Merge remote-tracking branch 'origin/main' into pr/mkitti/616

Author: Christopher Doris

.github/workflows/benchmark_pr.yml

@@ -0,0 +1,16 @@
+name: Benchmark PR
+on:
+  pull_request:
+
+jobs:
+  bench:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: MilesCranmer/AirspeedVelocity.jl@action-v1
+        with:
+          julia-version: "1"
+          tune: "true"
+          # Post to "summary" tab of workflow run:
+          job-summary: "true"
+          # Run benchmark using PR's version of the script:
+          bench-on: ${{ github.event.pull_request.head.sha }}

.github/workflows/docs.yml

@@ -16,14 +16,13 @@ jobs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
       - run: |
           julia --project=docs -e '
             using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
             Pkg.instantiate()'
       - run: |
           julia --project=docs -e '

.github/workflows/docscleanup.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           ref: gh-pages
 

.github/workflows/register-pypi.yml

@@ -11,11 +11,11 @@ jobs:
   register:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ref: ${{ inputs.git_ref }}
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: "3.10"
     - name: Install build

.github/workflows/tests-nightly.yml

@@ -10,7 +10,7 @@ on:
 
 jobs:
   tests:
-    name: Test (${{ matrix.os }}-${{ matrix.arch }}, julia ${{ matrix.jlversion }})
+    name: Test Julia (${{ matrix.jlversion }}, ${{ matrix.os }}-${{ matrix.arch }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -19,7 +19,7 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-latest]
         jlversion: ['~1.9.0-0', 'nightly']
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ inputs.jl_version }}

.github/workflows/tests.yml

@@ -12,70 +12,121 @@ on:
 
 jobs:
   julia:
-    name: Test (${{ matrix.os }}, julia ${{ matrix.jlversion }})
+    name: Test Julia (${{ matrix.jlversion }}, ${{ matrix.os }}, ${{ matrix.pythonexe }})
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
         arch: [x64] # x86 unsupported by MicroMamba
         os: [ubuntu-latest, windows-latest, macos-latest]
         jlversion: ['1','1.9']
+        pythonexe: ['@CondaPkg']
+        include:
+        - arch: x64
+          os: ubuntu-latest
+          jlversion: '1'
+          pythonexe: python
+
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
+
       - name: Set up Julia ${{ matrix.jlversion }}
         uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.jlversion }}
           arch: ${{ matrix.arch }}
+
       - uses: julia-actions/cache@v2
+
       - name: Build package
         uses: julia-actions/julia-buildpkg@v1
+        env:
+          PYTHON: python
+
       - name: Run tests
         uses: julia-actions/julia-runtest@v1
         env:
           JULIA_DEBUG: PythonCall
           JULIA_NUM_THREADS: '2'
+          PYTHON: python
+          JULIA_PYTHONCALL_EXE: ${{ matrix.pythonexe }}
+
       - name: Process coverage
         uses: julia-actions/julia-processcoverage@v1
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
   python:
-    name: Test (${{ matrix.os }}, python ${{ matrix.pyversion }})
+    name: Test Python (${{ matrix.pyversion }}, ${{ matrix.os }}, ${{ matrix.juliaexe }})
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        pyversion: ["3.x", "3.8"]
+        pyversion: ["3", "3.9"]
+        juliaexe: ["@JuliaPkg"]
+        include:
+        - os: ubuntu-latest
+          pyversion: 3
+          juliaexe: julia
+    env:
+      MANUAL_TEST_PROJECT: /tmp/juliacall-test-project
+      PYTHON_JULIACALL_THREADS: '2'
+      PYTHON_JULIACALL_HANDLE_SIGNALS: 'yes'
+
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
+
       - name: Set up Python ${{ matrix.pyversion }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.pyversion }}
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          python-version: ${{ matrix.pyversion }}
+  
       - name: Set up Julia
+        id: setup_julia
         uses: julia-actions/setup-julia@v2
         with:
           version: '1'
+
+      - name: Set up test Julia project
+        if: ${{ matrix.juliaexe == 'julia' }}
+        run: |
+          mkdir ${{ env.MANUAL_TEST_PROJECT }}
+          julia --project=${{ env.MANUAL_TEST_PROJECT }} -e 'import Pkg; Pkg.develop(path="."); Pkg.instantiate()'
+
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install flake8 pytest pytest-cov nbval numpy
           cp pysrc/juliacall/juliapkg-dev.json pysrc/juliacall/juliapkg.json
-          pip install -e .
+          uv sync --dev
+
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --ignore=F821 --show-source --statistics
+          uv run flake8 ./pysrc ./pytest --count --select=E9,F63,F7,F82 --ignore=F821 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-      - name: Run tests
+          uv run flake8 ./pysrc ./pytest --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Run tests (with JuliaPkg)
+        if: ${{ matrix.juliaexe == '@JuliaPkg' }}
         run: |
-          pytest -s --nbval --cov=pysrc ./pytest/
+          uv run pytest -s --nbval --cov=pysrc ./pytest/
+
+      - name: Run tests (without JuliaPkg)
+        if: ${{ matrix.juliaexe == 'julia' }}
+        run: |
+          uv run pytest -s --nbval --cov=pysrc ./pytest/
         env:
-          PYTHON_JULIACALL_THREADS: '2'
+          PYTHON_JULIACALL_EXE: "${{ steps.setup_julia.outputs.julia-bindir }}/julia"
+          PYTHON_JULIACALL_PROJECT: ${{ env.MANUAL_TEST_PROJECT }}
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5
         env:

