Skip to content

Commit 287154d

Browse files
jorgensdjuliusghrossbm1MPenaRdependabot[bot]
authored
Release (#282)
* Improve workflow handling (#118) * Create common action for all workflows and split them into multiple files * Dokken/update fspace and wmtgs (#127) * fix runs-on * Minor improvements in linearelasticity.md (#124) * Fix various things on release branch * Try adding trame * Revert fundamentals * Membrane code * More updates due to autoformatting * Lagrange -> CG back conversion * Change to github image --------- Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> * Update petsc arches * Fix bounding boxes and more (#135) * Start fixing code for nightly build * rerun all files * Try fixing subdomains * Fix meshio * PETSc python API update (#137) * Resolve #136 * Fixes related to: FEniCS/dolfinx#2703 * Update changelog * Make sure all notebooks run. Change to pathlib in some examples * Api changes related to: FEniCS/dolfinx#2763 (#142) * Bump version numbers * Bump version numbers (#149) * Fix petsc arch * Prepare v0.7.1 (#154) * Merge branch 'main' into release and bump versions * Delete obsolete file * Temporary shift path in nightly test * Make sure there are no warnigns in build * Tabulation * Updates compatible with nightly branch of DOLFINx (#156) * Replace VectorElement and FiniteElement with `basix.ufl.element`. Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace` * More updates * And more * Last vector element updates * Bump pyvista and dolfinx to v0.7.2 (#159) * Bump pyvista and dolfinx to v0.7.2 * remove -r * Add further pyvista deps * Bump versions * Update petsc solver and pc links. Resolves #143 (#160) * Fix typo and issue Issue on page /fem.html #122 (#161) * Compute entity-cell connectivity before calling locate_dofs_topological. Remove soon to be deprecated pyvista syntax for updating time dependent fields. Fix range->np.arange conversion * Update backend in workflow * Fix broken link (#140) + http:// to https:// (#162) * Run book build prior to parallel run * Add back write frame * Fix wrong link * Fix typo in changelog * Merge main into release (#189) * Merge main into release * Apply suggestions from code review * Various fixes when reading through the diff * Further fixes * add missing checkout (#191) * add missing checkout * Add test docker on release PR and release (only push on tag * Remove unused import * Update text to resolve #194 (#195) * Dokken/update nonlin options (#203) * Update options for non-linear solver to sensible choice, ref #200 * Update docker path * Update python file as well * Update config ptr (#207) * Pressure correction equation fix (#196) * Update fundamentals.md (#199) on line 110, updated a typesetting error in equation (3) * Change from vector to petsc_vec (#206) * dolfinx.fem.Form changed to dolfinx.fem.form (#213) * Update compiler_parameters.ipynb In the text it was mentioned that `dolfinx.fem.Form` was used to compile the form, instead of `dolfinx.fem.form`. Not matching the code cell. * jupytext sync * Form -> form in both py and ipynb and LinearProblem -> fem.petsc.LinearProblem * Update book_stable.yml * Update test_stable.yml * Fix python path in test * Fix CI (#227) * Bump docker/build-push-action from 5 to 6 (#221) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5 to 6. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v5...v6) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/configure-pages from 4 to 5 (#222) Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5. - [Release notes](https://github.com/actions/configure-pages/releases) - [Commits](actions/configure-pages@v4...v5) --- updated-dependencies: - dependency-name: actions/configure-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update book_stable.yml (#225) * Update book_stable.yml * Update test_stable.yml * resolve #224 (#226) * Update test_stable.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update test_stable.yml (#235) * Add libgl flag to ci (#238) * Dokken/bump release (#249) * Update elasticity_scaling.md (#242) * Improve workflow handling (#118) * Create common action for all workflows and split them into multiple files * Dokken/update fspace and wmtgs (#127) * fix runs-on * Minor improvements in linearelasticity.md (#124) * Fix various things on release branch * Try adding trame * Revert fundamentals * Membrane code * More updates due to autoformatting * Lagrange -> CG back conversion * Change to github image --------- Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> * Update petsc arches * Fix bounding boxes and more (#135) * Start fixing code for nightly build * rerun all files * Try fixing subdomains * Fix meshio * PETSc python API update (#137) * Resolve #136 * Fixes related to: FEniCS/dolfinx#2703 * Update changelog * Make sure all notebooks run. Change to pathlib in some examples * Api changes related to: FEniCS/dolfinx#2763 (#142) * Bump version numbers * Bump version numbers (#149) * Fix petsc arch * Prepare v0.7.1 (#154) * Merge branch 'main' into release and bump versions * Delete obsolete file * Temporary shift path in nightly test * Make sure there are no warnigns in build * Tabulation * Updates compatible with nightly branch of DOLFINx (#156) * Replace VectorElement and FiniteElement with `basix.ufl.element`. Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace` * More updates * And more * Last vector element updates * Bump pyvista and dolfinx to v0.7.2 (#159) * Bump pyvista and dolfinx to v0.7.2 * remove -r * Add further pyvista deps * Bump versions * Update petsc solver and pc links. Resolves #143 (#160) * Fix typo and issue Issue on page /fem.html #122 (#161) * Compute entity-cell connectivity before calling locate_dofs_topological. Remove soon to be deprecated pyvista syntax for updating time dependent fields. Fix range->np.arange conversion * Update backend in workflow * Fix broken link (#140) + http:// to https:// (#162) * Run book build prior to parallel run * Add back write frame * Fix wrong link * Fix typo in changelog * Merge main into release (#189) * Merge main into release * Apply suggestions from code review * Various fixes when reading through the diff * Further fixes * add missing checkout (#191) * add missing checkout * Add test docker on release PR and release (only push on tag * Remove unused import * Update text to resolve #194 (#195) * Dokken/update nonlin options (#203) * Update options for non-linear solver to sensible choice, ref #200 * Update docker path * Update python file as well * Update config ptr (#207) * Pressure correction equation fix (#196) * Update fundamentals.md (#199) on line 110, updated a typesetting error in equation (3) * Change from vector to petsc_vec (#206) * dolfinx.fem.Form changed to dolfinx.fem.form (#213) * Update compiler_parameters.ipynb In the text it was mentioned that `dolfinx.fem.Form` was used to compile the form, instead of `dolfinx.fem.form`. Not matching the code cell. * jupytext sync * Form -> form in both py and ipynb and LinearProblem -> fem.petsc.LinearProblem * Update book_stable.yml * Update test_stable.yml * Fix python path in test * Fix CI (#227) * Bump docker/build-push-action from 5 to 6 (#221) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5 to 6. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v5...v6) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/configure-pages from 4 to 5 (#222) Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5. - [Release notes](https://github.com/actions/configure-pages/releases) - [Commits](actions/configure-pages@v4...v5) --- updated-dependencies: - dependency-name: actions/configure-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update book_stable.yml (#225) * Update book_stable.yml * Update test_stable.yml * resolve #224 (#226) * Update test_stable.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update test_stable.yml (#235) * Add libgl flag to ci (#238) * Update elasticity_scaling.md --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com> Co-authored-by: Jørgen S. Dokken <dokken@simula.no> Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com> Co-authored-by: Manuel Pena <mpena991@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update navierstokes.md (#247) * Improve workflow handling (#118) * Create common action for all workflows and split them into multiple files * Dokken/update fspace and wmtgs (#127) * fix runs-on * Minor improvements in linearelasticity.md (#124) * Fix various things on release branch * Try adding trame * Revert fundamentals * Membrane code * More updates due to autoformatting * Lagrange -> CG back conversion * Change to github image --------- Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> * Update petsc arches * Fix bounding boxes and more (#135) * Start fixing code for nightly build * rerun all files * Try fixing subdomains * Fix meshio * PETSc python API update (#137) * Resolve #136 * Fixes related to: FEniCS/dolfinx#2703 * Update changelog * Make sure all notebooks run. Change to pathlib in some examples * Api changes related to: FEniCS/dolfinx#2763 (#142) * Bump version numbers * Bump version numbers (#149) * Fix petsc arch * Prepare v0.7.1 (#154) * Merge branch 'main' into release and bump versions * Delete obsolete file * Temporary shift path in nightly test * Make sure there are no warnigns in build * Tabulation * Updates compatible with nightly branch of DOLFINx (#156) * Replace VectorElement and FiniteElement with `basix.ufl.element`. Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace` * More updates * And more * Last vector element updates * Bump pyvista and dolfinx to v0.7.2 (#159) * Bump pyvista and dolfinx to v0.7.2 * remove -r * Add further pyvista deps * Bump versions * Update petsc solver and pc links. Resolves #143 (#160) * Fix typo and issue Issue on page /fem.html #122 (#161) * Compute entity-cell connectivity before calling locate_dofs_topological. Remove soon to be deprecated pyvista syntax for updating time dependent fields. Fix range->np.arange conversion * Update backend in workflow * Fix broken link (#140) + http:// to https:// (#162) * Run book build prior to parallel run * Add back write frame * Fix wrong link * Fix typo in changelog * Merge main into release (#189) * Merge main into release * Apply suggestions from code review * Various fixes when reading through the diff * Further