Merge remote-tracking branch 'origin/main' into less-getptr

Author: Christopher Doris

.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

.github/workflows/tests.yml

@@ -12,70 +12,88 @@ on:
 
 jobs:
   julia:
-    name: Test (${{ matrix.os }}, julia ${{ matrix.jlversion }})
+    name: Test Julia (${{ matrix.jlversion }}, ${{ matrix.os }})
     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']
+
     steps:
       - uses: actions/checkout@v4
+
       - 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
+
       - name: Run tests
         uses: julia-actions/julia-runtest@v1
         env:
           JULIA_DEBUG: PythonCall
           JULIA_NUM_THREADS: '2'
+
       - 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 }})
     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", "3.8"]
+
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Python ${{ matrix.pyversion }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.pyversion }}
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          python-version: ${{ matrix.pyversion }}
+  
       - name: Set up Julia
         uses: julia-actions/setup-julia@v2
         with:
           version: '1'
+
       - 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
+          uv run flake8 ./pysrc ./pytest --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
       - name: Run tests
         run: |
-          pytest -s --nbval --cov=pysrc ./pytest/
+          uv run pytest -s --nbval --cov=pysrc ./pytest/
         env:
           PYTHON_JULIACALL_THREADS: '2'
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5
         env:

docs/src/faq.md

@@ -89,3 +89,17 @@ Related issues: [#255](https://github.com/JuliaPy/PythonCall.jl/issues/255)
 Yes, it may be possible. A good example of that is having Julia running inside the Python that is running inside Blender, as presented in [this Discourse post](https://discourse.julialang.org/t/running-julia-inside-blender-through-vscode-using-pythoncall-juliacall/96838/6).
 From the point that one has JuliaCall running inside Python, if it has access to the terminal, one can even launch a Julia REPL there, and if needed connect with VSCode Julia extension to it.
 The full Python script to install, launch JuliaCall, and launch a Julia REPL in Blender is [here](https://gist.github.com/cdsousa/d820d27174238c0d48e5252355584172).
+
+## Using PythonCall.jl and CondaPkg.jl in a script
+
+If running from a script, make sure that [CondaPkg.jl](https://github.com/JuliaPy/CondaPkg.jl) is used before [PythonCall.jl](https://github.com/JuliaPy/PythonCall.jl) to ensure proper loading of Python packages in your path. E.g.,
+
+```julia
+using CondaPkg
+
+CondaPkg.add("numpy")
+
+using PythonCall
+
+np = pyimport("numpy")
+```

pyproject.toml

@@ -12,8 +12,17 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
 ]
-requires-python = ">=3.8"
-dependencies = ["juliapkg ~=0.1.17"]
+requires-python = ">=3.8, <4"
+dependencies = ["juliapkg >=0.1.17, <0.2"]
+
+[dependency-groups]
+dev = [
+    "flake8>=5.0",
+    "nbval>=0.11.0",
+    "numpy>=1.24",
+    "pytest>=8.3",
+    "pytest-cov>=5.0",
+]
 
 [tool.hatch.build.targets.wheel]
 packages = ["pysrc/juliacall"]

src/JlWrap/objectarray.jl

@@ -42,9 +42,11 @@ end
 
 @propagate_inbounds function Base.getindex(x::PyObjectArray, i::Integer...)
     @boundscheck checkbounds(x, i...)
-    @inbounds ptr = x.ptrs[i...]
-    ptr == C_NULL && throw(UndefRefError())
-    return pynew(incref(ptr))
+    Base.GC.@preserve x begin
+        @inbounds ptr = x.ptrs[i...]
+        ptr == C_NULL && throw(UndefRefError())
+        return pynew(incref(ptr))
+    end
 end
 
 @propagate_inbounds function Base.setindex!(x::PyObjectArray, v, i::Integer...)