Merge UWGeodynamics into Underworld #604
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Lets archive UWGeodynamics when we release UW 2.13 |
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Great stuff! |
julesghub
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Jul 12, 2022
* Updating development version to 2.13-dev * Release guidelines update * Add Changes to Changelog (#604) * Remoev UWGeodynamics installation from dockerfiles * Petsc 3.17 compatibility and removing duplicate examples python scripts * Add petsc variants to conda recipe * Add python 3.10 conda builds to actions. * Change PETSC and MPICH versions * Fix MPICH complaining... * Getting Dockerfiles ready: Ubuntu 22.04LTS and python 3.10. Note that this will fail for now because of h5py not being compatible. PR is on its way. * Update README * Update README * Transfer UWGeo documentation to Underworld * Remove python3-numpy-dbg for now * Fix Documentation Links (UWGeodynamics) Fix visualisation imports * Fix imports (UWGeodynamics) * Change Depth documentation toctree * UWGeodynamics Merging * Run tests * Move tests * H5py 3.7 is released, Use it in docker. * Typo in Petsc Dockerfile * Getting UWGeo internals to use uw2 mpi4py interface (#612) * Getting UWGeo internals to use uw2 mpi4py interface * Update CHANGES.md * Add pypi to github actions * Update PETSc Docker * Prepare Release 3.13 * Add Cython to Dockerfile for petsc4py * Fix Conda meta * Add comment to docker.md * Remove gadi install instructions * cython * Try this * Remove six(py2 compatibility) * Ad scipy for freesurface, surafeceprocesses etc. * Fix annoying error message when compiling * * Adding documentation re XDMF files (#614) * Removing obsolete python user_guides * Dockerfile fix. Switching from virtualenv -> venv for create python virtualenv. It appears the new Ubuntu/Python combo was causing the virtualenv paths to be different. Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
julesghub
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Aug 15, 2022
* Updating development version to 2.13-dev * Release guidelines update * Add Changes to Changelog (#604) * Remoev UWGeodynamics installation from dockerfiles * Petsc 3.17 compatibility and removing duplicate examples python scripts * Add petsc variants to conda recipe * Add python 3.10 conda builds to actions. * Change PETSC and MPICH versions * Fix MPICH complaining... * Getting Dockerfiles ready: Ubuntu 22.04LTS and python 3.10. Note that this will fail for now because of h5py not being compatible. PR is on its way. * Update README * Update README * Transfer UWGeo documentation to Underworld * Remove python3-numpy-dbg for now * Fix Documentation Links (UWGeodynamics) Fix visualisation imports * Fix imports (UWGeodynamics) * Change Depth documentation toctree * UWGeodynamics Merging * Run tests * Move tests * H5py 3.7 is released, Use it in docker. * Typo in Petsc Dockerfile * Getting UWGeo internals to use uw2 mpi4py interface (#612) * Getting UWGeo internals to use uw2 mpi4py interface * Update CHANGES.md * ask per 2.13 release (#615) 2.13 release Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Update _version.py * Fix for analytic ID, which changed during cmake update. Ganalytics should now be right * Typo fix for 3.10 * Dockerfile improvement - should be a single layer command * safer #define when not using an official release of petsc * Update PetscOptionsBegin() to be dev compatible. see https://gitlab.com/petsc/petsc/-/blob/f3ed01cd9ab452072c1a44e935347389f67d72c6/doc/docs/changes/dev.rst * cmake updates for $PETSC_DIR and $PETSC_ARCH. Now it displays $PKG_CONFIG_PATH * Remove some output files that shouldn't be stored. * Fixing the pytest interfaces to pick up ipynb Cleaning the test dir also * Add a RuntimeError exception for fields without units * Update tests - they weren't RUNNING! Need to workout how to run collective_fail.py under pytest. Think it's hard because the returncodes are non 0 by choice... but pytest picks up on it. * Only check rank==1 for collective test * Update CI.yml * Update CI.yml add nbmake for testing ipynb * Update _version.py * Update CHANGES.md Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
julesghub
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Nov 21, 2022
