pymstm 1.0.0__tar.gz

pymstm-1.0.0/.github/workflows/publish.yml

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+name: Continuous Delivery
+
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  testing:
+    uses: ./.github/workflows/test.yml
+
+  determine-version:
+    name: Determine next version (no side effects yet)
+    runs-on: ubuntu-latest
+    needs:
+      - testing
+    outputs:
+      released: ${{ steps.compute.outputs.released }}
+      version: ${{ steps.compute.outputs.version }}
+    steps:
+      - name: Setup | Checkout Repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup | Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Setup | Install python-semantic-release only
+        # --no-install-project: this job only ever calls `semantic-release
+        # version --print`, a pure dry run that never touches
+        # build_command -- unlike the real `release` job below, it never
+        # needs pymstm itself built, so it can skip gfortran entirely
+        # (confirmed locally: --print works fine against just the `build`
+        # extra's own deps).
+        run: uv sync --extra build --no-install-project
+
+      - name: Evaluate | Compute next version without tagging
+        id: compute
+        # `uv run <cmd>` implicitly re-syncs the venv first by default,
+        # regardless of an earlier separate `uv sync --no-install-project`
+        # -- that implicit sync doesn't inherit --no-install-project, so
+        # it tries to build/install pymstm itself again, which needs
+        # gfortran (deliberately not installed in this job, see the
+        # step above). That failure was hidden by this step's own
+        # `2>/dev/null` on the semantic-release line, so it looked like
+        # total silence rather than a build error -- confirmed locally:
+        # reproducible without --no-sync, gone with it. --no-sync trusts
+        # the venv exactly as the earlier `uv sync --no-install-project`
+        # left it.
+        run: |
+          CURRENT="$(python3 -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['version'])")"
+          NEXT="$(uv run --no-sync semantic-release version --print 2>/dev/null)"
+          echo "Current version: $CURRENT"
+          echo "Next version:    $NEXT"
+          echo "version=$NEXT" >> "$GITHUB_OUTPUT"
+          if [ "$NEXT" != "$CURRENT" ]; then
+            echo "released=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "released=false" >> "$GITHUB_OUTPUT"
+          fi
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    needs:
+      - determine-version
+    if: needs.determine-version.outputs.released == 'true'
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Linux only for now, deliberately -- macos-13/macos-14 legs
+        # both failed on the first real release run (macOS: Homebrew's
+        # latest gfortran links libgfortran/libquadmath requiring macOS
+        # 14+, tripping delocate-wheel's deployment-target check; see
+        # the CIBW_ENVIRONMENT_MACOS comment below for the fix, prepared
+        # but not yet re-verified end to end) -- narrowing to Linux
+        # avoids burning macOS runner minutes on repeated iterations
+        # while that's still being sorted out. Windows needs a whole
+        # separate MinGW/gfortran toolchain story, and Linux aarch64
+        # would mean QEMU-emulated compiles (slow, fragile for a first
+        # pass) -- both left as a follow-up too.
+        os: [ubuntu-latest]
+
+    steps:
+      - name: Setup | Checkout Repository
+        # No tag exists yet at this point -- that's the whole point of
+        # this reordering (see determine-version/release comments below).
+        # github.sha is fixed for the entire workflow run, so this and
+        # every other job here build from the exact same commit
+        # determine-version already computed a version for for.
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Setup | Stamp the version determine-version computed
+        # No tag/commit exists for this version yet -- release (below)
+        # only creates one once these wheels are confirmed good. Patch
+        # the version strings locally (uncommitted, this checkout is
+        # thrown away after the job) purely so the wheel filenames and
+        # METADATA carry the version that *will* be tagged, instead of
+        # whatever version.toml/`__init__.py` still say on plain main.
+        run: |
+          sed -i 's/^version = ".*"/version = "${{ needs.determine-version.outputs.version }}"/' pyproject.toml
+          sed -i 's/^__version__ = ".*"/__version__ = "${{ needs.determine-version.outputs.version }}"/' src/pymstm/__init__.py
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.21
+        env:
