Merge branch 'rel-0.3.0'

Author: mwtoews

.github/workflows/release.yml

@@ -1,6 +1,8 @@
 name: Build wheels
 
 on:
+  schedule:
+    - cron: '42 8 2-30/2 * *' # At 08:42 UTC on every 2nd day-of-month
   pull_request:
     paths:  # only run this with PRs that touch these files
       - ".github/workflows/release.yml"
@@ -31,9 +33,9 @@ jobs:
           arch: aarch64
         - os: windows-2022
           arch: AMD64
-        - os: macos-11
+        - os: macos-13
           arch: x86_64
-          macosx_deployment_target: "11.0"
+          macosx_deployment_target: "13.0"
           cmake_osx_architectures: x86_64
         - os: macos-14
           arch: arm64
@@ -66,14 +68,11 @@ jobs:
         shell: msys2 {0}
         env:
           LDFLAGS: -static-libgcc -static-libgfortran -static-libquadmath -Wl,-Bstatic,--whole-archive -lwinpthread -Wl,--no-whole-archive
-        run: |
-          bash scripts/build_lib.sh
+        run: bash scripts/build_lib.sh
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.18.0
+        uses: pypa/cibuildwheel@v2.22.0
         env:
-          CIBW_BUILD: "cp39-*"  # pick one version
-          CIBW_SKIP: "*-musllinux*"
           CIBW_ARCHS: ${{ matrix.arch }}
           CIBW_ENVIRONMENT_MACOS:
             FC=gfortran-13

.github/workflows/tests.yml

@@ -1,33 +1,30 @@
 name: Tests
 
-on: 
+on:
   schedule:
     - cron: '42 8 2-30/2 * *' # At 08:42 UTC on every 2nd day-of-month
   push:
   pull_request:
+  workflow_dispatch:
 
 jobs:
   tests:
-    name: Run tests on ${{ matrix.os }} Py${{ matrix.python }}
+    name: Tests on ${{ matrix.os }} Python-${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-12, windows-latest]
-        python-version: ["3.8", "3.11"]  # run lower and upper versions
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.13"]  # run lower and upper versions
 
     steps:
       - uses: actions/checkout@v4
 
       - name: Setup Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: astral-sh/setup-uv@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Update pip
-        run: |
-          python -m pip install --upgrade pip
-
       - name: Install MinGW-w64 tools (Windows)
         if: runner.os == 'Windows'
         uses: msys2/setup-msys2@v2
@@ -42,48 +39,29 @@ jobs:
 
       - name: Install GCC Fortran (macOS)
         if: runner.os == 'macOS'
-        uses: awvwgk/setup-fortran@main
+        uses: fortran-lang/setup-fortran@v1
         with:
           compiler: gcc
-          version: 11
-
-      - name: Install build dependencies (macOS)
-        if: runner.os == 'macOS'
-        run: |
-          pip install meson ninja pandas numpy matplotlib pyemu flopy jupyter notebook nbconvert
-
-      - name: Install build dependencies (macOS)
-        if: runner.os == 'Windows'
-        run: |
-          pip install meson ninja pandas numpy matplotlib pyemu flopy jupyter notebook nbconvert
-
+          version: 13
 
-      - name: Install build dependencies (Linux)
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y gfortran
-          pip install meson ninja pandas numpy matplotlib pyemu flopy jupyter notebook nbconvert
+      - name: Install build requirements
+        run: uv pip install meson ninja
 
       - name: Build pestutils (Windows)
         if: runner.os == 'Windows'
         shell: msys2 {0}
         env:
           LDFLAGS: -static-libgcc -static-libgfortran -static-libquadmath -Wl,-Bstatic,--whole-archive -lwinpthread -Wl,--no-whole-archive
-        run: |
-          bash scripts/build_lib.sh
+        run: bash scripts/build_lib.sh
 
       - name: Build pestutils (non-Windows)
         if: runner.os != 'Windows'
-        run: |
-          bash scripts/build_lib.sh
+        run: bash scripts/build_lib.sh
 
-      - name: Install package
-        run: |
-          pip install .[test,optional]
+      - name: Install package and all extras
+        run: uv sync --all-extras
 
       - name: Run tests
-        run: |
-          pytest -v
+        run: uv run pytest -v
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -1,3 +1,22 @@
+# General
+.DS_Store
+*.swp
+*.*~
+~$*
+
+# Modflow outputs
+*.lst
+*.list
+*.grb
+*.cbc
+*.cbb
+*.bud
+*.hds
+*.hed
+*.ucn
+*.out
+*.out.csv
+
 # Byte-compiled / optimized
 __pycache__/
 *.py[cod]
@@ -9,6 +28,7 @@ __pycache__/
 *.o
 *.obj
 *.so
+*.lib
 
