Dev container (#36)

* Create .python-version

* Create .gitignore

* Create Makefile

* remove Dockerfile

* remove docker workflow

* startup.sh

* devcontainer

* README with link

* Update Makefile

* obsolete python-version

* Update README.md

* Update README.md

* Update README.md

* Update devcontainer.json

no browser option for devContainer

* introducing a first test

* introducing a first test

* introducing a manual release job

* introducing a manual release job

* Update README.md

---------

Co-authored-by: Jonathan Taylor <jonathan.taylor@stanford.edu>

.devcontainer/devcontainer.json

@@ -0,0 +1,22 @@
+{
+    "name": "Jupyter Environment",
+    "image": "mcr.microsoft.com/devcontainers/python:3",
+    "features": {
+        "ghcr.io/devcontainers/features/python:1": {}
+    },
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "ms-python.python",
+                "ms-toolsai.jupyter",
+                "ms-toolsai.jupyter-keymap",
+                "ms-toolsai.jupyter-renderers",
+                "ms-toolsai.vscode-jupyter-cell-tags",
+                "ms-toolsai.vscode-jupyter-slideshow"
+            ]
+        }
+    },
+    "onCreateCommand": ".devcontainer/startup.sh",
+    "forwardPorts": [8888],
+    "postStartCommand": "uv run jupyter lab --no-browser --ip=0.0.0.0 --port=8888 --NotebookApp.token='' --NotebookApp.password=''"
+}

.devcontainer/startup.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+curl -LsSf https://astral.sh/uv/install.sh | sh
+uv venv --python 3.12
+uv pip install --no-cache-dir jupyterlab
+uv pip install --no-cache-dir -r requirements.txt

.docker/Dockerfile

@@ -1,11 +0,0 @@
-FROM docker.io/jupyter/base-notebook:lab-4.0.5
-
-COPY requirements.txt .
-
-# Install Python deps, the user approach is documented here:
-# https://pythonspeed.com/articles/multi-stage-docker-python/
-RUN pip install --user --no-cache-dir -r requirements.txt
-
-COPY --chown=jovyan:users . ${HOME}/work
-
-

.dockerignore

@@ -1,5 +0,0 @@
-.github
-.git
-.docker
-.dockerignore
-*.Rmd

.github/workflows/docker.yml

@@ -1,42 +0,0 @@
-name: Publish Docker image
-
-on:
-  workflow_dispatch:
-  push:
-    branches:
-      - stable
-    tags:
-      - v*
-
-jobs:
-
-  push_to_registry:
-    name: Push Docker image to Docker Hub
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out the repo
-        uses: actions/checkout@v3
-
-      - name: Log in to Docker Hub
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@v4
-        with:
-          images: jetaylor74/islp_labs
-          tags: |
-             type=ref,event=branch
-             type=semver,pattern={{raw}}
-
-      - name: Build and push Docker image
-        uses: docker/build-push-action@v4
-        with:
-          context: .
-          file: .docker/Dockerfile
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/release.yml

@@ -0,0 +1,21 @@
+name: Bump version and publish
+
+on:
+  #push:
+  workflow_dispatch
+
+permissions:
+  contents: write
+
+jobs:
+  tagging:
+    runs-on: ubuntu-latest
+    outputs:
+      new_tag: ${{ steps.tag_step.outputs.new_tag }}
+
+    steps:
+      - name: Generate Tag
+        id: tag_step
+        uses: tschm/cradle/actions/tag@v0.1.57
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test.yml

@@ -0,0 +1,60 @@
+# testing all notebooks
+name: TEST
+
+on:
+  - push
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ['3.11', '3.12']
+        #notebook: [ Ch02-statlearn-lab.ipynb ]. # Ch02 is tricky but we have a solution for it
+        notebook: [ Ch03-linreg-lab.ipynb ]
+        #            Ch04-classification-lab.ipynb,
+        #            Ch05-resample-lab.ipynb,
+        #            Ch06-varselect-lab.ipynb,
+        #            Ch07-nonlin-lab.ipynb,
+        #            Ch08-baggboost-lab.ipynb,
+        #            Ch09-svm-lab.ipynb,
+        #            Ch10-deeplearning-lab.ipynb,
+        #            Ch11-surv-lab.ipynb,
+        #            Ch12-unsup-lab.ipynb,
+        #            Ch13-multiple-lab.ipynb]
+        #exclude:
+        #  - python-version: '3.11'
+        #    notebook: Ch10-deeplearning-lab.ipynb
+
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      #with:
+      #  version: "0.5.15"
+
+
+    #- name: Set up Python
+    #  shell: bash
+    #  run: |
+    #    uv python install ${{ matrix.python-version }}
+
+    - name: Create venv
+      shell: bash
+      run: uv venv --python ${{ matrix.python-version }}
+
+    - name: Install requirements
+      shell: bash
+      run: |
+        uv pip install --upgrade pip
+        uv pip install -r requirements.txt
+        uv pip install pytest nbmake
+
+    - name: Test
+      shell: bash
+      run: |
+        uv run pytest --nbmake --nbmake-timeout=3600 -vv ${{ matrix.notebook }}

.gitignore

@@ -49,3 +49,4 @@ share/python-wheels/
 # IDEs
 .vscode/
 .idea/
+

Makefile

@@ -0,0 +1,23 @@
+.DEFAULT_GOAL := help
+
+venv:
+	@curl -LsSf https://astral.sh/uv/install.sh | sh
+	@uv venv --python 3.12
+
+
+.PHONY: install
+install: venv ## Install all dependencies (in the virtual environment) defined in requirements.txt
+	@uv pip install --upgrade pip
+	@uv pip install -r requirements.txt
+
+
+.PHONY: help
+help:  ## Display this help screen
+	@echo -e "\033[1mAvailable commands:\033[0m"
+	@grep -E '^[a-z.A-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "  \033[36m%-18s\033[0m %s\n", $$1, $$2}' | sort
+
+
+.PHONY: jupyter
+jupyter: install  ## Install and start jupyter Lab
+	@uv run pip install jupyterlab
+	@uv run jupyter lab

README.md

@@ -1,4 +1,7 @@
 # ISLP_labs
+
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/intro-stat-learning/ISLP_Labs)
+
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
 [![All Contributors](https://img.shields.io/badge/all_contributors-4-orange.svg?style=flat-square)](#contributors-)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
@@ -11,8 +14,6 @@
 
 - Daniela Witten
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/intro-stat-learning/ISLP_labs/v2.2)
-
 ### ISLP
 
 Please ensure you have followed the installation instructions for
@@ -23,7 +24,7 @@ if necessary, which is not included as a requirement of the labs.
 ### Up-to-date version of labs for ISLP. 
 
 This repo will track labs for ISLP as their source code changes.  The
-intent is that building a conda environment with
+intent is that building a virtual environment with
 `requirements.txt` will reproduce the results in this repo.
 
 To install the current version of the requirements run
@@ -32,7 +33,7 @@ To install the current version of the requirements run
 pip install -r https://raw.githubusercontent.com/intro-stat-learning/ISLP_labs/v2.2/requirements.txt;
 ```
 
-The labs can now be run from this directory:
+The labs can now be run via:
 
 ```
 jupyter lab Ch02-statlearn-lab.ipynb