Merge pull request #3 from ukhsa-collaboration/dev

Dev

.github/workflows/book.yml

@@ -0,0 +1,64 @@
+name: build-book
+
+# only run when specific files change
+# only run on install-fix-docs branch 
+# TODO change this to dev/main branch once integrated
+# TODO edit filepath once filepath levels are corrected
+
+on:
+  push:
+    branches:
+    - install-fix-docs
+    paths: 
+    - docs/**
+
+jobs:
+    build-book:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v2
+
+            - uses: actions/cache@v1
+              with:
+                path: ~/.cache/pip
+                key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+                restore-keys: |
+                  ${{ runner.os }}-pip-
+                    steps:
+            
+            - uses: actions/checkout@v3
+
+            - name: Setup Graphviz
+              uses: ts-graphviz/setup-graphviz@v1
+
+            # install python
+            - name: Set up Python 3.8
+              uses: actions/setup-python@v2
+              with:
+                python-version: 3.8
+
+            # install dependencies
+            - name: Install dependencies
+              run: |
+                python -m pip install --upgrade pip
+                pip install -r requirements.txt
+
+            # set up pygom
+            - name: Build and install pygom
+              run: |
+                  python setup.py build
+                  python setup.py install
+
+            # build the book
+            # TODO check which flags are needed, -W
+            - name: Build the book
+              run: |
+                jupyter-book build --all -v docs/pygom-doc
+
+            # deploy book to github-pages
+            - name: GitHub Pages 
+              uses: peaceiris/[email protected]
+              with:
+                github_token: ${{ secrets.GITHUB_TOKEN }}
+                publish_dir: docs/pygom-doc/_build/html
+

.github/workflows/main.yml

@@ -11,13 +11,16 @@ on:
     branches:
       - master
 
+env:
+  ACTIONS_ALLOW_UNSECURE_COMMANDS: true
+
 jobs:
   build:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.5, 3.6, 3.7, 3.8]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v2

.gitignore

@@ -7,6 +7,7 @@ cover/*
 __pycache__
 *.egg-info
 *.egg
+.vscode/
 
 # For jupyter / ipython
 */.ipynb_checkpoints
@@ -17,5 +18,8 @@ __pycache__
 .settings
 
 # For built documentation
-/doc/_build*
+/docs/pygom-doc/_build/*
+/doc/_build/
 /doc/source/savefig/*
+/docs/pygom-doc/_autosummary/
+*/_build/*

CONTRIBUTING.md

@@ -0,0 +1,32 @@
+# Contributor guidance 
+
+## suggested information for raising issues
+- is it possible to produce a template for a new issue?
+
+## requirements for amendments 
+- merge and pull requests should only be considered if the MR/PR explicitly states how the following has been addressed
+    - unit tests
+    - modified documentation
+    - justification
+    - successful execution of documentation (controlled by halting at errors in /docs/_config.yml, demonstrated by successful action)
+- #TODO is there a reasonable limit on the code quantity that is submitted per review? (e.g. 200 lines) to ensure a suitable review can be completed
+
+## workflow for incorporating merge and pull requests
+- dev and master are protected and require a code review by the project owner (or designated reviewer)
+- dev should contain all working amendments and collated before the next versioned merge request to master
+- only a merge request should be made to master from dev from the UKHSA repo
+- forked repo pull requests should be made into UKHSA dev branch (or others where appropriate)
+- master branch is for versioned releases, which should be tagged and a summary of alterations made to README.md
+- merge and pull requests to be made to dev, where builds and actions must run successfully before being incorporated
+- if closing a ticket, if possible, include the commit reference which addresses the issue
+- code reviewer should use the template to work through requirements (e.g. confirming tests have been added, documentation is appropriate, added to contributor file)
+
+## adding to the documentation how to add to the jupyterbook;
+
+## acknowledgements from contributors
+- what counts as a contribution?
+    - ticket? pr/mr?
+- how are contributors acknowledged?
+    - contributor md file?
+    - who adds the name to the contributor? suggest code reviewer on approval of MR/PR
+- provide citable repo link

README.rst

@@ -2,18 +2,18 @@
 pygom - ODE modelling in Python
 ===============================
 
-|Build status|  |Github actions|  |Documentation Status|  |pypi version|  |licence|
+|Build status|  |Github actions|  |Documentation Status|  |pypi version|  |licence|  |Jupyter Book Badge|
 
 .. |pypi version| image:: https://img.shields.io/pypi/v/pygom.svg
    :target: https://pypi.python.org/pypi/pygom
-.. |Build status| image:: https://travis-ci.org/PublicHealthEngland/pygom.svg?branch=master
-   :target: https://travis-ci.org/PublicHealthEngland/pygom
 .. |Documentation Status| image:: https://readthedocs.org/projects/pygom/badge/?version=master
    :target: https://pygom.readthedocs.io/en/master/?badge=master
 .. |licence| image:: https://img.shields.io/pypi/l/pygom?color=green   :alt: PyPI - License
    :target: https://raw.githubusercontent.com/PublicHealthEngland/pygom/master/LICENSE.txt
 .. |Github actions| image:: https://github.com/PublicHealthEngland/pygom/workflows/pygom/badge.svg
    :target: https://github.com/PublicHealthEngland/pygom/actions/
+.. |Jupyter Book Badge| image:: https://jupyterbook.org/badge.svg
+   :target: https://hwilliams-phe.github.io/pygom/intro.html
 
 A generic framework for ode models, specifically compartmental type problems.