Merge branch 'main' into stubs

Author: tlambert03

.github/workflows/build.yml

@@ -11,7 +11,7 @@ on:
       - main
 
 jobs:
-  build-cross-platform:
+  build:
     name: test ${{matrix.os}} - ${{matrix.python-version}} - ${{matrix.java-version}}
     runs-on: ${{ matrix.os }}
     strategy:
@@ -33,79 +33,30 @@ jobs:
             java-version: ''
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
-    - uses: actions/setup-python@v3
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{matrix.python-version}}
 
-    - uses: actions/setup-java@v3
+    - uses: actions/setup-java@v4
       if: matrix.java-version != ''
       with:
         java-version: ${{matrix.java-version}}
         distribution: 'zulu'
         cache: 'maven'
 
-    - name: Install ScyJava
+    - name: Set up uv
       run: |
         python -m pip install --upgrade pip
-        python -m pip install -e '.[dev]'
+        python -m pip install uv
 
-    - name: Test ScyJava
+    - name: Run tests
+      shell: bash
       run: |
-        bin/test.sh --color=yes
+        bin/test.sh
 
-  ensure-clean-code:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v3
-
-      - name: Lint code
-        run: |
-          python -m pip install ruff
-          ruff check
-          ruff format --check
-
-      - name: Validate pyproject.toml
-        run: |
-          python -m pip install validate-pyproject[all]
-          python -m validate_pyproject pyproject.toml
-
-  conda-dev-test:
-    name: Conda Setup & Code Coverage
-    runs-on: ubuntu-latest
-    defaults:
-      # Steps that rely on the activated environment must be run with this shell setup.
-      # See https://github.com/marketplace/actions/setup-miniconda#important
-      run:
-        shell: bash -l {0}
-    steps:
-      - uses: actions/checkout@v2
-      - name: Cache conda
-        uses: actions/cache@v4
-        env:
-          # Increase this value to reset cache if dev-environment.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('dev-environment.yml') }}
-      - uses: conda-incubator/setup-miniconda@v3
-        with:
-          # Create env with dev packages
-          auto-update-conda: true
-          python-version: 3.9
-          miniforge-version: latest
-          environment-file: dev-environment.yml
-          # Activate scyjava-dev environment
-          activate-environment: scyjava-dev
-          auto-activate-base: false
-          # Use mamba for faster setup
-          use-mamba: true
-      - name: Test scyjava
-        run: |
-          bin/test.sh --cov-report=xml --cov=.
-      # We could do this in its own action, but we'd have to setup the environment again.
-      - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v2
+    - name: Lint code
+      shell: bash
+      run: |
+        bin/lint.sh

.gitignore

@@ -23,3 +23,7 @@ coverage.xml
 # IDEA
 .idea/
 *.iml
+
+# uv
+/.venv/
+/uv.lock

Makefile

@@ -1,32 +1,22 @@
 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\
 		dist  - generate release archives\n\
-	\n\
-	Remember to 'mamba activate scyjava-dev' first!"
+	"
 
 clean:
 	bin/clean.sh
 
-setup:
-	bin/setup.sh
-
 check:
 	@bin/check.sh
 
 lint: check
 	bin/lint.sh
 
-fmt: check
-	bin/fmt.sh
-
 test: check
 	bin/test.sh
 
 dist: check clean
-	python -m build
-
-.PHONY: test
+	bin/dist.sh

bin/check.sh

@@ -1,10 +1,6 @@
 #!/bin/sh
 
-case "$CONDA_PREFIX" in
-  */scyjava-dev)
-    ;;
-  *)
-    echo "Please run 'make setup' and then 'mamba activate scyjava-dev' first."
-    exit 1
-    ;;
-esac
+if ! command -v uv >/dev/null 2>&1; then
+  echo "Please install uv (https://docs.astral.sh/uv/getting-started/installation/)."
+  exit 1
+fi

bin/setup.sh bin/dist.shbin/setup.sh renamed to bin/dist.sh

@@ -3,4 +3,4 @@
 dir=$(dirname "$0")
 cd "$dir/.."
 
