Jupytext updates

.github/workflows/build-publish.yml

@@ -34,50 +34,42 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
 
+      - name: Test complex notebooks in parallel
+        run: |
+          export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH
+          export PETSC_ARCH=linux-gnu-complex-32
+          export PYTHONPATH=/usr/local/dolfinx-complex/lib/python3.9/dist-packages:$PYTHONPATH
+          export LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH
+          cd chapter1
+          mpirun -n 2 python3 complex_mode.py
+
+
       - name: Install dependencies
         run: pip3 install notebook nbconvert jupyter-book --upgrade
       - name: Test notebooks in parallel
         run: |
           python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"
           cd chapter1
-          jupyter-nbconvert --to python fundamentals_code.ipynb
           mpirun -n 2 python3 fundamentals_code.py
-          jupyter-nbconvert --to python membrane_code.ipynb
           mpirun -n 2 python3 membrane_code.py
           cd ../chapter2
-          jupyter-nbconvert --to python diffusion_code.ipynb
           mpirun -n 2 python3 diffusion_code.py
-          jupyter-nbconvert --to python heat_code.ipynb
           mpirun -n 2 python3 heat_code.py
-          jupyter-nbconvert --to python linearelasticity_code.ipynb
           mpirun -n 2 python3 linearelasticity_code.py
-          jupyter-nbconvert --to python hyperelasticity.ipynb
           mpirun -n 2 python3 hyperelasticity.py
-          jupyter-nbconvert --to python nonlinpoisson_code.ipynb
           mpirun -n 2 python3 nonlinpoisson_code.py
-          jupyter-nbconvert --to python ns_code1.ipynb
           mpirun -n 2 python3 ns_code1.py
-          jupyter-nbconvert --to python ns_code2.ipynb
           mpirun -n 2 python3 ns_code2.py
           cd ../chapter3
-          jupyter-nbconvert --to python neumann_dirichlet_code.ipynb
           mpirun -n 3 python3 neumann_dirichlet_code.py
-          jupyter-nbconvert --to python multiple_dirichlet.ipynb
           mpirun -n 3 python3 multiple_dirichlet.py
-          jupyter-nbconvert --to python subdomains.ipynb
           mpirun -n 3 python3 subdomains.py
-          jupyter-nbconvert --to python robin_neumann_dirichlet.ipynb
           mpirun -n 3 python3 robin_neumann_dirichlet.py
-          jupyter-nbconvert --to python component_bc.ipynb
           mpirun -n 3 python3 component_bc.py
-          jupyter-nbconvert --to python em.ipynb
           mpirun -n 3 python3 em.py
           cd ../chapter4
-          jupyter-nbconvert --to python solvers.ipynb
           mpirun -n 3 python3 solvers.py
-          jupyter-nbconvert --to python convergence.ipynb
           mpirun -n 3 python3 convergence.py
-          jupyter-nbconvert --to python compiler_parameters.ipynb
           mpirun -n 3 python3 compiler_parameters.py
 
       # Runs a single command using the runners shell

.github/workflows/main-test.yml

@@ -23,7 +23,7 @@ jobs:
   test-against-master:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: dolfinx/dolfinx
+    container: dolfinx/lab
 
