Release 1.0.1

.github/workflows/ci.yml

@@ -22,10 +22,10 @@ jobs:
     steps:
 
     - name: Checkout repo
-      uses: actions/checkout@v4
+      uses: actions/checkout@v7
 
     - name: Setup uv
-      uses: astral-sh/setup-uv@v5
+      uses: astral-sh/setup-uv@v7
       with:
         cache-dependency-glob: "**/pyproject.toml"
 
@@ -43,10 +43,10 @@ jobs:
         shell: bash
     steps:
     - name: Checkout repo
-      uses: actions/checkout@v4
+      uses: actions/checkout@v7
 
     - name: Setup uv
-      uses: astral-sh/setup-uv@v5
+      uses: astral-sh/setup-uv@v7
       with:
         enable-cache: false
 
@@ -73,10 +73,10 @@ jobs:
         shell: bash
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           cache-dependency-glob: "**/pyproject.toml"
           python-version: ${{ matrix.python-version }}
@@ -85,6 +85,17 @@ jobs:
         run: uv sync --all-extras
 
       - name: Install modflow executables
+        id: install_modflow
+        continue-on-error: true
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          path: ${{ github.workspace }}/autotest
+          repo: modflow6-nightly-build
+
+      # the download reaches out to github and occasionally has its
+      # connection reset, failing the job before any test runs
+      - name: Install modflow executables (retry)
+        if: steps.install_modflow.outcome == 'failure'
         uses: modflowpy/install-modflow-action@v1
         with:
           path: ${{ github.workspace }}/autotest
@@ -113,10 +124,10 @@ jobs:
         shell: bash
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           cache-dependency-glob: "**/pyproject.toml"
           python-version: ${{ matrix.python-version }}
@@ -125,6 +136,18 @@ jobs:
         run: uv sync --all-extras
 
       - name: Install modflow executables
+        id: install_modflow
+        continue-on-error: true
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          path: ${{ github.workspace }}/autotest
+          repo: executables
+          tag: "14.0"
+
+      # the download reaches out to github and occasionally has its
+      # connection reset, failing the job before any test runs
+      - name: Install modflow executables (retry)
+        if: steps.install_modflow.outcome == 'failure'
         uses: modflowpy/install-modflow-action@v1
         with:
           path: ${{ github.workspace }}/autotest
@@ -138,7 +161,7 @@ jobs:
       - name: Run autotests
         working-directory: ./autotest
         shell: bash -l {0}
-        run: pytest -v -n auto -m "not mf6"     
+        run: uv run pytest -v -n auto -m "not mf6"
 
   autotest_mf6_examples:
     name: modflowapi mf6 examples autotests
@@ -154,10 +177,10 @@ jobs:
         shell: bash
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           cache-dependency-glob: "**/pyproject.toml"
           python-version: ${{ matrix.python-version }}
@@ -166,6 +189,17 @@ jobs:
         run: uv sync --all-extras
 
       - name: Install modflow6 nightly build
+        id: install_modflow
+        continue-on-error: true
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          path: ${{ github.workspace }}/autotest
+          repo: modflow6-nightly-build
+
+      # the download reaches out to github and occasionally has its
+      # connection reset, failing the job before any test runs
+      - name: Install modflow6 nightly build (retry)
+        if: steps.install_modflow.outcome == 'failure'
         uses: modflowpy/install-modflow-action@v1
         with:
           path: ${{ github.workspace }}/autotest

