Merge pull request #4 from matthias-baer/master

Migrate to pyproject.toml

.github/workflows/check.yml

@@ -4,37 +4,37 @@ on:
   push:
   pull_request:
   schedule:
-  - cron: "0 0 1 * *"
+    - cron: "0 0 1 * *"
 
 jobs:
   build:
 
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.7', '3.8']
-        os: [macos-latest, ubuntu-latest, windows-latest]
+        python-version: [ '3.9', '3.10', '3.12' ]
+        os: [ macos-latest, ubuntu-latest, windows-latest ]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        # prerequisites
-        python -m pip install --upgrade pip wheel
-        python -m pip install coverage flake8 pytest
-        # install dependencies
-        pip install -e .
-        # show installed packages
-        pip freeze
-    - name: Test with pytest
-      run: |
-        coverage run --source=flimage -m pytest tests
-    - name: Lint with flake8
-      run: |
-        flake8 --exclude _version.py .
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          # prerequisites
+          python -m pip install --upgrade pip wheel
+          python -m pip install coverage flake8 pytest
+          # install dependencies
+          pip install -e .
+          # show installed packages
+          pip freeze
+      - name: Test with pytest
+        run: |
+          coverage run --source=flimage -m pytest tests
+      - name: Lint with flake8
+        run: |
+          flake8 --exclude _version.py .
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3

.gitignore

@@ -104,3 +104,4 @@ venv.bak/
 .mypy_cache/
 _version_save.py
 .idea
+_version.py

pyproject.toml

@@ -0,0 +1,41 @@
+[build-system]
+requires = ["setuptools", "wheel", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "flimage"
+authors = [
+    {name = "Paul Müller", email = "[email protected]"}
+]
+description = "library for manipulating fluorescence microscopy series data"
+readme = "README.rst"
+license = {file = "LICENSE"}
+requires-python = ">=3.6, <4"
+dynamic = ["version"]
+keywords = ["fluorescence microscopy", "bleach correction"]
+classifiers = [
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Intended Audience :: Science/Research"
+]
+
+dependencies = [
+    "h5py>=2.7.0",
+    "lmfit>=0.9.8",
+    "numpy>=1.9.0",
+    "qpimage>=0.5.1",
+    "scikit-image>=0.11.0"
+]
+
+[project.urls]
+Homepage = "https://github.com/RI-imaging/flimage"
+
+[tool.setuptools_scm]
+write_to = "flimage/_version.py"
+version_scheme = "post-release"
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["flimage"]
+
+

tests/test_series.py

@@ -126,7 +126,7 @@ def test_series_meta():
         flimage.FLImage(h5file=h5file,
                         meta_data={"pixel size": 0.054e-6},
                         h5mode="r")
-    except (OSError, RuntimeError):
+    except (OSError, RuntimeError, KeyError):
         # no write intent on file
         pass
     else: