New workflow (#6)

* lots of tricks, it is now working

Author: jchiquet

.Rprofile

@@ -1,56 +1,22 @@
-name: build
+name: Main Workflows
 
 on:
-  workflow_dispatch:
   push:
-    branches: main
+    branches: ["main","master"]
+  repository_dispatch:
+    types: [custom-event] 
+  workflow_dispatch:
+  pull_request:
+    branches: ["main","master"]
+
 
 jobs:
-  build-and-publish:    
-    runs-on: ubuntu-latest
+  call_env_workflow:
+    uses: computorg/workflows/.github/workflows/global-env.yml@main
+  call_quartopublish_workflow:
     permissions:
+      id-token: write
       contents: write
-    steps:
-      - name: Checking out repository for Github action
-        uses: actions/checkout@v3
-        
-      - name: Installing quarto
-        uses: quarto-dev/quarto-actions/setup@v2
-        with:
-          tinytex: true
-
-      - name: Install Computo extension for Quarto
-        run: |
-          quarto add --no-prompt computorg/computo-quarto-extension
-
-      - name: register tinytex globally for diagram.lua
-        run: |
-          mkdir -p ~/.local/bin
-          ~/.TinyTeX/bin/x86_64-linux/tlmgr option sys_bin ~/.local/bin
-          ~/.TinyTeX/bin/x86_64-linux/tlmgr path add
-          ~/.TinyTeX/bin/x86_64-linux/tlmgr install libertinus-fonts
-          
-      - name: Install system dependencies
-        run: |+
-          sudo apt-get install libcurl4-openssl-dev libudunits2-dev libgdal-dev
-                   
-      - name: Setup R
-        uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: 4.2.2
-          
-      - name: Install R Dependencies
-        uses: r-lib/actions/setup-renv@v2
-        with:
-          cache-version: 1
-          
-      - name: Install fastai
-        run: |
-           R -e "fastai::install_fastai()"
-           
-      - name: Render and Publish
-        uses: quarto-dev/quarto-actions/publish@v2
-        with:
-          target: gh-pages
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      pages: write
+    uses: computorg/workflows/.github/workflows/publish-render.yml@main
+    needs: call_env_workflow

.github/workflows/build.yml

@@ -1,14 +1,31 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
 .Rhistory
 .RData
+.Rprofile
+.Rproj.user
+
+
 .quarto/
 /.joblib
-/_extensions/
-published-202304-gimenez-lynx.html
-published-202304-gimenez-lynx.ipynb
-published-202304-gimenez-lynx.tex
-published-202301-gimenez-lynx_files/
-published-202301-gimenez-lynx_files/*
-published-202301-gimenez-lynx_files/*/
 /.quarto/
+DS_Store
+/.luarc.json
+/*_files
+/*_cache
+/_freeze
+_extensions/
 
-.Rproj.user
+published-202204-gimenez-lynx.html
+published-202204-gimenez-lynx.pdf
+published-202204-gimenez-lynx.ipynb
+published-202204-gimenez-lynx.tex
+
+_environment
+/.micromamba/
+_site/
+logo_notext_white.png
+logo_text_white.pdf
+/renv/

.gitignore

@@ -2,6 +2,15 @@
 
 *A Reproducible `R` workflow integrating models in computer vision and ecological statistic*
 