* Updating development version to 2.13-dev * Release guidelines update * Add Changes to Changelog (#604) * Remoev UWGeodynamics installation from dockerfiles * Petsc 3.17 compatibility and removing duplicate examples python scripts * Add petsc variants to conda recipe * Add python 3.10 conda builds to actions. * Change PETSC and MPICH versions * Fix MPICH complaining... * Getting Dockerfiles ready: Ubuntu 22.04LTS and python 3.10. Note that this will fail for now because of h5py not being compatible. PR is on its way. * Update README * Update README * Transfer UWGeo documentation to Underworld * Remove python3-numpy-dbg for now * Fix Documentation Links (UWGeodynamics) Fix visualisation imports * Fix imports (UWGeodynamics) * Change Depth documentation toctree * UWGeodynamics Merging * Run tests * Move tests * H5py 3.7 is released, Use it in docker. * Typo in Petsc Dockerfile * Getting UWGeo internals to use uw2 mpi4py interface (#612) * Getting UWGeo internals to use uw2 mpi4py interface * Update CHANGES.md * ask per 2.13 release (#615) 2.13 release Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Update _version.py * Fix for analytic ID, which changed during cmake update. Ganalytics should now be right * Typo fix for 3.10 * Dockerfile improvement - should be a single layer command * safer #define when not using an official release of petsc * Update PetscOptionsBegin() to be dev compatible. see https://gitlab.com/petsc/petsc/-/blob/f3ed01cd9ab452072c1a44e935347389f67d72c6/doc/docs/changes/dev.rst * Petsc 3.18 updates Petsc error handling updates only. Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
julesghub
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Nov 23, 2022
* Dockerfile updates. * Adding mpi dockerfiles - only openmpi for now, mpich coming soon. * Removing `base` image for now. * Resultant UW image is ~2.4Gb rather than 3Gb. * Add some documentation * Activate UWGeo testing * Updates github actions for Dockerfile change * Update CI.yml Fix typo * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Updating versions of github actions * Fixing petsc image name * Rebuild UW is the dockerfile changes * Add checks * Forgot github action variable * checks variable is working or not? * Can't get underworld check in github action to work ???!!! * Fix? * Typo fix * Update CI.yml debug * Update CI.yml always! * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Including vim in find docker image * Better way to look for h5 units. Previous h5py interface was causing erros on the c level. * Updates to build docker * Enable tests round 1 * Update CI.yml * Update CI.yml * Renmae UWGeo test, they take a while, might reintroduce later * Revert "Renmae UWGeo test, they take a while, might reintroduce later" This reverts commit d8a2268. * Smarter way to disable UWgeo tests for CI * Typo fix * Typo underworldcode#2 * opss, fixes broken units check, thanks tests ;) * Typo underworldcode#3 * type underworldcode#4 * Enable multi arch build !!! * Update for dockerfiles and macos * Rename docker images * Update Dockerfile * Update Dockerfile new docker image names * Update Dockerfile new docker image names * CHAGES.md and checkin docker-builder.sh for manual docker image creation * docs/development/docker/docker-builder.sh * Updates for conda - still testing * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Testing conda-forge connection to github actions * Making petsc version a build-arg for the dockerfiles. * Typo and adding UW_VERSION to github actions too. * Update CI.yml Can't resolve tag in `container` of github actions!!! * Disable arm build for underworld image - easier for now. * Dockerfile go * Work please * Dockerfile madness * Pin down psutil as a dependency was updating it - breaking jupyter-lab * Updates * psutil set to 5.9.3 for github action builds * Touch Lavavu * Dockerfile touch ups * remove psutil confusion * setuptools 65.6.0 has an error, so use 65.5.1 * update lavavu * fix * Fix typo in docker label * v2.14 branch upto with dev development (underworldcode#640) * Updating development version to 2.13-dev * Release guidelines update * Add Changes to Changelog (underworldcode#604) * Remoev UWGeodynamics installation from dockerfiles * Petsc 3.17 compatibility