first version of the Python-based new template

Author: jchiquet

.github/workflows/build_n_publish.yml

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+name: Computo Build and Publish for Python
+
+on:
+  workflow_dispatch:
+  push:
+    branches: main
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+
+      - 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: Install Python and Dependencies
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+      - run: pip install -r requirements.txt
+
+      - name: Render and Publish
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

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+*_files/
+template-computo-python.html
+logo_text_white.pdf
+template-computo-python.pdf
+template-computo-python.ipynb
+template-computo-python.tex
+_extensions/
+/.quarto/
+/.joblib
+/_extensions/

README.md

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+
+# Template for contribution to Computo for Python users
+
+[![build output](https://github.com/computorg/template-computo-python/workflows/build/badge.svg)](https://computorg.github.io/template-computo-python/)
+
+Documentation and sample of a simple `Python`-based submission for the [Computo journal](https://computorg.github.io), using our Quarto-based template and `venv` for handling dependencies.
+
+Shows how to automatically setup and build the HTML and PDF outputs, ready to submit to our peer-review platform.
+
+Additional details can be found [in the template manuscript](https://computo.sfds.asso.fr/template-computo-python). 
+
+  ## Process overview
+
+Submissions to [Computo](https://computorg.github.io) require both scientific content (typically equations, codes and figures, data) and a proof that this content is reproducible. This is achieved by means of i) a notebook system, ii) a virtual environment fixing the dependencies and iii) continuous integration (plus, if needed, an external website to store large data files such a [Zenodo](https://zenodo.org/) or [OSF](https://osf.io/) ). 
+
+A Computo submission is thus a git(hub) repository like this one containing 
+
+- the source files of the notebook (a quarto .qmd file + a BibTeX .bib file + some statics files, _e.g._ figures or small .csv data tables)
+- configuration files to set up the dependencies in a virtual environment
+- configuration files to set up the continuous integration rendering the final documents
+
+In this template, we focus on `R` users and detail a solution based on
+
+- The `Jupyter` kernel of Quarto for rendering the document,
+- The `venv` Python built system for setting the virtual environment,
+- Github actions for handling the continuous integration.
+
+## Step-by-step procedure
+
+### Step 0: setup a git repository
+
+Use this repository as a template via the "use this template" button on the top of this page.
+
+**Note**: _You can use Gitlab for submitting for Computo. We hope giving more support in the future._
+
+### Step 1. setup Quarto and Computo extension on your system
+
+You need [quarto](https://quarto.org/) installed on your computer, as well as the [Computo extension](https://github.com/computorg/computo-quarto-extension) to prepare your document. 
+The latter can be installed as follows:
+
+```.bash
+quarto add computorg/computo-quarto-extension
+```
+
+### Step 2. write your contribution 
+
+Write your notebook as usual, [as demonstrated in the `template-computo-python.qmd` sample](https://computorg.github.io/template-computo-python/).
+
+**Note**: _Make sure that you are able to build your manuscript as a standard notebook on your system before proceeding to the next step._
+
+### Step 3: setup dependencies with `venv`
+
+Use the [`venv` package manager](https://cewing.github.io/training.python_web/html/presentations/venv_intro.html) to setup a reproducible environment handling your `Python` dependencies.
+
+### Step 4: proof reproducibility
+
+Put everything together and check that your work is indeed reproducible. To this end, you need to rely on a github action, whose default is pre-configured and found here: [.github/workflows/build_n_publish.yml](https://github.com/computorg/template-computo-R/blob/main/.github/workflows/build_n_publish.yml)
+
+This action will
+
+1. Check out repository on the ubuntu-latest machine
+2. Install quarto and dependencies, including the Computo extension for Quarto
+4. Install Python dependencies with `pip` and `venv`, using your `requirements.txt` file
+5. Render your .qmd file and Publish the results on a gh-page (both HTML and PDF)
+
+**Note**: _Gitlab CI can be used to obtained similar results._
+
+### Step 5. submit
+
+Once step 4 is successful, you should end up with an HTML version published as a gh-page, as well as a PDF version (see "Other format" at the end of the table of content of the rendered HTML). This PDF version can be submitted to the [Computo submission platform](https://computo.scholasticahq.com/):
+
+<div id="scholastica-submission-button" style="margin-top: 10px; margin-bottom: 10px;"><a href="https://computo.scholasticahq.com/for-authors" style="outline: none; border: none;"><img style="outline: none; border: none;" src="https://s3.amazonaws.com/docs.scholastica/law-review-submission-button/submit_via_scholastica.png" alt="Submit to Computo"></a></div>

_quarto.yml

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+project:
+  title: "template-computo-R"
+
+
+

references.bib

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+@Preamble{ " \newcommand{\noop}[1]{} " }
+
+@Manual{R-reticulate,
+  title = {reticulate: Interface to Python},
+  author = {Kevin Ushey and JJ Allaire and Yuan Tang},
+  year = {2020},
+  note = {R package version 1.18},
+  url = {https://github.com/rstudio/reticulate},
+}
+
+@article{computo,
+  title = {Computo: reproducible computational/algorithmic contributions in statistics and machine learning},
+  author = {{Computo Team}},
+  year = {2020},
+}
+
+@Manual{R-base,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2020},
+  url = {https://www.R-project.org/},
+}
+

requirements.txt

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+jupyter
+matplotlib
+numpy