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Add orthonym plugin - #72
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Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
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🔐 Plugin Security Scan ResultsScanned 3 plugin(s). 🔐 Security Scan:
|
| Metric | Value |
|---|---|
| Python files | 5 |
| Total Python lines | 239 |
| Plugin type | pypkg |
| Change type | modified |
Python files
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/__init__.py(36 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/mx2.py(43 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/nanotube.py(42 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/ribbon.py(40 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/slab.py(78 lines)
🔍 Bandit (Python Security Linter)
✅ No issues found.
🔎 Dangerous Pattern Check
Critical Patterns
✅ No critical patterns found.
Patterns Requiring Review
🟡 os.remove — file deletion
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/nanotube.py:32: os.remove(name)
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/slab.py:69: os.remove(name)
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/ribbon.py:30: os.remove(name)
🟡 tempfile — temp file creation
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/nanotube.py:9:import tempfile
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/nanotube.py:25: fd, name = tempfile.mkstemp(".xyz")
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/slab.py:9:import tempfile
🟡 file I/O — check paths are safe
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/nanotube.py:30: with open(name) as f:
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/slab.py:67: with open(name) as f:
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/ribbon.py:28: with open(name) as f:
🛡️ Semgrep Analysis
Found 1 issue(s):
| Severity | Count |
|---|---|
| ℹ️ INFO | 1 |
Issue details
- [INFO]
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_build_ase/__init__.py:36- Avogadro plugin scripts communicate via stdout (JSON). Use sys.stderr.write() for progress messages, not print().
(_this..github.avogadro-stderr-for-progress)
📦 Dependency Audit
Dependency files:
/home/runner/work/plugins/plugins/plugin-src/pyproject.toml
Dependency Source Check
✅ No non-PyPI dependency sources detected in static dependency files.
pip-audit
✅ No known vulnerabilities in dependencies.
🔐 Security Scan: generators
Repository: https://github.com/OpenChemistry/avogenerators.git
Commit: 16a0e73fbeea5dbeb41598326190d82c790f5a31
Change type: modified
📊 Code Overview
| Metric | Value |
|---|---|
| Python files | 29 |
| Total Python lines | 5621 |
| Plugin type | pypkg |
| Change type | modified |
Python files
/home/runner/work/plugins/plugins/plugin-src/scripts/write_orca_options.py(467 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/__init__.py(54 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/dalton/dalton.py(233 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/gamessuk/gamessuk.py(109 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/gaussian/gaussian.py(101 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/molpro/molpro.py(123 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/mopac/mopac.py(147 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/nwchem/nwchem.py(125 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/__init__.py(325 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/basis_sets.py(629 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/dft.py(240 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/implicit_solvation.py(365 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/input_blocks/__init__.py(5 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/input_blocks/basis.py(74 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/input_blocks/block_base.py(176 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/input_blocks/elprop.py(39 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/input_blocks/method.py(47 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/input_blocks/option_extras.py(478 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/input_blocks/scf.py(97 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/libxc.py(859 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/simple_keywords.py(172 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/wft.py(58 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/psi4/psi4.py(77 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/pyscf/pyscf.py(110 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/qchem/qchem.py(93 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/terachem/terachem.py(100 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/utilities/__init__.py(1 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/utilities/elements.py(143 lines)/home/runner/work/plugins/plugins/plugin-src/tests/inputgeneratortest.py(174 lines)
🔍 Bandit (Python Security Linter)
✅ No issues found.
🔎 Dangerous Pattern Check
Critical Patterns
🔴 compile() — dynamic code compilation
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/basis_sets.py:565: pople_pattern = re.compile(
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/basis_sets.py:569: def2_pattern = re.compile(
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/basis_sets.py:573: jensen_pattern = re.compile(
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/basis_sets.py:577: cc_pattern = re.compile(
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/orca/basis_sets.py:581: relativistic_pattern = re.compile(
Patterns Requiring Review
🟡 file I/O — check paths are safe
/home/runner/work/plugins/plugins/plugin-src/scripts/write_orca_options.py:466: with open(orca_toml, "w") as orca:
🛡️ Semgrep Analysis
Found 1 issue(s):
| Severity | Count |
|---|---|
| ℹ️ INFO | 1 |
Issue details
- [INFO]
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_generators/__init__.py:54- Avogadro plugin scripts communicate via stdout (JSON). Use sys.stderr.write() for progress messages, not print().
(_this..github.avogadro-stderr-for-progress)
📦 Dependency Audit
Dependency files:
/home/runner/work/plugins/plugins/plugin-src/pyproject.toml
Dependency Source Check
✅ No non-PyPI dependency sources detected in static dependency files.
pip-audit
✅ No known vulnerabilities in dependencies.
🔐 Security Scan: orthonym
Repository: https://github.com/ghutchis/avogadro-orthonym
Commit: 349b835096abbb5ba76d6a3895c5cacbf08b0abb
Change type: added
📊 Code Overview
| Metric | Value |
|---|---|
| Python files | 3 |
| Total Python lines | 173 |
| Plugin type | pypkg |
| Change type | added |
Python files
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_orthonym/__init__.py(35 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_orthonym/naming.py(117 lines)/home/runner/work/plugins/plugins/plugin-src/src/avogadro_orthonym/run.py(21 lines)
🔍 Bandit (Python Security Linter)
✅ No issues found.
🔎 Dangerous Pattern Check
Critical Patterns
✅ No critical patterns found.
Patterns Requiring Review
✅ No review-worthy patterns found.
🛡️ Semgrep Analysis
Found 2 issue(s):
| Severity | Count |
|---|---|
| ℹ️ INFO | 2 |
Issue details
- [INFO]
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_orthonym/__init__.py:34- Avogadro plugin scripts communicate via stdout (JSON). Use sys.stderr.write() for progress messages, not print().
(_this..github.avogadro-stderr-for-progress) - [INFO]
/home/runner/work/plugins/plugins/plugin-src/src/avogadro_orthonym/run.py:21- Avogadro plugin scripts communicate via stdout (JSON). Use sys.stderr.write() for progress messages, not print().
(_this..github.avogadro-stderr-for-progress)
📦 Dependency Audit
Dependency files:
/home/runner/work/plugins/plugins/plugin-src/pyproject.toml
Dependency Source Check
✅ No non-PyPI dependency sources detected in static dependency files.
pip-audit
✅ No known vulnerabilities in dependencies.
Note: Automated scans supplement but do not replace manual code review.
Please examine the flagged items before approving this PR.
Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
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