ci: updates (#1)

* feat: add funding

* ci: add dependabot

* ci: update julia and permission

* ci: quarto render

* feat: update julia to 1.10

* feat(python): simplify requirements

* ci: quarto render

* ci: julia-actions/cache

* ci: quarto-render

* ci: add IJulia

* ci: quarto-publish

.github/FUNDING.yml

@@ -0,0 +1,3 @@
+# These are supported funding model platforms
+
+github: storopoli

.github/dependabot.yml

@@ -0,0 +1,8 @@
+# Set update schedule for GitHub Actions
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/quarto-publish.yml

@@ -1,16 +1,24 @@
 on:
   push:
-    branches: main
+    branches:
+      - main
+      - master
   workflow_dispatch:
 
 name: Render and Publish
 
 jobs:
   build-deploy:
     runs-on: ubuntu-latest
+    permissions:
+      # For the push to `gh-pages` branch.
+      contents: write
+      pages: write
+    env:
+      JULIA_NUM_THREADS: "auto"
     steps:
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
@@ -20,28 +28,31 @@ jobs:
           # uncomment below and fill to pin a version
           # version: SPECIFIC-QUARTO-VERSION-HERE
 
-      - name: Set up Julia
-        uses: julia-actions/setup-julia@v1
-        with:
-          version: "1"
-      - name: Instantiate Julia project
-        run: julia --color=yes --project -e 'using Pkg; Pkg.instantiate()'
-
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
           python-version: '3.x' # Version range or exact version of a Python version to use, using SemVer's version range syntax
           cache: 'pip'
       - name: Install Jupyter
-        run: pip install jupyter # (if jupyter is not part of your requirements.txt)
+        run: pip install jupyter jupyter-cache
       - name: Install Python project
         run: pip install -r requirements.txt
       - run: echo "PYTHON=$(which python)" >> $GITHUB_ENV
 
+      - name: Set up Julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: "1"
+      - name: Cache Julia
+        uses: julia-actions/cache@v1
+      - name: Instantiate Julia project
+        run: julia --color=yes --project -e 'using Pkg; Pkg.instantiate()'
+
       - name: Publish to GitHub Pages (and render)
         uses: quarto-dev/quarto-actions/publish@v2
         with:
           target: gh-pages
+          path: index.qmd
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # this secret is always available for github actions
 

.github/workflows/quarto-render.yml

@@ -0,0 +1,62 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+  workflow_dispatch:
+
+name: Render
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      JULIA_NUM_THREADS: "auto"
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          # To install LaTeX to build PDF book 
+          tinytex: false # we don't need latex 
+          # uncomment below and fill to pin a version
+          # version: SPECIFIC-QUARTO-VERSION-HERE
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x' # Version range or exact version of a Python version to use, using SemVer's version range syntax
+          cache: 'pip'
+      - name: Install Jupyter
+        run: pip install jupyter jupyter-cache
+      - name: Install Python project
+        run: pip install -r requirements.txt
+      - run: echo "PYTHON=$(which python)" >> $GITHUB_ENV
+
+      - name: Set up Julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: "1"
+      - name: Cache Julia
+        uses: julia-actions/cache@v1
+      - name: Instantiate Julia project
+        run: julia --color=yes --project -e 'using Pkg; Pkg.instantiate()'
+
+      - name: Render Quarto Project
+        uses: quarto-dev/quarto-actions/render@v2
+        with:
+          to: html # If set, it will be equivalent to `quarto render --to html`
+          path: index.qmd
+
+      - name: Make preview available
+        if: ${{ github.event_name == 'pull_request' }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: html-preview
+          path: ./index.html

Project.toml

@@ -3,6 +3,7 @@ BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 Chain = "8be319e6-bccf-4806-a6f7-6fae938471bc"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

index.qmd

@@ -15,7 +15,6 @@ format:
 execute:
   echo: true
   cache: true
-jupyter: julia-1.8
 ---
 
 ```{julia}

requirements.txt

@@ -1,94 +1,3 @@
-anyio==3.6.2
-argon2-cffi==21.3.0
-argon2-cffi-bindings==21.2.0
-arrow==1.2.3
-asttokens==2.2.1
-attrs==22.2.0
-backcall==0.2.0
-beautifulsoup4==4.11.2
-bleach==6.0.0
-cffi==1.15.1
-click==8.1.3
-comm==0.1.2
-debugpy==1.6.6
-decorator==5.1.1
-defusedxml==0.7.1
-executing==1.2.0
-fastjsonschema==2.16.2
-fqdn==1.5.1
-greenlet==2.0.2
-idna==3.4
-importlib-metadata==6.0.0
-ipykernel==6.21.1
-ipython==8.9.0
-ipython-genutils==0.2.0
-ipywidgets==8.0.4
-isoduration==20.11.0
-jedi==0.18.2
-Jinja2==3.1.2
-jsonpointer==2.3
-jsonschema==4.17.3
-jupyter==1.0.0
-jupyter-cache==0.5.0
-jupyter-console==6.4.4
-jupyter-events==0.6.3
-jupyter_client==8.0.2
-jupyter_core==5.2.0
-jupyter_server==2.2.1
-jupyter_server_terminals==0.4.4
-jupyterlab-pygments==0.2.2
-jupyterlab-widgets==3.0.5
-MarkupSafe==2.1.2
-matplotlib-inline==0.1.6
-mistune==2.0.5
-nbclassic==0.5.1
-nbclient==0.5.13
-nbconvert==7.2.9
-nbformat==5.7.3
-nest-asyncio==1.5.6
-notebook==6.5.2
-notebook_shim==0.2.2
-numpy==1.24.2
-packaging==23.0
-pandas==1.5.3
-pandocfilters==1.5.0
-parso==0.8.3
-pexpect==4.8.0
-pickleshare==0.7.5
-platformdirs==3.0.0
-prometheus-client==0.16.0
-prompt-toolkit==3.0.36
-psutil==5.9.4
-ptyprocess==0.7.0
-pure-eval==0.2.2
-pycparser==2.21
-Pygments==2.14.0
-pyrsistent==0.19.3
-python-dateutil==2.8.2
-python-json-logger==2.0.4
-pytz==2022.7.1
-PyYAML==6.0
-pyzmq==25.0.0
-qtconsole==5.4.0
-QtPy==2.3.0
-rfc3339-validator==0.1.4
-rfc3986-validator==0.1.1
-scipy==1.10.0
-Send2Trash==1.8.0
-six==1.16.0
-sniffio==1.3.0
-soupsieve==2.3.2.post1
-SQLAlchemy==1.4.46
-stack-data==0.6.2
-tabulate==0.9.0
-terminado==0.17.1
-tinycss2==1.2.1
-tornado==6.2
-traitlets==5.9.0
-uri-template==1.2.0
-wcwidth==0.2.6
-webcolors==1.12
-webencodings==0.5.1
-websocket-client==1.5.1
-widgetsnbextension==4.0.5
-zipp==3.12.1
+numpy
+pandas
+scipy