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>
This commit is contained in:
Thomas Schmelzer
GitHub
22
.devcontainer/devcontainer.json
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22
.devcontainer/devcontainer.json
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@@ -0,0 +1,22 @@
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{
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"name": "Jupyter Environment",
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"image": "mcr.microsoft.com/devcontainers/python:3",
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"features": {
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"ghcr.io/devcontainers/features/python:1": {}
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},
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"customizations": {
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"vscode": {
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"extensions": [
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"ms-python.python",
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"ms-toolsai.jupyter",
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"ms-toolsai.jupyter-keymap",
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"ms-toolsai.jupyter-renderers",
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"ms-toolsai.vscode-jupyter-cell-tags",
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"ms-toolsai.vscode-jupyter-slideshow"
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]
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}
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},
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"onCreateCommand": ".devcontainer/startup.sh",
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"forwardPorts": [8888],
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"postStartCommand": "uv run jupyter lab --no-browser --ip=0.0.0.0 --port=8888 --NotebookApp.token='' --NotebookApp.password=''"
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}
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5
.devcontainer/startup.sh
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.devcontainer/startup.sh
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#!/bin/bash
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curl -LsSf https://astral.sh/uv/install.sh | sh
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uv venv --python 3.12
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uv pip install --no-cache-dir jupyterlab
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uv pip install --no-cache-dir -r requirements.txt
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@@ -1,11 +0,0 @@
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FROM docker.io/jupyter/base-notebook:lab-4.0.5
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COPY requirements.txt .
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# Install Python deps, the user approach is documented here:
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# https://pythonspeed.com/articles/multi-stage-docker-python/
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RUN pip install --user --no-cache-dir -r requirements.txt
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COPY --chown=jovyan:users . ${HOME}/work
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@@ -1,5 +0,0 @@
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.github
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.git
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.docker
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.dockerignore
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*.Rmd
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.github/workflows/docker.yml
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.github/workflows/docker.yml
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name: Publish Docker image
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on:
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workflow_dispatch:
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push:
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branches:
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- stable
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tags:
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- v*
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jobs:
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push_to_registry:
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name: Push Docker image to Docker Hub
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runs-on: ubuntu-latest
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steps:
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- name: Check out the repo
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uses: actions/checkout@v3
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- name: Log in to Docker Hub
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uses: docker/login-action@v2
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with:
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username: ${{ secrets.DOCKER_USERNAME }}
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password: ${{ secrets.DOCKER_PASSWORD }}
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@v4
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with:
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images: jetaylor74/islp_labs
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tags: |
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type=ref,event=branch
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type=semver,pattern={{raw}}
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- name: Build and push Docker image
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uses: docker/build-push-action@v4
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with:
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context: .
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file: .docker/Dockerfile
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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21
.github/workflows/release.yml
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.github/workflows/release.yml
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name: Bump version and publish
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on:
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#push:
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workflow_dispatch
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permissions:
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contents: write
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jobs:
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tagging:
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runs-on: ubuntu-latest
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outputs:
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new_tag: ${{ steps.tag_step.outputs.new_tag }}
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steps:
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- name: Generate Tag
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id: tag_step
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uses: tschm/cradle/actions/tag@v0.1.57
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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60
.github/workflows/test.yml
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.github/workflows/test.yml
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# testing all notebooks
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name: TEST
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on:
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- push
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jobs:
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.11', '3.12']
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#notebook: [ Ch02-statlearn-lab.ipynb ]. # Ch02 is tricky but we have a solution for it
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notebook: [ Ch03-linreg-lab.ipynb ]
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# Ch04-classification-lab.ipynb,
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# Ch05-resample-lab.ipynb,
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# Ch06-varselect-lab.ipynb,
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# Ch07-nonlin-lab.ipynb,
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# Ch08-baggboost-lab.ipynb,
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# Ch09-svm-lab.ipynb,
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# Ch10-deeplearning-lab.ipynb,
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# Ch11-surv-lab.ipynb,
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# Ch12-unsup-lab.ipynb,
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# Ch13-multiple-lab.ipynb]
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#exclude:
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# - python-version: '3.11'
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# notebook: Ch10-deeplearning-lab.ipynb
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fail-fast: false
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steps:
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- uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v5
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#with:
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# version: "0.5.15"
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#- name: Set up Python
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# shell: bash
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# run: |
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# uv python install ${{ matrix.python-version }}
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- name: Create venv
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shell: bash
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run: uv venv --python ${{ matrix.python-version }}
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- name: Install requirements
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shell: bash
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run: |
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uv pip install --upgrade pip
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uv pip install -r requirements.txt
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uv pip install pytest nbmake
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- name: Test
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shell: bash
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run: |
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uv run pytest --nbmake --nbmake-timeout=3600 -vv ${{ matrix.notebook }}
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1
.gitignore
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1
.gitignore
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# IDEs
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.vscode/
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.idea/
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23
Makefile
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Makefile
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.DEFAULT_GOAL := help
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venv:
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@curl -LsSf https://astral.sh/uv/install.sh | sh
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@uv venv --python 3.12
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.PHONY: install
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install: venv ## Install all dependencies (in the virtual environment) defined in requirements.txt
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@uv pip install --upgrade pip
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@uv pip install -r requirements.txt
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.PHONY: help
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help: ## Display this help screen
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@echo -e "\033[1mAvailable commands:\033[0m"
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@grep -E '^[a-z.A-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf " \033[36m%-18s\033[0m %s\n", $$1, $$2}' | sort
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.PHONY: jupyter
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jupyter: install ## Install and start jupyter Lab
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@uv run pip install jupyterlab
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@uv run jupyter lab
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# ISLP_labs
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[](https://codespaces.new/intro-stat-learning/ISLP_Labs)
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<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
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[](#contributors-)
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<!-- ALL-CONTRIBUTORS-BADGE:END -->
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@@ -11,8 +14,6 @@
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- Daniela Witten
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[](https://mybinder.org/v2/gh/intro-stat-learning/ISLP_labs/v2.2)
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### ISLP
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Please ensure you have followed the installation instructions for
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@@ -23,7 +24,7 @@ if necessary, which is not included as a requirement of the labs.
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### Up-to-date version of labs for ISLP.
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This repo will track labs for ISLP as their source code changes. The
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intent is that building a conda environment with
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intent is that building a virtual environment with
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`requirements.txt` will reproduce the results in this repo.
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To install the current version of the requirements run
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@@ -32,7 +33,7 @@ To install the current version of the requirements run
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pip install -r https://raw.githubusercontent.com/intro-stat-learning/ISLP_labs/v2.2/requirements.txt;
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```
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The labs can now be run from this directory:
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The labs can now be run via:
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```
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jupyter lab Ch02-statlearn-lab.ipynb
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