Merge pull request #4 from computorg/new-workflow

trying new workflow on chagneux

Author: jchiquet

.github/workflows/build.yml

@@ -1,54 +1,23 @@
-name: build
+name: Main Workflows
+
 on:
-  schedule:
-    - cron: '0 0 * * 0' 
   push:
-    branches:
-      - master
-      - main
-
-env: # Change this if needed
-  quarto_file: ${{ github.event.repository.name }}
-  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    branches: ["main","master"]
+  repository_dispatch:
+    types: [custom-event] 
+  workflow_dispatch:
+  pull_request:
+    branches: ["main","master"]
 
 
 jobs:
-  build-deploy:
-    if: "!contains(github.event.head_commit.message, 'skip build')"
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checking out repository for Github action
-        uses: actions/checkout@v3
-
-      - name: Installing dependencies with Micromamba
-        uses: mamba-org/provision-with-micromamba@main
-        with:
-          cache-env: true
-
-      - name: Set up Quarto
-        uses: quarto-dev/quarto-actions/setup@v2
-        with:
-          tinytex: true
-          version: pre-release
-  
-      - name: Install Computo extension for Quarto
-        run: |
-            quarto add --no-prompt computorg/computo-quarto-extension
-      - name: Rendering with Quarto
-        shell: bash -l {0}
-
-        run: |
-            quarto render ${{ env.quarto_file }}.qmd
-            mkdir _build
-            mv ${{ env.quarto_file }}.html _build/index.html
-            mv -vf ${{ env.quarto_file }}_files figures ${{ env.quarto_file }}.pdf _build/
-            cp environment.yml _build/
-            touch _build/.nojekyll
+  call_env_workflow:
+    uses: computorg/workflows/.github/workflows/global-env.yml@main
+  call_quartopublish_workflow:
+    permissions:
+      id-token: write
+      contents: write
+      pages: write
+    uses: computorg/workflows/.github/workflows/publish-render.yml@main
+    needs: call_env_workflow
 
-      - name: Deploying article on github pages
-        uses: JamesIves/github-pages-deploy-action@v4
-        with:
-          BRANCH: gh-pages
-          FOLDER: _build
-          CLEAN: true

.gitignore

@@ -1,6 +1,16 @@
-*.swp
-_build
-content.html
-__pycache__
-
 /.quarto/
+DS_Store
+.Rhistory
+/.luarc.json
+/.quarto/
+/*_files
+/*_cache
+/_freeze
+_extensions/
+.Rprofile
+published-202301-chagneux-macrolitter.html
+published-202301-chagneux-macrolitter.pdf
+_environment
+/.micromamba/
+/_siteg/
+/surfnet/

README.md

@@ -1,5 +1,8 @@
 # Macrolitter video counting on riverbanks using state space models and moving cameras
 
+[![build and publish](https://github.com/computorg/published-202301-chagneux-macrolitter/actions/workflows/build.yml/badge.svg)](https://github.com/computorg/published-202301-chagneux-macrolitter/actions/workflows/build.yml)
+
+Authors:
 
 - [Mathis Chagneux](https://www.linkedin.com/in/mathis-chagneux-140245158/?originalSubdomain=fr), Telecom Paris, LTCI
 - Sylvain Le Corff, Sorbonne Université, UMR 8001 (LPSM)
@@ -8,12 +11,8 @@
 - Océane Lepâtre, Surfrider Foundation Europe
 - Antoine Bruge, Surfrider Foundation Europe
 
-
-
-[![build status](https://github.com/computorg/published-202301-chagneux-macrolitter/workflows/build/badge.svg)](https://github.com/computorg/published-202301-chagneux-macrolitter/)
-[![](https://img.shields.io/github/last-commit/computorg/published-202301-chagneux-macrolitter.svg)](https://github.com/computorg/published-202301-chagneux-macrolitter/commits/main)
+[![DOI](https://img.shields.io/badge/DOI-10.57750%2F845m--f805-034E79.svg)](https://doi.org/10.57750/845m-f805)
 [![HTML](https://img.shields.io/badge/article-HTML-034E79)](https://computorg.github.io/published-202301-chagneux-macrolitter/)
-[![10.57750/845m-f805](https://img.shields.io/badge/DOI-10.57750%2F845m--f805-034E79.svg)](https://doi.org/10.57750/845m-f805)
 [![review 1](https://img.shields.io/badge/review-report%201-blue)](https://github.com/computorg/published-202301-chagneux-macrolitter/issues/1)
 [![review 2](https://img.shields.io/badge/review-report%202-blue)](https://github.com/computorg/published-202301-chagneux-macrolitter/issues/2)
 [![SWH](https://archive.softwareheritage.org/badge/origin/https://github.com/computorg/published-202301-chagneux-macrolitter/)](https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/computorg/published-202301-chagneux-macrolitter)

environment.yml

@@ -2,19 +2,18 @@ name: computo
 channels:
     - conda-forge
 dependencies:
-    - python==3.9
+    - jupyter
+    - numpy
+    - matplotlib
+    - scipy 
     - pip
+    - pandas 
+    - tqdm
+    - seaborn
+    - pycocotools
+    - filterpy
+    - scikit-image
+    - pykalman
     - pip:
-        - jupyter
-        - numpy
-        - matplotlib
-        - pycocotools
-        - scipy 
         - opencv_python
-        - pandas 
-        - pykalman
-        - filterpy
-        - scikit-image
-        - tqdm
-        - seaborn
         - pytk