Optimization - #1
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Code quality: - construct.py: extracted _write_positions helper (NumPy array → GROMACS position file) and _gmx_insert_cmd helper (centralises insert-molecules command building with optional -dr/-ip flags), replacing duplicated inline logic - actuate.py: shared folder/file path constants extracted from method-local variables to Actuate instance attributes; removes unused 're.A' import - simulate.py: Jinja2 analysis-script rendering refactored — single mol-metadata loop, has_fill derived once, template selection unified - Template scripts trimmed; dead sort.py template removed - tests/data/forhlr.sh: GROMACS module updated to 2024.3; GPU gres line added Tests: - Migrated test_simple.py (unittest) to pytest; split into test_unit.py and test_integration.py; new unit tests for Box API, Construct helpers Documentation: - docsrc/ RST sources migrated to MyST Markdown under docs/ - Sphinx theme updated to furo; sphinx-autoapi for API docs - Built HTML preserved under docs/v_old/ CI / tooling: - Added ruff lint and pip-audit security workflows - CI matrix extended to Python 3.10–3.13 Administrative: - setup.py: version 1.0.0, python_requires >=3.10, jinja2 unpinned
Drop Python 3.10 and 3.11 from CI matrix and classifiers; raise python_requires to >=3.12 in setup.py; update README and changelog.
Replace setup.py and MANIFEST.in with a single pyproject.toml; package-data absorbed into [tool.setuptools.package-data].
Switch all workflows from pip to uv (astral-sh/setup-uv@v5) for faster installs; remove requirements.txt (deps now declared solely in pyproject.toml); add explicit [tool.ruff] config to pyproject.toml.
Declare pytest and pytest-cov under [project.optional-dependencies] dev so the full test environment is installed with: pip install -e ".[dev]" CI updated to use the same extras group.
Replace manual venv setup with the dev install step so the README reflects the current pyproject.toml optional-dependencies setup.
Administrative section now reflects pyproject.toml and the new [project.optional-dependencies] dev group.
- Replace mutable defaults (area=[], box=[], kwargs_gmx={}) in add_mol
with None sentinels to prevent cross-call state sharing
- Modernize super(Benchmark, self).__init__() to bare super().__init__()
- Add encoding="utf-8" to all text-mode open() calls in analyze.py and
construct.py for cross-platform correctness
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- Remove tracked docs/v_old/ build snapshot (233 files); users should install the matching package version to get old docs - Remove cp -r v_old post-build hook from docs/Makefile - Remove v_old copy step from CI workflow - Enable MyST colon_fence extension so :::directives render correctly - Add _templates/base.html to default furo theme to light mode - Add custom style.css with brand colours (#c8860a) and dark-mode image fix (white background on transparent plots) - Wire templates_path, html_css_files, and myst_enable_extensions into conf.py - Clean up index.md: remove logo figure, remove v_old note, fix autoapi/index.html internal link suffix - Add docs/autoapi/ and docs/generated/ to .gitignore
- Convert docs/pics/pore_il.pdf and 2phase_il.pdf to SVG so images render in browsers (PDF is not supported as an <img> src in HTML) - Update simulation_complex.md and simulation_2ph.md figure directives to reference .svg files - Remove explicit width/height="100%" from logo_text.svg so furo can scale it by viewBox aspect ratio without clipping the top
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v1.0.0
Code quality
construct.py— extracted_write_positions(path, positions)helper: writes an (N, 3) NumPy position array to a GROMACS position file, replacing repeated inline loops; used for all molecule-insertion position filesconstruct.py— extracted_gmx_insert_cmd(folder_gro, file_box, mol, nmol, dr, pos_file)helper: centralises GROMACSinsert-moleculescommand construction with optional-drand-ipflags, eliminating duplicated string-building across pore/box/slit code pathsactuate.py— shared folder/file path constants (_gro/,_top/,_mdp/,box.gro,topol.top,index.ndx) extracted from local variables in each method to instance attributes onActuate.__init__; both_equilibrationand_simulationmethods now referenceself._folder_*/self._file_*actuate.py— removed unusedfrom re import Aimportsimulate.py— Jinja2 template rendering for analysis scripts (auto_dens.py/auto_dens_box.py) refactored: molecule metadata collected into a singlejinja2_dictloop;has_fillflag derived once instead of re-evaluated; template selection unified in a single branchauto_dens.pyandauto_dens_box.pytrimmed;sort.pytemplate removed (dead code)tests/data/forhlr.sh— GROMACS module updated from 2016.5 to 2024.3;#SBATCH --gresline added for GPU node supportTests
tests/test_simple.pyfrom unittest to pytesttest_unit.py(fast, no file I/O) andtest_integration.py(full output generation)test_unit.py— new unit tests:Boxgetter/setter round-trips,add_molvalidation,add_topolall types,Construct._write_positionsbyte-level output,Construct._gmx_insert_cmdall flag combinationsDocumentation
docsrc/todocs/; previous built HTML preserved atdocs/v_old/CI / tooling
lint.yml)security.yml)python_requiresbumped to>=3.12setup.py+MANIFEST.into a singlepyproject.toml(PEP 517/621);[tool.ruff]config addedpiptouv(astral-sh/setup-uv@v5);requirements.txtremoved (deps resolved viapyproject.toml)Administrative
pyproject.toml: version 1.0.0,requires-python = ">=3.12", author email updated, jinja2 unpinned;[project.optional-dependencies]dev group added (pytest,pytest-cov)