fixes * add missing checkout (#191) * add missing checkout * Add test docker on release PR and release (only push on tag * Remove unused import * Update text to resolve #194 (#195) * Dokken/update nonlin options (#203) * Update options for non-linear solver to sensible choice, ref #200 * Update docker path * Update python file as well * Update config ptr (#207) * Pressure correction equation fix (#196) * Update fundamentals.md (#199) on line 110, updated a typesetting error in equation (3) * Change from vector to petsc_vec (#206) * dolfinx.fem.Form changed to dolfinx.fem.form (#213) * Update compiler_parameters.ipynb In the text it was mentioned that `dolfinx.fem.Form` was used to compile the form, instead of `dolfinx.fem.form`. Not matching the code cell. * jupytext sync * Form -> form in both py and ipynb and LinearProblem -> fem.petsc.LinearProblem * Update book_stable.yml * Update test_stable.yml * Fix python path in test * Fix CI (#227) * Bump docker/build-push-action from 5 to 6 (#221) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5 to 6. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v5...v6) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/configure-pages from 4 to 5 (#222) Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5. - [Release notes](https://github.com/actions/configure-pages/releases) - [Commits](actions/configure-pages@v4...v5) --- updated-dependencies: - dependency-name: actions/configure-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update book_stable.yml (#225) * Update book_stable.yml * Update test_stable.yml * resolve #224 (#226) * Update test_stable.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update test_stable.yml (#235) * Add libgl flag to ci (#238) * Update navierstokes.md --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com> Co-authored-by: Jørgen S. Dokken <dokken@simula.no> Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com> Co-authored-by: Manuel Pena <mpena991@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Adding Acoustic Helmholtz equation to the tutorial (#232) * Acoustic Helmholtz scripts helmholtz.md contains the mathematical derivation of the variational formulation, while the helmholtz_code scripts contain the implementation. * Fix * equations rendering bug fixed * Update helmholtz.md Equations rendering second fix, missing spaces * Major updates to helmholtz * Add to toc * Updates to helmholtz * Update to work in parallel --------- Co-authored-by: jorgensd <dokken92@gmail.com> * Make helmholtz backwards compatible (#248) * Native arm build (#240) * Try new publish workflow * Fix platform choice * Update workflow to merge artifacts to one place * Set retention days to minimum * Fix name * change name to pattern * Minor improvements * Try new strategy * Remove duplicate tag * Revert platform tags * Use correct dockerfile * remove first login * Add merge skip if not pushing on release or tagging * Set push to false as we don't need the images before merging. * Remove push * Remove conditional to check that simpler code runs * Add back pushtrue * Revert comment --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: mleoni-pf <160495781+mleoni-pf@users.noreply.github.com> Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com> Co-authored-by: Manuel Pena <mpena991@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Antonio Baiano Svizzero <107617271+bayswiss@users.noreply.github.com> * Update linearelasticity_code.ipynb (#246) * Improve workflow handling (#118) * Create common action for all workflows and split them into multiple files * Dokken/update fspace and wmtgs (#127) * fix runs-on * Minor improvements in linearelasticity.md (#124) * Fix various things on release branch * Try adding trame * Revert fundamentals * Membrane code * More updates due to autoformatting * Lagrange -> CG back conversion * Change to github image --------- Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> * Update petsc arches * Fix bounding boxes and more (#135) * Start fixing code for nightly build * rerun all files * Try fixing subdomains * Fix meshio * PETSc python API update (#137) * Resolve #136 * Fixes related to: FEniCS/dolfinx#2703 * Update changelog * Make sure all notebooks run. Change to pathlib in some examples * Api changes related to: FEniCS/dolfinx#2763 (#142) * Bump version numbers * Bump version numbers (#149) * Fix petsc arch * Prepare v0.7.1 (#154) * Merge branch 'main' into release and bump versions * Delete obsolete file * Temporary shift path in nightly test * Make sure there are no warnigns in build * Tabulation * Updates compatible with nightly branch of DOLFINx (#156) * Replace VectorElement and FiniteElement with `basix.ufl.element`. Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace` * More updates * And more * Last vector element updates * Bump pyvista and dolfinx to v0.7.2 (#159) * Bump pyvista and dolfinx to v0.7.2 * remove -r * Add further pyvista deps * Bump versions * Update petsc solver and pc links. Resolves #143 (#160) * Fix typo and issue Issue on page /fem.html #122 (#161) * Compute entity-cell connectivity before calling locate_dofs_topological. Remove soon to be deprecated pyvista syntax for updating time dependent fields. Fix range->np.arange conversion * Update backend in workflow * Fix broken link (#140) + http:// to https:// (#162) * Run book build prior to parallel run * Add back write frame * Fix wrong link * Fix typo in changelog * Merge main into release (#189) * Merge main into release * Apply suggestions from code review * Various fixes when reading through the diff * Further fixes * add missing checkout (#191) * add missing checkout * Add test docker on release PR and release (only push on tag * Remove unused import * Update text to resolve #194 (#195) * Dokken/update nonlin options (#203) * Update options for non-linear solver to sensible choice, ref #200 * Update docker path * Update python file as well * Update config ptr (#207) * Pressure correction equation fix (#196) * Update fundamentals.md (#199) on line 110, updated a typesetting error in equation (3) * Change from vector to petsc_vec (#206) * dolfinx.fem.Form changed to dolfinx.fem.form (#213) * Update compiler_parameters.ipynb In the text it was mentioned that `dolfinx.fem.Form` was used to compile the form, instead of `dolfinx.fem.form`. Not matching the code cell. * jupytext sync * Form -> form in both py and ipynb and LinearProblem -> fem.petsc.LinearProblem * Update book_stable.yml * Update test_stable.yml * Fix python path in test * Fix CI (#227) * Bump docker/build-push-action from 5 to 6 (#221) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5 to 6. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v5...v6) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/configure-pages from 4 to 5 (#222) Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5. - [Release notes](https://github.com/actions/configure-pages/releases) - [Commits](actions/configure-pages@v4...v5) --- updated-dependencies: - dependency-name: actions/configure-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update book_stable.yml (#225) * Update book_stable.yml * Update test_stable.yml * resolve #224 (#226) * Update test_stable.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update test_stable.yml (#235) * Add libgl flag to ci (#238) * Update linearelasticity_code.ipynb * Add sync with `python3 -m jupytext --sync */*.ipynb` --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com> Co-authored-by: Jørgen S. Dokken <dokken@simula.no> Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com> Co-authored-by: Manuel Pena <mpena991@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update linearelasticity_code.ipynb (#245) * Improve workflow handling (#118) * Create common action for all workflows and split them into multiple files * Dokken/update fspace and wmtgs (#127) * fix runs-on * Minor improvements in linearelasticity.md (#124) * Fix various things on release branch * Try adding trame * Revert fundamentals * Membrane code * More updates due to autoformatting * Lagrange -> CG back conversion * Change to github image --------- Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> * Update petsc arches * Fix bounding boxes and more (#135) * Start fixing code for nightly build * rerun all files * Try fixing subdomains * Fix meshio * PETSc python API update (#137) * Resolve #136 * Fixes related to: FEniCS/dolfinx#2703 * Update changelog * Make sure all notebooks run. Change to pathlib in some examples * Api changes related to: FEniCS/dolfinx#2763 (#142) * Bump version numbers * Bump version numbers (#149) * Fix petsc arch * Prepare v0.7.1 (#154) * Merge branch 'main' into release and bump versions * Delete obsolete file * Temporary shift path in nightly test * Make sure there are no warnigns in build * Tabulation * Updates compatible with nightly branch of DOLFINx (#156) * Replace VectorElement and FiniteElement with `basix.ufl.element`. Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace` * More updates * And more * Last vector element updates * Bump pyvista and dolfinx to v0.7.2 (#159) * Bump pyvista and dolfinx to v0.7.2 * remove -r * Add further pyvista deps * Bump versions * Update petsc solver and pc links. Resolves #143 (#160) * Fix typo and issue Issue on page /fem.html #122 (#161) * Compute entity-cell connectivity before calling locate_dofs_topological. Remove soon to be deprecated pyvista syntax for updating time dependent fields. Fix range->np.arange conversion * Update backend in workflow * Fix broken link (#140) + http:// to https:// (#162) * Run book build prior to parallel run * Add back write frame * Fix wrong link * Fix typo in changelog * Merge main into release (#189) * Merge main into release * Apply suggestions from code review * Various fixes when reading through the diff * Further fixes * add missing checkout (#191) * add missing checkout * Add test docker on release PR and release (only push on tag * Remove unused import * Update text to resolve #194 (#195) * Dokken/update nonlin options (#203) * Update options for non-linear solver to sensible choice, ref #200 * Update docker path * Update python file as well * Update config ptr (#207) * Pressure correction equation fix (#196) * Update fundamentals.md (#199) on line 110, updated a typesetting error in equation (3) * Change from vector to petsc_vec (#206) * dolfinx.fem.Form changed to dolfinx.fem.form (#213) * Update compiler_parameters.ipynb In the text it was mentioned that `dolfinx.fem.Form` was used to compile the form, instead of `dolfinx.fem.form`. Not matching the code cell. * jupytext sync * Form -> form in both py and ipynb and LinearProblem -> fem.petsc.LinearProblem * Update book_stable.yml * Update test_stable.yml * Fix python path in test * Fix CI (#227) * Bump docker/build-push-action from 5 to 6 (#221) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5 to 6. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v5...v6) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/configure-pages from 4 to 5 (#222) Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5. - [Release notes](https://github.com/actions/configure-pages/releases) - [Commits](actions/configure-pages@v4...v5) --- updated-dependencies: - dependency-name: actions/configure-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update book_stable.yml (#225) * Update book_stable.yml * Update test_stable.yml * resolve #224 (#226) * Update test_stable.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update test_stable.yml (#235) * Add libgl flag to ci (#238) * Update linearelasticity_code.ipynb * Add sync with --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com> Co-authored-by: Jørgen S. Dokken <dokken@simula.no> Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com> Co-authored-by: Manuel Pena <mpena991@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update linearelasticity_code.ipynb (#244) * Improve workflow handling (#118) * Create common action for all workflows and split them into multiple files * Dokken/update fspace and wmtgs (#127) * fix runs-on * Minor improvements in linearelasticity.md (#124) * Fix various things on release branch * Try adding trame * Revert fundamentals * Membrane code * More updates due to autoformatting * Lagrange -> CG back conversion * Change to github image --------- Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> * Update petsc arches * Fix bounding boxes and more (#135) * Start fixing code for nightly build * rerun all files * Try fixing subdomains * Fix meshio * PETSc python API update (#137) * Resolve #136 * Fixes related to: FEniCS/dolfinx#2703 * Update changelog * Make sure all notebooks run. Change to pathlib in some examples * Api changes related to: FEniCS/dolfinx#2763 (#142) * Bump version numbers * Bump version numbers (#149) * Fix petsc arch * Prepare v0.7.1 (#154) * Merge branch 'main' into release and bump versions * Delete obsolete file * Temporary shift path in nightly test * Make sure there are no warnigns in build * Tabulation * Updates compatible with nightly branch of DOLFINx (#156) * Replace VectorElement and FiniteElement with `basix.ufl.element`. Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace` * More updates * And more * Last vector element updates * Bump pyvista and dolfinx to v0.7.2 (#159) * Bump pyvista and dolfinx to v0.7.2 * remove -r * Add further pyvista deps * Bump versions * Update petsc solver and pc links. Resolves #143 (#160) * Fix typo and issue Issue on page /fem.html #122 (#161) * Compute entity-cell connectivity before calling locate_dofs_topological. Remove soon to be deprecated pyvista syntax for updating time dependent fields. Fix range->np.arange conversion * Update backend in workflow * Fix broken link (#140) + http:// to https:// (#162) * Run book build prior to parallel run * Add back write frame * Fix wrong link * Fix typo in changelog * Merge main into release (#189) * Merge main into release * Apply suggestions from code review * Various fixes when reading through the diff * Further fixes * add missing checkout (#191) * add missing checkout * Add test docker on release PR and release (only push on tag * Remove unused import * Update text to resolve #194 (#195) * Dokken/update nonlin options (#203) * Update options for non-linear solver to sensible choice, ref #200 * Update docker path * Update python file as well * Update config ptr (#207) * Pressure correction equation fix (#196) * Update fundamentals.md (#199) on line 110, updated a typesetting error in equation (3) * Change from vector to petsc_vec (#206) * dolfinx.fem.Form changed to dolfinx.fem.form (#213) * Update compiler_parameters.ipynb In the text it was mentioned that `dolfinx.fem.Form` was used to compile the form, instead of `dolfinx.fem.form`. Not matching the code cell. * jupytext sync * Form -> form in both py and ipynb and LinearProblem -> fem.petsc.LinearProblem * Update book_stable.yml * Update test_stable.yml * Fix python path in test * Fix CI (#227) * Bump docker/build-push-action from 5 to 6 (#221) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5 to 6. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v5...v6) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/configure-pages from 4 to 5 (#222) Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5. - [Release notes](https://github.com/actions/configure-pages/releases) - [Commits](actions/configure-pages@v4...v5) --- updated-dependencies: - dependency-name: actions/configure-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update book_stable.yml (#225) * Update book_stable.yml * Update test_stable.yml * resolve #224 (#226) * Update test_stable.