CI: switch from Travis CI to GitHub Actions

.github/workflows/ci.yml

@@ -0,0 +1,22 @@
+---
+name: ci
+
+# yamllint disable-line rule:truthy
+on:
+  push:
+  pull_request:
+
+concurrency:
+  group: ci-${{github.ref}}-${{github.event.pull_request.number || github.run_number}}
+  cancel-in-progress: true
+
+jobs:
+  test-and-package:
+    uses: ./.github/workflows/test_and_package.yml
+    secrets: inherit
+  all:
+    needs: [test-and-package]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Success
+        run: "true"

.github/workflows/test_and_package.yml

@@ -0,0 +1,97 @@
+---
+# yamllint disable rule:line-length
+name: run tests and create installable packages
+
+# yamllint disable-line rule:truthy
+on:
+  workflow_dispatch:
+  workflow_call:
+
+concurrency:
+  group: test-${{github.ref}}-${{github.event.pull_request.number || github.run_number}}
+  cancel-in-progress: true
+
+jobs:
+
+  run-tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - 3.8
+          - 3.9
+          - "3.10"
+          - 3.11
+          # 3.12 has problems with older NumPy
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install test dependencies
+        run: |
+          python -m pip install -U setuptools pip
+          python -m pip install pytest pytest-cov
+      - name: Install package
+        run: |
+          python -m pip install .
+      - name: Test
+        run: |
+          python -m pytest --cov=loompy
+      - name: Install pypa/build
+        run: |
+          python -m pip install build
+      - name: Build distribution packages (binary wheel and source tarball)
+        run: |
+          python -m build
+      - name: Check packages with twine
+        run: |
+          python -m pip install twine
+          python -m twine check dist/*
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+        if: matrix.python-version == '3.11'
+
+  # We check the installation using all Python versions using the packages
+  # created from a single version, since the packages are platform and version
+  # independent.
+  check-installation:
+    needs:
+      - run-tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        install-method: [wheel, source]
+        python-version:
+          - 3.8
+          - 3.9
+          - "3.10"
+          - 3.11
+          # 3.12 has problems with older NumPy
+    steps:
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Download the distribution packages
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Update environment
+        run: |
+          python -m pip install -U setuptools pip
+      - name: Install from wheel
+        run: |
+          python -m pip install dist/*.whl
+        if: matrix.install-method == 'wheel'
+      - name: Install from source
+        run: |
+          python -m pip install dist/*.tar.gz
+        if: matrix.install-method == 'source'
+      - name: Check installation
+        run: |
+          cd ~
+          python -c 'import loompy; print(loompy.__version__)'

setup.py

@@ -1,3 +1,4 @@
+from pathlib import Path
 from setuptools import find_packages, setup
 
 # First update the version in loompy/_version.py, then:
@@ -17,8 +18,8 @@
 	name="loompy",
 	version=__version__,
 	packages=find_packages(),
-	python_requires='>=3.6',
-	install_requires=['h5py', 'numpy', 'scipy', 'setuptools', 'numba', 'click', "numpy-groupies"],
+	python_requires='>=3.6,<3.12',
+	install_requires=['h5py', 'numpy<1.24', 'scipy', 'setuptools', 'numba', 'click', "numpy-groupies"],
 	entry_points='''
 		[console_scripts]
 		loompy=loompy.commands:cli
@@ -27,6 +28,8 @@
 	author="Linnarsson Lab",
 	author_email="[email protected]",
 	description="Work with Loom files for single-cell RNA-seq data",
+	long_description=Path("README.md").read_text(encoding="utf-8"),
+	long_description_content_type="text/markdown",
 	license="BSD",
 	keywords="loom omics transcriptomics bioinformatics",
 	url="https://github.com/linnarsson-lab/loompy",

tests/test_file_attribute_manager.py

@@ -15,7 +15,7 @@ def setUp(self):
 		f = NamedTemporaryFile(suffix="loom")
 		f.close()
 		self.filename = f.name
-		self.file = h5py.File(f.name)
+		self.file = h5py.File(f.name, mode="w")
 		self.file.attrs["arr"] = self.VALUE_IN_FILE
 
 	def tearDown(self):