Remove pyxtal wrapper #405
Conversation
This lives now directly in the assyst package >0.8.1
WalkthroughRemoved PyXtal-based random structure generation code and its tests, eliminated pyxtal from docs, packaging, and CI environment files, and added hatch-vcs to Changes
Sequence Diagram(s)sequenceDiagram
autonumber
participant User
participant stk.build as stk.build API
participant PyXtal as PyXtal lib
Note over User,PyXtal: Previous behavior (before this PR)
User->>stk.build: call stk.build.pyxtal(...)
stk.build->>PyXtal: import and invoke PyXtal.from_random(...)
PyXtal-->>stk.build: Atoms / errors
stk.build-->>User: return Atoms / warnings / errors
rect rgb(235,245,255)
Note right of stk.build: After this PR
end
Note over User,stk.build: New behavior (after this PR)
User->>stk.build: call stk.build.pyxtal(...) (removed)
stk.build-->>User: NameError / missing symbol (function removed from API)
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~20 minutes Possibly related PRs
Suggested labels
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Pre-merge checks and finishing touches✅ Passed checks (3 passed)
✨ Finishing touches🧪 Generate unit tests (beta)
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #405 +/- ##
==========================================
- Coverage 83.13% 82.89% -0.25%
==========================================
Files 25 24 -1
Lines 1862 1818 -44
==========================================
- Hits 1548 1507 -41
+ Misses 314 311 -3 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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📒 Files selected for processing (7)
.ci_support/environment-old.yml(1 hunks).ci_support/environment.yml(0 hunks)README.md(0 hunks)pyproject.toml(0 hunks)structuretoolkit/build/__init__.py(0 hunks)structuretoolkit/build/random.py(0 hunks)tests/test_pyxtal.py(0 hunks)
💤 Files with no reviewable changes (6)
- .ci_support/environment.yml
- pyproject.toml
- structuretoolkit/build/random.py
- structuretoolkit/build/init.py
- README.md
- tests/test_pyxtal.py
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- GitHub Check: unittest_matrix (macos-latest, 3.13, osx-64-py-3-13)
- GitHub Check: unittest_matrix (windows-latest, 3.13, win-64-py-3-13)
| - sqsgenerator =0.2 | ||
| - hatchling =1.27.0 | ||
| - hatch-vcs =0.4.0 | ||
| - hatch-vcs =0.4.0 |
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🛠️ Refactor suggestion | 🟠 Major
🧩 Analysis chain
Validate need and compatibility of hatch-vcs here
- Is hatch-vcs required in this runtime CI env, or only via pyproject [build-system] during build? If the latter, consider dropping it from this env to reduce solve surface.
- Please verify hatch-vcs 0.4.0 is available on conda-forge for all CI OS/Python combos and is compatible with hatchling 1.27.0.
🌐 Web query:
Is hatch-vcs version 0.4.0 available on conda-forge and which Python versions does it support? Also, what hatchling version range does hatch-vcs 0.4.0 require?
💡 Result:
Short answer:
-
Is 0.4.0 on conda-forge? No — conda-forge currently shows 0.5.0; version 0.4.0 is available on the Anaconda/main channel (anaconda.org). [1][2]
-
Python versions supported by hatch-vcs (per PyPI): Requires Python >= 3.9 (classifiers list support for 3.9, 3.10, 3.11, 3.12, 3.13). [1]
-
hatchling requirement for hatch-vcs 0.4.0: I don't yet have a definitive packaged metadata line for the hatchling version range for the 0.4.0 release — would you like me to fetch the 0.4.0 release metadata (pyproject/setup metadata) and return the exact hatchling version requirement?
Sources: PyPI project page for hatch-vcs; Anaconda / conda-forge package listings. [1] PyPI hatch-vcs page. [2] Anaconda / conda-forge package pages.
🏁 Script executed:
#!/bin/bash
curl -s https://pypi.org/pypi/hatch-vcs/0.4.0/json | jq '.info.requires_dist'Length of output: 51
Update or remove hatch-vcs in environment-old.yml
- hatch-vcs 0.4.0 isn’t on conda-forge (only 0.5.0); pinning 0.4.0 forces use of the default channel.
- If this env only needs hatch-vcs at build time (via pyproject[build-system]), drop it here; otherwise bump to 0.5.0 (requires Python ≥ 3.9 and hatchling ≥ 1.1.0, satisfied by hatchling 1.27.0).
🤖 Prompt for AI Agents
In .ci_support/environment-old.yml around line 18, the pinned package "hatch-vcs
=0.4.0" is not available on conda-forge and forces use of the default channel;
either remove the entry if hatch-vcs is only required at build time (declared in
pyproject[build-system]), or update the version to "hatch-vcs =0.5.0" and ensure
the environment specifies Python >=3.9 and hatchling >=1.1.0 (e.g., hatchling
1.27.0) so the newer hatch-vcs can be installed from conda-forge instead of
falling back to the default channel.
This lives now directly in the assyst package >0.8.1
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