Merge pull request #9 from cfs-energy/patch39

Ensure project works for Python 3.9

.github/workflows/workflow_actions.yml

@@ -0,0 +1,97 @@
+# Largely based on https://github.com/cfs-energy/cfspopcon/blob/main/.github/workflows/workflow_actions.yml
+# This workflow will install Python dependencies and run tests
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: workflow_actions
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the "main" branch
+  pull_request: []
+  push:
+    tags:
+      - '*'
+    branches:
+      - 'main'
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+    tag: "Manual run"
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-22.04
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']  # should test the versions we allow for in pyproject.toml
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+
+      - name: Install Poetry
+        run: curl -sSL https://install.python-poetry.org | python - --version 1.8.2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'poetry'
+
+      - name: Setup
+        run: poetry install
+
+      - name: Tests
+        run: MPLBACKEND=Agg poetry run pytest tests
+
+      - name: Test package
+        run: |
+          poetry build -f wheel
+          python -m venv test_env
+          source ./test_env/bin/activate
+          pip install $(find ./dist -name "*.whl")
+          # enter tempdir so import cfspopcon doesn't find the cfspopcon directory
+          mkdir tmp_dir && cd tmp_dir
+          MPLBACKEND=Agg radas_config -o ./new_config.yaml
+          MPLBACKEND=Agg radas -s hydrogen -c ./new_config.yaml
+
+#   build_release:
+#     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+#     needs: build
+#     runs-on: ubuntu-22.04
+
+#     steps:
+#       - uses: actions/checkout@v3
+
+#       - name: Install Poetry
+#         run: curl -sSL https://install.python-poetry.org | python - --version 1.8.2
+
+#       - name: Poetry build
+#         run: poetry build
+
+#       - uses: actions/upload-artifact@v3
+#         with:
+#           name: pypi-build
+#           path: ./dist
+
+#   publish:
+#     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+#     needs: build_release
+#     runs-on: ubuntu-22.04
+#     environment:
+#       name: pypi-publish
+#       url: https://pypi.org/project/cfspopcon/
+#     permissions:
+#       id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+#     steps:
+#       - uses: actions/download-artifact@v3
+
+#       - name: Publish package distributions to PyPI
+#         uses: pypa/gh-action-pypi-publish@release/v1
+#         with:
+#           packages-dir: pypi-build/
+

README.md

@@ -39,7 +39,7 @@ The project is installed using [poetry](https://python-poetry.org/). If you have
 
 Once you have poetry installed, you can install `radas` by running
 ```
-poetry install --with dev
+poetry install
 ```
 
 Because we've added `in-project = true` in `poetry.toml`, the project will install in the `.venv` in the repository directory.
@@ -122,9 +122,9 @@ First, you should edit `pyproject.toml` and set `version="YYYY.MM.V"`, where `YY
 # Clean up any previous distributions
 rm -rf ./dist
 
-# Install the project
+# Install the project without dev dependencies
 poetry lock
-poetry install --with dev
+poetry install --with publish
 # Make sure the tests all pass!
 poetry run pytest
 

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "radas"
 # Version is year.month.version
-version = "2024.3.0"
+version = "2024.3.1"
 description = "Plasma radiated power calculated using OpenADAS"
 authors = ["Commonwealth Fusion Systems"]
 readme = "README.md"
@@ -24,26 +24,38 @@ run_radas = 'radas.cli:run_radas_cli'
 radas_config = 'radas.cli:write_config_template'
 
 [tool.poetry.dependencies]
-python = "<3.13,>=3.9"
-numpy = "^1.22"
-scipy = "^1.8"
-matplotlib = "^3.6"
-Pint = "^0.21"
-pyyaml = "^6.0"
+python = "<3.12,>=3.9"
+numpy = ">=1.22"
+scipy = ">=1.8"
+matplotlib = ">=3.6"
+Pint = ">=0.21"
+pyyaml = ">=6.0"
 xarray = ">=2023"
 pint-xarray = ">=0.3"
-click = "^8.1"
+click = ">=8.1"
 
