Update publish action

.github/workflows/python-package.yml

@@ -10,30 +10,89 @@ on:
     branches: [ main ]
 
 jobs:
-  build:
-
-    runs-on: ubuntu-latest
+  tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        include:
+
+          - name: Python 3.12 with Coverage
+            os: ubuntu-latest
+            python: '3.12'
+            toxenv: py312-test-cov
+
+          - name: Python 3.12
+            os: ubuntu-latest
+            python: '3.12'
+            toxenv: py312-test
+
+          - name: Python 3.10
+            os: ubuntu-latest
+            python: '3.10'
+            toxenv: py310-test
+
+          - name: Python 3.9
+            os: ubuntu-latest
+            python: 3.9
+            toxenv: py39-test
+
+          - name: Python 3.8
+            os: ubuntu-latest
+            python: 3.8
+            toxenv: py38-test
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - name: Checkout code
+      uses: actions/checkout@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        fetch-depth: 0
+
+    - name: Set up Python ${{ matrix.python }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest wheel
+        python -m pip install --upgrade tox
+        pip install flake8 pytest-cov wheel tox
         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
+    - name: Run Tests
       run: |
-        pytest
+        tox ${{ matrix.toxargs }} -e ${{ matrix.toxenv }} -- ${{ matrix.toxposargs }}
+    - name: Upload coverage to artifacts
+      if: ${{ contains(matrix.toxenv,'-cov') }}
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage_${{ matrix.toxenv }}.xml
+        path: coverage.xml
+        if-no-files-found: error
+
+  upload-coverage-report:
+    needs: ['tests']
+    permissions:
+      contents: none
+    runs-on: ubuntu-latest
+    name: Upload Coverage
+    steps:
+    - name: Download coverage artifacts
+      uses: actions/download-artifact@v4
+      with:
+        path: coverage
+        pattern: coverage_*
+        merge-multiple: true
+    - name: Upload to Codecov
+      if: ${{ hashFiles('coverage/') != ''}}
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        directory: coverage
+        fail_ci_if_error: true # optional (default = false)
+        verbose: true

.github/workflows/python-publish.yml

@@ -1,31 +1,45 @@
+
 # This workflows will upload a Python Package using Twine when a release is created
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
 name: Upload to PYPI
-
-on:
-  release:
-    types: [created]
+on: push
 
 jobs:
-  deploy:
-
+  release-build:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine build
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python -m build .
-        twine upload dist/*
+        python3 -m pip install build
+    - name: Build a binary wheel and source tarball
+      run: python3 -m build
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: release-dists
+        path: dist/
+
+  pypi-publish:
+    name: Publish Package to PyPI
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    needs:
+      - release-build
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Retrieve release distributions
+      uses: actions/download-artifact@v4
+      with:
+        name: release-dists
+        path: dist/
+    - name: Publish release distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -5,3 +5,8 @@ build/*
 *__pycache__*
 *.egg-info/*
 .tox/*
+/coverage.xml
+/.tox/
+/.coverage*
+/goodman_focus/version.py
+.DS_Store

.readthedocs.yml

@@ -1,6 +1,5 @@
 version: 2
 
-
 build:
   os: ubuntu-lts-latest
   tools:

README.md

@@ -4,7 +4,7 @@
 # Goodman Focus Finder
 
 ![Goodman Focus](https://github.com/soar-telescope/goodman_focus/workflows/Goodman%20Focus/badge.svg)
-[![Coverage Status](https://coveralls.io/repos/github/soar-telescope/goodman_focus/badge.svg?branch=master)](https://coveralls.io/github/soar-telescope/goodman_focus?branch=master)
+[![codecov](https://codecov.io/gh/soar-telescope/goodman_focus/graph/badge.svg?token=2ZK2DAMMYE)](https://codecov.io/gh/soar-telescope/goodman_focus)
 [![Documentation Status](https://readthedocs.org/projects/goodman-focus/badge/?version=latest)](https://goodman-focus.readthedocs.io/en/latest/?badge=latest)
 [![pypi](https://img.shields.io/pypi/v/goodman_focus.svg?style=flat)](https://pypi.org/project/goodman-focus/)
 
@@ -17,4 +17,4 @@ All the documentation is maintained in https://soardocs.readthedocs.io/projects/
 # Found a problem?
 
