[2023] A few fixes, software tests, and other modernizations

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

.github/workflows/tests.yml

@@ -0,0 +1,56 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+  # Allow job to be triggered manually.
+  workflow_dispatch:
+
+# Cancel in-progress jobs when pushing to the same branch.
+concurrency:
+  cancel-in-progress: true
+  group: ${{ github.workflow }}-${{ github.ref }}
+
+jobs:
+
+  tests:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ "ubuntu-latest" ]
+        python-version: [ "3.7", "3.8", "3.9", "3.10", "3.11" ]
+
+    name: Python ${{ matrix.python-version }} on OS ${{ matrix.os }}
+    steps:
+
+      - name: Acquire sources
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+          cache: 'pip'
+          cache-dependency-path: |
+            requirements-docs.txt
+            requirements-release.txt
+            requirements-test.txt
+            setup.py
+
+      - name: Run tests
+        run: make test
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          files: ./coverage.xml
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false

.gitignore

@@ -6,3 +6,5 @@
 /tmp
 /dist
 /doc/_build
+.coverage*
+coverage.xml

CHANGES.rst

@@ -4,6 +4,14 @@ phenodata changelog
 
 development
 ===========
+- Fix ``nearest-station`` with ``--format=json``
+- Fix filtering by ``int64``-type identifiers, see GH-7
+- Fix SQL filtering with DuckDB
+- Tests: Add software tests
+- Improve documentation
+- CI: Add GHA configuration to invoke software tests
+- CI/Tests: Fix installation on Python 3.7 to 3.9
+- Dependencies: Switch from ``appdirs`` to ``platformdirs``
 
 2020-12-29 0.11.0
 =================

Makefile

@@ -1,43 +1,67 @@
+# =============
+# Configuration
+# =============
+
+$(eval venv         := .venv)
+$(eval pip          := $(venv)/bin/pip)
+$(eval python       := $(venv)/bin/python)
+$(eval pytest       := $(venv)/bin/pytest)
+$(eval bumpversion  := $(venv)/bin/bumpversion)
+$(eval twine        := $(venv)/bin/twine)
+
+
 # ============
 # Main targets
 # ============
 
+# Run software tests.
+.PHONY: test
+test: install-package install-tests
+	$(pytest)
+
 # Release this piece of software
 # Synopsis:
 #   make release bump=minor  (major,minor,patch)
-release: bumpversion push sdist pypi-upload
+release: bumpversion push build pypi-upload
 
 # Build the documentation
 docs-html: install-doctools
-	$(eval venvpath := ".venv_project")
 	touch doc/index.rst
-	export SPHINXBUILD="`pwd`/$(venvpath)/bin/sphinx-build"; cd doc; make html
+	export SPHINXBUILD="`pwd`/$(venv)/bin/sphinx-build"; cd doc; make html
 
 
 # ===============
 # Utility targets
 # ===============
 bumpversion: install-releasetools
-	$(eval venvpath := ".venv_project")
-	@$(venvpath)/bin/bumpversion $(bump)
+	@$(bumpversion) $(bump)
 
 push:
 	git push && git push --tags
 
-sdist:
-	$(eval venvpath := ".venv_project")
-	@$(venvpath)/bin/python setup.py sdist
+build:
+	@$(python) -m build
 
 pypi-upload: install-releasetools
-	$(eval venvpath := ".venv_project")
-	@$(venvpath)/bin/twine upload --skip-existing dist/*.tar.gz
+	@$(twine) upload --skip-existing dist/*.tar.gz
+
+
+# =================
+# Installer targets
+# =================
+
+install-package:
+	@test -e $(python) || python3 -m venv $(venv)
+	$(pip) install --prefer-binary --editable=.[test,develop,release,sql]
 
 install-doctools:
-	$(eval venvpath := ".venv_project")
-	@test -e $(venvpath)/bin/python || `command -v virtualenv` --python=`command -v python` $(venvpath)
-	@$(venvpath)/bin/pip install --quiet --requirement requirements-docs.txt --upgrade
+	@test -e $(python) || python3 -m venv $(venv)
+	$(pip) install --requirement requirements-docs.txt --upgrade
 
 install-releasetools:
-	$(eval venvpath := ".venv_project")
-	@test -e $(venvpath)/bin/python || `command -v virtualenv` --python=`command -v python` $(venvpath)
-	@$(venvpath)/bin/pip install --quiet --requirement requirements-release.txt --upgrade
+	@test -e $(python) || python3 -m venv $(venv)
+	$(pip) install --requirement requirements-release.txt --upgrade
+
+install-tests:
+	@test -e $(python) || python3 -m venv $(venv)
+	$(pip) install --requirement requirements-tests.txt --upgrade