Merge branch 'v2.17.x' into uw2-pixi

Author: julesghub

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

@@ -22,15 +22,19 @@ jobs:
       - name: Set up Micromamba
         uses: mamba-org/setup-micromamba@v2
         with:
-          environment-file: conda/environment.yml
+          environment-file: conda/environment.yaml
+          environment-name: uw-2.17
+          generate-run-shell: true
           cache-environment: true
-          cache-downloads: true
-          init-shell: bash
+          #cache-downloads: false
 
-      - name: Compile the code, run tests
-        shell: micromamba-shell {0}
+      - name: compile and pytests
         run: | 
-          micromamba list
-          pip list
-          pip install .
+          micromamba env list 
+          micromamba list -v
+          env
+          pip install . --no-build-isolation
           pytest ./docs/pytests/tests.py ./docs/pytests/test_examples.py
+        shell: micromamba-shell {0}
+# name: Compile the code, run tests
+        

.github/workflows/publish-to-pypi.yaml

@@ -0,0 +1,81 @@
+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        persist-credentials: false
+    - name: Set up Micromamba
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-file: conda/environment.yaml
+        environment-name: uw-2.17
+        generate-run-shell: true
+        cache-environment: true
+        #cache-downloads: false
+    - name: Form tarball to publish
+      run: | 
+        micromamba env list 
+        micromamba list -v
+        env
+        python3 setup.py sdist
+      shell: micromamba-shell {0}
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/underworld  # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+## Currently need access from jmansour to this testpypi project
+  # publish-to-testpypi:
+  #   name: Publish Python 🐍 distribution 📦 to TestPyPI
+  #   needs:
+  #   - build
+  #   runs-on: ubuntu-latest
+
+  #   environment:
+  #     name: testpypi
+  #     url: https://test.pypi.org/p/testuw
+
+  #   permissions:
+  #     id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+  #   steps:
+  #   - name: Download all the dists
+  #     uses: actions/download-artifact@v4
+  #     with:
+  #       name: python-package-distributions
+  #       path: dist/
+  #   - name: Publish distribution 📦 to TestPyPI
+  #     uses: pypa/gh-action-pypi-publish@release/v1
+  #     with:
+  #       repository-url: https://test.pypi.org/legacy/
+  #       password: ${{ secrets.TEST_PYPI_API_TOKEN }}

CHANGES.md

@@ -1,5 +1,17 @@
 CHANGES: Underworld2
 =======================
+Release 2.17 [2025-07-08]
+-------------------------
+New:
+* Move container definitions to `./docs/development/container/`. Podman container is now preferred over docker and Dockerfiles.
+
+Changes:
+* UWGeodynamics - Badlands coupling imporvements.  See [blog](https://www.underworldcode.org/new-features-of-the-surface-coupling-framework-in-underworld-2/)
+
+Fixes:
+* Fix for Badlands coupling - Tectonic velocity now evaluated at surface, rather than Badlands basement recGrid. #725
+* UWGeo checkpoint times fix, e5d9ba1
+
 Release 2.16 [2025-03-03]
 ---------------------------
 New:

Installation.rst

@@ -1,16 +1,63 @@
 Underworld Installation
 =======================
 
-Detailed instructions for supported HPC platforms may be found at `docs/install_guides
-<https://github.com/underworldcode/underworld2/tree/master/docs/install_guides>`_. You may also find useful usage information (on docker/hpc/compilation/other) on the Underworld blog.
+Underworld 2 can be installed in multiple ways, using the container (preferred), from source code (advanced). It can also be installed on HPC clusters. These installation methods are documented below.
+
+Container
+----------
+
+Containers provide a type of lightweight virtualisation. The Underworld 2 container includes the latest version of Underworld 2 with all the dependencies packages and is the preferred method for usage on personal computers. 
+
+You will first need to install *podman* (recommended) or *docker* on your system. Both these tools can be used from the command line, but new users may wish to use the GUI Desktop versions to get started with it.
+
+The following script is the recommended way for launching the container with *podman*.
+
+.. code:: bash
+
+   sh ./docs/development/container/launch-container.sh
+
+This will take a moment to load up - be patient please. What you'll get is a container running a functioning Jupyterlab environment with the latest Underworld 2 installed at `localhost:20000 <localhost:20000>`_. A directory called **uw_space** will be create in the user's home directory which is (volume) mapped into the container, this acts as a tranfser directory for sending files to and from the container.
+
+Remember to take note of the Jupyterlab token from the start up messages. It will look something like.
+
+.. code:: bash
+   
+   http://127.0.0.1:8888/lab?token=e79006f4e441cf781440a9ea0cad8cf2a0dfd3b9c236a0ca
+
+The value must be copy-pasted into the jupyterlab launch page the first time.
+
+
+.. podman run -p 8888:8888 -v uw2-vol:/home/jovyan/workspace underworldcode/underworld2
+.. 
+.. Navigate to `localhost:8888 <localhost:8888>`_ to see the notebooks. Note that you can also use particular versions of Underworld using any of the Docker image tags. For example:
+.. 
+.. .. code:: bash
+.. 
+..    docker run -p 8888:8888 underworldcode/underworld2:2.7.1b
+.. 
+.. By default (ie, if no tag is provided), docker will use the latest stable release. A list of available tags may be found on `our DockerHub page <https://hub.docker.com/r/underworldcode/underworld2/tags>`_. Tags can also be accessed in Kitematic via the ellipsis button on container search results. 
+.. 
+.. A number of useful docker commands are provided within the `Underworld cheat-sheet <https://github.com/underworldcode/underworld2/tree/master/docs/cheatsheet/cheatsheet.pdf>`_.
+.. 
+.. see old `Notes on Installing Docker`_) and then you may install Underworld via Docker. Docker can be driven from the command line, but new users may wish to use the Docker Kitematic GUI instead for ease. Simply search for 'underworldcode/underworld2' within Kitematic, and then click 'CREATE' to launch a container. You will eventually wish to modify your container settings (again through Kitematic) to enable local folder volume mapping, which will allow you to access your local drives from within your container.
+.. 
+.. For Linux users, and those who prefer the command line, the following minimal command should be sufficient to access the Underworld2 Jupyter Notebook examples:
+.. 
+
 
