Claude/fix gpu wheels build yptx m

.github/release-drafter.yml

@@ -0,0 +1,133 @@
+# Configuration for Release Drafter
+# https://github.com/release-drafter/release-drafter
+#
+# Automatically drafts GitHub release notes from merged PRs.
+# PRs are categorized by their labels into changelog sections.
+
+name-template: 'v$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+
+# Determine the next version bump from PR labels
+version-resolver:
+  major:
+    labels:
+      - 'breaking'
+  minor:
+    labels:
+      - 'enhancement'
+      - 'feature'
+      - 'physics'
+  patch:
+    labels:
+      - 'bug'
+      - 'fix'
+      - 'performance'
+      - 'documentation'
+      - 'devops'
+      - 'dependencies'
+  default: patch
+
+# Map PR labels to changelog sections
+categories:
+  - title: '🔬 Physics & Solvers'
+    labels:
+      - 'physics'
+      - 'solver'
+  - title: '🚀 New Features'
+    labels:
+      - 'feature'
+      - 'enhancement'
+  - title: '⚡ Performance'
+    labels:
+      - 'performance'
+      - 'gpu'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'bug'
+      - 'fix'
+  - title: '📖 Documentation'
+    labels:
+      - 'documentation'
+  - title: '🔧 DevOps & CI'
+    labels:
+      - 'devops'
+      - 'ci'
+  - title: '📦 Dependencies'
+    labels:
+      - 'dependencies'
+  - title: '⚠️ Breaking Changes'
+    labels:
+      - 'breaking'
+  - title: '🧹 Maintenance'
+    labels:
+      - 'maintenance'
+      - 'refactor'
+
+# Exclude PRs with these labels from release notes
+exclude-labels:
+  - 'skip-changelog'
+
+# Template for the release body
+template: |
+  ## What's Changed
+
+  $CHANGES
+
+  **Full Changelog**: https://github.com/$OWNER/$REPOSITORY/compare/$PREVIOUS_TAG...v$RESOLVED_VERSION
+
+# Auto-label PRs based on file paths
+autolabeler:
+  - label: 'physics'
+    files:
+      - 'src/props/**'
+    title:
+      - '/tortuosity/i'
+      - '/diffusiv/i'
+      - '/solver/i'
+      - '/HYPRE/i'
+      - '/MLMG/i'
+  - label: 'io'
+    files:
+      - 'src/io/**'
+    title:
+      - '/reader/i'
+      - '/TIFF/i'
+      - '/HDF5/i'
+  - label: 'documentation'
+    files:
+      - 'docs/**'
+      - '*.md'
+      - 'Doxyfile'
+    title:
+      - '/docs/i'
+      - '/documentation/i'
+  - label: 'devops'
+    files:
+      - '.github/**'
+      - 'containers/**'
+      - 'pyproject.toml'
+      - 'CMakeLists.txt'
+    title:
+      - '/CI/i'
+      - '/workflow/i'
+      - '/wheel/i'
+      - '/PyPI/i'
+  - label: 'gpu'
+    files:
+      - 'src/props/*GPU*'
+      - 'src/props/*CUDA*'
+    title:
+      - '/CUDA/i'
+      - '/GPU/i'
+      - '/NVCC/i'
+  - label: 'python'
+    files:
+      - 'python/**'
+    title:
+      - '/python/i'
+      - '/pybind/i'
+      - '/binding/i'
+  - label: 'tests'
+    files:
+      - 'tests/**'
+      - 'python/tests/**'

.github/workflows/docs.yml

@@ -1,11 +1,12 @@
 # .github/workflows/docs.yml
-name: Deploy Doxygen Documentation
+name: Deploy Documentation
 
 on:
   push:
     branches: [master]
     paths:
       - 'src/**'
+      - 'python/**'
       - 'Doxyfile'
       - 'docs/**'
       - '.github/workflows/docs.yml'
@@ -24,7 +25,7 @@ concurrency:
 
 jobs:
   build-docs:
-    name: Build Doxygen Documentation
+    name: Build Documentation
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
@@ -35,15 +36,28 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y doxygen graphviz
           echo "Doxygen version: $(doxygen --version)"
-          echo "Dot version: $(dot -V 2>&1)"
 
-      - name: Generate documentation
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Sphinx and dependencies
+        run: pip install -r docs/requirements.txt
+
+      - name: Generate Doxygen XML and HTML
         run: doxygen Doxyfile
 
+      - name: Build Sphinx documentation
+        run: sphinx-build -b html docs/ docs/_build/html
+
+      - name: Copy Doxygen HTML into Sphinx output
+        run: cp -r docs/doxygen/html docs/_build/html/doxygen
+
       - name: Upload Pages artifact
         uses: actions/upload-pages-artifact@v3
         with:
-          path: docs/doxygen/html
+          path: docs/_build/html
 
   deploy:
     name: Deploy to GitHub Pages

.github/workflows/pypi-wheels-cpu.yml

@@ -16,6 +16,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive # Fetches Catch2, nlohmann/json, or pybind11 if needed
+          fetch-depth: 0
 
       - name: Set up Python
         uses: actions/setup-python@v5

.github/workflows/pypi-wheels-gpu.yml

@@ -16,6 +16,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
+          fetch-depth: 0
 
