New build system that includes smelib

.github/workflows/python-app.yml

@@ -1,127 +1,111 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Python application
- 
+
 on:
   push:
-    branches: [master]
-  pull_request:
-    branches: [master]
+    tags: ["v*"]
+  workflow_dispatch:
 
 jobs:
-  build:
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-15, macos-13]   # macos-15/14=arm64，macos-13=x86_64
-        py: ['3.9','3.10','3.11','3.12','3.13']
-    name: py${{ matrix.py }} on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    # strategy:
-    #   fail-fast: false
-    #   matrix:
-    #     include:
-    #       - name: ubuntu
-    #         runs_on: ubuntu-latest
-    #       - name: macos-intel
-    #         runs_on: macos-13
-    #       - name: macos-apple-silicon
-    #         runs_on: macos-15
-    # runs-on: ${{ matrix.runs_on }}
-    environment: release
-    permissions:
-      contents: write
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
+        os: [ubuntu-22.04, macos-14, windows-2022]
 
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 0
-      # - name: Install autoconf and gfortran (libgfortran) on macOS (GCC route)
-      #   if: ${{ matrix.name == 'macos-intel' || matrix.name == 'macos-apple-silicon' }}
-      #   run: |
-      #     brew update
-      #     # brew install autoconf automake libtool gcc
-      #     # brew link --force gcc
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.py }}
-        # run: |
-        #   python -V
-        #   python -c "import sys, sysconfig; print(sys.executable); print(sysconfig.get_platform())"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          # pip install flake8 pytest
-          python -m pip install .[dev]
-          # python setup.py version
-          pip install .
-
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-      - name: Test with pytest
-        run: pytest
-
-      - name: GitHub Tag
-        if: github.event_name != 'pull_request' && matrix.os == 'ubuntu-latest' && matrix.py == '3.12'
-        id: tag_release
-        uses: mathieudutour/github-tag-action@v6.2
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          submodules: recursive
 
-      - uses: actions/checkout@v4
-        if: github.event_name != 'pull_request' && matrix.os == 'ubuntu-latest' && matrix.py == '3.12'
+      - name: Install MSYS2 (Windows)
+        if: runner.os == 'Windows'
+        uses: msys2/setup-msys2@v2
         with:
-          ref: ${{ steps.tag_release.outputs.new_tag }}
-          clean: false
-
-      - name: Build Wheel
-        if: matrix.os == 'ubuntu-latest' && matrix.py == '3.12'
-        # run: pip install wheel && python setup.py sdist bdist_wheel
-        run: |
-          python -m pip install -U pip
-          python -m pip install -U wheel build
-          python -m build
-
-      - name: Zip data
-        if: matrix.os == 'ubuntu-latest' && matrix.py == '3.12'
-        id: zip_data
-        run: zip -r dist dist && echo "::set-output name=filename::dist.zip"
-
-      - name: Create Release
-        if: github.event_name != 'pull_request' && matrix.os == 'ubuntu-latest' && matrix.py == '3.12'
-        id: create_release
-        uses: actions/create-release@v1
+          msystem: MINGW64
+          update: false
+          install: mingw-w64-x86_64-gcc-fortran mingw-w64-x86_64-ninja
+
+      - name: Add MSYS2 to PATH (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: echo "C:\msys64\mingw64\bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.22
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
+          CIBW_BUILD_VERBOSITY: 1
+          CIBW_ENVIRONMENT_WINDOWS: 'FC=gfortran CC=gcc CXX=g++ CMAKE_GENERATOR=Ninja'
+
+      - uses: actions/upload-artifact@v4
         with:
-          tag_name: ${{ steps.tag_release.outputs.new_tag }}
-          release_name: Release ${{ steps.tag_release.outputs.new_tag }}
-          draft: false
-          prerelease: false
-
-      - name: Upload Release Asset
-        if: github.event_name != 'pull_request' && matrix.os == 'ubuntu-latest' && matrix.py == '3.12'
-        id: upload-release-asset
-        uses: actions/upload-release-asset@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  publish:
+    name: Publish to PyPI
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pysme-astro
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - uses: actions/download-artifact@v4
         with:
-          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
-          asset_path: ./dist.zip
-          asset_name: dist.zip
-          asset_content_type: application/zip
+          name: sdist
+          path: dist
 
-      - name: Publish a Python distribution to PyPI
-        if: github.event_name != 'pull_request' && matrix.os == 'ubuntu-latest' && matrix.py == '3.12'
+      - name: Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-        # with:
-        #   user: __token__
-        #   password: ${{ secrets.pypi_password }}
+
+  release:
+    name: Create GitHub Release
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+      - name: Create GitHub Release
+        run: gh release create ${{ github.ref_name }} dist/* --repo ${{ github.repository }} --title "${{ github.ref_name }}" --prerelease
+        env:
+          GH_TOKEN: ${{ github.token }}

.gitignore

@@ -164,4 +164,7 @@ paper/*.html
 local/
 atmo_ml/
 
-src/pysme/lib
+# Frontend build artifacts (webgui branch)
+src/pysme/gui/frontend/node_modules/
+src/pysme/gui/frontend/dist/
+docs/websme-reference/

.gitmodules

@@ -1,4 +1,3 @@
 [submodule "smelib"]
 	path = smelib
-	url = https://github.com/AWehrhahn/SMElib
-	update = checkout
+	url = https://github.com/MingjieJian/SMElib.git

