Merge pull request #1 from DavidStirling/master

Update bioformats dependencies

.github/workflows/build.yml

@@ -0,0 +1,37 @@
+name: Build
+
+on:
+  push:
+    branches: [ master ]
+    tags:
+      - '*'
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        architecture: x64
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip setuptools build numpy
+        pip install .[test]
+    - name: Run tests
+      run: pytest
+    - name: Build wheel
+      run: python -m build --wheel
+    - name: Upload Artifact
+      uses: actions/upload-artifact@v4
+      with:
+        path: dist/*.whl
+    - name: Release
+      uses: softprops/action-gh-release@v2
+      if: startsWith(github.ref, 'refs/tags/')
+      with:
+        files: dist/*.whl
+

bioformats/__init__.py

@@ -24,7 +24,7 @@
 
 _jars_dir = os.path.join(os.path.dirname(__file__), 'jars')
 
-JAR_VERSION = '6.5.1'
+JAR_VERSION = '7.3.1'
 
 JARS = javabridge.JARS + [os.path.realpath(os.path.join(_jars_dir, name + '.jar'))
                           for name in ['bioformats_package']]

setup.cfg

@@ -1,11 +1,3 @@
 [nosetests]
 with-javabridge = True
-classpath = bioformats/jars/loci_tools.jar
-
-[build_sphinx]
-source-dir = docs/
-build-dir  = docs/_build
-all_files  = 1
-
-[upload_sphinx]
-upload-dir = docs/_build/html
+classpath = bioformats/jars/bioformats_package.jar

setup.py

@@ -6,7 +6,6 @@
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "License :: OSI Approved :: GNU General Public License v2 (GPLv2)",
-        "Programming Language :: Python :: 2",
         "Programming Language :: Python :: 3",
         "Programming Language :: Java",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
@@ -15,7 +14,7 @@
     description="Read and write life sciences file formats",
     extras_require={
         "test": [
-            "pytest>=3.3.2,<4"
+            "pytest>=6.1"
         ]
     },
     install_requires=[
@@ -42,5 +41,5 @@
         "bioformats"
     ],
     url="http://github.com/CellProfiler/python-bioformats/",
-    version="4.1.0"
+    version="4.1.10001"
 )