Merge branch 'master' into review-next-steps

Author: fangohr

.github/workflows/deploy.yml

@@ -5,6 +5,7 @@ on:
     types: [created]
   push:
     # all
+  workflow_dispatch:
 
 jobs:
   docker-build-and-deploy:
@@ -54,7 +55,7 @@ jobs:
 
     # Deploy the book's HTML to gh-pages branch
     - name: GitHub Pages action
-      uses: peaceiris/actions-gh-pages@bbdfb200618d235585ad98e965f4aafc39b4c501
+      uses: peaceiris/actions-gh-pages@v3
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./book/_build/html

.github/workflows/nbval.yml

@@ -0,0 +1,41 @@
+name: nbval
+
+on:
+  push:
+    # all
+  workflow_dispatch:
+
+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

.github/workflows/stage.yml

@@ -3,6 +3,7 @@ name: Book Staging
 on:
   pull_request:
     branches: [ master ]
+  workflow_dispatch:
 
 jobs:
   docker-build-and-stage:

.gitignore

@@ -22,3 +22,4 @@ stock.csv
 .venv
 .venv/
 book/_build
+.DS_Store

Dockerfile

@@ -1,20 +1,26 @@
-FROM debian:bullseye-slim
+FROM debian:bookworm-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
+#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 wget
 
-COPY poetry.lock pyproject.toml /opt/
+RUN apt-get update -y && apt-get install -y python3 python3-pip texlive-xetex \
+    latexmk git zile wget texlive-fonts-extra python3-venv
 
-RUN pip install poetry==1.1.4
+COPY requirements.txt /opt/
 
 WORKDIR /opt/
-RUN poetry config virtualenvs.create false
-RUN poetry install -vvv
+RUN python3 -m venv venv
+RUN . venv/bin/activate && pip install -r requirements.txt
+RUN . venv/bin/activate && pip list
+# activate venv
+ENV PATH="/opt/venv/bin:$PATH"
 
 RUN mkdir -p /io
 WORKDIR /io
 
 # Need this for one nbval and chapter 1
 RUN ln -s /usr/bin/python3 /usr/local/bin/python
 
+# supress warning when running jupyter-book in container
+ENV PYDEVD_DISABLE_FILE_VALIDATION=1
 CMD ["/bin/bash"]

Makefile

@@ -3,7 +3,7 @@ all:
 	make pdf
 
 install:
-	poetry install -vvv 
+	pip install -r requirements.txt
 
 clean:
 	cd book; rm -rf \
@@ -13,16 +13,21 @@ clean:
 		_build .ipynb_checkpoints
 
 html:
-	poetry run jupyter-book build book --builder html
+	jupyter-book build book --builder html
 
 linkcheck:
-	poetry run jupyter-book build book --builder linkcheck
+	jupyter-book build book --builder linkcheck
 
 pdf: book/*-*.ipynb
-	poetry run jupyter-book build book --builder pdflatex
+	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"
+	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"
+	pytest -v --nbval-lax book/18-environments.ipynb
+
 
 
 docker-all:
@@ -39,16 +44,8 @@ docker-build:
 docker-build-nocache:
 	docker build -t python4compscience2 --no-cache .
 
-# Here we only bind the required directories and files into the docker container
-# at runtime to avoid potential conflicts with local files
-
 define DOCKER_RUN
-docker run --workdir=/io  \
-	-v $(CURDIR)/book:/io/book \
-	-v $(CURDIR)/Makefile:/io/Makefile \
-	-v $(CURDIR)/poetry.lock:/io/poetry.lock \
-	-v $(CURDIR)/pyproject.toml:/io/pyproject.toml \
-	python4compscience
+docker run --rm -v $(CURDIR):/io	python4compscience
 endef
 
 docker-bash:

Readme.md

@@ -119,7 +119,7 @@ and schools. Please send a message to the author if you do so.
 
 Hans Fangohr is a researcher and teacher (see
 [homepage](https://fangohr.github.io), [blog](https://fangohr.github.io/blog),
-[twitter](https://twitter.com/ProfCompMod)). His interests include effective
+[mastodon](https://fosstodon.org/@ProfCompMod)). His interests include effective
 software engineering for computational science and data science, researching
 computational modelling and data analysis methods, and education. He is a
 Professor at the [University of Southampton (UK)](https://www.southampton.ac.uk)