 We welcome feedback and support requests at our `github issue tracker <https://github.com/underworldcode/underworld2/issues>`_.
 
+HPC Installation
+----------------
+
+Detailed instructions for supported HPC platforms may be found at `docs/install_guides
+<https://github.com/underworldcode/underworld2/tree/master/docs/install_guides>`_. You may also find useful usage information (on docker/hpc/compilation/other) on the Underworld blog.
+
 Native Installation
 -------------------
 
 Requirements
-~~~~~~~~~~~~
+++++++++++++
 
 Build environment
 *****************
@@ -70,27 +117,6 @@ Note that some tests also require *matplotlib*
    pytest -vvv ./docs/pytests
 
 
-Docker
-------
-
-Docker is a type of lightweight virtualisation, and is the preferred method for Underworld usage on personal computers. You will first need to install Docker on your system (see `Notes on Installing Docker`_) and then you may install Underworld via Docker. Docker can be driven from the command line, but new users may wish to use the Docker Kitematic GUI instead for ease. Simply search for 'underworldcode/underworld2' within Kitematic, and then click 'CREATE' to launch a container. You will eventually wish to modify your container settings (again through Kitematic) to enable local folder volume mapping, which will allow you to access your local drives from within your container.
-
-For Linux users, and those who prefer the command line, the following minimal command should be sufficient to access the Underworld2 Jupyter Notebook examples:
-
-.. code:: bash
-
-   docker run -p 8888:8888 underworldcode/underworld2
-
-Navigate to `localhost:8888 <localhost:8888>`_ to see the notebooks. Note that you can also use particular versions of Underworld using any of the Docker image tags. For example:
-
-.. code:: bash
-
-   docker run -p 8888:8888 underworldcode/underworld2:2.7.1b
-
-By default (ie, if no tag is provided), docker will use the latest stable release. A list of available tags may be found on `our DockerHub page <https://hub.docker.com/r/underworldcode/underworld2/tags>`_. Tags can also be accessed in Kitematic via the ellipsis button on container search results. 
-
-A number of useful docker commands are provided within the `Underworld cheat-sheet <https://github.com/underworldcode/underworld2/tree/master/docs/cheatsheet/cheatsheet.pdf>`_.
-
 Notes on Installing Docker
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 

LICENSE.md

@@ -16,7 +16,8 @@ Underworld has been in development since 2003. It has always been released under
 
 ### Copyright holders
 
-Copyright Australian National University, 2020-2023
+Copyright Australian National University, 2020-2025
+Copyright The University of Sydney,       2020-2025
 Copyright Melbourne University,           2014-2021
 Copyright Monash University,              2003-2021
 Copyright VPAC,                           2003-2009

clean.sh

@@ -3,9 +3,10 @@
 set -x  # show commands
 
 rm -fr build
-find src/ -name \*.so -exec rm {} +
-find src/ -name __pycache__ -exec rm -r {} +
-find src/ -name '*.egg-info' -exec rm -r {} +
+
+find src -name '*.so' -exec rm {} +
+find src -name '*.__pycache__' -exec rm -r {} +
+find src -name '*.egg-info' -exec rm -r {} +
 rm -rf .pytest_cache
 ## To remove untracked git files
 #git clean -dfX ; git clean -dfx

conda/environment.yml conda/environment.yamlconda/environment.yml renamed to conda/environment.yaml

@@ -1,19 +1,21 @@
-name: uw-2.17.x
+name: uw-2.17
 channels:
   - conda-forge
 dependencies:
-  - python==3.11
+  - python==3.12
+  - numpy<2
   - compilers
   - pkg-config
-  - libxml2
+  - libxml2-devel
+  - make
   - cmake
   - swig>=4.0.0
   - ninja
   - pint
   - mpich
   - petsc==3.21.5
   - mesalib
-  - numpy<2
+  - git
   - scipy
   - mpi4py
   - h5py=*=mpi*
@@ -25,6 +27,7 @@ dependencies:
   - pip
   - pip:
     - lavavu
+    - lavavu-osmesa
     #- badlands comment out for the following for now
     - "badlands @ git+https://github.com/julesghub/badlands.git@julesghub/meson-build#subdirectory=badlands"