Compatibility with numpy 2

.binder/environment.yml

@@ -1 +1 @@
-../conda/environment.yaml
+../conda/environment.yml

.dockerignore

@@ -1,4 +1,3 @@
-libUnderworld/build
-libUnderworld/config.cfg
-libUnderworld/config.log
-.git/objects
+.git/
+__pycache__
+.ipynb_checkpoints/

.github/dependabot.yml

@@ -0,0 +1,9 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # see documentation for possible values
+    directory: "/" # location of package manifests
+    schedule:
+      interval: "monthly"
+

.github/workflows/conda-build-test.yml

@@ -8,7 +8,7 @@ on:
       - v2.*
   pull_request:
     branches:
-      - '**'
+      - "**"
   workflow_dispatch:
 
 jobs:
@@ -31,5 +31,7 @@ jobs:
       - name: Build Underworld2
         run: pixi run build
 
+      # disable ucx mpi comms as github runners can't run them
       - name: Run tests
-        run: pixi run test
+        run: |
+          OMPI_MCA_pml=^ucx pixi run test

.github/workflows/conda_deploy.yml

@@ -1,6 +1,6 @@
 name: Conda Deploy
 
-on: 
+on:
   release:
   workflow_dispatch:
 
@@ -18,7 +18,7 @@ jobs:
       - uses: actions/checkout@v6
         with:
           fetch-depth: 1
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           channels: conda-forge,defaults
           auto-update-conda: true
@@ -27,11 +27,11 @@ jobs:
       - name: Config Conda
         shell: bash -el {0}
         run: |
-            conda install --channel conda-forge conda-build anaconda-client conda-verify
-            conda config --add channels conda-forge
-            conda config --add channels underworldcode
-            conda config --set anaconda_upload no
-            anaconda logout
+          conda install --channel conda-forge conda-build anaconda-client conda-verify
+          conda config --add channels conda-forge
+          conda config --add channels underworldcode
+          conda config --set anaconda_upload no
+          anaconda logout
 
       - name: Config Conda For Upload
         if: github.event_name == 'release'
@@ -42,7 +42,7 @@ jobs:
         if: github.event_name == 'release'
         shell: bash -el {0}
         run: |
-            conda info
-            anaconda login --hostname github-actions-${{ matrix.os  }}-$RANDOM --username ${{ secrets.ANACONDA_USERNAME }} --password ${{ secrets.ANACONDA_PASSWORD }}
-            conda-build --channel conda-forge --user geo-down-under conda
-            anaconda logout
+          conda info
+          anaconda login --hostname github-actions-${{ matrix.os  }}-$RANDOM --username ${{ secrets.ANACONDA_USERNAME }} --password ${{ secrets.ANACONDA_PASSWORD }}
+          conda-build --channel conda-forge --user geo-down-under conda
+          anaconda logout

.github/workflows/docker_build.yml.disable

@@ -21,7 +21,7 @@ jobs:
       run_uw: ${{ steps.check_files.outputs.run_uw }}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
         with:
           fetch-depth: 2
 
@@ -84,22 +84,22 @@ jobs:
     steps:
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v4
 
       - name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build Base Docker Image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v7
         with:
           context: .
           push: true
@@ -116,22 +116,22 @@ jobs:
     steps:
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v4
 
       - name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build Base Docker Image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v7
         with:
           context: .
           push: true
@@ -149,22 +149,22 @@ jobs:
     steps:
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v4
 
       - name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build Petsc Docker Image
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v7
         with:
           context: .
           push: true
@@ -193,22 +193,22 @@ jobs:
     steps:
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v4
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v4
 
       - name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build Lavavu Docker Image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v7
         with:
           context: .
           push: true
@@ -225,22 +225,22 @@ jobs:
     steps:
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v4
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v4
 
       - name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build Underworld Docker Image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v7
         with:
           context: .
           push: true
@@ -271,7 +271,7 @@ jobs:
           pip uninstall -y underworld
 
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v6
 
       - name: Install Underworld
         run: |
@@ -297,7 +297,7 @@ jobs:
           #          os: ["ubuntu-latest", "macos-latest"]
           #          python-version: ["3.9", "3.10"]
           #      steps:
-          #        - uses: actions/checkout@v3
+          #        - uses: actions/checkout@v6
           #        - uses: conda-incubator/setup-miniconda@v2
           #          with:
           #            auto-update-conda: true
@@ -337,9 +337,9 @@ jobs:
   #        os: ["ubuntu-latest", "macos-latest"]
   #        python-version: ["3.9", "3.10"]
   #    steps:
-  #      - uses: actions/checkout@v3
+  #      - uses: actions/checkout@v6
   #      - name: Set up Python
-  #        uses: actions/setup-python@v2
+  #        uses: actions/setup-python@v6
   #        with:
   #          python-version: ${{ matrix.python-version }}
   #      - name: Package for Pypi

.github/workflows/issue-metrics.yml

@@ -35,7 +35,7 @@ jobs:
           SEARCH_QUERY: 'repo:underworldcode/underworld2 repo:underworldcode/underworld3 is:issue created:${{ env.last_month }} -reason:"not planned"'
 