and removing duplicate examples python scripts * Add petsc variants to conda recipe * Add python 3.10 conda builds to actions. * Change PETSC and MPICH versions * Fix MPICH complaining... * Getting Dockerfiles ready: Ubuntu 22.04LTS and python 3.10. Note that this will fail for now because of h5py not being compatible. PR is on its way. * Update README * Update README * Transfer UWGeo documentation to Underworld * Remove python3-numpy-dbg for now * Fix Documentation Links (UWGeodynamics) Fix visualisation imports * Fix imports (UWGeodynamics) * Change Depth documentation toctree * UWGeodynamics Merging * Run tests * Move tests * H5py 3.7 is released, Use it in docker. * Typo in Petsc Dockerfile * Getting UWGeo internals to use uw2 mpi4py interface (underworldcode#612) * Getting UWGeo internals to use uw2 mpi4py interface * Update CHANGES.md * ask per 2.13 release (underworldcode#615) 2.13 release Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Update _version.py * Fix for analytic ID, which changed during cmake update. Ganalytics should now be right * Typo fix for 3.10 * Dockerfile improvement - should be a single layer command * safer #define when not using an official release of petsc * Update PetscOptionsBegin() to be dev compatible. see https://gitlab.com/petsc/petsc/-/blob/f3ed01cd9ab452072c1a44e935347389f67d72c6/doc/docs/changes/dev.rst * Petsc 3.18 updates Petsc error handling updates only. Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Add build-args for openmpi Docker creation Co-authored-by: Julian Giordani <jgiordani@mini.staff.wireless.sydney.edu.au> Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
julesghub
added a commit
that referenced
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Dec 14, 2022
* Updating development version to 2.13-dev * Release guidelines update * Add Changes to Changelog (#604) * Remoev UWGeodynamics installation from dockerfiles * Petsc 3.17 compatibility and removing duplicate examples python scripts * Add petsc variants to conda recipe * Add python 3.10 conda builds to actions. * Change PETSC and MPICH versions * Fix MPICH complaining... * Getting Dockerfiles ready: Ubuntu 22.04LTS and python 3.10. Note that this will fail for now because of h5py not being compatible. PR is on its way. * Update README * Update README * Transfer UWGeo documentation to Underworld * Remove python3-numpy-dbg for now * Fix Documentation Links (UWGeodynamics) Fix visualisation imports * Fix imports (UWGeodynamics) * Change Depth documentation toctree * UWGeodynamics Merging * Run tests * Move tests * H5py 3.7 is released, Use it in docker. * Typo in Petsc Dockerfile * Getting UWGeo internals to use uw2 mpi4py interface (#612) * Getting UWGeo internals to use uw2 mpi4py interface * Update CHANGES.md * ask per 2.13 release (#615) 2.13 release Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Update _version.py * Fix for analytic ID, which changed during cmake update. Ganalytics should now be right * Typo fix for 3.10 * Dockerfile improvement - should be a single layer command * safer #define when not using an official release of petsc * Update PetscOptionsBegin() to be dev compatible. see https://gitlab.com/petsc/petsc/-/blob/f3ed01cd9ab452072c1a44e935347389f67d72c6/doc/docs/changes/dev.rst * Petsc 3.18 updates Petsc error handling updates only. * Dockerfile updates. * Adding mpi dockerfiles - only openmpi for now, mpich coming soon. * Removing `base` image for now. * Resultant UW image is ~2.4Gb rather than 3Gb. * Add some documentation * Activate UWGeo testing * Updates github actions for Dockerfile change * Update CI.yml Fix typo * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Updating versions of github actions * Fixing petsc image name * Rebuild UW is the dockerfile changes * Add checks * Forgot github action variable * checks variable is working or not? * Can't get underworld check in github action to work ???!!! * Fix? * Typo fix * Update CI.yml debug * Update CI.yml always! * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Including vim in find docker image * Better way to look for h5 units. Previous h5py interface was causing erros on the c level. * Updates to build docker * Enable tests round 1 * Update CI.yml * Update CI.yml * Renmae UWGeo test, they