.github/workflows/pull_request.yml

@@ -0,0 +1,43 @@
+name: pull request
+
+on:
+  pull_request:
+    types: [opened, edited, reopened, synchronize]
+    branches: [develop]
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+
+  title:
+    name: check title
+    # the release and reset pull requests are opened by a bot and are not
+    # squash merged, so their titles do not reach the changelog
+    if: github.event.pull_request.user.type != 'Bot'
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+
+      - name: Check conventional commit format
+        env:
+          TITLE: ${{ github.event.pull_request.title }}
+        run: |
+          # pull requests are squash merged, so the title becomes the commit
+          # message in develop, and the changelog is generated from those
+          # messages. a title that is not a conventional commit is dropped
+          # from the release notes without warning.
+          types="build|chore|ci|docs|feat|fix|perf|refactor|revert|style|test"
+          if [[ ! "$TITLE" =~ ^($types)(\([^\)]+\))?!?:\ .+ ]]; then
+            echo "::error::'$TITLE' is not a conventional commit header."
+            echo ""
+            echo "Use '<type>(<scope>): <subject>', for example:"
+            echo "  feat(runner): support adaptive time step retries"
+            echo ""
+            echo "Type is one of: ${types//|/, }."
+            echo "Only feat, fix, perf and refactor reach the release notes;"
+            echo "see cliff.toml. A user facing change needs one of those."
+            exit 1
+          fi
+          echo "'$TITLE' is a conventional commit header"

.github/workflows/release.yml

@@ -65,13 +65,13 @@ jobs:
           fi
 
       - name: Checkout source branch
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           ref: ${{ github.event_name == 'workflow_dispatch' && inputs.branch || github.ref_name }}
           fetch-depth: 0
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           cache-dependency-glob: "**/pyproject.toml"
 
@@ -104,14 +104,25 @@ jobs:
           uv run scripts/update_version.py -v "${{ steps.version.outputs.version }}"
           uv run python -c "import modflowapi; print('Version: ', modflowapi.__version__)"
 
-      - name: Lint and format
+      - name: Check style
         run: |
-          uvx ruff check --fix .
-          uvx ruff format .
+          uvx ruff check .
+          uvx ruff format --check .
           uvx codespell
 
       - name: Install modflow executables
         if: ${{ github.event_name != 'workflow_dispatch' || inputs.run_tests }}
+        id: install_modflow
+        continue-on-error: true
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          path: ${{ github.workspace }}/autotest
+          repo: modflow6-nightly-build
+
+      # the download reaches out to github and occasionally has its
+      # connection reset, failing the job before any test runs
+      - name: Install modflow executables (retry)
+        if: ${{ (github.event_name != 'workflow_dispatch' || inputs.run_tests) && steps.install_modflow.outcome == 'failure' }}
         uses: modflowpy/install-modflow-action@v1
         with:
           path: ${{ github.workspace }}/autotest
@@ -167,7 +178,7 @@ jobs:
           git config core.sharedRepository true
           git config user.name "github-actions[bot]"
           git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
-          git add -A
+          git add version.txt modflowapi/version.py CITATION.cff HISTORY.md
           git commit -m "ci(release): set version to $ver, update changelog"
           git push origin "v$ver"
 
@@ -200,7 +211,7 @@ jobs:
     steps:
 
       - name: Checkout main branch
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           ref: main
           fetch-depth: 0
@@ -251,12 +262,12 @@ jobs:
     steps:
 
       - name: Checkout main branch
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           ref: main
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           enable-cache: false
 
@@ -267,7 +278,7 @@ jobs:
         run: uvx twine check --strict dist/*
 
       - name: Upload package
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: dist
           path: dist
@@ -290,13 +301,13 @@ jobs:
     steps:
 
       - name: Checkout main branch
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           ref: main
           fetch-depth: 0
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           cache-dependency-glob: "**/pyproject.toml"
 
@@ -317,7 +328,7 @@ jobs:
           git config user.name "github-actions[bot]"
           git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
           git switch -c "$branch"
-          git add -A
+          git add version.txt modflowapi/version.py CITATION.cff
           git commit -m "ci(release): update version to $next"
           git push origin "$branch"
 

.gitignore

@@ -142,6 +142,15 @@ uv.lock
 # temporary test folders
 autotest/temp/**
 
+# modflow executables installed for testing
+autotest/mf6
+autotest/mf5to6
+autotest/zbud6
+autotest/libmf6.*
+autotest/mf6.exe
+autotest/mf5to6.exe
+autotest/zbud6.exe
+
 # notebooks
 docs/examples/notebooks/*.ipynb
 