       - name: Set up Python
         uses: actions/setup-python@v5

.github/workflows/release-drafter.yml

@@ -0,0 +1,21 @@
+# .github/workflows/release-drafter.yml
+name: Release Drafter
+
+on:
+  push:
+    branches:
+      - master
+  pull_request_target:
+    types: [opened, reopened, synchronize]
+
+permissions:
+  contents: read
+  pull-requests: write
+
+jobs:
+  update-release-draft:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: release-drafter/release-drafter@v6
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release.yml

@@ -15,6 +15,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: Set up Apptainer
         uses: eWaterCycle/setup-apptainer@v2
@@ -121,10 +123,14 @@ jobs:
           sudo apptainer build "$SIF_FILENAME" Singularity.final.def
           echo "SIF_FILENAME=$SIF_FILENAME" >> $GITHUB_ENV
 
-      - name: Create GitHub Release and Upload SIF
+      - name: Upload SIF to GitHub Release
         uses: softprops/action-gh-release@v2
         with:
           files: ${{ env.SIF_FILENAME }}
+          # Release notes are pre-populated by Release Drafter.
+          # Only fall back to auto-generated notes if the body is empty
+          # (e.g. tag was pushed without a prior draft).
           generate_release_notes: true
+          append_body: true
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

CMakeLists.txt

@@ -15,8 +15,37 @@
 
 cmake_minimum_required(VERSION 3.18)
 
+# ---------------------------------------------------------------------------
+# Derive project version from the latest Git tag (e.g. v4.0.1 → 4.0.1).
+# Falls back to 0.0.0 when building outside a Git repository or when no
+# tag is reachable (e.g. shallow clone without --tags).
+# ---------------------------------------------------------------------------
+set(OPENIMPALA_FALLBACK_VERSION "4.0.1")
+
+find_package(Git QUIET)
+if(GIT_FOUND)
+    execute_process(
+        COMMAND "${GIT_EXECUTABLE}" describe --tags --match "v[0-9]*" --abbrev=0
+        WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+        OUTPUT_VARIABLE _git_tag
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+        ERROR_QUIET
+        RESULT_VARIABLE _git_result
+    )
+    if(_git_result EQUAL 0 AND _git_tag MATCHES "^v([0-9]+\\.[0-9]+\\.[0-9]+)")
+        set(_detected_version "${CMAKE_MATCH_1}")
+    endif()
+endif()
+
+if(NOT _detected_version)
+    set(_detected_version "${OPENIMPALA_FALLBACK_VERSION}")
+    message(STATUS "Git tag not found — using fallback version ${_detected_version}")
+else()
+    message(STATUS "Version from Git tag: ${_detected_version}")
+endif()
+
 project(OpenImpala
-    VERSION 0.1.0
+    VERSION ${_detected_version}
     LANGUAGES C CXX Fortran
     DESCRIPTION "Image-based simulation of transport properties in porous media"
 )

Doxyfile

@@ -64,7 +64,8 @@ FULL_SIDEBAR           = NO
 GENERATE_LATEX         = NO
 GENERATE_RTF           = NO
 GENERATE_MAN           = NO
-GENERATE_XML           = NO
+GENERATE_XML           = YES
+XML_OUTPUT             = xml
 
 #---------------------------------------------------------------------------
 # Graphs (requires Graphviz dot)

docs/api/cpp.md

@@ -0,0 +1,75 @@
+# C++ API Reference
+
+The C++ API reference is generated from Doxygen comments in the source code
+using [Breathe](https://breathe.readthedocs.io/).
+
+## Namespace
+
+All OpenImpala classes live in the `OpenImpala` namespace.
+
+## Key classes
+
+### I/O Readers
+
+```{eval-rst}
+.. doxygenclass:: OpenImpala::TiffReader
+   :members:
+   :outline:
+
+.. doxygenclass:: OpenImpala::HDF5Reader
+   :members:
+   :outline:
+
+.. doxygenclass:: OpenImpala::RawReader
+   :members:
+   :outline:
+```
+
+### Transport Solvers
+
+```{eval-rst}
+.. doxygenclass:: OpenImpala::TortuosityHypre
+   :members:
+   :outline:
+
+.. doxygenclass:: OpenImpala::TortuosityMLMG
+   :members:
+   :outline:
+
+.. doxygenclass:: OpenImpala::EffectiveDiffusivityHypre
+   :members:
+   :outline:
+```
+
+### Utilities
+
+```{eval-rst}
+.. doxygenclass:: OpenImpala::VolumeFraction
+   :members:
+   :outline:
+
+.. doxygenclass:: OpenImpala::PercolationCheck
+   :members:
+   :outline:
+
+.. doxygenclass:: OpenImpala::TortuositySolverBase
+   :members:
+   :outline:
+
+.. doxygenclass:: OpenImpala::HypreStructSolver
+   :members:
+   :outline:
+```
+
+### Configuration
+
+```{eval-rst}
+.. doxygenstruct:: OpenImpala::PhysicsConfig
+   :members:
+   :outline:
+```
+
+## Full Doxygen output
+
+For the complete class hierarchy, include dependency graphs, and file-level
+documentation, see the [Doxygen pages](../doxygen/html/index.html).