+[![build and publish](https://github.com/computorg/published-202204-deeplearning-occupancy-lynx/actions/workflows/build.yml/badge.svg)](https://github.com/computorg/published-202204-deeplearning-occupancy-lynx/actions/workflows/build.yml)
+[![DOI:10.57750/yfm2-5f45 ](https://img.shields.io/badge/DOI-10.57750%2Fyfm2--5f45-034E79.svg)](https://doi.org/10.57750/yfm2-5f45)
+[![review](https://img.shields.io/badge/review-report-blue)](https://github.com/computorg/published-202204-deeplearning-occupancy-lynx/issues?q=is%3Aopen+is%3Aissue+label%3Areview)
+[![SWH](https://archive.softwareheritage.org/badge/origin/https://github.com/computorg/published-202204-deeplearning-occupancy-lynx/)](https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/computorg/published-202204-deeplearning-occupancy-lynx)
+[![Creative Commons License](https://i.creativecommons.org/l/by/4.0/80x15.png)](http://creativecommons.org/licenses/by/4.0/)
+ISSN 2824-7795
+
+Authors:
+
 - [Olivier Gimenez](https://oliviergimenez.github.io/) (CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France)
 - Maëlis Kervellec (CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France)
 - Jean-Baptiste Fanjul (Fédérations Départementales des Chasseurs du Jura, Arlay, France)
@@ -10,13 +19,3 @@
 - Yoann Bollet (Fédération Départementale des Chasseurs de l’Ain, Bourg-en-Bresse, France)
 - Christophe Duchamp (Office Français de la Biodiversité, Unité Espèces à enjeux, Gap, France)
 
-[![build status](https://github.com/computorg/published-202204-deeplearning-occupancy-lynx/workflows/build/badge.svg)](https://github.com/computorg/published-202204-deeplearning-occupancy-lynx/)
-[![](https://img.shields.io/github/last-commit/computorg/published-202204-deeplearning-occupancy-lynx.svg)](https://github.com/computorg/published-202204-deeplearning-occupancy-lynx/commits/main)
-[![HTML](https://img.shields.io/badge/article-HTML-034E79)](https://computorg.github.io/published-202204-deeplearning-occupancy-lynx/)
-<!-- [![PDF](https://img.shields.io/badge/article-PDF-034E79)](https://computorg.github.io/published-202204-deeplearning-occupancy-lynx/published-202204-gimenez-lynx.pdf) -->
-[![DOI:10.57750/yfm2-5f45 ](https://img.shields.io/badge/DOI-10.57750%2Fyfm2--5f45-034E79.svg)](https://doi.org/10.57750/yfm2-5f45)
-[![review 1](https://img.shields.io/badge/review-report%201-blue)](https://github.com/computorg/published-202204-deeplearning-occupancy-lynx/issues/1)
-[![review 2](https://img.shields.io/badge/review-report%202-blue)](https://github.com/computorg/published-202204-deeplearning-occupancy-lynx/issues/2)
-[![SWH](https://archive.softwareheritage.org/badge/origin/https://github.com/computorg/published-202204-deeplearning-occupancy-lynx/)](https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/computorg/published-202204-deeplearning-occupancy-lynx)
-[![Creative Commons License](https://i.creativecommons.org/l/by/4.0/80x15.png)](http://creativecommons.org/licenses/by/4.0/)
-ISSN 2824-7795

