From 1ec968e70531c607eb6ca6818b0a31bbaf4c8f5f Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Thu, 17 Oct 2024 11:36:01 +0100
Subject: [PATCH 1/4] Test upgrade bioformats

---
 .github/workflows/build.yml | 31 +++++++++++++++++++++++++++++++
 bioformats/__init__.py      |  2 +-
 setup.cfg                   | 10 +---------
 setup.py                    |  3 +--
 4 files changed, 34 insertions(+), 12 deletions(-)
 create mode 100644 .github/workflows/build.yml

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
new file mode 100644
index 0000000..a2d9ac2
--- /dev/null
+++ b/.github/workflows/build.yml
@@ -0,0 +1,31 @@
+name: Build
+
+on:
+  push:
+    branches: [ master ]
+  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
+
+
diff --git a/bioformats/__init__.py b/bioformats/__init__.py
index 4e012a6..4297961 100644
--- a/bioformats/__init__.py
+++ b/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']]
diff --git a/setup.cfg b/setup.cfg
index 29ac0d7..ef425da 100644
--- a/setup.cfg
+++ b/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
diff --git a/setup.py b/setup.py
index 74cdd65..f7c8738 100644
--- a/setup.py
+++ b/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",
@@ -42,5 +41,5 @@
         "bioformats"
     ],
     url="http://github.com/CellProfiler/python-bioformats/",
-    version="4.1.0"
+    version="4.1.10001"
 )

From ec72f31e2b2c5ea13499cba86a8842787aee2e4e Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Thu, 17 Oct 2024 11:50:29 +0100
Subject: [PATCH 2/4] Bump pytest

---
 .travis.yml | 25 -------------------------
 setup.py    |  2 +-
 2 files changed, 1 insertion(+), 26 deletions(-)
 delete mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 3c153da..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-language: python
-python:
-- 3.8
-sudo: false
-notifications:
-  email: false
-install:
-- pip install --upgrade pip wheel
-- pip install --upgrade numpy
-- pip install sphinx
-- pip install --upgrade .[test]
-script:
-- pytest
-- cd docs && make html && cd ..
-deploy:
-  provider: pypi
-  user: aether
-  password:
-    secure: Z88A/qARvvwFdogCnwiybg9g8+FTiJmTKh4rkfoOkFJP02dirWC3lDf8ZEUGo8Uk9QgO+M9BhcJR6vy7STGHYuVF+xC3lz9nuIQj39JkGfHOdy2aUOwiNQLES6jVGEzhJdDv4mJ5Wg481m0ZFGFxzjnAkpVBR2wxCyN80hcOXPc=
-  distributions: "sdist bdist_wheel"
-  on:
-    python: 3.8
-    tags: true
-    repo: CellProfiler/python-bioformats
-  skip_cleanup: true
diff --git a/setup.py b/setup.py
index f7c8738..ecfd203 100644
--- a/setup.py
+++ b/setup.py
@@ -14,7 +14,7 @@
     description="Read and write life sciences file formats",
     extras_require={
         "test": [
-            "pytest>=3.3.2,<4"
+            "pytest>=6.1"
         ]
     },
     install_requires=[

From fed48ec05b3ac37d9dec05f0e66404dfe310a703 Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 14:02:48 +0100
Subject: [PATCH 3/4] Releaser

---
 .github/workflows/build.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index a2d9ac2..cb390b3 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -27,5 +27,9 @@ jobs:
       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
 

From 0a45da77c908f4c35cb6ab08c6d9257bdca274dc Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 14:08:56 +0100
Subject: [PATCH 4/4] Releaser

---
 .github/workflows/build.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index cb390b3..8d7f1ad 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -3,6 +3,8 @@ name: Build
 on:
   push:
     branches: [ master ]
+    tags:
+      - '*'
   pull_request:
     branches: [ master ]