fixes for GHA tests

.github/workflows/release.yml

@@ -33,17 +33,13 @@ jobs:
           arch: aarch64
         - os: windows-2022
           arch: AMD64
-        - os: macos-13
-          arch: x86_64
-          macosx_deployment_target: "13.0"
-          cmake_osx_architectures: x86_64
         - os: macos-14
           arch: arm64
           macosx_deployment_target: "14.0"
           cmake_osx_architectures: arm64
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Set up QEMU
         if: runner.os == 'Linux' && matrix.arch == 'aarch64'
@@ -55,7 +51,7 @@ jobs:
         if: runner.os == 'Windows'
         uses: msys2/setup-msys2@v2
         with:
-          msystem: MINGW64
+          msystem: mingw64
           path-type: inherit
           install: >-
             mingw-w64-x86_64-gcc-fortran
@@ -71,15 +67,15 @@ jobs:
         run: bash scripts/build_lib.sh
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.22.0
+        uses: pypa/cibuildwheel@v3.2.1
         env:
           CIBW_ARCHS: ${{ matrix.arch }}
           CIBW_ENVIRONMENT_MACOS:
             FC=gfortran-13
             MACOSX_DEPLOYMENT_TARGET='${{ matrix.macosx_deployment_target }}'
             CMAKE_OSX_ARCHITECTURES='${{ matrix.cmake_osx_architectures }}'
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ matrix.arch }}
           path: ./wheelhouse/*.whl
@@ -88,12 +84,12 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Build sdist
         run: pipx run build --sdist
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         with:
           name: cibw-sdist
           path: dist/*.tar.gz
@@ -108,7 +104,7 @@ jobs:
     # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
     # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v6
         with:
           # unpacks all CIBW artifacts into dist/
           pattern: cibw-*

.github/workflows/tests.yml

@@ -15,21 +15,22 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.13"]  # run lower and upper versions
+        python-version: ["3.10", "3.14"]  # run lower and upper versions
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Setup Python ${{ matrix.python-version }}
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python-version }}
+          activate-environment: "true"
 
       - name: Install MinGW-w64 tools (Windows)
         if: runner.os == 'Windows'
         uses: msys2/setup-msys2@v2
         with:
-          msystem: MINGW64
+          msystem: mingw64
           path-type: inherit
           install: >-
             mingw-w64-x86_64-gcc-fortran

.pre-commit-config.yaml

@@ -3,14 +3,14 @@ ci:
 exclude: \.grb$
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     - id: check-yaml
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.3
+    rev: v0.14.10
     hooks:
-      # Run the linter.
-      - id: ruff
+      # Run the linter
+      - id: ruff-check
         args: [ --fix ]
-      # Run the formatter.
+      # Run the formatter
       - id: ruff-format

BUILD.md

@@ -26,6 +26,7 @@ Or manually with these steps:
 ```bash
 meson setup builddir  # options
 meson compile -C builddir
+meson install -C builddir
 ```
 
 After it is compiled, install to the Python module using:

etc/environment.yml

@@ -3,7 +3,7 @@ name: pypestutils
 
 channels:
   - conda-forge
-  - defaults
+  - nodefaults
 
 dependencies:
   - appdirs

examples/exploring_lowlevel_pypestutils_functions.ipynb

@@ -446,9 +446,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "usite = hdsdf.site.unique()\n",
+    "usite = hdsdf.site.unique().tolist()\n",
     "usite.sort()\n",
-    "usite_dict = {s: c for s, c in zip(usite, np.arange(usite.shape[0], dtype=int))}\n",
+    "usite_dict = {s: c for s, c in zip(usite, np.arange(len(usite), dtype=int))}\n",
     "hdsdf.loc[:, \"isite\"] = hdsdf.site.apply(lambda x: usite_dict[x])\n",
     "hdsdf.isite\n",
     "hdsdf.sort_values(by=[\"isite\", \"time\"], inplace=True)\n",

pypestutils/helpers.py

@@ -167,9 +167,9 @@ def mod2obs_mf6(
         print("WARNING: replacing existing 'totim' column in observation dataframe")
     obsdf.loc[:, "totim"] = obsdf.datetime.apply(lambda x: x - start_datetime).dt.days
 
-    usite = obsdf.site.unique()
+    usite = obsdf.site.unique().tolist()
     usite.sort()
-    usite_dict = {s: c for s, c in zip(usite, np.arange(usite.shape[0], dtype=int))}
+    usite_dict = {s: c for s, c in zip(usite, np.arange(len(usite), dtype=int))}
     obsdf.loc[:, "isite"] = obsdf.site.apply(lambda x: usite_dict[x])
     obsdf.sort_values(by=["isite", "totim"], inplace=True)
 

pypestutils/version.py

@@ -1,4 +1,4 @@
 """Package version."""
 
 # This is the only place to update version
-__version__ = "0.3.0"
+__version__ = "0.3.1.dev0"

pyproject.toml

@@ -12,25 +12,24 @@ authors = [
 readme = "README.md"
 description = "PEST utilities for MODFLOW"
 keywords = ["PEST", "MODFLOW", "groundwater", "model"]
-license = {text = "Unlicense"}
+license = "Unlicense"
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: The Unlicense (Unlicense)",
     "Operating System :: Unix",
     "Operating System :: MacOS",
     "Operating System :: Microsoft :: Windows",
     "Programming Language :: Fortran",
     "Programming Language :: Python :: 3 :: Only",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering :: Hydrology",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "numpy",
     "pandas",
@@ -59,7 +58,7 @@ version = {attr = "pypestutils.version.__version__"}
 include = ["pypestutils", "pypestutils.*"]
 
 [tool.cibuildwheel]
-build = "cp39-*"
+build = "cp310-*"
 build-verbosity = 3
 repair-wheel-command = "python scripts/repair_wheel.py -w {dest_dir} {wheel}"
 test-requires = "tox"

scripts/build_lib.sh

@@ -4,11 +4,14 @@ set -e
 # always run from top of repo
 cd $(dirname $0)/..
 
+
+echo "Running $0 for \$OSTYPE=$OSTYPE ..."
+
 # this needs bash
 case "$OSTYPE" in
-  darwin*)  libname=lib/libpestutils.dylib ;;
+  darwin*)  libname=lib/libpestutils.dylib && export LDFLAGS="$LDFLAGS -Wl,-ld_classic";;
   linux*)   libname=lib/libpestutils.so ;;
-  msys* )   libname=bin/pestutils.dll ;;
+  msys*|cygwin ) libname=bin/pestutils.dll ;;
   *) echo "unknown \$OSTYPE: $OSTYPE" && exit 1 ;;
 esac
 

tox.ini

@@ -1,7 +1,7 @@
 [tox]
 requires =
     tox>=4
-env_list = py{39,310,311,312,313}
+env_list = py{310,311,312,313,314}
 
 [testenv]
 description = run unit tests