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update test_stable.yml (#235) * Add libgl flag to ci (#238) * Update linearelasticity_code.ipynb * Sync file --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com> Co-authored-by: Jørgen S. Dokken <dokken@simula.no> Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com> Co-authored-by: Manuel Pena <mpena991@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update linearelasticity_code.ipynb (#243) * Improve workflow handling (#118) * Create common action for all workflows and split them into multiple files * Dokken/update fspace and wmtgs (#127) * fix runs-on * Minor improvements in linearelasticity.md (#124) * Fix various things on release branch * Try adding trame * Revert fundamentals * Membrane code * More updates due to autoformatting * Lagrange -> CG back conversion * Change to github image --------- Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> * Update petsc arches * Fix bounding boxes and more (#135) * Start fixing code for nightly build * rerun all files * Try fixing subdomains * Fix meshio * PETSc python API update (#137) * Resolve #136 * Fixes related to: FEniCS/dolfinx#2703 * Update changelog * Make sure all notebooks run. Change to pathlib in some examples * Api changes related to: FEniCS/dolfinx#2763 (#142) * Bump version numbers * Bump version numbers (#149) * Fix petsc arch * Prepare v0.7.1 (#154) * Merge branch 'main' into release and bump versions * Delete obsolete file * Temporary shift path in nightly test * Make sure there are no warnigns in build * Tabulation * Updates compatible with nightly branch of DOLFINx (#156) * Replace VectorElement and FiniteElement with `basix.ufl.element`. Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace` * More updates * And more * Last vector element updates * Bump pyvista and dolfinx to v0.7.2 (#159) * Bump pyvista and dolfinx to v0.7.2 * remove -r * Add further pyvista deps * Bump versions * Update petsc solver and pc links. Resolves #143 (#160) * Fix typo and issue Issue on page /fem.html #122 (#161) * Compute entity-cell connectivity before calling locate_dofs_topological. Remove soon to be deprecated pyvista syntax for updating time dependent fields. Fix range->np.arange conversion * Update backend in workflow * Fix broken link (#140) + http:// to https:// (#162) * Run book build prior to parallel run * Add back write frame * Fix wrong link * Fix typo in changelog * Merge main into release (#189) * Merge main into release * Apply suggestions from code review * Various fixes when reading through the diff * Further fixes * add missing checkout (#191) * add missing checkout * Add test docker on release PR and release (only push on tag * Remove unused import * Update text to resolve #194 (#195) * Dokken/update nonlin options (#203) * Update options for non-linear solver to sensible choice, ref #200 * Update docker path * Update python file as well * Update config ptr (#207) * Pressure correction equation fix (#196) * Update fundamentals.md (#199) on line 110, updated a typesetting error in equation (3) * Change from vector to petsc_vec (#206) * dolfinx.fem.Form changed to dolfinx.fem.form (#213) * Update compiler_parameters.ipynb In the text it was mentioned that `dolfinx.fem.Form` was used to compile the form, instead of `dolfinx.fem.form`. Not matching the code cell. * jupytext sync * Form -> form in both py and ipynb and LinearProblem -> fem.petsc.LinearProblem * Update book_stable.yml * Update test_stable.yml * Fix python path in test * Fix CI (#227) * Bump docker/build-push-action from 5 to 6 (#221) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5 to 6. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v5...v6) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/configure-pages from 4 to 5 (#222) Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5. - [Release notes](https://github.com/actions/configure-pages/releases) - [Commits](actions/configure-pages@v4...v5) --- updated-dependencies: - dependency-name: actions/configure-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update book_stable.yml (#225) * Update book_stable.yml * Update test_stable.yml * resolve #224 (#226) * Update test_stable.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update test_stable.yml (#235) * Add libgl flag to ci (#238) * Update linearelasticity_code.ipynb * sync --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com> Co-authored-by: Jørgen S. Dokken <dokken@simula.no> Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com> Co-authored-by: Manuel Pena <mpena991@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update ns_code2.ipynb (#241) * Improve workflow handling (#118) * Create common action for all workflows and split them into multiple files * Dokken/update fspace and wmtgs (#127) * fix runs-on * Minor improvements in linearelasticity.md (#124) * Fix various things on release branch * Try adding trame * Revert fundamentals * Membrane code * More updates due to autoformatting * Lagrange -> CG back conversion * Change to github image --------- Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> * Update petsc arches * Fix bounding boxes and more (#135) * Start fixing code for nightly build * rerun all files * Try fixing subdomains * Fix meshio * PETSc python API update (#137) * Resolve #136 * Fixes related to: FEniCS/dolfinx#2703 * Update changelog * Make sure all notebooks run. Change to pathlib in some examples * Api changes related to: FEniCS/dolfinx#2763 (#142) * Bump version numbers * Bump version numbers (#149) * Fix petsc arch * Prepare v0.7.1 (#154) * Merge branch 'main' into release and bump versions * Delete obsolete file * Temporary shift path in nightly test * Make sure there are no warnigns in build * Tabulation * Updates compatible with nightly branch of DOLFINx (#156) * Replace VectorElement and FiniteElement with `basix.ufl.element`. Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace` * More updates * And more * Last vector element updates * Bump pyvista and dolfinx to v0.7.2 (#159) * Bump pyvista and dolfinx to v0.7.2 * remove -r * Add further pyvista deps * Bump versions * Update petsc solver and pc links. Resolves #143 (#160) * Fix typo and issue Issue on page /fem.html #122 (#161) * Compute entity-cell connectivity before calling locate_dofs_topological. Remove soon to be deprecated pyvista syntax for updating time dependent fields. Fix range->np.arange conversion * Update backend in workflow * Fix broken link (#140) + http:// to https:// (#162) * Run book build prior to parallel run * Add back write frame * Fix wrong link * Fix typo in changelog * Merge main into release (#189) * Merge main into release * Apply suggestions from code review * Various fixes when reading through the diff * Further fixes * add missing checkout (#191) * add missing checkout * Add test docker on release PR and release (only push on tag * Remove unused import * Update text to resolve #194 (#195) * Dokken/update nonlin options (#203) * Update options for non-linear solver to sensible choice, ref #200 * Update docker path * Update python file as well * Update config ptr (#207) * Pressure correction equation fix (#196) * Update fundamentals.md (#199) on line 110, updated a typesetting error in equation (3) * Change from vector to petsc_vec (#206) * dolfinx.fem.Form changed to dolfinx.fem.form (#213) * Update compiler_parameters.ipynb In the text it was mentioned that `dolfinx.fem.Form` was used to compile the form, instead of `dolfinx.fem.form`. Not matching the code cell. * jupytext sync * Form -> form in both py and ipynb and LinearProblem -> fem.petsc.LinearProblem * Update book_stable.yml * Update test_stable.yml * Fix python path in test * Fix CI (#227) * Bump docker/build-push-action from 5 to 6 (#221) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5 to 6. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v5...v6) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/configure-pages from 4 to 5 (#222) Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5. - [Release notes](https://github.com/actions/configure-pages/releases) - [Commits](actions/configure-pages@v4...v5) --- updated-dependencies: - dependency-name: actions/configure-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update book_stable.yml (#225) * Update book_stable.yml * Update test_stable.yml * resolve #224 (#226) * Update test_stable.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update test_stable.yml (#235) * Add libgl flag to ci (#238) * Update ns_code2.ipynb * Update ns code --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com> Co-authored-by: Jørgen S. Dokken <dokken@simula.no> Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com> Co-authored-by: Manuel Pena <mpena991@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add files via upload (#250) * Remove dead link * Add fix from #253 + some other typs in that text. (#256) * Add propsoed solution to #205 (#257) * Add singular Poisson demo. Resolves: #139 (#263) * Add extra note on conversion from new python files (#265) * Adaptive mesh refinement with NetGen (#266) * Add amr demo * Update CI * Update pyproject.toml * Simplify dockerfile as vtk is now on pypi on linux arch * Fix indent * Make netgen optional as it is not on pypi on linux/arm * Build netgen from source * Add netgen to stable book build (#267) * Update text to reflect that there is a docker image (#268) * Strip output and adapt eta definition, ref comment from Jack Hale (#269) * Finish trailing sentence (#270) * Try removing xvfb for most tutorials (#278) * Try removing xvfb for most tutorials * INstall osmesa * Remove -W * Add offscreen false to jupyter build * Remove some more xvfb and move new variables * Lower bound on vtk * Change tag on release branch * Another rename --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com> Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com> Co-authored-by: Manuel Pena <mpena991@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mleoni-pf <160495781+mleoni-pf@users.noreply.github.com> Co-authored-by: Antonio Baiano Svizzero <107617271+bayswiss@users.noreply.github.com>
1 parent 84ef93b commit 287154d

