Various improvements (#220)

.github/dependabot.yml

@@ -0,0 +1,15 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "python/"
+    schedule:
+      interval: "weekly"

.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+- repo: https://github.com/kynan/nbstripout
+  rev: 0.7.1
+  hooks:
+    - id: nbstripout

README.md

@@ -1,7 +1,7 @@
 # The DOLFINx tutorial
 
-[![Test, build and publish](https://github.com/jorgensd/dolfinx-tutorial/actions/workflows/build-publish.yml/badge.svg)](https://github.com/jorgensd/dolfinx-tutorial/actions/workflows/build-publish.yml)
-[![Test release branch against DOLFINx nightly build](https://github.com/jorgensd/dolfinx-tutorial/actions/workflows/nightly.yml/badge.svg)](https://github.com/jorgensd/dolfinx-tutorial/actions/workflows/nightly.yml)
+[![Test, build and publish](https://github.com/jorgensd/dolfinx-tutorial/actions/workflows/deploy.yml/badge.svg)](https://github.com/jorgensd/dolfinx-tutorial/actions/workflows/deploy.yml)
+[![Test release branch against DOLFINx nightly build](https://github.com/jorgensd/dolfinx-tutorial/actions/workflows/test_nightly.yml/badge.svg)](https://github.com/jorgensd/dolfinx-tutorial/actions/workflows/test_nightly.yml)
 
 Author: Jørgen S. Dokken
 
@@ -26,6 +26,12 @@ python3 -m jupytext --sync  */*.ipynb
 
 Any code added to the tutorial should work in parallel.
 
+To strip notebook output, one can use pre-commit.
+
+```bash
+pre-commit run --all-files
+```
+
 ## Dependencies
 
 It is adviced to use a pre-installed version of DOLFINx, for instance through conda or docker. Remaining dependencies can be installed with
@@ -55,3 +61,4 @@ from the root of this repository, and run
 ```
 
 from the main directory.
+

chapter1/complex_mode.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "116651d1-d44d-471d-b13c-36855d8464ec",
+   "id": "0",
    "metadata": {},
    "source": [
     "# The Poisson problem with complex numbers\n",
@@ -40,7 +40,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b52b39d9-260d-4c54-b62a-7440c3b92e5a",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -59,7 +59,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "699ab6a9-4427-4c54-95c8-ce5de5d11b97",
+   "id": "2",
    "metadata": {},
    "source": [
     "However, as we would like to solve linear algebra problems of the form $Ax=b$, we need to be able to use matrices and vectors that support real and complex numbers. As [PETSc](https://petsc.org/release/) is one of the most popular interfaces to linear algebra packages, we need to be able to work with their matrix and vector structures.\n",
@@ -72,7 +72,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4d5b03e3-4d7f-45b7-95eb-9130a5141f34",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -84,7 +84,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9ea24650-5027-4491-a459-375d7cf69fe3",
+   "id": "4",
    "metadata": {},
    "source": [
     "## Variational problem\n",
@@ -94,7 +94,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "be8461a0-a089-4ff3-8bc8-61b016407e70",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +108,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d6f70a1e-d128-470b-9b32-b86dd807a0bf",
+   "id": "6",
    "metadata": {},
    "source": [
     "Note that we have used the `PETSc.ScalarType` to wrap the constant source on the right hand side. This is because we want the integration kernels to assemble into the correct floating type.\n",
@@ -121,7 +121,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "779ab267-4609-4628-9577-a280b9c18b6d",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -132,7 +132,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9efe0968-bf32-4184-85f7-4e8cc3401cfb",
+   "id": "8",
    "metadata": {},
    "source": [
     "Similarly, if we want to use the function `ufl.derivative` to take derivatives of functionals, we need to take some special care. As `ufl.derivative` inserts a `ufl.TestFunction` to represent the variation, we need to take the conjugate of this to be able to use it to assemble vectors.\n"
@@ -141,7 +141,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d61c477a-d364-4a81-9362-42f1eb4cd8ee",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -153,7 +153,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1b664480-fc11-404d-83ea-7e2548894904",
+   "id": "10",
    "metadata": {},
    "source": [
     "We define our Dirichlet condition and setup and solve the variational problem.\n",
@@ -163,7 +163,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "eb2357ae-ac71-4407-bf37-432f1b1e31d0",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -177,7 +177,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "053bfa60-c382-4216-beaf-c06e95e70067",
+   "id": "12",
    "metadata": {},
    "source": [
     "We compute the $L^2$ error and the max error.\n",
@@ -188,7 +188,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f51d9a7a-2cde-4d0f-8606-91f91c372c4b",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -203,7 +203,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "36431a2a-2063-4070-b1fc-3f58a3b7316b",
+   "id": "14",
    "metadata": {},
    "source": [
     "## Plotting\n",
@@ -214,7 +214,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7a3f89d0-4771-4cc3-a0cd-ce8451a414ba",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -232,7 +232,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9564e40a-ca18-497a-8de0-ef075aae3199",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -247,7 +247,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c179fdda-6ae6-4979-a19b-fadfebab2f0e",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -263,7 +263,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a63144b5-e3fc-445e-acea-b5d744bf7634",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": []