Merge pull request #248 from simphony/dev

Merge release 3.9.0

.dockerignore

@@ -1,2 +1,2 @@
 .vscode/
-build/
+build/

.github/workflows/ci.yml

@@ -4,24 +4,23 @@ on: pull_request
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.7
-    - name: Install OS dependencies
-      run: |
-        sudo apt-get update 
-        sudo apt-get install pandoc latexmk
-        sudo apt-get install texlive-fonts-recommended texlive-latex-recommended texlive-latex-extra
-    - name: Install python dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install wheel
-        pip install -r requirements.txt
-    - name: Build docs
-      run: sphinx-build docs/source docs/build/html
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+      - name: Install OS dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install pandoc latexmk
+          sudo apt-get install texlive-fonts-recommended texlive-latex-recommended texlive-latex-extra
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install wheel
+          pip install -r requirements.txt
+      - name: Build docs
+        run: sphinx-build docs/source docs/build/html

.gitignore

@@ -1,2 +1,2 @@
 .vscode/
-build/
+build/

.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+---
+ci:
+  autoupdate_branch: "dev"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+      - id: check-json
+      - id: pretty-format-json
+        args: ["--autofix", "--no-sort-keys"]
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.6.2
+    hooks:
+      - id: prettier
+        files: \.(js|ts|jsx|tsx|css|less|html|markdown|md|yaml|yml)$
+
+  - repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+      - id: black
+        args:
+          - --line-length=79
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        args:
+          - --profile=black
+          - --filter-files
+          - --line-length=79

README.md

@@ -1,52 +1,67 @@
 ## Build Status
-**latest** - [![Documentation latest](https://readthedocs.org/projects/simphony/badge/?version=latest)](https://simphony.readthedocs.io/en/latest/?badge=latest)  
+
+**latest** - [![Documentation latest](https://readthedocs.org/projects/simphony/badge/?version=latest)](https://simphony.readthedocs.io/en/latest/?badge=latest)
 **dev** - [![Documentation dev](https://readthedocs.org/projects/simphony/badge/?version=dev)](https://simphony.readthedocs.io/en/latest/?badge=dev)
 
 # SimPhoNy docs
+
 To access the documentation, please visit: [https://simphony.readthedocs.io](https://simphony.readthedocs.io).
 
 If you find any error or problem with the documentation, please [create an issue](https://github.com/simphony/docs/issues).
 
 ## Local Rendering
+
 ### HTML
+
 A server will start, generate the docs and listen for changes in the source files.
 This can be done by using docker or installing the development environment directly on the you machine. Next are installation guides for Docker and Linux OS.
 
 #### Docker
+
 First, build the Docker image by running the following command:
+
 ```shell
 $ docker build -f local_build.Dockerfile -t simphony-docs .
 ```
 
 Then, start the program by running:
+
 ```shell
 $ docker run --rm -v $PWD:/app -p 8000:8000 simphony-docs
 ```
 
 #### Linux
+
 At an OS level (these commands work on Linux Debian):
+
 ```shell
 $ sudo apt install pandoc graphviz default-jre
 $ sudo apt-get install texlive-latex-recommended \
                        texlive-latex-extra \
                        texlive-fonts-recommended \
-                       latexmk 
+                       latexmk
 ```
+
 The python dependencies:
+
 ```shell
 $ pip install -r requirements.txt
 ```
 
 Now you can start the server and render the docs:
+
 ```
 $ sphinx-autobuild docs/source docs/build/html
 ```
-The documentation will be available on [`http://127.0.0.1:8000`](http://127.0.0.1:8000).
 
+The documentation will be available on [`http://127.0.0.1:8000`](http://127.0.0.1:8000).
 
 ### PDF (LaTeX)
+
 To generate a PDF of the documentation, simply run (from the root project folder):
+
 ```sh
 make -C docs latexpdf
 ```
-The generated PDF can be found under docs/build/latex/SymPhoNy_docs.pdf
+
+The generated PDF can be found under docs/build/latex/SymPhoNy_docs.pdf

docs/source/_static/custom.css

@@ -0,0 +1,25 @@
+.caption-text,
+h1,
+h2,
+h3,
+h4 {
+  color: #6580a1 !important;
+}
+
+.btn-outline-primary {
+  border-color: #6580a1 !important;
+}
+
+.btn-outline-primary:hover {
+  background-color: #6580a1 !important;
+  color: azure !important;
+}
+
+@media (min-width: 1200px) {
+  .container-xl {
+    max-width: 1550px;
+  }
+  #site-navigation {
+    max-width: 20%;
+  }
+}