Merge pull request #31 from fangohr/nbval-review

- Making nbval pass
- Add additional workflow for nbval

Author: fangohr

.github/workflows/nbval.yml

@@ -0,0 +1,38 @@
+name: nbval
+
+on: [push]
+
+jobs:
+  docker-build-and-nbval:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v1
+
+    - name: Cache Docker layers
+      uses: actions/cache@v2
+      with:
+        path: /tmp/.buildx-cache
+        key: ${{ runner.os }}-buildx-${{ hashFiles('poetry.lock') }}
+        restore-keys: |
+          ${{ runner.os }}-buildx-${{ hashFiles('poetry.lock') }}
+
+    #  This build and push step does the same thing as `make docker-build`, but
+    #  makes it easier to store and load caches, which is why we use it instead
+    - name: Build and Save Layers Locally
+      uses: docker/build-push-action@v2
+      with:
+        context: ./
+        file: ./Dockerfile
+        load: true
+        cache-from: type=local,src=/tmp/.buildx-cache
+        cache-to: type=local,dest=/tmp/.buildx-cache
+        tags: python4compscience
+
+    - name: List Available Images
+      run: docker images
+
+    - name: Run NBVAL over all chapters
+      run: make docker-nbval

Dockerfile

@@ -1,7 +1,7 @@
 FROM debian:bullseye-slim
 
 RUN apt-get update -y && apt-get install -y texlive-xetex latexmk texlive-xetex \
-	texlive-fonts-extra fonts-freefont-otf python3 python3-pip git zile
+	texlive-fonts-extra fonts-freefont-otf python3 python3-pip git zile wget
 
 COPY poetry.lock pyproject.toml /opt/
 

Makefile

@@ -22,7 +22,12 @@ pdf: book/*-*.ipynb
 	poetry run jupyter-book build book --builder pdflatex
 
 nbval:
-	poetry run pytest -v --nbval book/*.ipynb --sanitize-with book/static/nbval_sanitize.cfg
+	@echo "Testing all chapters (apart from 18) with --nbval"
+	poetry run pytest -v --nbval book --sanitize-with book/static/nbval_sanitize.cfg \
+	    --ignore=book/18-environments.ipynb --ignore=book/_build
+	@echo "Testing chapter 18 with --nbval-lax"
+	poetry run pytest -v --nbval-lax book/18-environments.ipynb
+
 
 
 docker-all:

book/15-visualising-data.ipynb

@@ -1636,7 +1636,7 @@
    "id": "82715cd6",
    "metadata": {},
    "source": [
-    "**Tidy up**"
+    "**Tidy up**: remove files created in this section"
    ]
   },
   {
@@ -1647,16 +1647,9 @@
    "outputs": [],
    "source": [
     "!rm -rf /tmp/cowsay-python\n",
-    "!rm -rf myvirtualenv-copy"
+    "!rm -rf myvirtualenv-copy\n",
+    "!rm -f requirements.txt"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "bd9e1fa3",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

book/16-scipy.ipynb

@@ -0,0 +1,19 @@
+* <2022-01-05 Wed 07:42> Notes on nbval:
+
+** Chapters with matplotlib output
+- for chapter 15 (matplotlib) [and other with matplotlib], we run into fails if svg+xml output is saved
+  - For some of the fails, I have created entries in [file:static/nbvas_sanitize.cfg] to ignore the changes (and commented out)
+- Update on closer inspection: in the past, we didn't save the output, and thus the problem never occurred.
+- But what does nbval do if the cells are empty, and it computes output?    
+  - if we do not save output, then nbval will not complain about the empty cells
+  - if an exception occurs, it will report a fail.
+  - So --nbval on empty output cells behaves like --nbval-lax on saved output
+- So not saving the output might be the right way, as jupyter-book executes the
+  notebooks anyway when computing pdf and html
+  (And that's what we did before my recent changes, I just had to remind myself ...)
+
+** Extra treatment of Chapter 18 Environments
+  - should not execute automatically (because the description of creating
+    virtual envs is tailored to running it on a mac with Anaconda).
+  - achieved via instruction in [file:_config.yml]
+  - should be skipped by nbval for same reasons (use --ignore switch for that)

book/18-environments.ipynb

@@ -13,3 +13,25 @@ replace: TIMEIT-OUTPUT
 [dictionary-keys-values-items]
 regex: dict_[\s\S]*\(\[[\s\S]*\]\)
 replace: DICTIONARY-DATA
+
+# The following rules are helpful if we attempt to include the svg+xml output from matplotlib in the notebooks.
+#
+#[matplotlib-path-id]
+#regex:  id="[0-9a-zA-Z]+"
+#replace: PATH-ID
+#
+#[matplotlib-clip-path-url]
+#regex: clip-path="url\(#[0-9a-zA-Z]+\)"
+#replace: CLIPPATH-URL
+#
+#[matplotlib-xlink-href]
+#regex: xlink:href="#[0-9a-zA-Z]+"
+#replace: XLINK-HREF
+#
+#[date-stamp]
+#regex: \d{2,4}-\d{1,2}-\d{2,4}
+#replace: DATE-STAMP
+#
+#[time-stamp]
+#regex: \d{2}:\d{2}:\d{2}.\d{6}
+#replace: TIME-STAMP