README.md

@@ -1,142 +1,9 @@
-name: renv-python
+name: gimenez
 channels:
+  - fastai
   - conda-forge
-  - defaults
 dependencies:
-  - _libgcc_mutex=0.1=conda_forge
-  - _openmp_mutex=4.5=2_gnu
-  - ca-certificates=2022.12.7=ha878542_0
-  - ld_impl_linux-64=2.40=h41732ed_0
-  - libffi=3.4.2=h7f98852_5
-  - libgcc-ng=12.2.0=h65d4601_19
-  - libgomp=12.2.0=h65d4601_19
-  - libnsl=2.0.0=h7f98852_0
-  - libsqlite=3.40.0=h753d276_0
-  - libstdcxx-ng=12.2.0=h46fd767_19
-  - libzlib=1.2.13=h166bdaf_4
-  - ncurses=6.3=h27087fc_1
-  - openssl=3.0.7=h0b41bf4_2
-  - pip=23.0=pyhd8ed1ab_0
-  - python=3.7.12=hf930737_100_cpython
-  - readline=8.1.2=h0f457ee_0
-  - setuptools=66.1.1=pyhd8ed1ab_0
-  - sqlite=3.40.0=h4ff8645_0
-  - tk=8.6.12=h27826a3_0
-  - wheel=0.38.4=pyhd8ed1ab_0
-  - xz=5.2.6=h166bdaf_0
-  - pip:
-      - absl-py==1.4.0
-      - aiohttp==3.8.3
-      - aiosignal==1.3.1
-      - async-timeout==4.0.2
-      - asynctest==0.13.0
-      - attrs==22.2.0
-      - backcall==0.2.0
-      - blis==0.7.9
-      - catalogue==2.0.8
-      - certifi==2022.12.7
-      - charset-normalizer==2.1.1
-      - click==8.1.3
-      - confection==0.0.4
-      - cycler==0.11.0
-      - cymem==2.0.7
-      - datasets==2.9.0
-      - decorator==5.1.1
-      - descartes==1.1.0
-      - dill==0.3.6
-      - et-xmlfile==1.1.0
-      - fastai==2.7.10
-      - fastcore==1.5.27
-      - fastdownload==0.0.7
-      - fastinference==0.0.36
-      - fastprogress==1.0.3
-      - filelock==3.9.0
-      - fonttools==4.38.0
-      - frozenlist==1.3.3
-      - fsspec==2023.1.0
-      - huggingface-hub==0.12.0
-      - idna==3.4
-      - imageio==2.25.0
-      - importlib-metadata==6.0.0
-      - ipython==7.34.0
-      - jedi==0.18.2
-      - jinja2==3.1.2
-      - joblib==1.2.0
-      - kiwisolver==1.4.4
-      - kornia==0.6.8
-      - langcodes==3.3.0
-      - markupsafe==2.1.2
-      - matplotlib==3.5.3
-      - matplotlib-inline==0.1.6
-      - mizani==0.7.3
-      - multidict==6.0.4
-      - multiprocess==0.70.14
-      - murmurhash==1.0.9
-      - networkx==2.6.3
-      - nltk==3.8.1
-      - numpy==1.21.6
-      - ohmeow-blurr==1.0.5
-      - opencv-python==4.7.0.68
-      - openpyxl==3.0.10
-      - packaging==23.0
-      - palettable==3.3.0
-      - pandas==1.3.5
-      - parso==0.8.3
-      - pathy==0.10.1
-      - patsy==0.5.3
-      - pexpect==4.8.0
-      - pickleshare==0.7.5
-      - pillow==9.4.0
-      - plotly==5.13.0
-      - plotnine==0.8.0
-      - preshed==3.0.8
-      - prompt-toolkit==3.0.36
-      - ptyprocess==0.7.0
-      - pyarrow==11.0.0
-      - pydantic==1.10.4
-      - pydicom==2.3.1
-      - pygments==2.14.0
-      - pyparsing==3.0.9
-      - python-dateutil==2.8.2
-      - pytz==2022.7.1
-      - pywavelets==1.3.0
-      - pyyaml==6.0
-      - regex==2022.10.31
-      - requests==2.28.2
-      - responses==0.18.0
-      - rouge-score==0.1.2
-      - scikit-image==0.19.3
-      - scikit-learn==1.0.2
-      - scipy==1.7.3
-      - sentencepiece==0.1.97
-      - seqeval==1.2.2
-      - shap==0.35.0
-      - six==1.16.0
-      - smart-open==6.3.0
-      - spacy==3.5.0
-      - spacy-legacy==3.0.12
-      - spacy-loggers==1.0.4
-      - srsly==2.4.5
-      - statsmodels==0.13.5
-      - tenacity==8.1.0
-      - thinc==8.1.7
-      - threadpoolctl==3.1.0
-      - tifffile==2021.11.2
-      - timm==0.6.12
-      - tokenizers==0.13.2
-      - torch==1.9.0+cpu
-      - torchaudio==0.9.0
-      - torchvision==0.10.0+cpu
-      - tqdm==4.64.1
-      - traitlets==5.9.0
-      - transformers==4.26.0
-      - typer==0.7.0
-      - typing-extensions==4.4.0
-      - urllib3==1.26.14
-      - wasabi==1.1.1
-      - wcwidth==0.2.6
-      - xlrd==2.0.1
-      - xxhash==3.2.0
-      - yarl==1.8.2
-      - zipp==3.12.0
-prefix: renv-python
+  - jupyter
+  - jupyter-cache  
+  - fastai
+