Modernize package

.github/workflows/pytest.yml

@@ -1,41 +1,56 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python package
+name: Pyfive Test
 
 on:
   push:
-    branches: [ master ]
+    branches: [ master, modernize_package ]  # leave only "master" after PR69 is merged
   pull_request:
     branches: [ master ]
+  schedule:
+    - cron: '0 0 * * *'  # nightly
+
+# Required shell entrypoint to have properly configured bash shell
+defaults:
+  run:
+    shell: bash -l {0}
 
 jobs:
   build:
 
+    name: Test Python ${{ matrix.python-version }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        python -m pip install -e .
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: pyfive
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          miniforge-version: "latest"
+          use-mamba: true
+      - name: Install Pyfive Test Mode
+        run: |
+          mamba install -c conda-forge pip
+          pip install -e .[test]
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Check environment contents
+        run: |
+          conda list
+          pip list
+      - name: Test with pytest
+        run: |
+          pytest -n 2

.gitignore

@@ -1,2 +1,6 @@
 .coverage
 build
+pyfive.egg-info/
+pyfive/__pycache__/
+tests/__pycache__/
+test-reports

codecov.yml

@@ -0,0 +1,6 @@
+coverage:
+  status:
+    project: off
+    patch:
+      default:
+        target: 100%

environment.yml

@@ -0,0 +1,9 @@
+---
+name: pyfive
+channels:
+  - conda-forge
+  - nodefaults
+
+dependencies:
+  - numpy
+  - python >=3.9

pyproject.toml

@@ -0,0 +1,105 @@
+[build-system]
+requires = [
+    "setuptools >= 40.6.0",
+    "setuptools_scm>=6.2",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+authors = [
+    {name = "Pyfive Development Team", email = "jjhelmus@gmail.com"}
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Operating System :: POSIX :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Atmospheric Science",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dynamic = [
+    "readme",
+    "version",
+]
+dependencies = [
+    "numpy",
+]
+description = "A pure python HDF5 reader"
+license = {text = "BSD License, Version 3-Clause"}
+name = "pyfive"
+requires-python = ">=3.9"
+
+[project.optional-dependencies]
+test = [
+    "pytest>6.0.0",
+    "pytest-cov>=2.10.1",
+    "pytest-html!=2.1.0",
+    "pytest-xdist",
+    "dask",
+    "flake8",
+    "flask",
+    "flask-cors",
+    "h5netcdf",
+    "h5py",
+    "netCDF4",
+    "moto",
+    "s3fs",
+]
+
+# very possible these will be needed
+# at some point in the near future
+# doc = [
+#     "sphinx>=6.1.3",
+#     "pydata_sphinx_theme",
+# ]
+# develop = [
+#     "pre-commit",
+#     "pylint",
+#     "pydocstyle",
+# ]
+
+
+[project.urls]
+Code = "https://github.com/jjhelmus/pyfive"
+# Documentation = ""
+Issues = "https://github.com/jjhelmus/pyfive/issues"
+
+[tool.setuptools]
+include-package-data = true
+license-files = ["LICENSE"]
+packages = ["pyfive"]
+zip-safe = false  # possibly yes
+
+[tool.setuptools.dynamic]
+readme = {file = "README.md", content-type = "text/markdown"}
+
+[tool.setuptools_scm]
+version_scheme = "release-branch-semver"
+
+[tool.pytest.ini_options]
+addopts = [
+    "--cov-report=xml:test-reports/coverage.xml",
+    "--cov-report=html:test-reports/coverage_html",
+    "--html=test-reports/report.html",
+]
+
+[tool.coverage.run]
+parallel = true
+source = ["pyfive"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
+]