CondaPkg.toml

@@ -1,3 +1,6 @@
+[deps.libstdcxx]
+version = "<=julia"
+
 [deps.libstdcxx-ng]
 version = "<=julia"
 
@@ -6,4 +9,4 @@ version = "<=julia"
 
 [deps.python]
 build = "**cpython**"
-version = ">=3.8,<4"
+version = ">=3.9,<4"

Project.toml

@@ -1,7 +1,7 @@
 name = "PythonCall"
 uuid = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
 authors = ["Christopher Doris <github.com/cjdoris>"]
-version = "0.9.25"
+version = "0.9.27"
 
 [deps]
 CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
@@ -10,31 +10,41 @@ Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 UnsafePointers = "e17b2a0c-0bdf-430a-bd0c-3a23cae4ff39"
 
 [compat]
 Aqua = "0 - 999"
-CondaPkg = "0.2.23"
+CategoricalArrays = "0.10, 1"
+CondaPkg = "0.2.30"
 Dates = "1"
 Libdl = "1"
 MacroTools = "0.5"
 Markdown = "1"
 Pkg = "1"
-Requires = "1"
+PyCall = "1"
 Serialization = "1"
 Tables = "1"
 Test = "1"
 TestItemRunner = "0 - 999"
 UnsafePointers = "1"
 julia = "1.9"
 
+[extensions]
+PyCallExt = "PyCall"
+CategoricalArraysExt = "CategoricalArrays"
+
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
+PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
 
 [targets]
-test = ["Aqua", "Test", "TestItemRunner"]
+test = ["Aqua", "PyCall", "Test", "TestItemRunner"]
+
+[weakdeps]
+CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
+PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"

README.md

@@ -14,7 +14,7 @@ Bringing [**Python®**](https://www.python.org/) and [**Julia**](https://juliala
 - Fast non-copying conversion of numeric arrays in either direction: modify Python arrays (e.g. `bytes`, `array.array`, `numpy.ndarray`) from Julia or Julia arrays from Python.
 - Helpful wrappers: interpret Python sequences, dictionaries, arrays, dataframes and IO streams as their Julia counterparts, and vice versa.
 - Beautiful stack-traces.
-- Supports modern systems: tested on Windows, MacOS and Linux, 64-bit, Julia 1.9 upwards and Python 3.8 upwards.
+- Supports modern systems: tested on Windows, MacOS and Linux, 64-bit, Julia 1.9 upwards and Python 3.9 upwards.
 
 ⭐ If you like this, a GitHub star would be lovely thank you. ⭐
 

benchmark/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"