+          # cp39/cp310 dropped for good (see pyproject.toml's
+          # requires-python comment) -- two independent, real cibuildwheel
+          # failures below cp311: cp39 segfaulted (SIGSEGV) deep in a
+          # two-sphere solve (ruled out compiler version and f2py's
+          # legacy distutils backend as causes, both survived); cp310
+          # crashed earlier, during the f2py build itself (KeyError:
+          # 'void' in numpy's own crackfortran). Both are the only builds
+          # resolving a numpy old enough to hit these, and both Python
+          # versions are in their final year of upstream support anyway
+          # -- not worth separately chasing two legacy-numpy-version bugs
+          # for them.
+          # PyPy/musllinux skipped -- Fortran extensions aren't a realistic
+          # target there and it doubles build time for no real benefit.
+          CIBW_BUILD: "cp311-* cp312-* cp313-*"
+          CIBW_SKIP: "*-musllinux*"
+          # cibuildwheel's own default architecture set for a Linux
+          # x86_64 runner also includes i686 (32-bit) -- confirmed via a
+          # real run: cp311/cp312/cp313 x86_64 wheels all built cleanly,
+          # then it moved on to cp311-manylinux_i686, where numpy has no
+          # prebuilt wheel, forcing a ~3+ minute from-source numpy build
+          # just to get started. Nobody needs 32-bit wheels for this.
+          CIBW_ARCHS_LINUX: "x86_64"
+          CIBW_ARCHS_MACOS: "auto"
+          CIBW_BUILD_VERBOSITY: "1"
+          # manylinux images are AlmaLinux/CentOS-based -- gcc-gfortran is
+          # in the base repos on both manylinux2014 and manylinux_2_28.
+          CIBW_BEFORE_ALL_LINUX: "yum install -y gcc-gfortran"
+          # No CIBW_BEFORE_ALL_MACOS `brew install gcc` -- GitHub's macOS
+          # runner images ship gfortran-13/14/15 pre-installed (see
+          # actions/runner-images' own macos-14-arm64-Readme.md), and
+          # NumPy's own wheels.yml uses exactly this pinned-version
+          # approach (`FC=gfortran-13`, no brew install at all) rather
+          # than installing Homebrew's *latest* gcc fresh. That distinction
+          # matters here, not just for speed: the first real run's macOS
+          # legs failed because a freshly `brew install`ed gcc links
+          # libgfortran/libquadmath requiring macOS 14+, which
+          # delocate-wheel then refuses to repair for an 11.0-targeted
+          # wheel -- the older, pre-installed gfortran-13 doesn't have
+          # that mismatch. Not yet re-verified end to end (matrix is
+          # Linux-only above until that's settled) -- prepared so macOS
+          # can be re-added with a real fix instead of the guess that
+          # failed the first time.
+          CIBW_ENVIRONMENT_MACOS: "FC=gfortran-13"
+          # Smoke test: actually import and run a tiny solve inside the
+          # built wheel (in an isolated venv cibuildwheel creates), not
+          # just an import check -- catches a wheel that imports fine but
+          # is missing/mislinked its compiled extension.
+          #
+          # `import pymstm;` MUST stay on the same source line as the
+          # opening quote below -- YAML's `>` folding replaces every line
+          # break with a single space, so a break right after `python -c
+          # "` folds into a *leading space inside the quoted string*
+          # (`python -c " import pymstm; ...`), and `python -c` raises
+          # IndentationError: unexpected indent on any leading whitespace
+          # in top-level exec'd code. Confirmed via a real failed run.
+          CIBW_TEST_COMMAND: >
+            python -c "import pymstm;
+            m = pymstm.MSTM();
+            m.set_spheres(radii=[1.0,1.0], positions=[[-1.5,0,0],[1.5,0,0]], orders=[6,6], ref_re=[1.5,1.5], ref_im=[0.01,0.01]);
+            m.set_medium_ref(1.0, 0.0);
+            m.set_incident(alpha_deg=0.0, beta_deg=0.0);
+            m.set_solver_params(eps=1e-3, max_iter=200);
+            m.set_verbose(False);
+            m.prepare();
+            r = m.solve();
+            m.finalize();
+            assert r['qext_tot'] > 0"
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  release:
+    name: Tag and create the GitHub Release (wheels already verified)
+    runs-on: ubuntu-latest
+    needs:
+      - determine-version
+      - build_wheels
+
+    concurrency:
+      group: ${{ github.workflow }}-release-${{ github.ref_name }}
+      cancel-in-progress: false
+    permissions:
+      contents: write
+
+    outputs:
+      released: ${{ steps.release.outputs.released }}
+      tag: ${{ steps.release.outputs.tag }}
+      version: ${{ steps.release.outputs.version }}
+
+    steps:
