Fix GitHub actions and docs generation (#10)

* Fix GitHub workflows and docs generation

* Remove superfluous workflows yml

* Update pyproject.toml

* Remove docs/requirements.txt, adapt github/workflows/build.yml

* Adapt setup.py

* Adapt setup.cfg metadata fields to hold underscore-separated fields

* Add path to .readthedocs.yml

* Adapt docs/conf.py

* Add setuptools and wheel to build.yml, remove specific python version from .readthedocs.yml

* Fix typo in env.yml, adapt setup.cfg

* Bugfix setup.cfg

* Update pyproject.toml, remove .travis.yml, update Automated Tests badge link

.github/workflows/build.yml

@@ -9,8 +9,9 @@ name: Automated Tests
 on:
   push:
   pull_request:
+  workflow_dispatch:
   schedule:
-    - cron: "0 11 * * 1" # Every Monday at 11 UTC
+    - cron: "0 9 * * 1" # Every Monday at 9 UTC
 
 jobs:
   build:
@@ -25,33 +26,32 @@ jobs:
         with:
           submodules: true
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2.0.1
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
+          channel-priority: flexible
           environment-file: environment.yml
           activate-environment: flagit
           auto-activate-base: false
       - name: Print environment infos
         shell: bash -l {0}
         run: |
           conda info -a
-          conda list
-          pip list
           which pip
           which python
-      - name: Export Environment
+      - name: Install base package and run tests
         shell: bash -l {0}
         run: |
-          mkdir -p .artifacts
-          filename=env_py${{ matrix.python-version }}_${{ matrix.os }}.yml
-          conda env export --no-builds | grep -v "prefix" > .artifacts/$filename
-      - name: Install package and test
+          pip install -e .[testing]
+          pytest  # run only basic tests, see setup.cfg
+      - name: Export Environment
         shell: bash -l {0}
         run: |
-          pip install .
-          pytest
+          mkdir -p artifacts
+          filename=env_py${{ matrix.python-version }}_${{ matrix.os }}.yml
+          conda env export --no-builds | grep -v "prefix" > artifacts/$filename
       - name: Upload Coverage
         shell: bash -l {0}
         run: |
@@ -63,15 +63,23 @@ jobs:
       - name: Create wheel and dist package
         shell: bash -l {0}
         run: |
-          pip install setuptools_scm
-          # build dist on linux
-          python setup.py sdist --dist-dir .artifacts/dist
-          ls .artifacts/dist
+          pip install setuptools setuptools_scm wheel
+
+          # Create source distribution (sdist) and wheel distribution
+          python setup.py sdist --dist-dir artifacts/dist
+          python setup.py bdist_wheel --dist-dir artifacts/dist
+
+          # Verify the contents of the artifacts directory
+          ls artifacts/dist
+
+          # Validate the built distribution files
+          pip install twine
+          twine check artifacts/dist/*
       - name: Upload Artifacts
         uses: actions/upload-artifact@v4
         with:
-          name: Artifacts
-          path: .artifacts/*
+          name: Artifacts-py${{ matrix.python-version }}-${{ matrix.os }}
+          path: artifacts/*
   coveralls:
     name: Submit Coveralls 👚
     needs: build
@@ -95,6 +103,10 @@ jobs:
           echo "GITHUB_REPOSITORY = $GITHUB_REPOSITORY"
       - name: Download Artifacts
         uses: actions/download-artifact@v4
+        with:
+          path: Artifacts
+          pattern: Artifacts-*
+          merge-multiple: true
       - name: Display downloaded files
         run: ls -aR
       - name: Upload to PyPI
@@ -105,4 +117,4 @@ jobs:
           verify_metadata: true
           packages_dir: Artifacts/dist/
           user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }} # this needs to be uploaded to github actions secrets
+          password: ${{ secrets.PYPI_API_TOKEN }} # this needs to be uploaded to github actions secrets

.readthedocs.yml

@@ -1,12 +1,17 @@
 version: 2
 
-sphinx:
-  configuration: docs/conf.py
-
-formats:
-  - pdf
+build:
+  os: ubuntu-20.04
+  tools:
+    python: mambaforge-4.10
 
 python:
-  version: 3.7
   install:
-    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+
+sphinx:
+  configuration: docs/conf.py
+
+conda:
+  environment: docs/env.yml

