Merge branch 'better-testing'

* Test both Fiji-Stable and Fiji-Latest.
* Test both Java 8 and Java 21 via cjdk.
* Work around JPMS encapsulation woes.
* Switch to uv for environment management.

Author: ctrueden

.github/workflows/build.yml

@@ -18,7 +18,6 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ["3.9", "3.13"]
-        java-version: ["8", "21"]
 
 
     steps:
@@ -28,11 +27,6 @@ jobs:
       with:
         python-version: ${{matrix.python-version}}
 
-    - uses: actions/setup-java@v3
-      with:
-        java-version: ${{matrix.java-version}}
-        distribution: 'zulu'
-
     - name: Install PyImageJ
       run: |
         python -m pip install --upgrade pip

.gitignore

@@ -7,8 +7,10 @@
 /dist/
 /doc/_build/
 /src/pyimagej.egg-info/
+/Fiji
 /Fiji.app
-/fiji-nojre.zip
+/fiji-*.zip
+/uv.lock
 MANIFEST
 .vscode/settings.json
 .vscode/launch.json

Makefile

@@ -1,36 +1,28 @@
 help:
 	@echo "Available targets:\n\
 		clean - remove build files and directories\n\
-		setup - create mamba developer environment\n\
 		lint  - run code formatters and linters\n\
 		test  - run automated test suite\n\
 		docs  - generate documentation site\n\
 		dist  - generate release archives\n\
-	\n\
-	Remember to 'mamba activate pyimagej-dev' first!"
+	"
 
 clean:
 	bin/clean.sh
 
-setup:
-	bin/setup.sh
-
-check:
-	@bin/check.sh
-
-lint: check
+lint:
 	bin/lint.sh
 
-fmt: check
+fmt:
 	bin/fmt.sh
 
-test: check
+test:
 	bin/test.sh
 
-docs: check
+docs:
 	cd doc && $(MAKE) html
 
-dist: check clean
-	python -m build
+dist: clean
+	uv run python -m build
 
 .PHONY: tests

README.md

@@ -43,32 +43,30 @@ PyImageJ has been tested on the following operating systems:
 
 PyImageJ requires the following packages:
 
-* Python >= 3.7
+* Python >= 3.9
 * [imglyb] >= 2.1.0
 * [jgo] >= 1.0.3
 * [JPype] >= 1.3.0
 * [labeling] >= 0.1.14
 * [matplotlib] \(optional, for `ij.py.show` function only)
 * [NumPy]
-* [scyjava] >= 1.8.0
+* [scyjava] >= 1.12.0
 * [xarray]
 
 PyImageJ will not function properly if dependency versions are too old.
 
-In addition, PyImageJ requires [OpenJDK] and [Maven] to be installed.
-
 ## Installation
 
-On Mac and Linux, PyImageJ can be installed using [Conda]+[Mamba]. Here is how to create
-and activate a new conda environment with PyImageJ available:
+On Mac and Linux, PyImageJ can be installed using [Conda]+[Mamba]. Here is
+how to create and activate a new conda environment with PyImageJ available:
 
 ```
 conda install mamba -n base -c conda-forge
-mamba create -n pyimagej -c conda-forge pyimagej openjdk=8
+mamba create -n pyimagej -c conda-forge pyimagej
 conda activate pyimagej
 ```
 
-You can also `pip install pyimagej`, but will then need to install OpenJDK and Maven manually.
+Alternately, you can `pip install pyimagej`.
 
 Installation time takes approximately 20 seconds. Initializing PyImageJ
 takes an additional ~30 seconds to ~2-3 minutes (depending on bandwidth)
@@ -150,7 +148,5 @@ For details on how to develop the PyImageJ codebase, see
 [NumPy]: https://numpy.org/
 [scyjava]: https://github.com/scijava/scyjava
 [xarray]: https://docs.xarray.dev/
-[OpenJDK]: https://en.wikipedia.org/wiki/OpenJDK
-[Maven]: https://maven.apache.org/
 [Conda]: https://conda.io/
 [Mamba]: https://mamba.readthedocs.io/

bin/fmt.sh

@@ -4,8 +4,8 @@ dir=$(dirname "$0")
 cd "$dir/.."
 