-mamba env create -f dev-environment.yml
+uv run python -m build

bin/fmt.sh

@@ -4,10 +4,19 @@ dir=$(dirname "$0")
 cd "$dir/.."
 
 exitCode=0
-ruff check
+
+# Check for errors and capture non-zero exit codes.
+uv run validate-pyproject pyproject.toml
+code=$?; test $code -eq 0 || exitCode=$code
+uv run ruff check >/dev/null 2>&1
 code=$?; test $code -eq 0 || exitCode=$code
-ruff format --check
+uv run ruff format --check >/dev/null 2>&1
 code=$?; test $code -eq 0 || exitCode=$code
-validate-pyproject pyproject.toml
+
+# Do actual code reformatting.
+uv run ruff check --fix
 code=$?; test $code -eq 0 || exitCode=$code
+uv run ruff format
+code=$?; test $code -eq 0 || exitCode=$code
+
 exit $exitCode

bin/lint.sh

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-# Executes the pytest framework in both JPype and Jep modes.
+# Runs the unit tests.
 #
 # Usage examples:
 #   bin/test.sh
@@ -13,26 +13,26 @@ dir=$(dirname "$0")
 cd "$dir/.."
 
 echo
-echo "-------------------------------------------"
-echo "| Testing JPype mode (Java inside Python) |"
-echo "-------------------------------------------"
+echo "----------------------"
+echo "| Running unit tests |"
+echo "----------------------"
 
 if [ $# -gt 0 ]
 then
-  python -m pytest -p no:faulthandler $@
+  uv run python -m pytest -v -p no:faulthandler $@
 else
-  python -m pytest -p no:faulthandler tests/
+  uv run python -m pytest -v -p no:faulthandler tests/
 fi
 jpypeCode=$?
 
 echo
-echo "-------------------------------------------"
-echo "| Running integration tests (JPype only)  |"
-echo "-------------------------------------------"
+echo "-----------------------------"
+echo "| Running integration tests |"
+echo "-----------------------------"
 itCode=0
 for t in tests/it/*.py
 do
-  python "$t"
+  uv run python "$t"
   code=$?
   printf -- "--> %s " "$t"
   if [ "$code" -eq 0 ]
@@ -44,64 +44,6 @@ do
   fi
 done
 
-echo
-echo "-------------------------------------------"
-echo "|  Testing Jep mode (Python inside Java)  |"
-echo "-------------------------------------------"
-
-# Discern the Jep installation.
-site_packages=$(python -c 'import sys; print(next(p for p in sys.path if p.endswith("site-packages")))')
-test -d "$site_packages/jep" || {
-  echo "[ERROR] Failed to detect Jep installation in current environment!" 1>&2
-  exit 1
-}
-
-# We execute the pytest framework through Jep via jgo, so that
-# the surrounding JVM includes scijava-table on the classpath.
-#
-# Arguments to the shell script are translated into an argument
-# list to the pytest.main function. A weak attempt at handling
-# special characters, e.g. single quotation marks and backslashes,
-# is made, but there are surely other non-working cases.
-
-if [ $# -gt 0 ]
-then
-  a=$(echo "$@" | sed 's/\\/\\\\/g')     # escape backslashes
-  a=$(echo "$a" | sed 's/'\''/\\'\''/g') # escape single quotes
-  a=$(echo "$a" | sed 's/ /'\'','\''/g') # replace space with ','
-  argString="['-v', '$a']"
-else
-  argString=""
-fi
-if ! java -version 2>&1 | grep -q '^openjdk version "\(1\.8\|9\|10\|11\|12\|13\|14\|15\|16\)\.'
-then
-  echo "Skipping jep tests due to unsupported Java version:"
-  java -version || true
-  jepCode=0
-elif [ "$(uname -s)" = "Darwin" ]
-then
-  echo "Skipping jep tests on macOS due to flakiness"
-  jepCode=0
-else
-  echo "# AUTOGENERATED test file for jep; safe to delete.
-import logging, sys, pytest, scyjava
-scyjava._logger.addHandler(logging.StreamHandler(sys.stderr))
-scyjava._logger.setLevel(logging.INFO)
-scyjava.config.set_verbose(2)
-result = pytest.main($argString)
-if result:
-  sys.exit(result)
-" > jep_test.py
-  jgo -vv \
-    -r scijava.public=https://maven.scijava.org/content/groups/public \
-    -Djava.library.path="$site_packages/jep" \
-    black.ninia:jep:jep.Run+org.scijava:scijava-table \
-    jep_test.py
-  jepCode=$?
-  rm -f jep_test.py
-fi
-
 test "$jpypeCode" -ne 0 && exit "$jpypeCode"
 test "$itCode" -ne 0 && exit "$itCode"
-test "$jepCode" -ne 0 && exit "$jepCode"
 exit 0