AUTHORS.rst

@@ -5,3 +5,4 @@ Contributors
 * Daniel Aberer <[email protected]>
 * Angelika Xaver <[email protected]>
 * Wolfgang Preimesberger <[email protected]>
+* Kasjen Kramer <[email protected]>

CHANGELOG.rst

@@ -13,3 +13,10 @@ Version 0.2
 - Adapt code for internal use
 - Bugfix D06 rolling mean calculation
 - Bugfix case of multiple precipitation sensors
+
+Version 0.3
+===========
+
+- Detect ancillary column
+- Fix automated tests and docs
+- Use list as only optional input to specify flag procedures

README.rst

@@ -2,7 +2,7 @@
 flagit
 ======
 
-.. image:: https://github.com/TUW-GEO/flagit/workflows/Automated%20Tests/badge.svg?branch=main
+.. image:: https://github.com/TUW-GEO/flagit/actions/workflows/build.yml/badge.svg?branch=main
    :target: https://github.com/TUW-GEO/flagit/actions
 
 .. image:: https://coveralls.io/repos/github/TUW-GEO/flagit/badge.svg?branch=main

docs/conf.py

@@ -13,8 +13,9 @@
 import inspect
 import shutil
 
-__location__ = os.path.join(os.getcwd(), os.path.dirname(
-    inspect.getfile(inspect.currentframe())))
+__location__ = os.path.join(
+    os.getcwd(), os.path.dirname(inspect.getfile(inspect.currentframe()))
+)
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -43,30 +44,42 @@
 
 try:
     import sphinx
-    from pkg_resources import parse_version
 
-    cmd_line_template = "sphinx-apidoc -f -o {outputdir} {moduledir}"
+
+    cmd_line_template = (
+        "sphinx-apidoc --implicit-namespaces -f -o {outputdir} {moduledir}"
+    )
     cmd_line = cmd_line_template.format(outputdir=output_dir, moduledir=module_dir)
 
     args = cmd_line.split(" ")
-    if parse_version(sphinx.__version__) >= parse_version('1.7'):
+    if tuple(sphinx.__version__.split(".")) >= ("1", "7"):
+        # This is a rudimentary parse_version to avoid external dependencies
         args = args[1:]
 
     apidoc.main(args)
 except Exception as e:
     print("Running `sphinx-apidoc` failed!\n{}".format(e))
 
-# -- General configuration -----------------------------------------------------
+# -- General configuration ---------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
 # needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.todo',
-              'sphinx.ext.autosummary', 'sphinx.ext.viewcode', 'sphinx.ext.coverage',
-              'sphinx.ext.doctest', 'sphinx.ext.ifconfig', 'sphinx.ext.mathjax',
-              'sphinx.ext.napoleon']
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.coverage",
+    "sphinx.ext.doctest",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "nbsphinx",
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -262,11 +275,12 @@
 # -- External mapping ------------------------------------------------------------
 python_version = '.'.join(map(str, sys.version_info[0:2]))
 intersphinx_mapping = {
-    'sphinx': ('http://www.sphinx-doc.org/en/stable', None),
-    'python': ('https://docs.python.org/' + python_version, None),
-    'matplotlib': ('https://matplotlib.org', None),
-    'numpy': ('https://docs.scipy.org/doc/numpy', None),
-    'sklearn': ('http://scikit-learn.org/stable', None),
-    'pandas': ('http://pandas.pydata.org/pandas-docs/stable', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+    "sphinx": ("http://www.sphinx-doc.org/en/stable", None),
+    "python": ("https://docs.python.org/" + python_version, None),
+    "matplotlib": ("https://matplotlib.org", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "sklearn": ("https://scikit-learn.org/stable", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "pyscaffold": ("https://pyscaffold.org/en/stable", None),
 }

docs/env.yml

@@ -0,0 +1,17 @@
+# To keep the RTD build as small as possible, we define a separate .yml here
+name: docs
+channels:
+- conda-forge
+- defaults
+dependencies:
+- python=3.10
+- ipykernel
+- nbsphinx
+- mock
+- pillow
+- sphinx<7
+- sphinx_rtd_theme
+- pip
+- pip:
+  - recommonmark
+  - readthedocs-sphinx-ext

pyproject.toml

@@ -1,2 +1,11 @@
+[build-system]
+# AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD!
+requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+version_scheme = "no-guess-dev"
+
 [tool.pytest.ini_options]
-pythonpath = ["src"]
+pythonpath = ["src"]
+addopts = "--cov=flagit --cov-report=term-missing --verbose"