take a while, might reintroduce later * Revert "Renmae UWGeo test, they take a while, might reintroduce later" This reverts commit d8a2268. * Smarter way to disable UWgeo tests for CI * Typo fix * Typo #2 * opss, fixes broken units check, thanks tests ;) * Typo #3 * type #4 * Enable multi arch build !!! * Update for dockerfiles and macos * Rename docker images * Update Dockerfile * Update Dockerfile new docker image names * Update Dockerfile new docker image names * CHAGES.md and checkin docker-builder.sh for manual docker image creation * docs/development/docker/docker-builder.sh * Updates for conda - still testing * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Testing conda-forge connection to github actions * Making petsc version a build-arg for the dockerfiles. * Typo and adding UW_VERSION to github actions too. * Update CI.yml Can't resolve tag in `container` of github actions!!! * Disable arm build for underworld image - easier for now. * Dockerfile go * Work please * Dockerfile madness * Pin down psutil as a dependency was updating it - breaking jupyter-lab * Updates * psutil set to 5.9.3 for github action builds * Touch Lavavu * Dockerfile touch ups * remove psutil confusion * setuptools 65.6.0 has an error, so use 65.5.1 * update lavavu * fix * Fix typo in docker label * v2.14 branch upto with dev development (#640) * Updating development version to 2.13-dev * Release guidelines update * Add Changes to Changelog (#604) * Remoev UWGeodynamics installation from dockerfiles * Petsc 3.17 compatibility and removing duplicate examples python scripts * Add petsc variants to conda recipe * Add python 3.10 conda builds to actions. * Change PETSC and MPICH versions * Fix MPICH complaining... * Getting Dockerfiles ready: Ubuntu 22.04LTS and python 3.10. Note that this will fail for now because of h5py not being compatible. PR is on its way. * Update README * Update README * Transfer UWGeo documentation to Underworld * Remove python3-numpy-dbg for now * Fix Documentation Links (UWGeodynamics) Fix visualisation imports * Fix imports (UWGeodynamics) * Change Depth documentation toctree * UWGeodynamics Merging * Run tests * Move tests * H5py 3.7 is released, Use it in docker. * Typo in Petsc Dockerfile * Getting UWGeo internals to use uw2 mpi4py interface (#612) * Getting UWGeo internals to use uw2 mpi4py interface * Update CHANGES.md * ask per 2.13 release (#615) 2.13 release Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Update _version.py * Fix for analytic ID, which changed during cmake update. Ganalytics should now be right * Typo fix for 3.10 * Dockerfile improvement - should be a single layer command * safer #define when not using an official release of petsc * Update PetscOptionsBegin() to be dev compatible. see https://gitlab.com/petsc/petsc/-/blob/f3ed01cd9ab452072c1a44e935347389f67d72c6/doc/docs/changes/dev.rst * Petsc 3.18 updates Petsc error handling updates only. Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Add build-args for openmpi Docker creation * Dockerfile updates (#1) * Dockerfile updates. * Adding mpi dockerfiles - only openmpi for now, mpich coming soon. * Removing `base` image for now. * Resultant UW image is ~2.4Gb rather than 3Gb. * Add some documentation * Activate UWGeo testing * Updates github actions for Dockerfile change * Update CI.yml Fix typo * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Updating versions of github actions * Fixing petsc image name * Rebuild UW is the dockerfile changes * Add checks * Forgot github action variable * checks variable is working or not? * Can't get underworld check in github action to work ???!!! * Fix? * Typo fix * Update CI.yml debug * Update CI.yml always! * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Including vim in find docker image * Better way to look for h5 units. Previous h5py interface was causing erros on the c level. * Updates to build docker * Enable tests round 1 * Update CI.yml * Update CI.yml * Renmae UWGeo test, they take a while, might reintroduce later * Revert "Renmae UWGeo test, they take a while, might reintroduce later" This reverts commit d8a2268. * Smarter way to disable UWgeo tests for CI * Typo fix * Typo #2 * opss, fixes broken units check, thanks tests ;) * Typo #3 * type #4 * Enable multi arch build !!! * Update for dockerfiles and macos * Rename docker images * Update Dockerfile * Update Dockerfile new docker image names * Update Dockerfile new docker image names * CHAGES.md and checkin docker-builder.sh for manual docker image creation * docs/development/docker/docker-builder.sh * Updates for conda - still testing * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Testing conda-forge connection to github actions * Making petsc version a build-arg for the dockerfiles. * Typo and adding UW_VERSION to github actions too. * Update CI.yml Can't resolve tag in `container` of github actions!!! * Disable arm build for underworld image - easier for now. * Dockerfile go * Work please * Dockerfile madness * Pin down psutil as a dependency was updating it - breaking jupyter-lab * Updates * psutil set to 5.9.3 for github action builds * Touch Lavavu * Dockerfile touch ups * remove psutil confusion * setuptools 65.6.0 has an error, so use 65.5.1 * update lavavu * fix * Fix typo in docker label * v2.14 branch upto with dev development (#640) * Updating development version to 2.13-dev * Release guidelines update * Add Changes to Changelog (#604) * Remoev UWGeodynamics installation from dockerfiles * Petsc 3.17 compatibility and removing duplicate examples python scripts * Add petsc variants to conda recipe * Add python 3.10 conda builds to actions. * Change PETSC and MPICH versions * Fix MPICH complaining... * Getting Dockerfiles ready: Ubuntu 22.04LTS and python 3.10. Note that this will fail for now because of h5py not being compatible. PR is on its way. * Update README * Update README * Transfer UWGeo documentation to Underworld * Remove python3-numpy-dbg for now * Fix Documentation Links (UWGeodynamics) Fix visualisation imports * Fix imports (UWGeodynamics) * Change Depth documentation toctree * UWGeodynamics Merging * Run tests * Move tests * H5py 3.7 is released, Use it in docker. * Typo in Petsc Dockerfile * Getting UWGeo internals to use uw2 mpi4py interface (#612) * Getting UWGeo internals to use uw2 mpi4py interface * Update CHANGES.md * ask per 2.13 release (#615) 2.13 release Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Update _version.py * Fix for analytic ID, which changed during cmake update. Ganalytics should now be right * Typo fix for 3.10 * Dockerfile improvement - should be a single layer command * safer #define when not using an official release of petsc * Update PetscOptionsBegin() to be dev compatible. see https://gitlab.com/petsc/petsc/-/blob/f3ed01cd9ab452072c1a44e935347389f67d72c6/doc/docs/changes/dev.rst * Petsc 3.18 updates Petsc error handling updates only. Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Add build-args for openmpi Docker creation Co-authored-by: Julian Giordani <jgiordani@mini.staff.wireless.sydney.edu.au> Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Enable the default args * disable petsc in github workflows * Update to underworldcode docker hub * update for 2.14 release (#642) * Images will push to underworldcode docker hub now * Change to kick off underworld2 image build * fix spacing in version file * Update CHANGES.md * Adding mpich Dockerfile * Disable github actions build of petsc and uw * Adding ARG smarts to petsc and UW image. Now MPI_IMAGE for petsc/Dockerfile and PETSC_IMAGE for uw2/Dockerfile are options that can we used to specify the exact docker image name. This will be used by github actions in future. * Update CI.yml * Update CI.yml Fix indenting of yaml * Update CI.yml * workdispatch only for openmpi/mpich and lavavu * Update CI.yml Adding MPICH_VERSION as an env var * Clean up docker-builder script * Smarts for docker-builder.sh Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> Co-authored-by: Julian Giordani <jgiordani@mini.staff.wireless.sydney.edu.au>
julesghub
added a commit
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Oct 31, 2023
