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Commit a5975f3

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First commit of dev container and mkdocs (#92)
* First commit of dev container and mkdocs * Referenced correct env file * Moving to SSH remote * Add pre-commit hooks * Updated gitignore * Starting the docs * Added config for black inside pyproject.toml * Update environment file * WIP working on explaining basic probability distributions * Add networkx for PGM visualization * Starting section on PGMs. * Start of day commit to save state of previous changes * Continued on to likelihoods * Continued writing about likelihoods * Progress made to spaces of models and data * Nearly at the end for introduction piece! * Almost done with simulation nb * Updated notebooks on the basics of probability and simulation * started notebook on inference * More on the fundamentals of probability * Finished probability notebook * Finished up main prose of basic inference notebook * Add starter solutions for Inference notebooks Still left todo: - Place in better prompts - Refactor solutions out into solutions library * Massive commit adding new content - Estimation notebook is done - First pass at hierarchical model is done - Updated TOC - Ice cream shop data is ready :) * Adding further prose to hierarchical notebook Probably snuck in some other changes that I can't remember. * More updates - Shrinkage section - Funnel preview * Updated hierarchical notebook prose * Ignoring auto-generated ice cream shop trace file * Moved model out of notebook into custom source * Added notebooks on reparametrization * Started notebooks on sampling * Updating reparametrization, sampling and adding diagnostics * Restored execution of notebooks * Guaranteed execution of notebooks * Added notebook on dirichlet processes (DP) - CRP (Chinese Restaurant Process) - Stick-breaking process - Generation of Gaussian Mixtures from a DP
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‎.devcontainer/Dockerfile‎

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#-------------------------------------------------------------------------------------------------------------
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# Copyright (c) Microsoft Corporation. All rights reserved.
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# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
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#-------------------------------------------------------------------------------------------------------------
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FROM continuumio/miniconda3
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# Avoid warnings by switching to noninteractive
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ENV DEBIAN_FRONTEND=noninteractive
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# This Dockerfile adds a non-root user with sudo access. Use the "remoteUser"
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# property in devcontainer.json to use it. On Linux, the container user's GID/UIDs
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# will be updated to match your local UID/GID (when using the dockerFile property).
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# See https://aka.ms/vscode-remote/containers/non-root-user for details.
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ARG USERNAME=vscode
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ARG USER_UID=1000
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ARG USER_GID=$USER_UID
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# Copy environment.yml (if found) to a temp locaition so we update the environment. Also
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# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
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COPY binder/environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
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# Configure apt and install packages
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RUN apt-get update \
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&& apt-get -y install --no-install-recommends apt-utils dialog 2>&1 \
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#
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# Verify git, process tools, lsb-release (common in install instructions for CLIs) installed
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&& apt-get -y install git openssh-client less iproute2 procps iproute2 lsb-release \
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#
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# Install pylint
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&& /opt/conda/bin/pip install pylint \
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#
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# Update Python environment based on environment.yml (if present)
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&& if [ -f "/tmp/conda-tmp/environment.yml" ]; then /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \
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&& rm -rf /tmp/conda-tmp \
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#
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# Create a non-root user to use if preferred - see https://aka.ms/vscode-remote/containers/non-root-user.
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&& groupadd --gid $USER_GID $USERNAME \
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&& useradd -s /bin/bash --uid $USER_UID --gid $USER_GID -m $USERNAME \
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# [Optional] Add sudo support for the non-root user
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&& apt-get install -y sudo \
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&& echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME\
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&& chmod 0440 /etc/sudoers.d/$USERNAME \
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#
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# Clean up
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&& apt-get autoremove -y \
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&& apt-get clean -y \
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&& rm -rf /var/lib/apt/lists/*
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# Switch back to dialog for any ad-hoc use of apt-get
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ENV DEBIAN_FRONTEND=dialog

‎.devcontainer/devcontainer.json‎

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// For format details, see https://aka.ms/vscode-remote/devcontainer.json or this file's README at:
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// https://github.com/microsoft/vscode-dev-containers/tree/v0.117.1/containers/python-3-miniconda
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{
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"name": "Python 3 - Miniconda",
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"context": "..",
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"dockerFile": "Dockerfile",
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"terminal.integrated.shell.linux": "/bin/bash",
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"python.pythonPath": "/opt/conda/bin/python",
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"python.linting.enabled": true,
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"python.linting.pylintEnabled": true,
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"python.linting.pylintPath": "/opt/conda/bin/pylint"
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},
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": [
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"ms-python.python"
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],
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// Use 'forwardPorts' to make a list of ports inside the container available locally.
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"forwardPorts": [
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5959,
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8000,
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8888,
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8889,
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8890,
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8891,
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],
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// Use 'postCreateCommand' to run commands after the container is created.
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// "postCreateCommand": "python --version",
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// Uncomment to connect as a non-root user. See https://aka.ms/vscode-remote/containers/non-root.
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// "remoteUser": "vscode"
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}

‎.devcontainer/noop.txt‎

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This file is copied into the container along with environment.yml* from the
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parent folder. This is done to prevent the Dockerfile COPY instruction from
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failing if no environment.yml is found.

