memilio-simulation PyPI package

.github/actions/build-py/action.yml

@@ -13,12 +13,18 @@ runs:
     - name: Make artifact dir
       shell: bash
       run: |
-        cd pycode/memilio-${{ inputs.package }}/
+        if [ "${{ inputs.package }}" != "simulation" ]; then
+          cd pycode/memilio-${{ inputs.package }}/
+        // else stay in root directory
+        fi
         mkdir wheelhouse
     - name: Build Python Wheels
       shell: bash
       run: |
-        cd pycode/memilio-${{ inputs.package }}/
+        if [ "${{ inputs.package }}" != "simulation" ]; then
+          cd pycode/memilio-${{ inputs.package }}/
+        // else stay in root directory
+        fi
         /opt/python/cp38-cp38/bin/python -m pip install --upgrade pip setuptools wheel
         /opt/python/cp38-cp38/bin/python -m pip install scikit-build scikit-build-core
         /opt/python/cp38-cp38/bin/python -m build --no-isolation --wheel
@@ -35,7 +41,8 @@ runs:
         fi
         cp -r wheelhouse ..
     - name: Upload Python Wheels
-      uses: actions/upload-artifact@v4
+      uses: actions/upload-artifact@v6
       with:
         name: python-wheels-${{ inputs.package }}
         path: pycode/wheelhouse
+

.github/workflows/build_wheels.yml

@@ -0,0 +1,59 @@
+name: Build wheels 
+
+on: [pull_request, release]
+
+jobs:
+
+  build_wheels:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+
+      - uses: pypa/cibuildwheel@v2.16
+
+      - uses: actions/upload-artifact@v6
+        with:
+          name: cibw-wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist: 
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v5
+      with:
+          fetch-depth: 0
+
+    - run: pipx run build --sdist
+
+    - uses: actions/upload-artifact@v6
+      with:
+        name: cibw-sdist
+        path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true
+          # To test uploads to TestPyPI, uncomment the following:
+          repository-url: https://test.pypi.org/legacy/

CMakeLists.txt

@@ -0,0 +1,10 @@
+cmake_minimum_required(VERSION 3.13)
+project(memilio-simulation)
+
+set(CMAKE_CXX_STANDARD "20")
+set(CMAKE_CXX_STANDARD_REQUIRED "20")
+
+# add in C++ library
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/cpp ${CMAKE_CURRENT_BINARY_DIR}/cpp EXCLUDE_FROM_ALL)
+
+add_subdirectory(pycode/memilio-simulation)

README.md

@@ -1,6 +1,6 @@
 # MEmilio - a high performance Modular EpideMIcs simuLatIOn software #
 
-![memilio_logo](docs/memilio-small.png)
+![memilio_logo](https://github.com/SciCompMod/memilio/blob/main/docs/memilio-small.png)
 
 [![CI](https://github.com/SciCompMod/memilio/actions/workflows/main.yml/badge.svg)](https://github.com/SciCompMod/memilio/actions/workflows/main.yml)
 [![codecov](https://codecov.io/gh/SciCompMod/memilio/branch/main/graph/badge.svg?token=DVQXIQJHBM)](https://codecov.io/gh/SciCompMod/memilio)

pycode/memilio-simulation/CMakeLists.txt

@@ -1,9 +1,3 @@
-cmake_minimum_required(VERSION 3.13)
-project(memilio-python)
-
-set(CMAKE_CXX_STANDARD "20")
-set(CMAKE_CXX_STANDARD_REQUIRED "20")
-
 option(MEMILIO_USE_BUNDLED_PYBIND11 "Use pybind11 bundled with this library." ON)
 mark_as_advanced(MEMILIO_USE_BUNDLED_PYBIND11)
 
@@ -52,9 +46,6 @@ else()
     find_package(pybind11 REQUIRED)
 endif()
 
-# add in C++ library
-add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/../../cpp ${CMAKE_CURRENT_BINARY_DIR}/cpp EXCLUDE_FROM_ALL)
-
 # a list of all "LINKED_LIBRARIES" that are given to add_pymio_module. will contain duplicates
 # used for wheel installation
 set(PYMIO_MEMILIO_LIBS_LIST)

pycode/memilio-simulation/README.md

@@ -6,10 +6,10 @@ This package contains Python bindings for the MEmilio C++ library. It enables se
 
 This project is configured via ``pyproject.toml`` and is built with [scikit-build-core](https://scikit-build-core.readthedocs.io). CMake and Ninja must be available on the system. The package uses the [Pybind11 C++ library](https://pybind11.readthedocs.io) to create the bindings.
 
-To install the package, use the command (from the directory containing ``pyproject.toml``)
+To install the package, use the command
 
 ```bash
-pip install .
+pip install memilio-simulation
 ```
 
 This builds the C++ library and C++ Python extension module and copies everything required to your site-packages.
@@ -30,7 +30,7 @@ Alternatively, edit the `CMakeCache.txt` in the directory created by scikit-buil
 
 ## Development
 
-For developement of the cpp bindings use
+For developement of the cpp bindings use the following command from the root of this repository (i.e. the directory containing ``pyproject.toml``)
 
 ```bash
 pip install -e .[dev]

pyproject.toml

@@ -1,3 +1,53 @@
+[project]
+name = "memilio-simulation"
+version = "2.3.0" 
+# dynamic = ["version"] 
+description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
+readme = "README.md"
+requires-python = ">=3.8"
+license = { text = "Apache-2.0" }
+authors = [{ name = "MEmilio Team" }]
+maintainers = [
+  { email = "martin.kuehn@dlr.de" }
+]
+dependencies = [
+  # smaller numpy versions cause a security issue, 1.25 does not work together with pyfakefs
+  "numpy>=1.22,!=1.25.*",
+  # smaller pandas versions contain a bug that sometimes prevents reading
+  "pandas>=2.0.0"
+]
+
+[project.optional-dependencies]
+dev = []
+
+[project.urls]
+Homepage = "https://github.com/SciCompMod/memilio"
+Team = "https://memilio.readthedocs.io/en/latest/team.html"
+
+[build-system]
+requires = [
+  "scikit-build-core>=0.9.0",
+  "setuptools>=68",
+  "setuptools-scm>=8",
+  "wheel"
+]
+build-backend = "scikit_build_core.build"
+
+[tool.scikit-build]
+cmake.version = ">=3.13"
+cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
+wheel.packages = ["pycode/memilio-simulation/memilio"]
+wheel.install-dir = "memilio/simulation"
+build-dir = "pycode/build/memilio-simulation"
+metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
+
+[tool.setuptools_scm]  
+local_scheme = "no-local-version"
+
+[tool.cibuildwheel]
+# Disable some wheels
+skip = ["pp*", "*musllinux*", "*-win32"] 
+
 [tool.autopep8]
 max-line-length = 79