Python packaging (#346)

* Updated packaging

* use extras_require for optional dependencies

* Add python 3.10 in tests

* Add python 3.10 in tests

* Ensure a c99 compliant C compiler

* separate C anc C++ extensions

Author: lfarv

.github/workflows/build-python-wheels.yml

@@ -6,6 +6,7 @@ on:
   push:
     tags:
       - pyat-*
+  workflow_dispatch:
 
 defaults:
   run:
@@ -20,41 +21,52 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-
-      - uses: actions/setup-python@v2
-        name: Install Python
         with:
-          python-version: '3.7'
-
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel
+          # Necessary to fetch tags and allow setuptools_scm
+          # see: https://github.com/pypa/setuptools_scm/issues/480
+          fetch-depth: 0
 
-      - name: Prepare source
-        run: |
-          pip install -e .
+      - name: Install Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
 
-      - name: Remove built files
-        if: (! contains(matrix.os, 'windows'))
-        run: rm -rf build
+      - name: Set build configuration
+        run: cp githubproject.toml pyproject.toml
 
       - name: Build wheels
-        run: python -m cibuildwheel --output-dir wheelhouse
-        env:
-          # We don't yet support Python 3.10.
-          # Pypy does not have Scipy so we cannot support it.
-          CIBW_SKIP: cp310* pp*
-          CIBW_BUILD_VERBOSITY: 1
-
-      - name: Build sdist
-        run: python setup.py sdist
+        uses: pypa/[email protected]
+        with:
+          package-dir: pyat
 
       - name: Upload wheels
         uses: actions/upload-artifact@v2
         with:
           name: wheels
-          path: ./pyat/wheelhouse/*.whl
+          path: ./wheelhouse/*.whl
           if-no-files-found: error
 
+  build_sdist:
+    runs-on: ubuntu-18.04
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          # Necessary to fetch tags and allow setuptools_scm
+          # see: https://github.com/pypa/setuptools_scm/issues/480
+          fetch-depth: 0
+
+      - name: Install Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
+
+      - name: Install build tools
+        run: python -m pip install build
+
+      - name: Build sdist
+        run: python -m build --sdist
+
       - name: Upload sdist
         uses: actions/upload-artifact@v2
         with:

.github/workflows/python-tests.yml

@@ -19,7 +19,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.6', '3.7', '3.8', '3.9']
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
         os: [macos-latest, ubuntu-latest, windows-latest]
 
     steps:
@@ -31,15 +31,8 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8
-        python -m pip install -r requirements.txt
-        python -m pip install pytest-cov
-
-    - name: Build and install at
-      run: python -m pip install -e .
+    - name: Build and install at with tests
+      run: python -m pip install -e ".[dev]"
 
     - name: Lint with flake8
       run: |

.gitignore

@@ -24,6 +24,7 @@ pyat/dist
 pyat/at.egg-info
 pyat/prefix
 pyat/integrator-src
+pyat/at/_version.py
 *.egg-info
 .pytest_cache
 .coverage

jupyter/at.dockerfile

@@ -42,8 +42,9 @@ RUN git clone --depth 1 -b $AT_BRANCH $AT_REPO /home/$USERNAME/at \
 	&& octave --eval 'bootstrap(:,true);savepath'
 
 RUN cd /home/$USERNAME/at/pyat \
-	&& pip3 install -r requirements.txt \
 	&& pip3 install matplotlib \
+	&& pip3 install numpy \
+	&& pip3 install scipy \
 	&& python3 setup.py install --user
 
 WORKDIR $DOCKER_NOTEBOOK_DIR

pyat/MANIFEST.in

@@ -1,2 +1,2 @@
 
-recursive-include integrator-src *.c *.h
+global-include *.c *.h *.cc

pyat/at/__init__.py

@@ -1,7 +1,16 @@
 """Python port of the Accelerator Toolbox"""
 
-# Make all functions visible in the at namespace:
 import sys
+if sys.version_info.minor < 8:
+    from importlib_metadata import version, PackageNotFoundError
+else:
+    from importlib.metadata import version, PackageNotFoundError
+try:
+    __version__ = version('accelerator-toolbox')
+except PackageNotFoundError:
+    __version__ = "0.0.0"
+# from ._version import version as __version__
+# Make all functions visible in the at namespace:
 from .lattice import *
 from .tracking import *
 from .physics import *

pyat/developers.rst

@@ -19,6 +19,12 @@ Install the Python development package for your OS. For example, using yum:
 