 # Local installation and misc. dirs
 inst/

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+ci:
+  autoupdate_schedule: quarterly
+exclude: \.grb$
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    - id: check-yaml
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.3
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format

CHANGELOG.md

@@ -4,6 +4,22 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+### Added
+### Changed
+### Fixed
+
+## [0.3.0] - 2025-02-12
+### Changed
+- Set minimum Python 3.9 (#36)
+- Updated cibuildwheel workflow, build macos arm64 wheels from GHA (#30, #32)
+- Fix finder.load() for conda and LD path search
+- Fix typos (#37)
+- Use ruff format, apply ruff check rules, add pre-commit (#38, #45)
+
+### Fixed
+- Fix in `mod2obs_mf6` with different depvar names (#33)
+
 ## [0.2.1] - 2024-01-23
 ### Fixed
 - Fix AttributeError: 'DataFrame' object has no attribute 'site' (#21)
@@ -25,6 +41,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Initial pre-alpha release
 
+[Unreleased]: https://github.com/pypest/pypestutils/compare/v0.3.0...develop
+[0.3.0]: https://github.com/pypest/pypestutils/compare/v0.2.1...v0.3.0
 [0.2.1]: https://github.com/pypest/pypestutils/compare/v0.2.0...v0.2.1
 [0.2.0]: https://github.com/pypest/pypestutils/compare/v0.1.0...v0.2.0
 [0.1.0]: https://github.com/pypest/pypestutils/releases/tag/v0.1.0

docs/helpers.html

@@ -161,7 +161,7 @@ <h1 class="title">Module <code>pypestutils.helpers</code></h1>
     return {&#34;all_results&#34;:allresults_df,&#34;interpolated_results&#34;:obsdf}
 
 def get_grid_info_from_gridspec(gridspec_fname: str) -&gt; dict:
-    &#34;&#34;&#34;Read structured grid info from a PEST-style grid specificatin file
+    &#34;&#34;&#34;Read structured grid info from a PEST-style grid specification file
     Parameters
     ----------
     gridspec_fname : str
@@ -728,7 +728,7 @@ <h1 class="title">Module <code>pypestutils.helpers</code></h1>
         the zone array
     varioaniso: float or numpy.ndarray
         the variogram anisotropy ratio.  Either a scalar or array of shape nnodes.
-    variobearing: flaot or numpy.ndarray
+    variobearing: float or numpy.ndarray
         the variogram anisotropy bearing.  Either a scalar or array of shape nnodes
     random_seed: int
         the random seed.  Default is 12345
@@ -1225,7 +1225,7 @@ <h2 class="section-title" id="header-functions">Functions</h2>
 <dt><strong><code>varioaniso</code></strong> :&ensp;<code>float</code> or <code>numpy.ndarray</code></dt>
 <dd>the variogram anisotropy ratio.
 Either a scalar or array of shape nnodes.</dd>
-<dt><strong><code>variobearing</code></strong> :&ensp;<code>flaot</code> or <code>numpy.ndarray</code></dt>
+<dt><strong><code>variobearing</code></strong> :&ensp;<code>float</code> or <code>numpy.ndarray</code></dt>
 <dd>the variogram anisotropy bearing.
 Either a scalar or array of shape nnodes</dd>
 <dt><strong><code>random_seed</code></strong> :&ensp;<code>int</code></dt>
@@ -1283,7 +1283,7 @@ <h2 id="returns">Returns</h2>
         the zone array
     varioaniso: float or numpy.ndarray
         the variogram anisotropy ratio.  Either a scalar or array of shape nnodes.
-    variobearing: flaot or numpy.ndarray
+    variobearing: float or numpy.ndarray
         the variogram anisotropy bearing.  Either a scalar or array of shape nnodes
     random_seed: int
         the random seed.  Default is 12345
@@ -1643,7 +1643,7 @@ <h2 id="returns">Returns</h2>
 <span>def <span class="ident">get_grid_info_from_gridspec</span></span>(<span>gridspec_fname: str) ‑> dict</span>
 </code></dt>
 <dd>
-<div class="desc"><p>Read structured grid info from a PEST-style grid specificatin file
+<div class="desc"><p>Read structured grid info from a PEST-style grid specification file
 Parameters</p>
 <hr>
 <dl>
@@ -1660,7 +1660,7 @@ <h2 id="returns">Returns</h2>
 <span>Expand source code</span>
 </summary>
 <pre><code class="python">def get_grid_info_from_gridspec(gridspec_fname: str) -&gt; dict:
-    &#34;&#34;&#34;Read structured grid info from a PEST-style grid specificatin file
+    &#34;&#34;&#34;Read structured grid info from a PEST-style grid specification file
     Parameters
     ----------
     gridspec_fname : str