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Fix multi-review findings: Gibbs ranking, worker-death hang, fp64 energies, FIRE decoupling #173

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Fix multi-review findings: Gibbs ranking, worker-death hang, fp64 energies, FIRE decoupling

Fix multi-review findings: Gibbs ranking, worker-death hang, fp64 energies, FIRE decoupling #173

Workflow file for this run

.github/workflows/docs.yml at 9e79099
name: Documentation
on:
push:
branches: [main]
paths:
- 'docs/**'
- 'src/**'
- 'example/**'
- '.github/workflows/docs.yml'
pull_request:
paths:
- 'docs/**'
- 'src/**'
- 'example/**'
- '.github/workflows/docs.yml'
jobs:
build:
name: Build Documentation
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4
- name: Set up Python
uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
with:
python-version: "3.12"
- name: Install system dependencies
run: |
sudo apt-get update
sudo apt-get install -y pandoc
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -e .
pip install -r docs/requirements.txt
- name: Build Sphinx documentation
run: |
cd docs
make html
- name: Check for Sphinx warnings
run: |
cd docs
make html 2>&1 | tee build.log
# Fail if there are errors (warnings are ok)
if grep -q "ERROR" build.log; then
echo "Documentation build has errors!"
exit 1
fi
- name: Upload documentation artifact
uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
with:
name: documentation
path: docs/build/html/
retention-days: 7
linkcheck:
name: Check Links
runs-on: ubuntu-latest
needs: build
steps:
- uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4
- name: Set up Python
uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
with:
python-version: "3.12"
- name: Install system dependencies
run: |
sudo apt-get update
sudo apt-get install -y pandoc
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -e .
pip install -r docs/requirements.txt
- name: Check links
run: |
cd docs
make linkcheck || true # Don't fail on broken external links
continue-on-error: true
# Parses the notebooks. Does NOT run them.
#
# This job was called "Test Notebooks", ran a step called "Test notebooks
# execute", and installed `pytest nbmake` -- then never invoked nbmake. What
# it actually did, and still does, is assert each file is JSON with the two
# keys a notebook must have. Naming it accurately is the point of this job's
# current shape: the misleading version read as coverage nobody had.
#
# Executing them belongs in the slow tier, next to the model cache: every one
# of the 20 needs a neural network potential. Exactly one runs there for real
# (see `Execute the single-point notebook` in tests.yml). The limit is CPU
# time, measured rather than guessed: a single point over four records takes
# 5.9 s, the same four records through `opt_geometry` take over 600 s, and
# every other notebook either optimizes or runs `main()` end to end.
#
# So 19 are still parse-checked only, and an API change can invalidate them
# without turning anything red. The narrower guard that does cover all 20 is
# tests/test_notebook_properties.py, which fails when a notebook reads an SD
# property no Auto3D writer sets.
validate-notebooks:
name: Validate Notebooks (JSON only)
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4
- name: Set up Python
uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
with:
python-version: "3.12"
# No dependencies: the check is stdlib `json` over files on disk. It
# previously installed the package plus pytest and nbmake for a step that
# imported none of them.
- name: Validate notebook JSON
run: |
python -c "
import json, sys
from pathlib import Path
bad = []
notebooks = sorted(Path('example').glob('*.ipynb'))
if not notebooks:
sys.exit('no notebooks found under example/')
for nb in notebooks:
try:
data = json.loads(nb.read_text())
if 'cells' not in data or 'nbformat' not in data:
bad.append(f'{nb}: missing cells/nbformat')
else:
print(f'ok {nb} ({len(data[\"cells\"])} cells)')
except json.JSONDecodeError as e:
bad.append(f'{nb}: {e}')
if bad:
sys.exit('invalid notebooks:\n ' + '\n '.join(bad))
print(f'{len(notebooks)} notebooks parsed; none executed')
"