+      - name: Setup | Checkout Repository on Release Branch
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.ref_name }}
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Setup | Force release branch to be at workflow sha
+        run: git reset --hard ${{ github.sha }}
+
+      - name: Setup | Install gfortran
+        # `uv sync` also builds/installs pymstm itself (not just the
+        # `build` extra's own deps), and pyproject.toml's
+        # no-build-isolation-package = ["pymstm"] means that build needs
+        # gfortran and meson-python already present in *this* venv --
+        # same reason test.yml installs it before syncing.
+        run: sudo apt-get update && sudo apt-get install -y gfortran
+
+      - name: Setup | Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Setup | Install build dependencies
+        # `build-ext` for meson/ninja/meson-python (needed to build
+        # pymstm itself, see gfortran step above) without pytest/
+        # pytest-cov along for the ride -- this job never runs the test
+        # suite, that's test.yml's job. `build` for
+        # python-semantic-release.
+        run: uv sync --extra build --extra build-ext
+
+      - name: Evaluate | Verify upstream has NOT changed
+        # Wheels take a while to build -- more important here than it
+        # was before this job moved to run last, since there's now a
+        # longer window for main to have drifted between our checkout
+        # above and the push below.
+        shell: bash
+        run: |
+          set +o pipefail
+
+          UPSTREAM_BRANCH_NAME="$(git status -sb | head -n 1 | cut -d' ' -f2 | grep -E '\.{3}' | cut -d'.' -f4)"
+          printf '%s\n' "Upstream branch name: $UPSTREAM_BRANCH_NAME"
+
+          set -o pipefail
+
+          if [ -z "$UPSTREAM_BRANCH_NAME" ]; then
+              printf >&2 '%s\n' "::error::Unable to determine upstream branch name!"
+              exit 1
+          fi
+
+          git fetch "${UPSTREAM_BRANCH_NAME%%/*}"
+
+          if ! UPSTREAM_SHA="$(git rev-parse "$UPSTREAM_BRANCH_NAME")"; then
+              printf >&2 '%s\n' "::error::Unable to determine upstream branch sha!"
+              exit 1
+          fi
+
+          HEAD_SHA="$(git rev-parse HEAD)"
+
+          if [ "$HEAD_SHA" != "$UPSTREAM_SHA" ]; then
+              printf >&2 '%s\n' "[HEAD SHA] $HEAD_SHA != $UPSTREAM_SHA [UPSTREAM SHA]"
+              printf >&2 '%s\n' "::error::Upstream has changed, aborting release..."
+              exit 1
+          fi
+
+          printf '%s\n' "Verified upstream branch has not changed, continuing with release..."
+
+      - name: Action | Semantic Version Release
+        # Bumps pyproject.toml/src/pymstm/__init__.py's version, builds
+        # the sdist (build_command below), commits, tags, pushes, and
+        # creates the GitHub Release (sdist attached as an asset) --
+        # only reached after build_wheels has already succeeded, so
+        # (unlike the very first version of this pipeline) a tag/release
+        # only ever gets created once we already know real wheels exist
+        # for it. Recomputes the same version determine-version already
+        # printed (nothing has changed the commit history since), so the
+        # wheels build_wheels already built and stamped stay correct.
+        id: release
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          git config user.name "github-actions"
+          git config user.email "actions@users.noreply.github.com"
+          uv run semantic-release -v version
+
+      - name: Publish | Upload sdist to GitHub Release Assets
+        if: steps.release.outputs.released == 'true'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: uv run semantic-release publish
+
+  publish:
+    name: Publish to PyPI and attach wheels to the GitHub Release
+    needs:
+      - release
+      - build_wheels
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pymstm
+    permissions:
+      id-token: write
+      contents: write
+
+    steps:
+      - name: Download all wheels
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - name: Download sdist from the GitHub Release
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh release download ${{ needs.release.outputs.tag }} \
+            --repo ${{ github.repository }} \
+            --pattern '*.tar.gz' \
+            --dir dist
+
+      - name: Publish | Upload wheels to GitHub Release Assets
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh release upload ${{ needs.release.outputs.tag }} dist/*.whl \
+            --repo ${{ github.repository }} \
+            --clobber
+
+      - name: Setup | Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Publish | Publish to PyPI
+        run: uv publish dist/*

