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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.
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‎.github/workflows/build.yml‎

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

‎.gitignore‎

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/dist/
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/doc/_build/
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/src/pyimagej.egg-info/
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/Fiji
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/Fiji.app
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/fiji-nojre.zip
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/fiji-*.zip
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/uv.lock
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MANIFEST
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.vscode/settings.json
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.vscode/launch.json

‎Makefile‎

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

‎README.md‎

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

‎bin/fmt.sh‎

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cd "$dir/.."
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exitCode=0
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ruff check --fix
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uv run ruff check --fix
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code=$?; test $code -eq 0 || exitCode=$code
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ruff format
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uv run ruff format
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code=$?; test $code -eq 0 || exitCode=$code
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exit $exitCode

‎bin/lint.sh‎

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cd "$dir/.."
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exitCode=0
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ruff check
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uv run ruff check
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code=$?; test $code -eq 0 || exitCode=$code
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ruff format --check
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uv run ruff format --check
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code=$?; test $code -eq 0 || exitCode=$code
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validate-pyproject pyproject.toml
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uv run validate-pyproject pyproject.toml
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code=$?; test $code -eq 0 || exitCode=$code
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exit $exitCode

‎bin/test.sh‎

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| Testing ImageJ2 + original ImageJ |--legacy=true
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| Testing ImageJ2 standalone |--legacy=false
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| Testing Fiji Is Just ImageJ(2) |--ij=sc.fiji:fiji
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| Testing locally wrapped Fiji.app |--ij=Fiji.app
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| Testing local Fiji-Stable |--ij=Fiji.app
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| Testing local Fiji-Latest |--ij=Fiji
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| Testing ImageJ2 version 2.10.0 |--ij=2.10.0
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| Testing ImageJ2 version 2.14.0 |--ij=2.14.0
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"
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if [ ! -d Fiji.app ]
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then
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# No locally available Fiji.app; download one.
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echo "-- Downloading and unpacking Fiji.app --"
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# No locally available Fiji-Stable; download one.
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echo "-- Downloading and unpacking Fiji-Stable --"
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curl -fsLO https://downloads.imagej.net/fiji/stable/fiji-stable-portable-nojava.zip
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unzip fiji-stable-portable-nojava.zip
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echo
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fi
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if [ ! -d Fiji ]
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then
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# No locally available Fiji-Latest; download one.
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echo "-- Downloading and unpacking Fiji-Latest --"
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curl -fsLO https://downloads.imagej.net/fiji/latest/fiji-latest-portable-nojava.zip
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unzip fiji-latest-portable-nojava.zip
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echo
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fi
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echo "$modes" | while read mode
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do
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test "$mode" || continue
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msg="${mode%|*}|"
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flag=${mode##*|}
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echo "-------------------------------------"
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echo "$msg"
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echo "-------------------------------------"
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if [ $# -gt 0 ]
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then
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python -m pytest -p no:faulthandler $flag $@
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else
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python -m pytest -p no:faulthandler $flag tests
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fi
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code=$?
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if [ $code -ne 0 ]
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then
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# HACK: `while read` creates a subshell, which can't modify the parent
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# shell's variables. So we save the failure code to a temporary file.
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echo $code >exitCode.tmp
44-
fi
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for java in 8 21
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do
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# Fiji-Latest requires Java 21; skip Fiji-Latest + Java 8.
42+
echo "$msg" | grep -q Fiji-Latest && test "$java" -eq 8 && continue
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echo "-------------------------------------"
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echo "$msg"
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printf "| < OpenJDK %2s > |\n" "$java"
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echo "-------------------------------------"
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if [ $# -gt 0 ]
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then
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uv run python -m pytest -p no:faulthandler $flag --java $java $@
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else
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uv run python -m pytest -p no:faulthandler $flag --java $java tests
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fi
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code=$?
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if [ $code -eq 0 ]
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then
57+
echo "==> TESTS PASSED with code 0"
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else
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# HACK: `while read` creates a subshell, which can't modify the parent
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# shell's variables. So we save the failure code to a temporary file.
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echo
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echo "==> TESTS FAILED with code $code"
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echo $code >exitCode.tmp
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fi
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echo
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done
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done
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exitCode=0
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if [ -f exitCode.tmp ]

