Minor configs to get binder to work

Dockerfile

@@ -2,13 +2,22 @@
 
 FROM ubuntu:22.04
 
+
 RUN apt-get update && \
-    apt-get install -y python3-pip
+    apt-get install -y python3-pip git
 
 # Use modern setuptools from pip instead of apt
 RUN pip3 install pip setuptools --upgrade
 
-RUN apt-get purge python3-setuptools
+RUN apt-get purge -y python3-setuptools
+
+
+# Install mypackage
+WORKDIR /tmp/
+RUN git clone https://github.com/jorgensd/reproducibility && \
+    pip3 install ./reproducibility[docs]
+
+RUN rm -rf /tmp
 
 # Create user with a home directory
 ARG NB_USER

Makefile

@@ -10,8 +10,9 @@ doc: # Generate Sphinx HTML documentation, including API docs
 	@for file in ${DOCS}; do \
 		cp $$file docs/. ;\
 	done 
+# We use --set-kernel with jupytext to make it possible for binder to pick it up
 	@for demo in ${DEMOS}; do \
-		jupytext --to=ipynb demo/$$demo.py --output=docs/$$demo.ipynb ;\
+		jupytext --to=ipynb --set-kernel=python3 demo/$$demo.py --output=docs/$$demo.ipynb ;\
 		jupyter book build -W docs ;\
 	done
 

README.md

@@ -6,8 +6,7 @@ This repository is a template for how to set up a reproducible python environmen
 
 ## Python-packaging
 
-To be able to create a python package, we need a folder with the name of the package (in this repository `mypackage`), and a `pyproject.toml` file.
-
+To be able to create a python package, we need a folder with the name of the package (in this repository it is called `mypackage`, located under `src/mypackage`), and a `pyproject.toml` file.
 
 
 ## Make a repository citable

docs/_config.yml

@@ -15,33 +15,28 @@ execute:
 # Information about where the book exists on the web
 repository:
   url: https://github.com/jorgensd/reproducibility # Online location of your book
-  path_to_book: docs # Optional path to your book, relative to the repository root
-  branch: main # Which branch of the repository should be used when creating links (optional)
-
-
-sphinx:
-  extra_extensions:
-  - 'sphinx.ext.autodoc'
-  - 'sphinx.ext.napoleon'
-  - 'sphinx.ext.viewcode'
-
+  path_to_book: _sources # Optional path to your book, relative to the repository root
+  branch: gh-pages  # Which branch of the repository should be used when creating links (optional)
 
 launch_buttons:
   notebook_interface: "jupyterlab" # The interface interactive links will activate ["classic", "jupyterlab"]
   binderhub_url: "https://mybinder.org"
-  colab_url: "https://colab.research.google.com"
-
-
 
-# Add GitHub buttons to your book
-# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
 html:
   use_issues_button: true
   use_repository_button: true
 
-
 parse:
   myst_enable_extensions:
     - amsmath
     - dollarmath
-    - linkify
+    - linkify
+
+sphinx:
+  extra_extensions:
+  - 'sphinx.ext.autodoc'
+  - 'sphinx.ext.napoleon'
+  - 'sphinx.ext.viewcode'
+
+
+