     env:
       HDF5_MPI: "ON"
@@ -45,51 +45,42 @@ jobs:
           jupyter nbextension enable --py --sys-prefix ipygany 
           rm -rf /usr/local/share/.cache/*
           jupyter-book -h
-      - name: Test building the book
-        run: 
-          PYVISTA_JUPYTER_BACKEND=static PYVISTA_OFF_SCREEN=false jupyter-book build  -W .
-      - name: Test notebooks in parallel
+      - name: Test complex notebooks in parallel
+        run: |
+          export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH
+          export PETSC_ARCH=linux-gnu-complex-32
+          export PYTHONPATH=/usr/local/dolfinx-complex/lib/python3.10/dist-packages:$PYTHONPATH
+          export LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH
+          cd chapter1
+          mpirun -n 2 python3 complex_mode.py
+
+      - name: Test real notebooks in parallel
         run: |
           cd chapter1
           python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"
-          jupyter-nbconvert --to python fundamentals_code.ipynb
           mpirun -n 2 python3 fundamentals_code.py
-          jupyter-nbconvert --to python nitsche.ipynb
           mpirun -n 2 python3 nitsche.py
-          jupyter-nbconvert --to python membrane_code.ipynb
           mpirun -n 2 python3 membrane_code.py
           cd ../chapter2
-          jupyter-nbconvert --to python diffusion_code.ipynb
           mpirun -n 2 python3 diffusion_code.py
-          jupyter-nbconvert --to python heat_code.ipynb
           mpirun -n 2 python3 heat_code.py
-          jupyter-nbconvert --to python linearelasticity_code.ipynb
           mpirun -n 2 python3 linearelasticity_code.py
-          jupyter-nbconvert --to python hyperelasticity.ipynb
           mpirun -n 2 python3 hyperelasticity.py
-          jupyter-nbconvert --to python nonlinpoisson_code.ipynb
           mpirun -n 2 python3 nonlinpoisson_code.py
-          jupyter-nbconvert --to python ns_code1.ipynb
           mpirun -n 2 python3 ns_code1.py
-          jupyter-nbconvert --to python ns_code2.ipynb
           mpirun -n 2 python3 ns_code2.py
           cd ../chapter3
-          jupyter-nbconvert --to python neumann_dirichlet_code.ipynb
           mpirun -n 3 python3 neumann_dirichlet_code.py
-          jupyter-nbconvert --to python multiple_dirichlet.ipynb
           mpirun -n 3 python3 multiple_dirichlet.py
-          jupyter-nbconvert --to python subdomains.ipynb
           mpirun -n 3 python3 subdomains.py
-          jupyter-nbconvert --to python robin_neumann_dirichlet.ipynb
           mpirun -n 3 python3 robin_neumann_dirichlet.py
-          jupyter-nbconvert --to python component_bc.ipynb
           mpirun -n 3 python3 component_bc.py
-          jupyter-nbconvert --to python em.ipynb
           mpirun -n 3 python3 em.py
           cd ../chapter4
-          jupyter-nbconvert --to python solvers.ipynb
           mpirun -n 3 python3 solvers.py
-          jupyter-nbconvert --to python convergence.ipynb
           mpirun -n 3 python3 convergence.py
-          jupyter-nbconvert --to python compiler_parameters.ipynb
           mpirun -n 3 python3 compiler_parameters.py
+
+      - name: Test building the book
+        run: 
+          PYVISTA_JUPYTER_BACKEND=static PYVISTA_OFF_SCREEN=false jupyter-book build  -W .

.gitignore

@@ -5,4 +5,7 @@ _build
 *.vtu
 */.ipynb_checkpoints/*
 .ipynb_checkpoints/*
-**/.cache
+**/.cache
+*.png
+*.pvtu
+*.msh

Changelog.md

@@ -1,6 +1,10 @@
 # Changelog
 
 ## Dev
+- Change all notebooks to use [jupytext](https://jupytext.readthedocs.io/en/latest/install.html) to automatically sync `.ipynb` with `.py` files.
+- Add dummy complex mode test
+
+## 0.4.1
 - No changes
 
 ## 0.4.0 (05.02.2021)

_toc.yml

@@ -10,6 +10,7 @@ parts:
       - file: chapter1/fundamentals
         sections:
           - file: chapter1/fundamentals_code
+          - file: chapter1/complex_mode
       - file: chapter1/nitsche
       - file: chapter1/membrane
         sections:

chapter1/complex_mode.ipynb

@@ -0,0 +1,63 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "116651d1-d44d-471d-b13c-36855d8464ec",
+   "metadata": {},
+   "source": [
+    "# Running DOLFINx in complex mode\n",
+    "\n",
+    "Author: Jørgen S. Dokken\n",
+    "\n",
+    "This section will explain how to run DOLFINx in complex mode, and its peculiarities.\n",
+    "\n",
+    "## TODO: Add complex example"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "4d5b03e3-4d7f-45b7-95eb-9130a5141f34",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import dolfinx\n",
+    "from petsc4py import PETSc\n",
+    "import numpy as np\n",
+    "assert np.dtype(PETSc.ScalarType).kind == 'c'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "be8461a0-a089-4ff3-8bc8-61b016407e70",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "jupytext": {
+   "formats": "ipynb,py:light"
+  },
+  "kernelspec": {
+   "display_name": "Python 3 (DOLFINx complex)",
+   "language": "python",
+   "name": "python3-complex"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

chapter1/complex_mode.py

@@ -0,0 +1,29 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:light
+#     text_representation:
+#       extension: .py
+#       format_name: light
+#       format_version: '1.5'
+#       jupytext_version: 1.13.8
+#   kernelspec:
+#     display_name: Python 3 (DOLFINx complex)
+#     language: python
+#     name: python3-complex
+# ---
+
+# # Running DOLFINx in complex mode
+#
+# Author: Jørgen S. Dokken
+#
+# This section will explain how to run DOLFINx in complex mode, and its peculiarities.
+#
+# ## TODO: Add complex example
+
+import dolfinx
+from petsc4py import PETSc
+import numpy as np
+assert np.dtype(PETSc.ScalarType).kind == 'c'
+
+