V0.7.0 (#150)

* 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 <[email protected]>

* 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

---------

Co-authored-by: Julius Herb <[email protected]>

Author: jorgensd

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

@@ -1,17 +1,10 @@
 name: Install dependencies
 
-
 runs:
   using: composite
   steps:
       - name: Install apt dependencies and upgrade pip
         shell: bash -el {0}
         run: |
           apt-get update && apt-get install -y libgl1-mesa-glx libxrender1 xvfb
-          python3 -m pip install -U pip
-      # Install `h5py` master branch
-      # https://github.com/hl5py/h5py/issues/2222
-      - name: Install h5py and pip requirements
-        shell: bash -el {0}
-        run: |
-          python3 -m pip install --no-binary=h5py git+https://github.com/h5py/h5py@master
+          python3 -m pip install -U pip

.github/workflows/book_stable.yml

@@ -15,7 +15,7 @@ env:
 jobs:
   build-book:
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/lab:v0.6.0-r1
+    container: ghcr.io/fenics/dolfinx/lab:v0.7.0
 
     env:
       PYVISTA_TRAME_SERVER_PROXY_PREFIX: "/proxy/"

.github/workflows/test_nightly.yml

@@ -17,7 +17,7 @@ jobs:
   test-nightly:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: dolfinx/lab:nightly
+    container: ghcr.io/fenics/dolfinx/lab:nightly
 
     env:
       HDF5_MPI: "ON"

.github/workflows/test_stable.yml

@@ -20,7 +20,7 @@ jobs:
   test:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/lab:v0.6.0-r1
+    container: ghcr.io/fenics/dolfinx/lab:v0.7.0
     env:
       PYVISTA_OFF_SCREEN: true
 
@@ -37,7 +37,7 @@ jobs:
       - name: Test complex notebooks in parallel
         run: |
           export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH
-          export PETSC_ARCH=linux-gnu-complex-32
+          export PETSC_ARCH=linux-gnu-complex128-32
           export PYTHONPATH=/usr/local/dolfinx-complex/lib/python3.10/dist-packages:$PYTHONPATH
           export LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH
           python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"

Changelog.md

@@ -1,18 +1,24 @@
 # Changelog
 
-## main
-- No changes
+## v0.7.0
+
+- Renamed `dolfinx.graph.create_adjacencylist` to `dolfinx.graph.adjacencylist`
+- Renamed `dolfinx.plot.create_vtk_mesh` to `dolfinx.plot.vtk_mesh`
+- `dolfinx.geometry.BoundingBoxTree` has been changed to `dolfinx.geometry.bb_tree`
+- `create_mesh` with Meshio has been modified. Note that you now need to pass dtype `np.int32` to the cell_data.
+- Update dolfinx petsc API. Now one needs to explicitly import `dolfinx.fem.petsc` and `dolfinx.fem.nls`, as PETSc is no longer a strict requirement. Replace `petsc4py.PETSc.ScalarType` with `dolfinx.default_scalar_type` in demos where we do not use `petsc4py` explicitly.
 
 ## v0.6.0
+
 - Remove `ipygany` and `pythreejs` as plotting backends. Using `panel`.
 - Add gif-output to [chapter2/diffusion_code] and [chapter2/hyperelasticity].
 - Replace `dolfinx.fem.Function.geometric_dimension` with `len(dolfinx.fem.Function)`
 - Improve [chapter2/ns_code2] to have better splitting scheme and density.
 - Improve mesh quality in [chapter3/em].
 - `jit_params` and `form_compiler_params` renamed to `*_options`.
 
-
 ## v0.5.0
+
 - Using new GMSH interface in DOLFINx (`dolfinx.io.gmshio`) in all demos using GMSH
 - Added a section on custom Newton-solvers, see [chapter4/newton-solver].
 - Various minor DOLFINx API updates. `dolfinx.mesh.compute_boundary_facets` -> `dolfinx.mesh.exterior_facet_indices` with slightly different functionality. Use `dolfinx.mesh.MeshTagsMetaClass.find` instead of `mt.indices[mt.values==value]`.
@@ -21,9 +27,11 @@
 - Add example of how to use `DOLFINx` in complex mode, see [chapter1/complex_mode].
 
 ## 0.4.1
+
 - No changes
 
 ## 0.4.0 (05.02.2021)
+
 - All `pyvista` plotting has been rewritten to use `ipygany` and `pythreejs` as well as using a cleaner interface.
 - `dolfinx.plot.create_vtk_topology` has been renamed to `dolfinx.plot.create_vtk_mesh` and can now be directly used as input to `pyvista.UnstructuredGrid`.
 - `dolfinx.fem.Function.compute_point_values` has been deprecated. Interpolation into a CG-1 is now the way of getting vertex values.
@@ -34,14 +42,14 @@
 - Various API changes relating to the import structure of DOLFINx
 
 ## 0.3.0 (09.09.2021)
+
 - Major improvements in [Form compiler parameters](chapter4/compiler_parameters), using pandas and seaborn for visualization of speed-ups gained using form compiler parameters.
 - API change: `dolfinx.cpp.la.scatter_forward(u.x)` -> `u.x.scatter_forward`
 - Various plotting updates due to new version of pyvista.
 - Updating of the [Hyperelasticity demo](chapter2/hyperelasticity), now using DOLFINx wrappers to create the non-linear problem
 - Internal updates due to bumping of jupyter-book versions
 - Various typos and capitalizations fixed by @mscroggs in [PR 35](https://github.com/jorgensd/dolfinx-tutorial/pull/35).
 
-
-
 ## 0.1.0 (11.05.2021)
-- First tagged release of DOLFINx Tutorial, compatible with [DOLFINx 0.1.0](https://github.com/FEniCS/dolfinx/releases/tag/0.1.0).
+
+- First tagged release of DOLFINx Tutorial, compatible with [DOLFINx 0.1.0](https://github.com/FEniCS/dolfinx/releases/tag/0.1.0).

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/jorgensd/dolfinx-tutorial:v0.6.0.post0
+FROM ghcr.io/jorgensd/dolfinx-tutorial:v0.7.0
 
 # create user with a home directory
 ARG NB_USER=jovyan