       - name: Create issue
-        uses: peter-evans/create-issue-from-file@v5
+        uses: peter-evans/create-issue-from-file@v6
         with:
           title: Monthly issue metrics report
           token: ${{ secrets.GH_TOKEN }}

.github/workflows/kaiju.yml

@@ -20,4 +20,3 @@ jobs:
           SERVER: ${{ secrets.GB_SERVER }}
           KAIJUPASSWD: ${{secrets.KAIJU_PASSWORD}}
           KAIJUUSER: ${{secrets.KAIJU_USERNAME}}
-

.github/workflows/release.yml.disable

@@ -13,7 +13,7 @@ jobs:
 
     steps:
     - name: Check out code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v6
       with:
         fetch-depth: 0
         ref: 'development'

AGENTS.md

@@ -0,0 +1,39 @@
+# AGENTS.md — Underworld2
+
+## Setup & build
+
+- **Python**: >=3.9,<3.13 (conda build pins to <3.12). **numpy <2** required.
+- **Env manager**: pixi (`pixi.toml` at root). Commands: `pixi install` → `pixi run build` → `pixi run test`.
+- **C/C++ build** requires: PETSc (found via `pkg-config`; set `PETSC_DIR`), MPI compilers (`MPICC`, `MPICXX`, `MPIF90`), SWIG >=4.0, CMake >=4.0, Ninja, libxml2, MPI-enabled h5py (`h5py=*=mpi*`).
+- **Install**: `pip install .` or `pip install . --no-build-isolation` (CI style). Pass CMake options via `python setup.py build_ext -D"FOO=BAR"`.
+- **Clean**: `bash clean.sh` (removes build artifacts, compiled `.so`, `_uwid.py`, caches).
+
+## Tests
+
+- **Run all**: `pytest ./docs/pytests/tests.py ./docs/pytests/test_examples.py ./docs/pytests/test_user_guide.py ./docs/pytests/test_UWGeo_examples.py ./docs/pytests/test_UWGeo_tutorial11.py`
+- **CI subset** (fastest check): `pytest ./docs/pytests/tests.py ./docs/pytests/test_examples.py ./docs/pytests/test_UWGeo_examples.py`
+- All test runners use `subprocess` to execute `.py` or `.ipynb` files. Notebooks are run via `pytest --nbmake`.
+- Test notebooks live in `docs/test/`, `docs/examples/`, `docs/user_guide/`, `docs/UWGeodynamics/examples/`, `docs/UWGeodynamics/tutorials/`.
+
+## Package structure
+
+| Path | Role |
+|---|---|
+| `src/underworld/` | Main Python package (set `package_dir={"":"src"}` in setup.py) |
+| `src/underworld/libUnderworld/` | C/C++ core + SWIG wrappers, built via CMake |
+| `src/underworld/UWGeodynamics/` | High-level geodynamics API |
+| `src/underworld/visualisation/` | LavaVu-based viz |
+
+## Critical quirks
+
+1. **dlopen flags**: `__init__.py` sets `RTLD_GLOBAL` before importing `.so` modules. This must happen early — do not reorder imports.
+2. **h5py first**: h5py is imported before anything else to avoid HDF5 library conflicts with PETSc.
+3. **`_uwid.py`**: Auto-generated on first install if missing (random UUID for usage metrics). Safe to delete/recreate.
+4. **Usage metrics**: Opt out via `UW_NO_USAGE_METRICS` env var. In MPI, only rank 0 sends data.
+5. **MPI exception handling**: In multi-process runs, exceptions are caught and broadcast via barrier. Set `UW_ALL_MESSAGES` to see all ranks' tracebacks.
+6. **PRs**: Target `development` branch. Must update `CHANGELOG.md` and docstrings. See `CONTRIBUTING.rst`.
+
+## Docs
+
+- ReadTheDocs: https://underworld2.readthedocs.io (Sphinx config at `docs/development/docs_generator/conf.py`).
+- Build docs via `docs/development/docs_generator/requirements.txt` deps.

CHANGELOG.md

@@ -1,6 +1,19 @@
 CHANGELOG: Underworld2
 =======================
 
+Release 2.18.0 [2026-06-29]
+-------------------------
+New:
+* `numpy 2` and `numpy 1` compatibility, default is `numpy 1`. Badlands yet to support `numpy 2` #764
+* Enabling `pixi` package management #0fe4355 
+
+Changes:
+* github action workflow package updates, `dependabot.yml` included for future.
+* `conda/environment.yml` updated, no longer source of truth in CI testing, move to pixi instead.
+
+Fixes:
+* Fix for UWGeo losing BCs and unknown field. #762
+
 Release 2.17.3 [2026-05-14]
 ---------------------------
 New:

README.md

@@ -54,7 +54,9 @@ Note that it can take a while for the site to fire up and that it will time-out
 
 | | |
 |-|-|
+| Try v2.18.x | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/v2.18.x) |
 | Try v2.17.x | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/v2.17.x) | 
+| Try v2.16.4 | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/v2.16.4) | 
 | Try dev | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/development) |