File tree

7 files changed

+23
-14
lines changed

7 files changed

+23
-14
lines changed

.github/actions/install-dependencies/action.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,4 +6,4 @@ runs:
66
- name: Install apt dependencies and upgrade pip
77
shell: bash -el {0}
88
run: |
9-
apt-get update && apt-get install -y libxrender1
9+
apt-get update && apt-get install -y libxrender1 libgl1-mesa-dev mesa-utils

.github/workflows/book_stable.yml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@ jobs:
2020

2121
env:
2222
PYVISTA_OFF_SCREEN: false
23-
PYVISTA_JUPYTER_BACKEND: "html"
23+
PYVISTA_JUPYTER_BACKEND: html
2424

2525
steps:
2626
- uses: actions/checkout@v5
@@ -34,7 +34,7 @@ jobs:
3434
python3 -m pip install --no-binary=h5py .[netgen]
3535
3636
- name: Build the book
37-
run: jupyter-book build . -W
37+
run: jupyter-book build .
3838

3939
- uses: actions/upload-artifact@v4
4040
if: always()

.github/workflows/test_stable.yml

Lines changed: 5 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -5,19 +5,18 @@ on:
55
workflow_call:
66
pull_request:
77
branches: ["release"]
8-
env:
9-
HDF5_MPI: "ON"
10-
HDF5_DIR: "/usr/local/"
11-
DISPLAY: ":99.0"
12-
DEB_PYTHON_INSTALL_LAYOUT: deb_system
13-
LIBGL_ALWAYS_SOFTWARE: 1
148

159
jobs:
1610
test:
1711
runs-on: ubuntu-latest
1812
container: ghcr.io/fenics/dolfinx/lab:stable
1913
env:
14+
HDF5_MPI: "ON"
15+
HDF5_DIR: "/usr/local/"
16+
DEB_PYTHON_INSTALL_LAYOUT: deb_system
2017
PYVISTA_OFF_SCREEN: true
18+
PYVISTA_JUPYTER_BACKEND: html
19+
LIBGL_ALWAYS_SOFTWARE: 1
2120

2221
# Steps represent a sequence of tasks that will be executed as part of the job
2322
steps:

Dockerfile

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
FROM ghcr.io/jorgensd/dolfinx-tutorial:release
1+
FROM ghcr.io/jorgensd/dolfinx-tutorial:v0.9.1
22

33
# create user with a home directory
44
ARG NB_USER=jovyan

chapter4/compiler_parameters.ipynb

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -82,7 +82,8 @@
8282
"id": "4",
8383
"metadata": {},
8484
"source": [
85-
"We start by considering the different levels of optimization that the C compiler can use on the optimized code. A list of optimization options and explanations can be found [here](https://gcc.gnu.org/onlinedocs/gcc/Optimize-Options.html)"
85+
"We start by considering the different levels of optimization that the C compiler can use on the optimized code.\n",
86+
"A list of optimization options and explanations can be found [here](https://gcc.gnu.org/onlinedocs/gcc/Optimize-Options.html)"
8687
]
8788
},
8889
{
@@ -100,7 +101,9 @@
100101
"id": "6",
101102
"metadata": {},
102103
"source": [
103-
"The next option we can choose is if we want to compile the code with `-march=native` or not. This option enables instructions for the local machine, and can give different results on different systems. More information can be found [here](https://gcc.gnu.org/onlinedocs/gcc/AArch64-Options.html#g_t-march-and--mcpu-Feature-Modifiers)"
104+
"The next option we can choose is if we want to compile the code with `-march=native` or not.\n",
105+
"This option enables instructions for the local machine, and can give different results on different systems.\n",
106+
"More information can be found [here](https://gcc.gnu.org/onlinedocs/gcc/AArch64-Options.html#g_t-march-and--mcpu-Feature-Modifiers)"
104107
]
105108
},
106109
{

chapter4/compiler_parameters.py

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -64,11 +64,14 @@ def compile_form(space: str, degree: int, jit_options: Dict):
6464
return end - start
6565

6666

67-
# We start by considering the different levels of optimization that the C compiler can use on the optimized code. A list of optimization options and explanations can be found [here](https://gcc.gnu.org/onlinedocs/gcc/Optimize-Options.html)
67+
# We start by considering the different levels of optimization that the C compiler can use on the optimized code.
68+
# A list of optimization options and explanations can be found [here](https://gcc.gnu.org/onlinedocs/gcc/Optimize-Options.html)
6869

6970
optimization_options = ["-O1", "-O2", "-O3", "-Ofast"]
7071

71-
# The next option we can choose is if we want to compile the code with `-march=native` or not. This option enables instructions for the local machine, and can give different results on different systems. More information can be found [here](https://gcc.gnu.org/onlinedocs/gcc/AArch64-Options.html#g_t-march-and--mcpu-Feature-Modifiers)
72+
# The next option we can choose is if we want to compile the code with `-march=native` or not.
73+
# This option enables instructions for the local machine, and can give different results on different systems.
74+
# More information can be found [here](https://gcc.gnu.org/onlinedocs/gcc/AArch64-Options.html#g_t-march-and--mcpu-Feature-Modifiers)
7275

7376
march_native = [True, False]
7477

docker/Dockerfile

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -47,4 +47,8 @@ ENV PYVISTA_OFF_SCREEN="false"
4747
ENV PYVISTA_JUPYTER_BACKEND="trame"
4848
ENV LIBGL_ALWAYS_SOFTWARE=1
4949

50+
ENV PYVISTA_OFF_SCREEN="false"
51+
ENV PYVISTA_JUPYTER_BACKEND="trame"
52+
ENV LIBGL_ALWAYS_SOFTWARE=1
53+
5054
ENTRYPOINT ["jupyter", "lab", "--ip", "0.0.0.0", "--no-browser", "--allow-root"]

0 commit comments

Comments
 (0)