 * ``sudo yum install python3-devel``
 
+Source download
+---------------
+Download the latest version of AT:
+    ``$ git clone https://github.com/atcollab/at.git``
+
+
 Installation (all platforms)
 ----------------------------
 
@@ -30,9 +36,18 @@ It is easiest to do this using a virtualenv. inside pyat:
 
 Then:
 
-* ``source venv/bin/activate  # or venv\Scripts\activate on Windows``
-* ``pip install -r requirements.txt``
-* ``pip install -e .``
+* activate the virtual environment:
+
+  ``source venv/bin/activate  # or venv\Scripts\activate on Windows``
+* make sure you have a recent pip installer:
+
+  ``pip install --upgrade pip``
+* Go to the pyat root directory:
+
+  ``cd <atroot>/pyat``
+* install AT:
+
+  ``pip install -e .``
 
 Finally, you should be able to run the tests:
 
@@ -58,17 +73,17 @@ recompiled.  To force recompilation, remove the build directory:
 Any changes to .py files are automatically reinstalled in the build, but to
 ensure any changes to .c files are reinstalled rerun:
 
-* ``python setup.py develop``
+* ``pip install -e .``
 
-If you get strange behaviour even after running setup.py develop again, then
+If you get strange behaviour even after running pip install develop again, then
 running the following, inside pyat, should fix it:
 
 * ``rm -rf build``
 * ``find at -name "*.pyc" -exec rm '{}' \;``
 * ``find at -name "*.so" -exec rm '{}' \;``
-* ``python setup.py develop``
+* ``pip install -e .``
 
-N.B. setup.py develop needs to be run with the same version of Python (and
+N.B. ``pip install -e .`` needs to be run with the same version of Python (and
 numpy) that you are using to run pyAT.
 
 Releasing a version to PyPI
@@ -91,12 +106,10 @@ For testing any version that you have installed, the simple snippet in
 ``README.rst`` is sufficient.
 
 * Decide the Python versions that should be supported in the release
-   * Set these Python versions in setup.py
-   * Set at least these Python versions as python-version in .github/workflows/python-tests.yml
+   * Set these Python versions in ``python_requires`` in ``setup.cfg``
+   * Set at least these Python versions as ``python-version`` in ``.github/workflows/python-tests.yml``
 * Determine the minimum Numpy version that is required for those Python versions
-   * Set this numpy version in install_requires in setup.py
-   * Set this numpy version in requirements.txt
-* Update the pyat version in setup.py to x.y.z
+   * Set this numpy version in ``install_requires`` in ``setup.cfg``
 * Push a tag ``pyat-x.y.z`` to Github
 
 If all goes well, there will be a build of "Build and upload wheels and sdist"

pyat/githubproject.toml

@@ -0,0 +1,25 @@
+[build-system]
+requires = [
+    "numpy == 1.16.6;python_version<'3.10'",
+    "numpy == 1.21.5;python_version>='3.10'",
+    "setuptools >= 45",
+    "setuptools_scm>=6.2",
+    "wheel",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.cibuildwheel]
+# Pypy does not have Scipy so we cannot support it.
+build = ["cp3{6,7,8,9,10}*"]
+build-verbosity = "1"
+# "build" frontend fails on windows
+# build-frontend = "build"
+
+[tool.cibuildwheel.macos]
+archs = ["x86_64", "arm64"]
+
+[tool.setuptools_scm]
+root = ".."
+# write_to = "pyat/at/_version.py"
+git_describe_command = "git describe --tags --long --match pyat-[0-9]* HEAD"
+fallback_version = "0.0.0"

pyat/pyproject.toml

@@ -1,7 +1,25 @@
 [build-system]
 requires = [
-    "numpy == 1.16.6",
-    "setuptools >= 40.9.0",
+    "numpy >= 1.16.6;python_version<'3.10'",
+    "numpy >= 1.21.5;python_version>='3.10'",
+    "setuptools >= 45",
+    "setuptools_scm>=6.2",
     "wheel",
 ]
 build-backend = "setuptools.build_meta"
+
+[tool.cibuildwheel]
+# Pypy does not have Scipy so we cannot support it.
+build = ["cp3{6,7,8,9}*", "cp310*"]
+build-verbosity = "1"
+# "build" frontend fails on windows
+# build-frontend = "build"
+
+[tool.cibuildwheel.macos]
+archs = ["x86_64", "arm64"]
+
+[tool.setuptools_scm]
+root = ".."
+# write_to = "pyat/at/_version.py"
+git_describe_command = "git describe --dirty --tags --long --match pyat-[0-9]*"
+fallback_version = "0.0.0"