pybmds

.github/workflows/python-test-windows.yml

@@ -2,10 +2,10 @@ name: Python test windows
 
 on:
   workflow_dispatch:
-  pull_request:
-  push:
-    branches:
-      - main
+  # pull_request:
+  # push:
+  #   branches:
+  #     - main
 
 env:
   PYTHON_LIBRARY_DIR: $Env:CONDA\Lib\site-packages
@@ -32,7 +32,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
-      - name: set dependency direcory
+      - name: set dependency directory
         run: echo "DEPENDENCY_DIR=$HOME\github-deps" >> $env:GITHUB_ENV
       - name: restore github dependencies from cache
         id: cache-github
@@ -73,22 +73,18 @@ jobs:
           echo "EIGEN_DIR=${{ env.DEPENDENCY_DIR }}\eigen" >> $env:GITHUB_ENV
           echo "NLOPT_DIR=${{ env.DEPENDENCY_DIR }}\nlopt\src\api;${{ env.DEPENDENCY_DIR }}\nlopt\build\Release;${{ env.DEPENDENCY_DIR }}\nlopt\build" >> $env:GITHUB_ENV
           echo "GSL_DIR=${{ env.DEPENDENCY_DIR }}\gsl\build\Release;${{ env.DEPENDENCY_DIR }}\gsl\build" >> $env:GITHUB_ENV
-      - name: build bmds with cmake
-        shell: pwsh
-        run: |
-          mkdir build
-          cd build
-          cmake ..
-          cmake --build . --config Release
-      - name: Install dependencies
+      - name: Cache python build
+        uses: actions/cache@v4
+        with:
+          path: |
+            src/pybmds/bmdscore*
+          key: ${{ runner.os }}-${{ matrix.python-version }}-python-build
+      - name: Build package
         run: |
           python -m pip install -U pip wheel
-          python -m pip install -r requirements_dev.txt
-      - name: Build pybmds
-        run: |
-          python setup.py develop
+          python -m pip install -e ".[dev,docs]"
           stubgen -p pybmds.bmdscore -o src
-          ruff format src\pybmds\bmdscore.pyi
+          ruff format src/pybmds/bmdscore.pyi
           python setup.py bdist_wheel
       - uses: actions/upload-artifact@v4
         with:

.github/workflows/python-test.yml

@@ -3,9 +3,9 @@ name: Python test linux
 on:
   workflow_dispatch:
   pull_request:
-  push:
-    branches:
-      - main
+  # push:
+  #   branches:
+  #     - main
 
 jobs:
   test:
@@ -22,24 +22,42 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
-      - name: Install dependencies
+      - name: Cache build
+        uses: actions/cache@v4
+        with:
+          path: |
+            ./.egg-info/
+            ./pybmds.egg-info/
+            ./src/.egg-info/
+            ./src/pybmds.egg-info/
+            ./src/pybmds/bmdscore*
+          key: pybmds2-${{ runner.os }}-${{ matrix.python-version }}
+      - name: Install dependencies and build pybmds
         run: |
+          source ./tools/linux_ci.sh
           python -m pip install -U pip wheel
-          python -m pip install -r requirements_dev.txt
+          python -m pip install -e ".[dev,docs]"
+          stubgen -p pybmds.bmdscore -o src
+          ruff format src/pybmds/bmdscore.pyi
       - name: Check linting
         run: |
+          ls -laht
+          ls src -laht
           make lint
-      - name: Compile bmdscore and build pybmds
-        run: |
-          source ./tools/linux_ci.sh
-          make build
       - name: Test with pytest
         run: |
-          make test
-      - name: Build package
+          coverage run -m pytest
+          echo "# Python coverage report" >> $GITHUB_STEP_SUMMARY
+          coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
+      - name: Build documentation
         run: |
-          source ./tools/linux_ci.sh
-          make dist
+          make docs
       - uses: actions/upload-artifact@v4
         with:
-          path: ./dist/*.whl
+          path: |
+            ./docs/build/html
+            ./dist/*.whl
+            ./.egg-info/
+            ./pybmds.egg-info/
+            ./src/.egg-info/
+            ./src/pybmds.egg-info/

