(chore): a modern python package

.github/workflows/test.yml

@@ -0,0 +1,28 @@
+name: Python Tests
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.10, 3.11, 3.12]
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Install UV
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "0.5.0"
+          enable-cache: true
+          cache-dependency-glob:  |
+            pyproject.toml
+
+      - name: Install python deps
+        run: |
+          uv pip install --system -e ".[test]"
+
+      - name: Python Tests
+        run: pytest

.gitignore

@@ -24,6 +24,7 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+/generate_tiff_offsets/_version.py
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+build-backend = "hatchling.build"
+requires = ["hatchling", "hatch-vcs"]
+
+[project]
+name = "generate-tiff-offsets"
+description = "A package to generate TIFF offsets"
+authors = [
+    { name = "Ilan Gold", email = "[email protected]" }
+]
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "Environment :: Console",
+    "Framework :: Jupyter",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Visualization",
+]
+license = { text = "MIT" }
+dependencies = ["tifffile>=2023.9.26"]
+dynamic = ["version"]
+[project.optional-dependencies]
+test = ["pytest"]
+
+[tool.hatch.version]
+source = "vcs"
+[tool.hatch.build.hooks.vcs]
+version-file = "generate_tiff_offsets/_version.py"
+[tool.hatch.build.targets.wheel]
+packages = ["src/anndata", "src/testing"]

tests/test_generate_tiff_offsets.py

@@ -1,21 +1,14 @@
 #!/usr/bin/env python
 
 """Tests for `generate_tiff_offsets` package."""
-
-
-import unittest
 import json
 
 from generate_tiff_offsets.generate_tiff_offsets import generate_tiff_offsets
 
-
-class TestGenerate_tiff_offsets(unittest.TestCase):
-    """Tests for `generate_tiff_offsets` package."""
-
-    def test_offsets(self):
-        generate_tiff_offsets('./tests/test-input/multi-channel.ome.tif')
-        with open('./tests/test-output-expected/multi-channel.offsets.json', 'r') as f:
-            expected = json.loads(f.read())
-        with open('./tests/test-input/multi-channel.offsets.json', 'r') as f:
-            actual = json.loads(f.read())
-        assert(actual == expected)
+def test_offsets():
+    generate_tiff_offsets('./tests/test-input/multi-channel.ome.tif')
+    with open('./tests/test-output-expected/multi-channel.offsets.json', 'r') as f:
+        expected = json.loads(f.read())
+    with open('./tests/test-input/multi-channel.offsets.json', 'r') as f:
+        actual = json.loads(f.read())
+    assert(actual == expected)