pymstm-1.0.0/.github/workflows/test.yml

@@ -0,0 +1,49 @@
+name: Testing
+on:
+  workflow_call:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches: [main]
+jobs:
+  unittest:
+    name: PyTest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: Install gfortran
+        # Needed for `uv sync` to build the f2py extension (meson-python
+        # drives numpy.f2py -c against external/mstm/, see meson.build).
+        run: sudo apt-get update && sudo apt-get install -y gfortran
+      - name: Install uv
+        id: setup-python
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+      - name: Install dependencies (builds the f2py extension)
+        run: uv sync --extra dev
+      - name: Cache | MSTM CLI reference binary
+        id: cache-cli
+        uses: actions/cache@v4
+        with:
+          path: build/mstm
+          # external/mstm is a git submodule pinned to a fixed commit in
+          # .gitmodules -- it essentially never changes between runs, so
+          # hashing its checked-out content (plus the Makefile that
+          # compiles it) is a reliable "did the CLI's own inputs change"
+          # key, letting most runs skip recompiling it entirely.
+          key: ${{ runner.os }}-mstm-cli-${{ hashFiles('external/mstm/december2023/**', 'Makefile') }}
+
+      - name: Build the standalone MSTM CLI reference binary
+        # test_compatibility.py skips itself if this isn't present -- but
+        # we want that cross-check to actually run in CI, not silently
+        # skip. Skipped entirely on a cache hit above -- `make`'s own
+        # mtime-based staleness check isn't reliable here since a fresh
+        # checkout + cache restore don't produce trustworthy relative
+        # timestamps between sources and the cached binary.
+        if: steps.cache-cli.outputs.cache-hit != 'true'
+        run: make cli
+      - name: Test with pytest
+        run: uv run pytest tests/ -v

pymstm-1.0.0/.gitignore

@@ -0,0 +1,304 @@
+build/
+src/pymstm/libmstm.so
+
+## Devenv
+.devenv*
+devenv.local.nix
+devenv.local.yaml
+
+# direnv
+.direnv
+
+# pre-commit
+.pre-commit-config.yaml
+
+## Python
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+*.lcov
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+# Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+# poetry.lock
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi/*
+!.pixi/config.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule*
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#   and can be added to the global gitignore or merged into this file.  For a more nuclear
+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+# .idea/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer,
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+# Temporary file for partial code execution
+tempCodeRunnerFile.py
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml
+
+## C++
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Linker files
+*.ilk
+
+# Debugger Files
+*.pdb
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+*.so.*
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Build directories
+build/
+Build/
+build-*/
+
+# CMake generated files
+CMakeFiles/
+CMakeCache.txt
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+
+# Temporary files
+*.tmp
+*.log
+*.bak
+*.swp
+
+# vcpkg
+vcpkg_installed/
+
+# debug information files
+*.dwo
+
+# test output & cache
+Testing/
+.cache/

pymstm-1.0.0/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "external/mstm"]
+	path = external/mstm
+	url = https://github.com/dmckwski/MSTM