• Add setup-venv.sh script to automate Python venv creation with dependencies
• Add make venv and make venv-nopy targets for convenient environment setup
• Replace exact version pins with minimum constraints in requirements.txt
• Remove invalid [project.package-data] section from pyproject.toml
• Add .venv/ directory to .gitignore

New venv setup automation script

• New bash script that creates and configures Python virtual environment
• Installs all dependencies from requirements.txt using pip
• Optionally builds pysimple Fortran-Python bindings via CMake
• Supports --no-pysimple flag for dependencies-only installation
• Includes comprehensive help documentation and error handling

setup-venv.sh

Add venv setup make targets

• Add venv and venv-nopy targets to .PHONY declaration
• Implement venv target that calls ./setup-venv.sh
• Implement venv-nopy target that calls ./setup-venv.sh --no-pysimple

Makefile

Replace exact pins with minimum versions

• Replace exact version pins with minimum version constraints (e.g., ==2.2.6 → >=2.2)
• Update comment to explain minimum versions for Python compatibility
• Keep f90wrap==0.2.16 pinned due to API sensitivity
• Affects: numpy, scikit-build-core, pytest, pytest-cov, netCDF4, matplotlib, scipy, shapely

requirements.txt

Description

setup-venv.sh only configures CMake when build/build.ninja is missing, so an existing build/
configured with ENABLE_PYTHON_INTERFACE=OFF can be reused and pysimple won’t be built correctly.
This can lead to pip install -e . producing a package that fails to import because the python/
subdirectory is skipped by CMake.

Code

setup-venv.sh[R49-58]

+    if [ ! -f "${SCRIPT_DIR}/build/build.ninja" ]; then
+        echo "  Configuring CMake ..."
+        cmake -S "$SCRIPT_DIR" -B"${SCRIPT_DIR}/build" -GNinja \
+            -DCMAKE_BUILD_TYPE=Release -DCMAKE_COLOR_DIAGNOSTICS=ON
+    fi
+    echo "  Building Fortran library ..."
+    cmake --build "${SCRIPT_DIR}/build" --config Release
+
+    echo "  Installing pysimple in editable mode ..."
+    pip install --no-build-isolation -e "$SCRIPT_DIR"

Evidence

The script’s “configure only if build.ninja is missing” logic can reuse a cached build/ that was
explicitly configured without Python bindings. This repo’s Makefile has a target that configures
build/ with ENABLE_PYTHON_INTERFACE=OFF, and the top-level CMakeLists.txt only adds the python/
subtree when ENABLE_PYTHON_INTERFACE is ON. Because scikit-build-core is configured to use build/ as
its build directory, pip’s editable install will also be impacted by the cached build settings.

setup-venv.sh[46-58]
Makefile[73-85]
CMakeLists.txt[498-500]
pyproject.toml[13-19]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

### Issue description
`setup-venv.sh` reuses an existing `build/` directory if `build/build.ninja` exists, without ensuring `-DENABLE_PYTHON_INTERFACE=ON`. If a developer previously ran `make build-deterministic-nopy` (which configures `build/` with `ENABLE_PYTHON_INTERFACE=OFF`), the venv setup will reuse that cache and the Python bindings won’t be built/installed correctly.

### Issue Context
- `Makefile` has a `build-deterministic-nopy` target that configures `build/` with `-DENABLE_PYTHON_INTERFACE=OFF`.
- Top-level `CMakeLists.txt` only adds `python/` when `ENABLE_PYTHON_INTERFACE` is enabled.
- `pyproject.toml` sets scikit-build-core `build-dir = "build"`, so pip editable installs will interact with the same build directory.

### Fix Focus Areas
- setup-venv.sh[46-58]
- Makefile[73-85]
- pyproject.toml[13-19]

### Implementation direction
Do one of the following (preferred options first):
1. Use a dedicated build directory for the venv workflow (e.g. `build_venv/`), so it cannot conflict with `make build-deterministic-nopy`.
2. Always run an explicit reconfigure step when `BUILD_PYSIMPLE=1`, passing `-DENABLE_PYTHON_INTERFACE=ON` (and optionally `-DSIMPLE_ENABLE_PYTHON_TOOLS=ON`) even when `build/build.ninja` exists.
3. Detect a cached `CMakeCache.txt` with `ENABLE_PYTHON_INTERFACE:BOOL=OFF` and either error out with a clear message or automatically reconfigure/clean.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

Description

Makefile defines a venv-nopy target but does not include it in .PHONY, so a file named venv-nopy in
the repo root would prevent the recipe from running. This makes the new convenience target slightly
fragile.

Code

Makefile[17]

+.PHONY: all configure reconfigure build build-deterministic build-deterministic-nopy test test-nopy test-fast test-slow test-regression test-all test-golden-main test-golden-tag test-golden install clean venv nvfortran nvfortran-test nvfortran-test-nopy nvfortran-configure nvfortran-clean

Evidence

The .PHONY list includes venv but omits the newly-added venv-nopy target, while the target is
defined later in the file.

Makefile[17-18]
Makefile[101-106]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

### Issue description
`venv-nopy` is a new Makefile target but it is not listed in `.PHONY`, so Make may treat it as a file target if `./venv-nopy` exists.

### Issue Context
This is a small robustness fix for the new venv workflow targets.

### Fix Focus Areas
- Makefile[17-18]

### Suggested change
Add `venv-nopy` to the `.PHONY:` declaration alongside `venv`.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools