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Minor fixes #554

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merged 1 commit into from
Jul 7, 2021
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@jmansour jmansour commented Jul 7, 2021

  • Import scaling into uw.
  • Fix docstrings & doctests.
  • Rename pull request template as Github doesn't appear
    to register it with upper case naming.
  • Fix test in config which Py3.8 is complaining about.

* Fix docstrings & doctests.
* Rename pull request template as Github doesn't appear
  to register it with upper case naming.
* Fix test in config which Py3.8 is complaining about.
@jmansour jmansour requested a review from julesghub July 7, 2021 02:39
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Nice

@julesghub julesghub merged commit 19d3c5d into underworldcode:v2.11_release Jul 7, 2021
julesghub added a commit that referenced this pull request Aug 17, 2021
* Fix issue 537 - vrms typo

* Making sure the factor is an appropriate numpy type

* Updates for docker image generation: (#550)

* Switch deprecated `MAINTAINER` tag for new `LABEL` construct.
* Set `/opt` to ugo+rwx to allow users to install new pip packages.
* Remove `tini` which no longer appears to be required (and wasn't
  being used previously in any case).
* Remove extras for notebook MPI usage, as this wasn't being used
  and is easy to reinstall.
* Update UW image to point to newest base file image.
* Update to CHANGES.md

* Renaming guidelines.md -> development_guidelines.md

* * Fixes h5 file save mode (underworldcode/underworld2/#533)
* Minor documentation updates.
* Minor redundant code removal.
* Adding a pull request template!
* Update `CHANGES.md`

* Update to fix broken ReadTheDocs generation.

* * Import scaling into uw. (#554)

* Fix docstrings & doctests.
* Rename pull request template as Github doesn't appear
  to register it with upper case naming.
* Fix test in config which Py3.8 is complaining about.

* * Added a check to ensure that the selected solver is available at runtime. (#553)

The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* Solver check (#555)

* * Added a check to ensure that the selected solver is available at runtime.
  The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* I've updated these models to run with "mumps" if available,
and fallback to the default solver otherwise.

* Using a relative path to reload swarm files

* * For sequential IO operations, need to ensure that
  non-root procs open file with `append` mode instead
  of `write` mode (otherwise a new file is created by
  each proc, effectively deleting all data previously
  written).
* Update mesh file mode to `write` mode.

* Making test_long.sh executable

* Adding a EBA example to the tests for now. Documentation will come next
release when it's moved into examples.
The 2 extra terms in the heat equation, viscous dissipation and
adiabatic heating, should have equal volume integrals in the model, as
per King et al.

* Update CHANGES

* github actions docker images

* * Documentation, version numbers, and docker file updates. (#559)

* File creation mode should be "w" here too. Interesting, "append"
  mode causes a test failure in the Docker container, but not baremetal
  Ubuntu.

* Update docker_build_push.yml

* Update docker_build_push.yml

* Update docker_build_push.yml

* Adding symlink to `LICENSE.md` for conda.

Co-authored-by: John Mansour <mansourjohn@gmail.com>
julesghub added a commit that referenced this pull request Aug 24, 2021
* Forcing h5py version 2.10.0 in the latest gadi install.
And UwGeo 2.10.2

* Update Gadi install script, use  in LD_PRELOAD

* Updating gadi install scripts to use the nci specific compiler wrappers.

* * H5py v3 is more strict in allowed indexing array shapes. Updated our
  structures to accomodate.
* Tester uses `jupyter-nbconvert` which no longer defaults to Python. Update
  to explicitly select Python.

* Scons 4.1 compatibility fixes.

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* Add some tests on the mesh

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* * Update `CHANGES.md`.
* Add `pint` to `setup.py` requirements.

* Fix warning messages when downcasting units to numpy array.

* Fix issue 537 - vrms typo

* Making sure the factor is an appropriate numpy type

* Updates for docker image generation: (#550)

* Switch deprecated `MAINTAINER` tag for new `LABEL` construct.
* Set `/opt` to ugo+rwx to allow users to install new pip packages.
* Remove `tini` which no longer appears to be required (and wasn't
  being used previously in any case).
* Remove extras for notebook MPI usage, as this wasn't being used
  and is easy to reinstall.
* Update UW image to point to newest base file image.
* Update to CHANGES.md

* Renaming guidelines.md -> development_guidelines.md

* * Fixes h5 file save mode (underworldcode/underworld2/#533)
* Minor documentation updates.
* Minor redundant code removal.
* Adding a pull request template!
* Update `CHANGES.md`

* Update to fix broken ReadTheDocs generation.

* * Import scaling into uw. (#554)

* Fix docstrings & doctests.
* Rename pull request template as Github doesn't appear
  to register it with upper case naming.
* Fix test in config which Py3.8 is complaining about.

* * Added a check to ensure that the selected solver is available at runtime. (#553)

The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* Solver check (#555)

* * Added a check to ensure that the selected solver is available at runtime.
  The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* I've updated these models to run with "mumps" if available,
and fallback to the default solver otherwise.

* Using a relative path to reload swarm files

* * For sequential IO operations, need to ensure that
  non-root procs open file with `append` mode instead
  of `write` mode (otherwise a new file is created by
  each proc, effectively deleting all data previously
  written).
* Update mesh file mode to `write` mode.

* Making test_long.sh executable

* Adding a EBA example to the tests for now. Documentation will come next
release when it's moved into examples.
The 2 extra terms in the heat equation, viscous dissipation and
adiabatic heating, should have equal volume integrals in the model, as
per King et al.

* Update CHANGES

* * Documentation, version numbers, and docker file updates. (#559)

* File creation mode should be "w" here too. Interesting, "append"
  mode causes a test failure in the Docker container, but not baremetal
  Ubuntu.

* Fix/Revert these version identifiers.

* * Update CHANGES.md
* Adding github action: docker build push

* Forgot to push

push = true to always push after

Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
Co-authored-by: jmansour <mansourjohn@gmail.com>
rbeucher added a commit that referenced this pull request Jan 10, 2022
* Forcing h5py version 2.10.0 in the latest gadi install.
And UwGeo 2.10.2

* Update Gadi install script, use  in LD_PRELOAD

* Updating gadi install scripts to use the nci specific compiler wrappers.

* * H5py v3 is more strict in allowed indexing array shapes. Updated our
  structures to accomodate.
* Tester uses `jupyter-nbconvert` which no longer defaults to Python. Update
  to explicitly select Python.

* Scons 4.1 compatibility fixes.

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* Add some tests on the mesh

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* * Update `CHANGES.md`.
* Add `pint` to `setup.py` requirements.

* Fix warning messages when downcasting units to numpy array.

* Fix issue 537 - vrms typo

* Making sure the factor is an appropriate numpy type

* Updates for docker image generation: (#550)

* Switch deprecated `MAINTAINER` tag for new `LABEL` construct.
* Set `/opt` to ugo+rwx to allow users to install new pip packages.
* Remove `tini` which no longer appears to be required (and wasn't
  being used previously in any case).
* Remove extras for notebook MPI usage, as this wasn't being used
  and is easy to reinstall.
* Update UW image to point to newest base file image.
* Update to CHANGES.md

* Renaming guidelines.md -> development_guidelines.md

* * Fixes h5 file save mode (underworldcode/underworld2/#533)
* Minor documentation updates.
* Minor redundant code removal.
* Adding a pull request template!
* Update `CHANGES.md`

* Update to fix broken ReadTheDocs generation.

* * Import scaling into uw. (#554)

* Fix docstrings & doctests.
* Rename pull request template as Github doesn't appear
  to register it with upper case naming.
* Fix test in config which Py3.8 is complaining about.

* * Added a check to ensure that the selected solver is available at runtime. (#553)

The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* Solver check (#555)

* * Added a check to ensure that the selected solver is available at runtime.
  The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* I've updated these models to run with "mumps" if available,
and fallback to the default solver otherwise.

* Using a relative path to reload swarm files

* * For sequential IO operations, need to ensure that
  non-root procs open file with `append` mode instead
  of `write` mode (otherwise a new file is created by
  each proc, effectively deleting all data previously
  written).
* Update mesh file mode to `write` mode.

* Making test_long.sh executable

* Adding a EBA example to the tests for now. Documentation will come next
release when it's moved into examples.
The 2 extra terms in the heat equation, viscous dissipation and
adiabatic heating, should have equal volume integrals in the model, as
per King et al.

* Update CHANGES

* * Documentation, version numbers, and docker file updates. (#559)

* File creation mode should be "w" here too. Interesting, "append"
  mode causes a test failure in the Docker container, but not baremetal
  Ubuntu.

* Fix/Revert these version identifiers.

* * Update CHANGES.md
* Adding github action: docker build push

* Forgot to push

push = true to always push after

Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
Co-authored-by: jmansour <mansourjohn@gmail.com>
rbeucher added a commit that referenced this pull request Jan 18, 2022
* Initial work on implementing the FSSA stabilisation term.

The FSSA algorithm introduced by

Kaus, B.J.P., et al., A stabilization algorithm for geodynamic numerical simulations with a free surface. Phys.
Earth Planet. In. (2010), doi:10.1016/j.pepi.2010.04.007

This is only the C++ backend implementation as it stands the matrix term is yet to incorporate the disagonalisation and still
requires testing.

* Lastest updates for fssa

Adding a python later to use the c-code.
Now stokes takes an `_fn_fssa` argument.

* FSSA implementation updates.

* Bug fix - using the right determinant now.
* Implementing the FSSA2 algorithm, ie. just diagonal entries now, not
the full, non-symmetric, matrix.

* updating fssa-algo with development (#570)

* Forcing h5py version 2.10.0 in the latest gadi install.
And UwGeo 2.10.2

* Update Gadi install script, use  in LD_PRELOAD

* Updating gadi install scripts to use the nci specific compiler wrappers.

* * H5py v3 is more strict in allowed indexing array shapes. Updated our
  structures to accomodate.
* Tester uses `jupyter-nbconvert` which no longer defaults to Python. Update
  to explicitly select Python.

* Scons 4.1 compatibility fixes.

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* Add some tests on the mesh

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* * Update `CHANGES.md`.
* Add `pint` to `setup.py` requirements.

* Fix warning messages when downcasting units to numpy array.

* Fix issue 537 - vrms typo

* Making sure the factor is an appropriate numpy type

* Updates for docker image generation: (#550)

* Switch deprecated `MAINTAINER` tag for new `LABEL` construct.
* Set `/opt` to ugo+rwx to allow users to install new pip packages.
* Remove `tini` which no longer appears to be required (and wasn't
  being used previously in any case).
* Remove extras for notebook MPI usage, as this wasn't being used
  and is easy to reinstall.
* Update UW image to point to newest base file image.
* Update to CHANGES.md

* Renaming guidelines.md -> development_guidelines.md

* * Fixes h5 file save mode (underworldcode/underworld2/#533)
* Minor documentation updates.
* Minor redundant code removal.
* Adding a pull request template!
* Update `CHANGES.md`

* Update to fix broken ReadTheDocs generation.

* * Import scaling into uw. (#554)

* Fix docstrings & doctests.
* Rename pull request template as Github doesn't appear
  to register it with upper case naming.
* Fix test in config which Py3.8 is complaining about.

* * Added a check to ensure that the selected solver is available at runtime. (#553)

The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* Solver check (#555)

* * Added a check to ensure that the selected solver is available at runtime.
  The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* I've updated these models to run with "mumps" if available,
and fallback to the default solver otherwise.

* Using a relative path to reload swarm files

* * For sequential IO operations, need to ensure that
  non-root procs open file with `append` mode instead
  of `write` mode (otherwise a new file is created by
  each proc, effectively deleting all data previously
  written).
* Update mesh file mode to `write` mode.

* Making test_long.sh executable

* Adding a EBA example to the tests for now. Documentation will come next
release when it's moved into examples.
The 2 extra terms in the heat equation, viscous dissipation and
adiabatic heating, should have equal volume integrals in the model, as
per King et al.

* Update CHANGES

* * Documentation, version numbers, and docker file updates. (#559)

* File creation mode should be "w" here too. Interesting, "append"
  mode causes a test failure in the Docker container, but not baremetal
  Ubuntu.

* Fix/Revert these version identifiers.

* * Update CHANGES.md
* Adding github action: docker build push

* Forgot to push

push = true to always push after

Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
Co-authored-by: jmansour <mansourjohn@gmail.com>

* Building a docker automatically 

It will be at
julesg/underworld2:jgiordani/fssa-algo

The name of the docker needs to update at some stage... it's awful.

* Update docker_build_push.yml

* Update docker_build_push.yml

* Cleaning up the code

* opps

* Automatic border gauss swarm population.

Using the volume element GaussIntSwarm to inform the surface integration GaussSwarm population.

* Some updates to test

* Delete github action

* Delete github action, Add cpp file to CMakeList

* Fix some header paths for CMake compilation...

* Update fssa implementation

* Typo fix

* Adding the matrix surface assembly term for the fssa algorithm

Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
Co-authored-by: jmansour <mansourjohn@gmail.com>
rbeucher added a commit that referenced this pull request Jan 18, 2022
* Forcing h5py version 2.10.0 in the latest gadi install.
And UwGeo 2.10.2

* Update Gadi install script, use  in LD_PRELOAD

* Updating gadi install scripts to use the nci specific compiler wrappers.

* * H5py v3 is more strict in allowed indexing array shapes. Updated our
  structures to accomodate.
* Tester uses `jupyter-nbconvert` which no longer defaults to Python. Update
  to explicitly select Python.

* Scons 4.1 compatibility fixes.

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* Add some tests on the mesh

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* * Update `CHANGES.md`.
* Add `pint` to `setup.py` requirements.

* Fix warning messages when downcasting units to numpy array.

* Fix issue 537 - vrms typo

* Making sure the factor is an appropriate numpy type

* Updates for docker image generation: (#550)

* Switch deprecated `MAINTAINER` tag for new `LABEL` construct.
* Set `/opt` to ugo+rwx to allow users to install new pip packages.
* Remove `tini` which no longer appears to be required (and wasn't
  being used previously in any case).
* Remove extras for notebook MPI usage, as this wasn't being used
  and is easy to reinstall.
* Update UW image to point to newest base file image.
* Update to CHANGES.md

* Renaming guidelines.md -> development_guidelines.md

* * Fixes h5 file save mode (underworldcode/underworld2/#533)
* Minor documentation updates.
* Minor redundant code removal.
* Adding a pull request template!
* Update `CHANGES.md`

* Update to fix broken ReadTheDocs generation.

* * Import scaling into uw. (#554)

* Fix docstrings & doctests.
* Rename pull request template as Github doesn't appear
  to register it with upper case naming.
* Fix test in config which Py3.8 is complaining about.

* * Added a check to ensure that the selected solver is available at runtime. (#553)

The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* Solver check (#555)

* * Added a check to ensure that the selected solver is available at runtime.
  The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* I've updated these models to run with "mumps" if available,
and fallback to the default solver otherwise.

* Using a relative path to reload swarm files

* * For sequential IO operations, need to ensure that
  non-root procs open file with `append` mode instead
  of `write` mode (otherwise a new file is created by
  each proc, effectively deleting all data previously
  written).
* Update mesh file mode to `write` mode.

* Making test_long.sh executable

* Adding a EBA example to the tests for now. Documentation will come next
release when it's moved into examples.
The 2 extra terms in the heat equation, viscous dissipation and
adiabatic heating, should have equal volume integrals in the model, as
per King et al.

* Update CHANGES

* * Documentation, version numbers, and docker file updates. (#559)

* File creation mode should be "w" here too. Interesting, "append"
  mode causes a test failure in the Docker container, but not baremetal
  Ubuntu.

* Fix/Revert these version identifiers.

* * Update CHANGES.md
* Adding github action: docker build push

* Forgot to push

push = true to always push after

Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
Co-authored-by: jmansour <mansourjohn@gmail.com>
rbeucher added a commit that referenced this pull request Jan 18, 2022
* Initial work on implementing the FSSA stabilisation term.

The FSSA algorithm introduced by

Kaus, B.J.P., et al., A stabilization algorithm for geodynamic numerical simulations with a free surface. Phys.
Earth Planet. In. (2010), doi:10.1016/j.pepi.2010.04.007

This is only the C++ backend implementation as it stands the matrix term is yet to incorporate the disagonalisation and still
requires testing.

* Lastest updates for fssa

Adding a python later to use the c-code.
Now stokes takes an `_fn_fssa` argument.

* FSSA implementation updates.

* Bug fix - using the right determinant now.
* Implementing the FSSA2 algorithm, ie. just diagonal entries now, not
the full, non-symmetric, matrix.

* updating fssa-algo with development (#570)

* Forcing h5py version 2.10.0 in the latest gadi install.
And UwGeo 2.10.2

* Update Gadi install script, use  in LD_PRELOAD

* Updating gadi install scripts to use the nci specific compiler wrappers.

* * H5py v3 is more strict in allowed indexing array shapes. Updated our
  structures to accomodate.
* Tester uses `jupyter-nbconvert` which no longer defaults to Python. Update
  to explicitly select Python.

* Scons 4.1 compatibility fixes.

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* Add some tests on the mesh

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* * Update `CHANGES.md`.
* Add `pint` to `setup.py` requirements.

* Fix warning messages when downcasting units to numpy array.

* Fix issue 537 - vrms typo

* Making sure the factor is an appropriate numpy type

* Updates for docker image generation: (#550)

* Switch deprecated `MAINTAINER` tag for new `LABEL` construct.
* Set `/opt` to ugo+rwx to allow users to install new pip packages.
* Remove `tini` which no longer appears to be required (and wasn't
  being used previously in any case).
* Remove extras for notebook MPI usage, as this wasn't being used
  and is easy to reinstall.
* Update UW image to point to newest base file image.
* Update to CHANGES.md

* Renaming guidelines.md -> development_guidelines.md

* * Fixes h5 file save mode (underworldcode/underworld2/#533)
* Minor documentation updates.
* Minor redundant code removal.
* Adding a pull request template!
* Update `CHANGES.md`

* Update to fix broken ReadTheDocs generation.

* * Import scaling into uw. (#554)

* Fix docstrings & doctests.
* Rename pull request template as Github doesn't appear
  to register it with upper case naming.
* Fix test in config which Py3.8 is complaining about.

* * Added a check to ensure that the selected solver is available at runtime. (#553)

The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* Solver check (#555)

* * Added a check to ensure that the selected solver is available at runtime.
  The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* I've updated these models to run with "mumps" if available,
and fallback to the default solver otherwise.

* Using a relative path to reload swarm files

* * For sequential IO operations, need to ensure that
  non-root procs open file with `append` mode instead
  of `write` mode (otherwise a new file is created by
  each proc, effectively deleting all data previously
  written).
* Update mesh file mode to `write` mode.

* Making test_long.sh executable

* Adding a EBA example to the tests for now. Documentation will come next
release when it's moved into examples.
The 2 extra terms in the heat equation, viscous dissipation and
adiabatic heating, should have equal volume integrals in the model, as
per King et al.

* Update CHANGES

* * Documentation, version numbers, and docker file updates. (#559)

* File creation mode should be "w" here too. Interesting, "append"
  mode causes a test failure in the Docker container, but not baremetal
  Ubuntu.

* Fix/Revert these version identifiers.

* * Update CHANGES.md
* Adding github action: docker build push

* Forgot to push

push = true to always push after

Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
Co-authored-by: jmansour <mansourjohn@gmail.com>

* Building a docker automatically 

It will be at
julesg/underworld2:jgiordani/fssa-algo

The name of the docker needs to update at some stage... it's awful.

* Update docker_build_push.yml

* Update docker_build_push.yml

* Cleaning up the code

* opps

* Automatic border gauss swarm population.

Using the volume element GaussIntSwarm to inform the surface integration GaussSwarm population.

* Some updates to test

* Delete github action

* Delete github action, Add cpp file to CMakeList

* Fix some header paths for CMake compilation...

* Update fssa implementation

* Typo fix

* Adding the matrix surface assembly term for the fssa algorithm

* Update Lavavu and Petsc Dockerfiles

* Initial work on implementing the FSSA stabilisation term.

The FSSA algorithm introduced by

Kaus, B.J.P., et al., A stabilization algorithm for geodynamic numerical simulations with a free surface. Phys.
Earth Planet. In. (2010), doi:10.1016/j.pepi.2010.04.007

This is only the C++ backend implementation as it stands the matrix term is yet to incorporate the disagonalisation and still
requires testing.

* Lastest updates for fssa

Adding a python later to use the c-code.
Now stokes takes an `_fn_fssa` argument.

* FSSA implementation updates.

* Bug fix - using the right determinant now.
* Implementing the FSSA2 algorithm, ie. just diagonal entries now, not
the full, non-symmetric, matrix.

* updating fssa-algo with development (#570)

* Forcing h5py version 2.10.0 in the latest gadi install.
And UwGeo 2.10.2

* Update Gadi install script, use  in LD_PRELOAD

* Updating gadi install scripts to use the nci specific compiler wrappers.

* * H5py v3 is more strict in allowed indexing array shapes. Updated our
  structures to accomodate.
* Tester uses `jupyter-nbconvert` which no longer defaults to Python. Update
  to explicitly select Python.

* Scons 4.1 compatibility fixes.

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* Add some tests on the mesh

* Option to Add units to the swarm, mesh and associated variables when saving to HDF5.

* * Update `CHANGES.md`.
* Add `pint` to `setup.py` requirements.

* Fix warning messages when downcasting units to numpy array.

* Fix issue 537 - vrms typo

* Making sure the factor is an appropriate numpy type

* Updates for docker image generation: (#550)

* Switch deprecated `MAINTAINER` tag for new `LABEL` construct.
* Set `/opt` to ugo+rwx to allow users to install new pip packages.
* Remove `tini` which no longer appears to be required (and wasn't
  being used previously in any case).
* Remove extras for notebook MPI usage, as this wasn't being used
  and is easy to reinstall.
* Update UW image to point to newest base file image.
* Update to CHANGES.md

* Renaming guidelines.md -> development_guidelines.md

* * Fixes h5 file save mode (underworldcode/underworld2/#533)
* Minor documentation updates.
* Minor redundant code removal.
* Adding a pull request template!
* Update `CHANGES.md`

* Update to fix broken ReadTheDocs generation.

* * Import scaling into uw. (#554)

* Fix docstrings & doctests.
* Rename pull request template as Github doesn't appear
  to register it with upper case naming.
* Fix test in config which Py3.8 is complaining about.

* * Added a check to ensure that the selected solver is available at runtime. (#553)

The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* Solver check (#555)

* * Added a check to ensure that the selected solver is available at runtime.
  The previous behaviour resulted in solves continuing unaware of solve
  difficulties, and failing elsewhere, or worse.
* Added test for the solver check.

* I've updated these models to run with "mumps" if available,
and fallback to the default solver otherwise.

* Using a relative path to reload swarm files

* * For sequential IO operations, need to ensure that
  non-root procs open file with `append` mode instead
  of `write` mode (otherwise a new file is created by
  each proc, effectively deleting all data previously
  written).
* Update mesh file mode to `write` mode.

* Making test_long.sh executable

* Adding a EBA example to the tests for now. Documentation will come next
release when it's moved into examples.
The 2 extra terms in the heat equation, viscous dissipation and
adiabatic heating, should have equal volume integrals in the model, as
per King et al.

* Update CHANGES

* * Documentation, version numbers, and docker file updates. (#559)

* File creation mode should be "w" here too. Interesting, "append"
  mode causes a test failure in the Docker container, but not baremetal
  Ubuntu.

* Fix/Revert these version identifiers.

* * Update CHANGES.md
* Adding github action: docker build push

* Forgot to push

push = true to always push after

Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
Co-authored-by: jmansour <mansourjohn@gmail.com>

* Building a docker automatically 

It will be at
julesg/underworld2:jgiordani/fssa-algo

The name of the docker needs to update at some stage... it's awful.

* Update docker_build_push.yml

* Update docker_build_push.yml

* Cleaning up the code

* opps

* Automatic border gauss swarm population.

Using the volume element GaussIntSwarm to inform the surface integration GaussSwarm population.

* Some updates to test

* Delete github action

* Delete github action, Add cpp file to CMakeList

* Fix some header paths for CMake compilation...

* Update fssa implementation

* Typo fix

* Adding the matrix surface assembly term for the fssa algorithm

* Update Lavavu and Petsc Dockerfiles

Co-authored-by: julian <house.of.jules@gmail.com>
Co-authored-by: Julian Giordani <julesghub@users.noreply.github.com>
Co-authored-by: jmansour <mansourjohn@gmail.com>
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2 participants