 Please [Open an Issue](https://github.com/soar-telescope/goodman_focus/issues) on
-GitHub.
+GitHub.

docs/conf.py

@@ -16,7 +16,8 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
-__version__ = __import__('goodman_focus').__version__
+from importlib.metadata import version
+__version__ = version('goodman_focus')
 
 # -- Project information -----------------------------------------------------
 
@@ -43,8 +44,8 @@
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.intersphinx',
-    'sphinxcontrib.napoleon',
     'matplotlib.sphinxext.plot_directive',
+    'sphinx.ext.napoleon'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -170,4 +171,4 @@
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}

environment.yml

@@ -1,6 +1,6 @@
 name: goodman_focus
 dependencies:
-  - python=3.8
+  - python=3.12
   - astropy
   - matplotlib
   - numpy

goodman_focus/__init__.py

@@ -1,3 +1,6 @@
-from .version import __version__  # noqa: F401
+from importlib.metadata import version
+
 from .goodman_focus import GoodmanFocus  # noqa: F401
 from .goodman_focus import run_goodman_focus  # noqa: F401
+
+__version__ = version('goodman_focus')

pyproject.toml

@@ -1,7 +1,72 @@
 [build-system]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
 
-requires = ["setuptools",
-            "setuptools_scm",
-            "wheel"]
+[project]
+name = "goodman_focus"
+dynamic = ["version"]
+description = "Finds best focus for Goodman HTS based on a series of images obtained with different focus values"
+readme = "README.md"
+requires-python = ">=3.8"
+license = {file = "LICENSE"}
+keywords = [
+    "soar",
+    "pipelines",
+    "astronomy",
+    "images",
+    "spectroscopy",
+    "focus"
+]
 
-build-backend = 'setuptools.build_meta'
+authors = [
+  {name = "Simón Torres", email = "[email protected]"}
+]
+maintainers = [
+  {name = "Simón Torres", email = "[email protected]"}
+]
+
+classifiers = [
+  'Development Status :: 5 - Production/Stable',
+  'Environment :: Console',
+  'Intended Audience :: Developers',
+  'Intended Audience :: Education',
+  'Intended Audience :: Science/Research',
+  'License :: OSI Approved :: BSD License',
+  'Programming Language :: Python :: 3.8',
+  'Programming Language :: Python :: 3.9',
+  'Programming Language :: Python :: 3.10',
+  'Programming Language :: Python :: 3.11',
+  'Programming Language :: Python :: 3.12',
+  'Natural Language :: English',
+  'Operating System :: POSIX :: Linux',
+  'Operating System :: POSIX :: Other',
+  'Operating System :: MacOS :: MacOS X',
+  'Topic :: Scientific/Engineering :: Astronomy',
+  'Topic :: Scientific/Engineering :: Information Analysis',
+  'Topic :: Software Development :: Libraries :: Python Modules',
+]
+
+dependencies = [
+  "astropy",
+  "ccdproc",
+  "matplotlib",
+  "numpy",
+  "packaging",
+  "pandas",
+  "scipy",
+]
+
+[project.urls]
+"Homepage" = "https://soardocs.readthedocs.io/projects/goodmanfocus/en/latest/"
+"Bug Reports" = "https://github.com/soar-telescope/goodman_focus/issues"
+"Source" = "https://github.com/soar-telescope/goodman_focus"
+
+[project.scripts]
+goodman-focus = "goodman_focus:run_goodman_focus"
+
+[tool.setuptools]
+[tool.setuptools.packages.find]
+where = ["goodman_focus"]
+
+[tool.setuptools_scm]
+version_file = "goodman_focus/version.py"

setup.cfg

@@ -11,25 +11,3 @@ build_dir = docs/_build
 [upload_docs]
 upload_dir = docs/_build/html
 show_response = 1
-
-[metadata]
-package_name = goodman_focus
-description = Finds best focus for Goodman HTS based on a series of images obtained with different focus values
-long_description = Standalone app to get the best focus.
-author = Simon Torres
-author_email = [email protected]
-license = BSD-3-Clause
-# url =
-edit_on_github = False
-github_project = soar-telescope/goodman_focus
-install_requires =
-    astropy
-    matplotlib
-    numpy
-    pandas
-    scipy
-    ccdproc
-    sphinx
-
-# version should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440)
-version = 2.0.3