 exitCode=0
-ruff check --fix
+uv run ruff check --fix
 code=$?; test $code -eq 0 || exitCode=$code
-ruff format
+uv run ruff format
 code=$?; test $code -eq 0 || exitCode=$code
 exit $exitCode

bin/lint.sh

@@ -4,10 +4,10 @@ dir=$(dirname "$0")
 cd "$dir/.."
 
 exitCode=0
-ruff check
+uv run ruff check
 code=$?; test $code -eq 0 || exitCode=$code
-ruff format --check
+uv run ruff format --check
 code=$?; test $code -eq 0 || exitCode=$code
-validate-pyproject pyproject.toml
+uv run validate-pyproject pyproject.toml
 code=$?; test $code -eq 0 || exitCode=$code
 exit $exitCode

bin/test.sh

@@ -7,41 +7,63 @@ modes="
 | Testing ImageJ2 + original ImageJ |--legacy=true
 |    Testing ImageJ2 standalone     |--legacy=false
 |  Testing Fiji Is Just ImageJ(2)   |--ij=sc.fiji:fiji
-|  Testing locally wrapped Fiji.app |--ij=Fiji.app
+|  Testing local Fiji-Stable        |--ij=Fiji.app
+|  Testing local Fiji-Latest        |--ij=Fiji
 |  Testing ImageJ2 version 2.10.0   |--ij=2.10.0
 |  Testing ImageJ2 version 2.14.0   |--ij=2.14.0
 "
 
 if [ ! -d Fiji.app ]
 then
-  # No locally available Fiji.app; download one.
-  echo "-- Downloading and unpacking Fiji.app --"
+  # No locally available Fiji-Stable; download one.
+  echo "-- Downloading and unpacking Fiji-Stable --"
   curl -fsLO https://downloads.imagej.net/fiji/stable/fiji-stable-portable-nojava.zip
   unzip fiji-stable-portable-nojava.zip
   echo
 fi
 
+if [ ! -d Fiji ]
+then
+  # No locally available Fiji-Latest; download one.
+  echo "-- Downloading and unpacking Fiji-Latest --"
+  curl -fsLO https://downloads.imagej.net/fiji/latest/fiji-latest-portable-nojava.zip
+  unzip fiji-latest-portable-nojava.zip
+  echo
+fi
+
 echo "$modes" | while read mode
 do
   test "$mode" || continue
   msg="${mode%|*}|"
   flag=${mode##*|}
-  echo "-------------------------------------"
-  echo "$msg"
-  echo "-------------------------------------"
-  if [ $# -gt 0 ]
-  then
-    python -m pytest -p no:faulthandler $flag $@
-  else
-    python -m pytest -p no:faulthandler $flag tests
-  fi
-  code=$?
-  if [ $code -ne 0 ]
-  then
-    # HACK: `while read` creates a subshell, which can't modify the parent
-    # shell's variables. So we save the failure code to a temporary file.
-    echo $code >exitCode.tmp
-  fi
+  for java in 8 21
+  do
+    # Fiji-Latest requires Java 21; skip Fiji-Latest + Java 8.
+    echo "$msg" | grep -q Fiji-Latest && test "$java" -eq 8 && continue
+
+    echo "-------------------------------------"
+    echo "$msg"
+    printf "|           < OpenJDK %2s >          |\n" "$java"
+    echo "-------------------------------------"
+    if [ $# -gt 0 ]
+    then
+      uv run python -m pytest -p no:faulthandler $flag --java $java $@
+    else
+      uv run python -m pytest -p no:faulthandler $flag --java $java tests
+    fi
+    code=$?
+    if [ $code -eq 0 ]
+    then
+      echo "==> TESTS PASSED with code 0"
+    else
+      # HACK: `while read` creates a subshell, which can't modify the parent
+      # shell's variables. So we save the failure code to a temporary file.
+      echo
+      echo "==> TESTS FAILED with code $code"
+      echo $code >exitCode.tmp
+    fi
+    echo
+  done
 done
 exitCode=0
 if [ -f exitCode.tmp ]