* Updating development version to 2.13-dev * Release guidelines update * Add Changes to Changelog (#604) * Remoev UWGeodynamics installation from dockerfiles * Petsc 3.17 compatibility and removing duplicate examples python scripts * Add petsc variants to conda recipe * Add python 3.10 conda builds to actions. * Change PETSC and MPICH versions * Fix MPICH complaining... * Getting Dockerfiles ready: Ubuntu 22.04LTS and python 3.10. Note that this will fail for now because of h5py not being compatible. PR is on its way. * Update README * Update README * Transfer UWGeo documentation to Underworld * Remove python3-numpy-dbg for now * Fix Documentation Links (UWGeodynamics) Fix visualisation imports * Fix imports (UWGeodynamics) * Change Depth documentation toctree * UWGeodynamics Merging * Run tests * Move tests * H5py 3.7 is released, Use it in docker. * Typo in Petsc Dockerfile * Getting UWGeo internals to use uw2 mpi4py interface (#612) * Getting UWGeo internals to use uw2 mpi4py interface * Update CHANGES.md * ask per 2.13 release (#615) 2.13 release Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Update _version.py * Fix for analytic ID, which changed during cmake update. Ganalytics should now be right * Typo fix for 3.10 * Dockerfile improvement - should be a single layer command * safer #define when not using an official release of petsc * Update PetscOptionsBegin() to be dev compatible. see https://gitlab.com/petsc/petsc/-/blob/f3ed01cd9ab452072c1a44e935347389f67d72c6/doc/docs/changes/dev.rst * Dockerfile updates. * Adding mpi dockerfiles - only openmpi for now, mpich coming soon. * Removing `base` image for now. * Resultant UW image is ~2.4Gb rather than 3Gb. * Add some documentation * Activate UWGeo testing * Updates github actions for Dockerfile change * Update CI.yml Fix typo * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Updating versions of github actions * Fixing petsc image name * Rebuild UW is the dockerfile changes * Add checks * Forgot github action variable * checks variable is working or not? * Can't get underworld check in github action to work ???!!! * Fix? * Typo fix * Update CI.yml debug * Update CI.yml always! * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Including vim in find docker image * Better way to look for h5 units. Previous h5py interface was causing erros on the c level. * Updates to build docker * Enable tests round 1 * Update CI.yml * Update CI.yml * Renmae UWGeo test, they take a while, might reintroduce later * Revert "Renmae UWGeo test, they take a while, might reintroduce later" This reverts commit d8a2268. * Smarter way to disable UWgeo tests for CI * Typo fix * Typo #2 * opss, fixes broken units check, thanks tests ;) * Typo #3 * type #4 * Enable multi arch build !!! * Update for dockerfiles and macos * Rename docker images * Update Dockerfile * Update Dockerfile new docker image names * Update Dockerfile new docker image names * CHAGES.md and checkin docker-builder.sh for manual docker image creation * docs/development/docker/docker-builder.sh * Updates for conda - still testing * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Testing conda-forge connection to github actions * Making petsc version a build-arg for the dockerfiles. * Typo and adding UW_VERSION to github actions too. * Update CI.yml Can't resolve tag in `container` of github actions!!! * Disable arm build for underworld image - easier for now. * Dockerfile go * Work please * Dockerfile madness * Pin down psutil as a dependency was updating it - breaking jupyter-lab * Updates * psutil set to 5.9.3 for github action builds * Touch Lavavu * Dockerfile touch ups * remove psutil confusion * setuptools 65.6.0 has an error, so use 65.5.1 * update lavavu * fix * Fix typo in docker label * v2.14 branch upto with dev development (#640) * Updating development version to 2.13-dev * Release guidelines update * Add Changes to Changelog (#604) * Remoev UWGeodynamics installation from dockerfiles * Petsc 3.17 compatibility and removing duplicate examples python scripts * Add petsc variants to conda recipe * Add python 3.10 conda builds to actions. * Change PETSC and MPICH versions * Fix MPICH complaining... * Getting Dockerfiles ready: Ubuntu 22.04LTS and python 3.10. Note that this will fail for now because of h5py not being compatible. PR is on its way. * Update README * Update README * Transfer UWGeo documentation to Underworld * Remove python3-numpy-dbg for now * Fix Documentation Links (UWGeodynamics) Fix visualisation imports * Fix imports (UWGeodynamics) * Change Depth documentation toctree * UWGeodynamics Merging * Run tests * Move tests * H5py 3.7 is released, Use it in docker. * Typo in Petsc Dockerfile * Getting UWGeo internals to use uw2 mpi4py interface (#612) * Getting UWGeo internals to use uw2 mpi4py interface * Update CHANGES.md * ask per 2.13 release (#615) 2.13 release Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Update _version.py * Fix for analytic ID, which changed during cmake update. Ganalytics should now be right * Typo fix for 3.10 * Dockerfile improvement - should be a single layer command * safer #define when not using an official release of petsc * Update PetscOptionsBegin() to be dev compatible. see https://gitlab.com/petsc/petsc/-/blob/f3ed01cd9ab452072c1a44e935347389f67d72c6/doc/docs/changes/dev.rst * Petsc 3.18 updates Petsc error handling updates only. Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Add build-args for openmpi Docker creation * Dockerfile updates (#1) * Dockerfile updates. * Adding mpi dockerfiles - only openmpi for now, mpich coming soon. * Removing `base` image for now. * Resultant UW image is ~2.4Gb rather than 3Gb. * Add some documentation * Activate UWGeo testing * Updates github actions for Dockerfile change * Update CI.yml Fix typo * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Updating versions of github actions * Fixing petsc image name * Rebuild UW is the dockerfile changes * Add checks * Forgot github action variable * checks variable is working or not? * Can't get underworld check in github action to work ???!!! * Fix? * Typo fix * Update CI.yml debug * Update CI.yml always! * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Including vim in find docker image * Better way to look for h5 units. Previous h5py interface was causing erros on the c level. * Updates to build docker * Enable tests round 1 * Update CI.yml * Update CI.yml * Renmae UWGeo test, they take a while, might reintroduce later * Revert "Renmae UWGeo test, they take a while, might reintroduce later" This reverts commit d8a2268. * Smarter way to disable UWgeo tests for CI * Typo fix * Typo #2 * opss, fixes broken units check, thanks tests ;) * Typo #3 * type #4 * Enable multi arch build !!! * Update for dockerfiles and macos * Rename docker images * Update Dockerfile * Update Dockerfile new docker image names * Update Dockerfile new docker image names * CHAGES.md and checkin docker-builder.sh for manual docker image creation * docs/development/docker/docker-builder.sh * Updates for conda - still testing * Update CI.yml * Update CI.yml * Update CI.yml * Update CI.yml * Testing conda-forge connection to github actions * Making petsc version a build-arg for the dockerfiles. * Typo and adding UW_VERSION to github actions too. * Update CI.yml Can't resolve tag in `container` of github actions!!! * Disable arm build for underworld image - easier for now. * Dockerfile go * Work please * Dockerfile madness * Pin down psutil as a dependency was updating it - breaking jupyter-lab * Updates * psutil set to 5.9.3 for github action builds * Touch Lavavu * Dockerfile touch ups * remove psutil confusion * setuptools 65.6.0 has an error, so use 65.5.1 * update lavavu * fix * Fix typo in docker label * v2.14 branch upto with dev development (#640) * Updating development version to 2.13-dev * Release guidelines update * Add Changes to Changelog (#604) * Remoev UWGeodynamics installation from dockerfiles * Petsc 3.17 compatibility and removing duplicate examples python scripts * Add petsc variants to conda recipe * Add python 3.10 conda builds to actions. * Change PETSC and MPICH versions * Fix MPICH complaining... * Getting Dockerfiles ready: Ubuntu 22.04LTS and python 3.10. Note that this will fail for now because of h5py not being compatible. PR is on its way. * Update README * Update README * Transfer UWGeo documentation to Underworld * Remove python3-numpy-dbg for now * Fix Documentation Links (UWGeodynamics) Fix visualisation imports * Fix imports (UWGeodynamics) * Change Depth documentation toctree * UWGeodynamics Merging * Run tests * Move tests * H5py 3.7 is released, Use it in docker. * Typo in Petsc Dockerfile * Getting UWGeo internals to use uw2 mpi4py interface (#612) * Getting UWGeo internals to use uw2 mpi4py interface * Update CHANGES.md * ask per 2.13 release (#615) 2.13 release Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Update _version.py * Fix for analytic ID, which changed during cmake update. Ganalytics should now be right * Typo fix for 3.10 * Dockerfile improvement - should be a single layer command * safer #define when not using an official release of petsc * Update PetscOptionsBegin() to be dev compatible. see https://gitlab.com/petsc/petsc/-/blob/f3ed01cd9ab452072c1a44e935347389f67d72c6/doc/docs/changes/dev.rst * Petsc 3.18 updates Petsc error handling updates only. Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Add build-args for openmpi Docker creation Co-authored-by: Julian Giordani <jgiordani@mini.staff.wireless.sydney.edu.au> Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Enable the default args * disable petsc in github workflows * Update to underworldcode docker hub * update for 2.14 release (#642) * Images will push to underworldcode docker hub now * Change to kick off underworld2 image build * fix spacing in version file * Update CHANGES.md * Adding mpich Dockerfile * Disable github actions build of petsc and uw * Adding ARG smarts to petsc and UW image. Now MPI_IMAGE for petsc/Dockerfile and PETSC_IMAGE for uw2/Dockerfile are options that can we used to specify the exact docker image name. This will be used by github actions in future. * Update CI.yml * Update CI.yml Fix indenting of yaml * Update CI.yml * workdispatch only for openmpi/mpich and lavavu * Update CI.yml Adding MPICH_VERSION as an env var * Clean up docker-builder script * Smarts for docker-builder.sh * Include 'temperatureDot' checkpointing for UWGeo models by default * Adding pragmatric to petsc * cleanup of underworld2 dockerfile * Update version and disable conda for conda-forge staging process * Adding a fix for swarmvariable reloading. Thanks Arijit! * Removing unused imports * Disable openmpi. * Will delete this conda directory once the conda-forge feedstock is accepted. * Update for 2.14.2 * Fixes for temperatureDot checkpoint/restarting. * Petsc Dockerfile updates for h5py * Fixing the np.int deprecation issue. fixes #652 * Fixing some test. nbmark and matplotlib are needed for the tests. * Fixing/Shortening some models so they pass CI * removing ipynb version * Fixing all test in ./doc/test/* to not require matplotlib * update workflow with the new script name * Updating python dependencies. * Swig is a build dependency * Numpy version reducing to 1.20.3 for setonix * Fixes for checkpointing/restart with freeSurface's in UWGeo * Fix for #657 * Added path check in utils/_io.py * 1st cut adding Ben Knight's 3D surface veclocity code. Test model to come * Upload 3D SP example * Adding setonix install guide * starting for new release uw2.15 * Update surfaceProcesses.py Update timeField to record time of deposition of sediment in SP functions * Update surfaceProcesses.py Fix typo in 3D surface. Also reset time of the air material to the model time * Update surfaceProcesses.py fixed typo in func * updating the setonix jobs runners * Update surfaceProcesses.py Simplify 2D velocity and diffusivity SP functions * Update surfaceProcesses.py Didn't create object to bcast surface function to * Update surfaceProcesses Revert back to MPI gather of data over evaluate_global Update the examples * Adding melt dynamic heating to the advection diffusion solver see issue #669 * docker utils updates * Adding some final fixes to the dockerfile scripts * Update CHANGES.md * Remove obsolete glucifer bits * Update dockerfile Badlands install and CHANGES.md * Update CI for docker builds * Fixing the velocitySurface 2D and 3D implementation to handle restarts. Changes also include: * Renaming the surface tracers to prevent unexpected overwrites * The surfaceProcess class saving the passive tracer key to use during initialisation and solve. This is to make the code not save an instance of the pt to the swarm incase the pt is swapped in/out of Model memory. And helps with code readability. * Get the latest release of badlands from pypi --------- Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> Co-authored-by: Julian Giordani <jgiordani@mini.staff.wireless.sydney.edu.au> Co-authored-by: Ben Knight <55677727+bknight1@users.noreply.github.com>
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