Various improvements (#26)

* Add info about badges
Add coverage report to github pages

* Remove link in README

Author: jorgensd

.github/workflows/build_docs.yml

@@ -4,10 +4,13 @@ on:
   push:
     branches:
       - main
-
 jobs:
   deploy:
     runs-on: ubuntu-22.04
+    env:
+      # Directory that will be published on github pages
+      PUBLISH_DIR: ./docs/_build/html
+
     steps:
       - uses: actions/checkout@v3
 
@@ -17,12 +20,22 @@ jobs:
           python-version: "3.10"
 
       - name: Install dependencies
-        run: python -m pip install ".[docs]"
+        run: python -m pip install ".[test,docs]"
+                
       - name: Build docs
         run: make doc
 
+      - name: Copy Dockerfile into gh-pages
+        run: cp Dockerfile ${PUBLISH_DIR}
+
+      - name: Add coverage report to github pages
+        run: |
+          python -m pytest --cov=mypackage test 
+          python -m coverage html
+          cp -r htmlcov ${PUBLISH_DIR} 
+
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./docs/_build/html
+          publish_dir: ${PUBLISH_DIR}

Dockerfile

@@ -15,7 +15,7 @@ RUN apt-get purge -y python3-setuptools
 # Install mypackage
 WORKDIR /tmp/
 RUN git clone https://github.com/jorgensd/reproducibility && \
-    pip3 install ./reproducibility[docs]
+    pip install ./reproducibility[docs]
 
 RUN rm -rf /tmp
 

README.md

@@ -1,9 +1,26 @@
 # Reproducible workflow for researchers
-[![Jupyter Book Badge](https://jupyterbook.org/badge.svg)](https://jorgensd.github.io/reproducibility)
-[![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://choosealicense.com/licenses/mit/)
 
 This repository is a template for how to set up a reproducible python environment with GitHub.
 
+## Badges
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jorgensd/reproducibility/gh-pages?labpath=_sources)
+
+To get the `Launch Binder` badge, go to: [https://mybinder.org/](https://mybinder.org/) and fill in (specifics for this repo in brackets):
+- Your Github repository (https://github.com/jorgensd/reproducibility)
+- Git ref (`gh-pages`, see: [How to create github pages](#ghpages))
+- Path to notebook file (`_sources`, as generated by `jupyter-book`, see [Jupyter-book](#jupyterbook))
+
+Then press `Launch`, and then `Expand to see the text below, paste it into your README to show a binder badge` and copy the markdown code. If you render the README.md file as plaintext, you can see all the settings explicitly in the image link
+
+[![Jupyter Book Badge](https://jupyterbook.org/badge.svg)](https://jorgensd.github.io/reproducibility)
+
+Replace link in image (https://jorgensd.github.io/reproducibility) with your [Github pages url](#ghpages)
+
+![MIT License](https://img.shields.io/github/license/jorgensd/reproducibility)
+
+Replace `username/repo` in image link with appropriate user/respository.
+
 ## Python-packaging
 
 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.
@@ -24,4 +41,13 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for ways to get started.
 
 A good idea is to look at the [issue tracker](https://github.com/jorgensd/reproducibility/issues) and see if you can resolve any open issues.  A list of good first issues can be found [here](https://github.com/jorgensd/reproducibility/contribute)
 
-If you find a bug in the source code, please [open an issue](https://github.com/jorgensd/reproducibility/issues/new/choose).
+If you find a bug in the source code, please [open an issue](https://github.com/jorgensd/reproducibility/issues/new).
+
+
+## <a id="ghpages"></a> Auto-publish to Github Pages
+
+Add text
+
+## <a id="jupyterbook"></a> Jupyter-book
+
+Add text