conftest.py

@@ -3,12 +3,13 @@
 import pytest
 
 import imagej
+import imagej.doctor
 from scyjava import config
 
 
 def pytest_addoption(parser):
     """
-    Set up the command line parser for ImageJ location and headless mode
+    Set up the command line parser for ImageJ2 location and headless mode
     :param parser: pytest's parser, passed in automatically
     :return: None
     """
@@ -32,59 +33,41 @@ def pytest_addoption(parser):
         default=True,
         help="Include the original ImageJ",
     )
+    parser.addoption(
+        "--java",
+        action="store",
+        default=None,
+        help="version of Java to cache and use (e.g. 8, 11, 17, 21)",
+    )
 
 
 @pytest.fixture(scope="session")
 def ij(request):
     """
-    Create an ImageJ instance to be used by the whole testing environment
+    Create an ImageJ2 gateway to be used by the whole testing environment
     :param request: Pytest variable passed in to fixtures
     """
+    # enable debug logging
+    imagej.doctor.debug_to_stderr()
     # get test configuration
     ij_dir = request.config.getoption("--ij")
     legacy = request.config.getoption("--legacy")
     headless = request.config.getoption("--headless")
-    # add the nashorn (JavaScript) endpoint if needed,
-    # nashorn was bundled with the JDK from Java 8 to 14
-    if capture_java_version() > 14:
+    java_version = request.config.getoption("--java")
+    config.set_java_constraints(fetch=True, vendor='zulu', version=java_version)
+    # JavaScript is used in the tests. But the Nashorn engine was
+    # dropped from the JDK at v15, so we readd it here if needed.
+    if int(java_version) >= 15:
         config.endpoints.append("org.openjdk.nashorn:nashorn-core")
-    imagej.when_imagej_starts(lambda ij: setattr(ij, "_testing", True))
-    # initialize the ImageJ gateway
+    imagej.when_imagej_starts(lambda ij: setattr(ij, "_java_version", java_version))
+    # initialize the ImageJ2 gateway
     mode = "headless" if headless else "interactive"
     ij = imagej.init(ij_dir, mode=mode, add_legacy=legacy)
-
     yield ij
 
     ij.dispose()
 
 
-def capture_java_version() -> int:
-    """Capture the installed Java version.
-
-    This function captures the JDK version installed in the current
-    venv without starting the JVM by parsing the Java "-version"
-    output string.
-
-    :return: The major Java version (8, 11, 21 etc...).
-    """
-    try:
-        # capture the Java version string
-        java_ver_str = subprocess.run(
-            ["java", "-version"], capture_output=True, text=True
-        )
-        # extract the Java version from the string
-        java_ver = java_ver_str.stderr.split("\n")[0].split(" ")[2]
-        java_ver = java_ver.strip('"').split(".")
-        major_ver_arr = [int(java_ver[i]) for i in range(2)]
-        # find major Java version
-        if major_ver_arr[0] == 1:
-            return major_ver_arr[1]  # Java 8-10
-        else:
-            return major_ver_arr[0]  # Java 11+
-    except FileNotFoundError:
-        raise RuntimeError("No Java installation found.")
-
-
 def str2bool(v):
     """
     Convert string inputs into bool

dev-environment.yml

@@ -3,13 +3,8 @@
 There are two supported ways to install PyImageJ: via
 [conda](https://conda.io/)/[mamba](https://mamba.readthedocs.io/) or via
 [pip](https://packaging.python.org/guides/tool-recommendations/).
-Although both tools are great
-[for different reasons](https://www.anaconda.com/blog/understanding-conda-and-pip),
-if you have no strong preference then we suggest using mamba because it will
-manage PyImageJ's non-Python dependencies:
-[Java](https://www.azul.com/downloads/?version=java-8-lts&package=jdk#zulu) (a.k.a. Java) and
-[Maven](https://maven.apache.org/install.html). If you use pip, you will need to install
-those two things separately.
+Both tools are great
+[for different reasons](https://www.anaconda.com/blog/understanding-conda-and-pip).
 
 ## Installing via conda/mamba