CLAUDE.md

@@ -0,0 +1,130 @@
+# PySME Development Guide
+
+## Quick Start
+
+```bash
+uv sync                    # Install in dev mode (compiles native code)
+uv run pytest              # Run tests
+```
+
+## Project Overview
+
+PySME (Spectroscopy Made Easy) is a Python package for stellar spectroscopy analysis. It includes a native library (`libsme`) written in Fortran/C++ that handles the computationally intensive spectral synthesis.
+
+## Build System
+
+Uses **scikit-build-core** with CMake to compile the native extension:
+- `smelib/` - Git submodule containing Fortran/C++ source (from MingjieJian/SMElib)
+- `CMakeLists.txt` - Builds `libsme` shared library and `_smelib` Python extension
+- `pyproject.toml` - Build configuration and cibuildwheel settings
+
+The native code is compiled at build time (not runtime), producing platform-specific wheels.
+
+### smelib Submodule
+
+The `smelib/` directory is a git submodule pointing to `ivh/SMElib` (forked from `MingjieJian/SMElib`, which is the active upstream). The original repo `AWehrhahn/SMElib` is abandoned.
+
+PySME's CMakeLists.txt compiles these smelib sources:
+- `smelib/src/sme/sme_synth_faster.cpp` - main C++ synthesis code
+- `smelib/src/sme/*.f`, `smelib/src/eos/*.f` - Fortran routines
+- `smelib/pymodule/_smelib.cpp` - Python extension wrapper
+- `smelib/src/data/` - runtime data files
+
+Into:
+- `libsme.so/.dylib/.dll` - shared library with Fortran routines
+- `_smelib` - Python extension module
+
+#### smelib cleanup
+
+The fork has been cleaned of files not needed by PySME:
+- Removed: CI configs (`.github/`, `.travis.yml`, `travis/`), test suite, debug scripts, backup files
+- Kept: autotools build system (`bootstrap`, `configure.ac`, `Makefile.am`, etc.) and `pymodule/smelib.py` for standalone/IDL use
+
+#### Build system history
+
+**Old approach** (before current build system):
+1. `pip install pysme-astro` installed pure Python
+2. At runtime, PySME detected platform and downloaded pre-built `libsme` binaries from SMElib GitHub releases
+3. Those releases were built by SMElib's own CI workflows (now removed from our fork)
+
+**Current approach**:
+1. `pip install pysme-astro` installs a wheel with compiled `libsme` included
+2. Compilation happens at wheel build time via PySME's CI (CMake/scikit-build-core)
+3. No runtime downloads needed
+
+The standalone SMElib releases (from MingjieJian/SMElib) are still produced for IDL users who use SME without Python.
+
+## CI/CD
+
+GitHub Actions workflow (`.github/workflows/python-app.yml`):
+- Triggers on version tags (`v*`) or manual dispatch
+- Builds wheels for:
+  - Linux x86_64 (manylinux)
+  - macOS arm64
+  - Windows AMD64
+- Publishes to PyPI via trusted publishing (OIDC)
+
+### Platform-specific notes
+
+- **macOS**: Uses Homebrew gcc/gfortran-14, MACOSX_DEPLOYMENT_TARGET=14.0
+- **Windows**: Uses MSYS2 MinGW gfortran, Ninja generator, custom wheel repair script
+- **Linux**: Uses manylinux container with gfortran
+
+## Release Process
+
+1. Update version in `pyproject.toml`:
+   ```
+   version = "X.Y.Z"      # stable release
+   version = "X.Y.ZaN"    # alpha (not installed by default)
+   version = "X.Y.ZbN"    # beta
+   version = "X.Y.ZrcN"   # release candidate
+   ```
+
+2. Sync lockfile and commit:
+   ```bash
+   uv sync
+   git add pyproject.toml uv.lock
+   git commit -m "Release vX.Y.Z"
+   git tag vX.Y.Z
+   git push && git push origin vX.Y.Z
+   ```
+
+3. GitHub Actions builds wheels and publishes to PyPI automatically.
+
+4. If PyPI publish fails (permissions), create GitHub release manually:
+   ```bash
+   gh run download <run-id> --dir release-artifacts
+   gh release create vX.Y.Z --prerelease --title "vX.Y.Z" \
+     release-artifacts/sdist/* release-artifacts/wheels-*/*
+   ```
+
+## Key Files
+
+- `src/pysme/` - Main Python package
+- `src/pysme/smelib/` - Native library interface
+- `smelib/` - Fortran/C++ source (submodule)
+- `CMakeLists.txt` - Native build configuration
+- `pyproject.toml` - Package metadata, build config, cibuildwheel config
+
+## Dependencies
+
+Runtime: numpy, scipy, pandas, astropy, tqdm, emcee, plotly, matplotlib, etc.
+Build: scikit-build-core, numpy, CMake, Fortran compiler (gfortran)
+
+## Testing
+
+```bash
+uv run pytest                           # Run all tests
+uv run python -c "from pysme.sme import SME_Structure"  # Quick import test
+```
+
+## Local Development Setup
+
+After cloning, initialize submodules and install:
+
+```bash
+git submodule update --init --recursive
+uv sync
+```
+
+This compiles the native code and installs in editable mode. After editing C/Fortran code in `smelib/`, re-run `uv sync` to rebuild.