‎conftest.py‎

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import pytest
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import imagej
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import imagej.doctor
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from scyjava import config
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def pytest_addoption(parser):
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"""
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Set up the command line parser for ImageJ location and headless mode
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Set up the command line parser for ImageJ2 location and headless mode
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:param parser: pytest's parser, passed in automatically
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:return: None
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"""
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default=True,
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help="Include the original ImageJ",
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)
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parser.addoption(
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"--java",
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action="store",
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default=None,
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help="version of Java to cache and use (e.g. 8, 11, 17, 21)",
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)
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@pytest.fixture(scope="session")
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def ij(request):
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"""
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Create an ImageJ instance to be used by the whole testing environment
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Create an ImageJ2 gateway to be used by the whole testing environment
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:param request: Pytest variable passed in to fixtures
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"""
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# enable debug logging
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imagej.doctor.debug_to_stderr()
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# get test configuration
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ij_dir = request.config.getoption("--ij")
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legacy = request.config.getoption("--legacy")
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headless = request.config.getoption("--headless")
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# add the nashorn (JavaScript) endpoint if needed,
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# nashorn was bundled with the JDK from Java 8 to 14
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if capture_java_version() > 14:
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java_version = request.config.getoption("--java")
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config.set_java_constraints(fetch=True, vendor='zulu', version=java_version)
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# JavaScript is used in the tests. But the Nashorn engine was
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# dropped from the JDK at v15, so we readd it here if needed.
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if int(java_version) >= 15:
5061
config.endpoints.append("org.openjdk.nashorn:nashorn-core")
51-
imagej.when_imagej_starts(lambda ij: setattr(ij, "_testing", True))
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# initialize the ImageJ gateway
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imagej.when_imagej_starts(lambda ij: setattr(ij, "_java_version", java_version))
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# initialize the ImageJ2 gateway
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mode = "headless" if headless else "interactive"
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ij = imagej.init(ij_dir, mode=mode, add_legacy=legacy)
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yield ij
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ij.dispose()
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def capture_java_version() -> int:
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"""Capture the installed Java version.
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This function captures the JDK version installed in the current
65-
venv without starting the JVM by parsing the Java "-version"
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output string.
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:return: The major Java version (8, 11, 21 etc...).
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"""
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try:
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# capture the Java version string
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java_ver_str = subprocess.run(
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["java", "-version"], capture_output=True, text=True
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)
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# extract the Java version from the string
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java_ver = java_ver_str.stderr.split("\n")[0].split(" ")[2]
77-
java_ver = java_ver.strip('"').split(".")
78-
major_ver_arr = [int(java_ver[i]) for i in range(2)]
79-
# find major Java version
80-
if major_ver_arr[0] == 1:
81-
return major_ver_arr[1] # Java 8-10
82-
else:
83-
return major_ver_arr[0] # Java 11+
84-
except FileNotFoundError:
85-
raise RuntimeError("No Java installation found.")
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def str2bool(v):
8972
"""
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Convert string inputs into bool

‎dev-environment.yml‎

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‎doc/Install.md‎

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There are two supported ways to install PyImageJ: via
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[conda](https://conda.io/)/[mamba](https://mamba.readthedocs.io/) or via
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[pip](https://packaging.python.org/guides/tool-recommendations/).
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Although both tools are great
7-
[for different reasons](https://www.anaconda.com/blog/understanding-conda-and-pip),
8-
if you have no strong preference then we suggest using mamba because it will
9-
manage PyImageJ's non-Python dependencies:
10-
[Java](https://www.azul.com/downloads/?version=java-8-lts&package=jdk#zulu) (a.k.a. Java) and
11-
[Maven](https://maven.apache.org/install.html). If you use pip, you will need to install
12-
those two things separately.
6+
Both tools are great
7+
[for different reasons](https://www.anaconda.com/blog/understanding-conda-and-pip).
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## Installing via conda/mamba
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