Added template license, readme, action to render quarto to GH Pages (#1)

Added template license, readme, action to render quarto to GH Pages
https://github.com/pranavmishra90/project-template/tree/develop

.datalad/config

@@ -1,8 +1,12 @@
 [datalad "dataset"]
-	id = f9026e7b-8c71-4092-ba3a-72408294523c
+  id = f9026e7b-8c71-4092-ba3a-72408294523c
 
 [datalad "ui"]
-        suppress-similar-results = off
+  suppress-similar-results = off
+  progressbar=tqdm
+
+[datalad "save"]
+  no-message=interactive
 
 [push]
-        autoSetupRemote = true
+  autoSetupRemote = true

.devcontainer/devcontainer.json

@@ -9,6 +9,9 @@
     "updateRemoteUserUID": true,
     "forwardPorts": [3334],
     "postCreateCommand": ["/bin/bash"],
+    "containerEnv": {
+        "ENV_NAME": "base"
+    },
 
     // If you need GPUs to be passed into the devcontainer, uncomment the following line
     // "runArgs": ["--gpus", "0"],

.github/workflows/test-quarto-publish.yml

@@ -0,0 +1,46 @@
+on:
+  push:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}
+  cancel-in-progress: true
+
+name: Render and Publish
+
+# you need these permissions to publish to GitHub pages
+permissions: 
+    contents: write
+    pages: write
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+
+      - uses: actions/setup-python@v4
+        name: Install python packages
+        with:
+          python-version: '3.11'
+      - run: pip install jupyter jupyter-cache
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tinytex: true 
+          # version: SPECIFIC-QUARTO-VERSION-HERE
+
+
+      # Remember, you have to first run `quarto publish gh-pages` locally 1 time to initilize this branch
+      - name: Publish to GitHub Pages (and render) 
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # this secret is always available for github actions

.pre-commit-config.yaml

@@ -0,0 +1,18 @@
+repos:
+  - repo: "https://github.com/pre-commit/pre-commit-hooks"
+    rev: v4.6.0
+    hooks:
+      # Lint files
+      - id: check-yaml
+      - id: check-json
+        exclude: |
+            (?x)^(
+                .devcontainer/devcontainer.json|
+                exclude.this.file
+            )$
+      - id: mixed-line-ending
+        args: ["--fix=lf"]
+      # Prevent adding private keys in files
+      - id: detect-private-key
+      # Detect problematic referenced files
+      - id: check-symlinks

_quarto.yml

@@ -5,6 +5,7 @@ project:
         - "*.qmd"
         - "*.md"
         - "docs/"
+        - "!readme.md"
 
         # Do not render
         - "!code/"
@@ -15,23 +16,23 @@ project:
         timeout: 300
 
 website:
-    title: "Facsimilab - Template for Datalad Datasets"
+    title: "FacsimiLab - Project Template for Datalad Datasets"
     navbar:
         search: true
         left:
             - text: Home
-              href: readme.md
+              href: index.qmd
             - text: About
               href: notebook/about.qmd
     open-graph: true
     sidebar:
         style: "docked"
         contents: auto
     reader-mode: true
-    repo-url: https://github.com/FacsimiLab/datalad-dataset-template
+    repo-url: https://github.com/FacsimiLab/project-template
     repo-actions: [issue, edit]
     repo-link-target: "_blank"
-    page-footer: "Copyright 2024: Pranav Mishra"
+    page-footer: "Copyright 2024: Pranav Kumar Mishra"
 
 bibliography:
     - ./notebook/references.bib

index.qmd

@@ -0,0 +1,24 @@
+---
+execute:
+  echo: false
+  output: asis
+---
+
+
+<!-- Automatically render the readme as the index page -->
+
+```{python}
+with open("readme.md", "r") as file:
+    markdown_content = file.read()
+
+    print(markdown_content)
+
+import datetime as date
+
+print("------")
+print("<br>")
+
+print(f"This page was generated automatically from the repository `readme.md` on {date.datetime.now()}")
+```
+
+

licenses/FacsimiLab-Project-Template-Repository.md

@@ -0,0 +1,23 @@
+# FacsimiLab Template
+
+### MIT License
+
+Copyright (c) 2024 Pranav Kumar Mishra
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

licenses/readme.md

@@ -14,6 +14,9 @@ listing:
 
 The repository code, unless otherwise specified, is licensed under the [MIT License](./MIT-license.md).
 
+
+Note: This repository was generated using the [FacsimiLab project template repository](https://github.com/FacsimiLab/project-template) created by [Pranav Mishra](https://drpranavmishra.com), which is licensed under the [MIT License](./FacsimiLab-Project-Template-Repository.md).
+
 ## Repository Media
 
 <img alt="media_CCBY4" src="https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2Fpranavmishra90%2Fbadges%2Fmain%2Fone-sided-badge/media_CCBY4.json&color=3e4c75">
@@ -28,10 +31,11 @@ This repository uses code and/or files from other sources. You can find the lice
 
 All other works in this repository are copyrighted without explicit useage / sharing permissions from the authors.
 
-### Copyright © 2024 Pranav Kumar Mishra (Rush University, Chicago, IL, USA)
+### Copyright © 2024 Pranav Kumar Mishra
 
 ---
 
+
 ## List of Licenses {#sec-licenses-list}
 
 :::{#licenses-list}

readme.md

@@ -1,9 +1,14 @@
-# Dataset template for reproducible research
+# [`FacsimiLab`] Project Template for Reproducible Research
 
-# Licensing
+## Project Details
 
-## Default copyright
+This is a datalad repository for the **FacsimiLab** project. Additional dataset information to go here.
 
-All works (research data) in this repository, unless otherwise specified, are copyrighted without explicit useage / sharing permissions from the author(s). Please visit [Licenses](licenses/readme.md) for further details
 
-**Copyright © 2024 Pranav Kumar Mishra (Rush University, Chicago, IL, USA)**
+## Licensing
+
+**Default copyright**
+
+All research data in this repository, unless explicitly stated otherwise, is protected by copyright and does not include permissions for use or sharing from the author(s). This includes raw data, analysis / intermediate data, and research output data. Code, select source files, and specific research output may have other licenses. For more information, please consult the [Licenses](licenses/readme.md) section.
+
+**Copyright © 2024 Pranav Kumar Mishra**