.gitignore

@@ -1,18 +1,10 @@
-*.html
-*.docx
 *.o
-# *.tar.gz
 *.a
 *.la
 *.so
-*.Rproj.user
-*.tgz
-.Rproj.user
 .DS_Store
-*.o
 *.so
-.Rhistory
-build/
+
 create_dll_compile.bash
 
 # python
@@ -21,11 +13,13 @@ create_dll_compile.bash
 .ipynb_checkpoints/
 .mypy_cache/
 .pytest_cache/
+.ruff_cache/
 .vscode/
+build/
 dist/
 htmlcov/
 venv/
 *.log
 *.py[cod]
-.coverage
+.coverage/
 .env

MANIFEST.in

@@ -1,3 +1,3 @@
-recursive-include * *.pyi
+recursive-include * *.pyi *.json *.csv *.docx
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

Makefile

@@ -1,4 +1,4 @@
-.PHONY: clean lint format test coverage build develop
+.PHONY: clean lint format test coverage build dist docs docs-clean
 .DEFAULT_GOAL := help
 
 define PRINT_HELP_PYSCRIPT
@@ -40,3 +40,10 @@ build: ## Rebuild in development environment
 dist: ## Build wheel package for distribution
 	@python setup.py bdist_wheel
 	@ls -lh dist
+
+docs: ## Build documentation {html}
+	sphinx-build -W -b html docs/source docs/build/html
+	@echo "HTML: \"docs/build/html/index.html\""
+
+docs-clean: ## Clean documentation
+	@$(MAKE) -C docs clean

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/_static/css/style.css

@@ -0,0 +1,7 @@
+code {
+    font-family: Consolas, Menlo, Monaco, Lucida Console, Liberation Mono, DejaVu Sans Mono, Bitstream Vera Sans Mono, Courier New, monospace, serif;
+}
+
+.bd-page-width {
+    max-width: 100%;
+}

docs/source/conf.py

@@ -0,0 +1,49 @@
+project = "pybmds"
+copyright = "Public Domain"
+author = "U.S. EPA"
+
+extensions = ["myst_nb"]
+souce_suffix = {
+    ".md": "markdown",
+    ".rst": "restructuredtext",
+}
+templates_path = ["_templates"]
+
+exclude_patterns = []
+
+# HTML settings
+html_theme = "pydata_sphinx_theme"
+html_static_path = ["_static"]
+html_css_files = ["css/style.css"]
+html_sidebars = {"**": ["globaltoc.html"]}
+html_theme_options = {
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/USEPA/bmds-private",
+            "icon": "fa-brands fa-github",
+            "type": "fontawesome",
+        },
+        {
+            "name": "U.S. Environmental Protection Agency",
+            "url": "https://epa.gov/bmds",
+            "icon": "_static/img/epa_logo.png",
+            "type": "local",
+        },
+    ],
+    "use_edit_page_button": False,
+    "show_toc_level": 2,
+    "navbar_end": [
+        "theme-switcher.html",
+        "navbar-icon-links.html",
+    ],
+}
+
+# Latex / PDF settings
+latex_elements = {
+    "printindex": "",
+    "sphinxsetup": "hmargin={0.9in,0.9in}, vmargin={0.9in,0.9in}, marginpar=1.0in",
+    "papersize": "letterpaper",
+    "pointsize": "10pt",
+    "figure_align": "htbp",
+}

docs/source/index.md

@@ -0,0 +1,23 @@
+---
+html_theme.sidebar_secondary.remove: true
+---
+
+# pybmds
+
+A Python package for executing the U.S. EPA Benchmark Dose Modeling Software (BMDS).
+
+## User's Guide
+
+```{toctree}
+:maxdepth: 2
+
+reference/index
+```
+
+## Recipes
+
+```{toctree}
+:maxdepth: 2
+
+recipes/index
+```