notebooks, coverage, benchmark-tests, pip-check, unit-tests/macos, pypi-release) failed with `libmamba Could not solve for environment specs`. Main has been red since 5701c50. Fix-forward: pull ase / pandas / scipy back to the largest values that satisfy ALL of {pwa 0.0.7, pyiron_lammps 0.5.4, pysqa 0.4.0}, and bump pyiron_lammps + pysqa themselves so the rest of the upgrade we already shipped doesn't have to revert: ase 3.28.0 -> 3.27.0 (cap from pyiron_lammps 0.5.4) pandas 3.0.2 -> 3.0.0 (cap from pyiron_lammps 0.5.4) scipy 1.17.1 -> 1.17.0 (cap from pyiron_lammps 0.5.4) pyiron_lammps 0.4.6 -> 0.5.4 (latest; needed to lift the conda pin `ase <=3.26.0` from 0.4.6) pysqa 0.3.0 -> 0.4.0 (latest; lifts pandas cap) Verified locally with `pixi add` against conda-forge: full env solves clean. API check for pyiron_lammps 0.5.4 vs the two functions pwl uses (`write_lammps_structure`, `parse_lammps_output_files`): - write_lammps_structure: only added a trailing optional kwarg `atom_type='atomic'`. Pwl call site at lammps.py:24-30 uses only the original kwargs. Backward-compatible. - parse_lammps_output_files: signature identical, output dict structure (generic.cells/positions/indices/energy_tot/forces/ pressures/steps) unchanged. Updated in lockstep across: - pyproject.toml (runtime + cluster extra) - .ci_support/environment.yml - .ci_support/lower-bound.yml - .binder/environment.yml - docs/environment.yml Supersedes #35 (pysqa) and #36 (pyiron_lammps) -- close after merge. Co-authored-by: Han Mai <ligerzerof@gmail.com> Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Bumps the runtime pin block to be compatible with
pyiron-workflow-atomistics==0.0.7(latest, released 2026-05-14).pwa 0.0.7switched from exact==Xpins to bounded ranges (e.g.numpy <1.27.0,>=1.22.0,ase <3.29.0,>=3.21.0,pymatgen <2026.6.0,>=2024.8.8), which is much easier on the resolver. The version values picked here all sit comfortably inside those ranges, while still matching what pwa 0.0.6 used to pin exactly — so installs are clean against either.pyiron-lammpsstays at0.4.6— its bump to 0.5.4 is tracked in #36 and needs a parser-API review before merging.Updated in lockstep:
pyproject.toml.ci_support/environment.yml.ci_support/lower-bound.yml.binder/environment.ymldocs/environment.ymlSupersedes (close on merge)
<1.27.0)Test plan
pip install -e .resolves cleanly alongsidepyiron-workflow-atomistics==0.0.7(no resolver conflict warnings).notebooks/EnginePrototype_lammps.ipynbstill runs end-to-end against a LAMMPS build with theMANYBODYpackage.🤖 Generated with Claude Code