 [tool.poetry.group.dev.dependencies]
-twine = ">=4.0"
-black = ">=23.0"
-ipdb = "^0.13"
-pytest = "^7.2"
-pytest-order = "^1.1"
-pytest-cov = "^4.1"
+# Install pytest into all development environments
+# (don't set optional = true)
+pytest = ">=7.2"
+pytest-order = ">=1.1"
+pytest-cov = ">=4.1"
 coverage = ">=7.2"
+black = ">=23.0"
+
+[tool.poetry.group.ipykernel]
+optional = true
+
+[tool.poetry.group.ipykernel.dependencies]
+ipdb = ">=0.13"
 ipykernel = ">=6.20"
 
+[tool.poetry.group.publish]
+optional = true
+
+[tool.poetry.group.publish.dependencies]
+twine = ">=4.0"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

radas/adas_interface/compile_with_f2py.py

@@ -13,7 +13,7 @@ def compile_with_f2py(
     def compile_fortran_files(quiet: bool):
         command = (
             ["python3", "-m", "numpy.f2py", "-c"]
-            + files_to_compile
+            + [str(path) for path in files_to_compile]
             + ["-m", module_name]
         )
 

radas/cli.py

@@ -3,6 +3,7 @@
 import multiprocessing as mp
 from pathlib import Path
 from functools import partial
+from typing import Optional
 
 from .shared import open_yaml_file, default_config_file
 from .adas_interface.prepare_adas_readers import prepare_adas_fortran_interface
@@ -43,7 +44,7 @@
 )
 def run_radas_cli(
     directory: Path,
-    config: str | None,
+    config: Optional[str],
     species: list[str],
     verbose: int,
 ):
@@ -67,7 +68,7 @@ def run_radas_cli(
 
 def run_radas(
     directory: Path,
-    config: str | None,
+    config: Optional[str],
     species: list[str],
     verbose: int,
 ):
@@ -86,7 +87,7 @@ def run_radas(
         if verbose:
             print("Skipping computation.")
     else:
-        config_file = default_config_file if config is None else Path(config)
+        config_file = default_config_file if config is None else Path(config).absolute()
         if verbose:
             print(f"Opening config file at {config_file}")
         configuration = open_yaml_file(config_file)
@@ -181,6 +182,7 @@ def run_radas_computation(dataset: xr.Dataset, output_dir: Path, verbose: int):
     help="Output path for a config file. DEFAULT: ./config.yaml",
 )
 def write_config_template(output: Path):
-    print(f"Copying {default_config_file} to {output.absolute()}")
-    Path(output).absolute().write_text(default_config_file.read_text())
+    output = Path(output).absolute()
+    print(f"Copying {default_config_file} to {output}")
+    output.write_text(default_config_file.read_text())
     print("Done")

radas/read_rate_coeffs.py

@@ -24,20 +24,18 @@ def read_rate_coeff(reader_dir, data_file_dir, species_name, config):
             config["data_file_config"], dataset_type
         )
 
-        match reader_key:
-
-            case "adf11":
-                rate_dataset = build_adf11_rate_dataset(
-                    reader_dir,
-                    data_file_dir,
-                    species_name,
-                    dataset_type,
-                    dataset_config,
-                )
-            case _:
-                raise NotImplementedError(
-                    f"No implementation for reading {reader_key} files."
-                )
+        if reader_key == "adf11":
+            rate_dataset = build_adf11_rate_dataset(
+                reader_dir,
+                data_file_dir,
+                species_name,
+                dataset_type,
+                dataset_config,
+            )
+        else:
+            raise NotImplementedError(
+                f"No implementation for reading {reader_key} files."
+            )
 
         determine_coordinates(dataset, rate_dataset)
         dataset[dataset_type] = rate_dataset.rate_coefficient

radas/shared.py

@@ -1,7 +1,7 @@
 """Bits and pieces shared by many other parts of radas."""
 
 from pathlib import Path
-from importlib_resources import files
+from importlib.resources import files
 import subprocess
 import yaml