CITATION.cff

@@ -3,8 +3,8 @@ message: If you use this software, please cite both the article from preferred-c
   and the software itself.
 type: software
 title: MODFLOW API
-version: 1.0.0
-date-released: '2026-09-05'
+version: 1.0.1
+date-released: '2026-09-06'
 abstract: An extension to xmipy for the MODFLOW API.
 repository-artifact: https://pypi.org/project/modflowapi
 repository-code: https://github.com/MODFLOW-ORG/modflowapi

HISTORY.md

@@ -1,4 +1,10 @@
 # Changelog
+### Version 1.0.1
+
+#### Bug fixes
+
+* [fix(dependencies)](https://github.com/MODFLOW-ORG/modflowapi/commit/adbfd151b14861360fbb9fb67f48bcff87f7d43f): Require a pandas that supports numpy 2 (#118). Committed by Joseph Hughes on 2026-09-06.
+
 ### Version 1.0.0
 
 This is the first stable release. modflowapi now follows semantic versioning, so a breaking change to the `modflowapi` or `modflowapi.extensions` interface will increment the major version. The Python interface is unchanged from 0.2.0, but Python 3.9 and 3.10 are no longer supported; Python 3.11 or later is required.

guide-to-publish.md

@@ -4,6 +4,14 @@ Releases are automated by [`.github/workflows/release.yml`](.github/workflows/re
 Publishing to PyPI uses [trusted publishing](https://docs.pypi.org/trusted-publishers/), so no
 API token is needed, but the repository must have a `release` environment configured.
 
+> [!IMPORTANT]
+> PyPI matches a trusted publisher on the organisation name, the repository name, the workflow
+> filename and the environment name. Renaming any of them silently invalidates the publisher, and
+> nothing reports it until the next release fails with `invalid-publisher`. This happened when the
+> organisation was renamed from `MODFLOW-USGS` to `MODFLOW-ORG`, and went unnoticed for the
+> eighteen months until the next release. After any such rename, update the publisher at
+> https://pypi.org/manage/project/modflowapi/settings/publishing/ to match.
+
 ## 1. Start the release
 
 From the [Actions tab](https://github.com/MODFLOW-ORG/modflowapi/actions/workflows/release.yml),
@@ -46,7 +54,16 @@ Merge the reset pull request to finish the release.
 
 ## Changelog conventions
 
-Release notes are generated from commit messages, so commits merged to `develop` should follow the
+Release notes are generated from commit messages, so commits merged to `develop` must follow the
 [conventional commits](https://www.conventionalcommits.org/) format (`feat:`, `fix:`, `refactor:`,
-etc.). Commits that do not follow the convention are omitted from the changelog. See
-[`cliff.toml`](cliff.toml) for the commit groups and which ones are skipped.
+etc.). Commits that do not follow the convention are omitted from the changelog without warning.
+See [`cliff.toml`](cliff.toml) for the commit groups and which ones are skipped.
+
+Pull requests are squash merged, so the title becomes the commit message the notes are generated
+from. [`.github/workflows/pull_request.yml`](.github/workflows/pull_request.yml) rejects a title
+that is not a conventional commit header, but it cannot tell whether the type is the right one: a
+user facing change titled `chore:` still passes the check and is still dropped from the notes.
+
+Read the generated changelog on the release pull request before merging it. Anything missing is
+added there, into the section for the version being cut, not to `develop`; the section does not
+exist until the release workflow generates it.

modflowapi/version.py

@@ -1,3 +1,3 @@
 # modflowapi version file automatically created using...update_version.py
-# created on...September 05, 2026 12:54:22
-__version__ = "1.0.0"
+# created on...September 06, 2026 12:36:39
+__version__ = "1.0.1"

pyproject.toml

@@ -34,7 +34,7 @@ classifiers = [
 requires-python = ">=3.11"
 dependencies = [
     "numpy>=1.23",
-    "pandas>=1.5",
+    "pandas>=2.2.2",
     "xmipy>=1.5.0",
 ]
 

version.txt

@@ -1 +1 @@
-1.0.0
+1.0.1