Merge pull request #125 from ken-lauer/bld_pypi

BLD/CI: specify and test against pip (PyPI) dependencies

Author: ChristopherMayes

.github/actions/conda-setup/action.yml

@@ -13,10 +13,6 @@ inputs:
     description: "Conda environment name to create"
     required: false
     default: "beamphysics-dev"
-  extras:
-    description: "Package extras to install"
-    required: true
-    default: "dev"
 runs:
   using: "composite"
   steps:
@@ -54,7 +50,3 @@ runs:
           mamba install -n ${{ inputs.env_name }} python=${{ inputs.python-version }}
         fi
       if: steps.cache.outputs.cache-hit != 'true'
-    - name: Setup the environment
-      shell: bash -l {0}
-      run: |
-        python -m pip install .[${{ inputs.extras }}]

.github/workflows/gh-pages.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     name: "Build docs"
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - uses: ./.github/actions/conda-setup

.github/workflows/lint.yml

@@ -8,7 +8,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 1
 

.github/workflows/pypi_upload.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Set up Python 3.9

.github/workflows/tests-pip.yml

@@ -0,0 +1,38 @@
+name: pypi - tests
+
+on:
+  pull_request:
+  push:
+  release:
+    types:
+      - published
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+    name: Test Suite
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "${{ matrix.python-version }}"
+      - name: Install openPMD-beamphysics (pypi deps)
+        shell: bash -l -e -o pipefail {0}
+        run: |
+          python -m pip install .[dev]
+      - name: Test environment conda package list
+        shell: bash -l {0}
+        run: |
+          conda list
+      - name: Run unit tests
+        shell: bash -l -e -o pipefail {0}
+        run: |
+          echo -e '## Test results\n\n```' >> "$GITHUB_STEP_SUMMARY"
+          pytest -v 2>&1 | tee -a "$GITHUB_STEP_SUMMARY"
+          echo '```' >> "$GITHUB_STEP_SUMMARY"

.github/workflows/tests.yaml

@@ -1,4 +1,4 @@
-name: Run tests
+name: conda - tests
 
 on:
   pull_request:
@@ -13,23 +13,26 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
 
     name: Test Suite
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - uses: ./.github/actions/conda-setup
         with:
           python-version: ${{ matrix.python-version }}
-          extras: "dev"
+      - name: Install openPMD-beamphysics (conda deps)
+        shell: bash -l -e -o pipefail {0}
+        run: |
+          python -m pip install --no-deps .
       - name: Test environment conda package list
         shell: bash -l {0}
         run: |
           conda list
       - name: Run unit tests
-        shell: bash -l {0}
+        shell: bash -l -e -o pipefail {0}
         run: |
           echo -e '## Test results\n\n```' >> "$GITHUB_STEP_SUMMARY"
           pytest -v 2>&1 | tee -a "$GITHUB_STEP_SUMMARY"

README.md

@@ -1,15 +1,14 @@
 # openPMD-beamphysics
 
-**`Documentation`** |
-------------------- |
-[![Documentation](https://img.shields.io/badge/beamphysics-documentation-blue.svg)](https://christophermayes.github.io/openPMD-beamphysics/)  |
+| **`Documentation`**                                                                                                                          |
+| -------------------------------------------------------------------------------------------------------------------------------------------- |
+| [![Documentation](https://img.shields.io/badge/beamphysics-documentation-blue.svg)](https://christophermayes.github.io/openPMD-beamphysics/) |
 
 Tools for analyzing and viewing particle data in the openPMD standard, extension beamphysics.
 
-https://github.com/openPMD/openPMD-standard/blob/upcoming-2.0.0/EXT_BeamPhysics.md
+<https://github.com/openPMD/openPMD-standard/blob/upcoming-2.0.0/EXT_BeamPhysics.md>
 
-Installing openpmd-beamphysics
-==============================
+# Installing openpmd-beamphysics
 
 Installing `openpmd-beamphysics` from the `conda-forge` channel can be achieved by adding `conda-forge` to your channels with:
 
@@ -27,3 +26,30 @@ It is possible to list all of the versions of `openpmd-beamphysics` available on
 
 ```
 conda search openpmd-beamphysics --channel conda-forge
+```
+
+## Development environment
+
+A conda environment file is provided in this repository and may be used for a
+development environment.
+
+To create a new conda environment using this file, do the following:
+
+```bash
+git clone https://github.com/ChristopherMayes/openPMD-beamphysics
+cd openPMD-beamphysics
+conda env create -n pmd_beamphysics-dev -f environment.yml
+conda activate beamphysics-dev
+python -m pip install --no-deps -e .
+```
+
+Alternatively, with a virtualenv and pip:
+
+```bash
+git clone https://github.com/ChristopherMayes/openPMD-beamphysics
+cd openPMD-beamphysics
+
+python -m venv beamphysics-venv
+source pmd_beamphysics-venv/bin/activate
+python -m pip install -e .
+```

environment.yml

@@ -14,12 +14,11 @@ dependencies:
   - pytest-benchmark
   - pytest-cov
   - jupyterlab>=3
-  - pygments
+  # Documentation
   - mkdocs
   - mkdocstrings
   - mkdocs-material
   - mkdocs-jupyter
   - mkdocstrings-python
+  - pygments
   - pip
-  - pip:
-      - mkdocstrings-python

mkdocs.yml

@@ -112,6 +112,3 @@ plugins:
             show_submodules: false
             group_by_category: true
             unwrap_annotated: true
-            import:
-              - https://docs.python.org/3/objects.inv
-              - https://docs.h5py.org/en/stable/objects.inv

pyproject.toml

@@ -11,8 +11,11 @@ classifiers = [
   "Topic :: Scientific/Engineering",
 ]
 dependencies = [
-  # All core dependencies must be sourced from conda (conda-forge).
-  # See ``environment.yml`` for further information.
+  "numpy",
+  "scipy>=1.0.0",
+  "matplotlib",
+  "h5py",
+  "python-dateutil",
 ]
 description = "Tools for analyzing and viewing particle data in the openPMD standard, extension beamphysics."
 dynamic = ["version"]
@@ -22,10 +25,10 @@ readme = { file = "README.md", content-type = "text/markdown" }
 requires-python = ">=3.9"
 
 [project.optional-dependencies]
-dev = ["pytest", "pytest-cov"]
+dev = ["pytest", "pytest-cov", "pytest-benchmark"]
 doc = [
-  "mkdocs==1.5.2",
-  "mkdocs-jupyter==0.24.6",
+  "mkdocs",
+  "mkdocs-jupyter",
   "mkdocs-macros-plugin",
   "mkdocs-material",
   "mkdocstrings",
@@ -49,8 +52,8 @@ file = "LICENSE"
 
 [tool.pytest.ini_options]
 addopts = "--cov=pmd_beamphysics/"
-log_cli_level = "info"
-log_level = "debug"
+log_cli_level = "INFO"
+log_level = "DEBUG"
 testpaths = ["tests"]
 
 [tool.setuptools_scm]