‎.gitignore‎

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# Custom
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docs/*
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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# mypy
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.mypy_cache/
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# Custom
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*.md.tmp
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.vscode/*

‎.pre-commit-config.yaml‎

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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v2.4.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- repo: https://github.com/kynan/nbstripout
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rev: master
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hooks:
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- id: nbstripout
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files: ".ipynb"
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- repo: https://github.com/psf/black
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rev: stable
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hooks:
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- id: black

‎README.md‎

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git clone https://github.com/ericmjl/bayesian-stats-modelling-tutorial
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```
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Alternatively, you can download the zip file of the repository at the top of the main page of the repository.
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Alternatively, you can download the zip file of the repository at the top of the main page of the repository.
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If you prefer not to use git or don't have experience with it, this a good option.
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## 2. Download Anaconda (if you haven't already)
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If you do not already have the [Anaconda distribution](https://www.anaconda.com/download/) of Python 3,
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go get it
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(note: you can also set up your project environment w/out Anaconda using `pip` to install the required packages;
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If you do not already have the [Anaconda distribution](https://www.anaconda.com/download/) of Python 3,
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go get it
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(note: you can also set up your project environment w/out Anaconda using `pip` to install the required packages;
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however Anaconda is great for Data Science and we encourage you to use it).
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## 3. Set up your environment
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### 3a. `conda` users
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If this is the first time you're setting up your compute environment,
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use the `conda` package manager
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to **install all the necessary packages**
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If this is the first time you're setting up your compute environment,
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use the `conda` package manager
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to **install all the necessary packages**
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from the provided `environment.yml` file.
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```bash
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### 3b. `pip` users
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Please install all of the packages listed in the `environment.yml` file manually.
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Please install all of the packages listed in the `environment.yml` file manually.
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```bash
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Navigate to the notebooks directory
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and open the notebook `01-Student-Probability_a_simulated_introduction.ipynb`.
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### 4b. Open your Jupyter notebook in Jupyter Lab!
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In the terminal, execute `jupyter lab`.
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Navigate to the notebooks directory
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and open the notebook `01-Student-Probability_a_simulated_introduction.ipynb`.
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Now, if you're using Jupyter lab, for Notebook 2, you'll need to get ipywidgets working.
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Now, if you're using Jupyter lab, for Notebook 2, you'll need to get ipywidgets working.
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The documentation is [here](https://ipywidgets.readthedocs.io/en/latest/user_install.html#installing-the-jupyterlab-extension).
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In short, you'll need node installed & you'll need to run the following in your terminal:
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### 4d. Want to view static HTML notebooks
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If you're interested in only viewing the static HTML versions of the notebooks,
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the links are provided below:
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Part 1: Bayesian Data Science by Simulation
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# Acknowledgements
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Development of this type of material is almost always a result of years of discussions between members of a community.
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We'd like to thank the community and to mention several people who have played pivotal roles in our understanding the the material:
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Michael Betancourt,
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Justin Bois,
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Allen Downey,
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Chris Fonnesbeck,
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Jake VanderPlas.
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Development of this type of material is almost always a result of years of discussions between members of a community.
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We'd like to thank the community and to mention several people who have played pivotal roles in our understanding the the material:
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Michael Betancourt,
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Justin Bois,
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Allen Downey,
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Chris Fonnesbeck,
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Jake VanderPlas.
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Also, Andrew Gelman rocks!
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# Feedback
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Please leave feedback for us [here](https://ericma1.typeform.com/to/j88n8P)!
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Please leave feedback for us [here](https://ericma1.typeform.com/to/j88n8P)!
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We'll use this information to help improve the teaching and delivery of the material.
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# data credits

‎binder/environment.yml‎

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- ericmjl
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dependencies:
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- python=3.7
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- jupyter=1.0.0
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- pymc3=3.7
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- pip=19.2.3
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- seaborn=0.9.0
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- matplotlib=3.1.1
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- numpy=1.16.4
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- scipy=1.3.1
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- pandas=0.25.1
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- jupyterlab=1.0.9
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- tqdm=4.35.0
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- missingno=0.4.2
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- scikit-learn=0.21.3
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- cython=0.29.13
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- nodejs=12.8.1
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- pyjanitor=0.18.1
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- xarray=0.12.3
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- pandoc=2.7.3
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- black=19.3b0
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- nbstripout=0.3.6
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- pylint=2.3.1
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- arviz=0.4.1
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- theano=1.0.4
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- ipykernel=5.1.2
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- hvplot=0.4.0
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- bokeh=1.3.4
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- holoviews=1.12.5
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- mkl=2019.4
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- mkl-service=2.2.0
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- jupyter
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- jupyterlab
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- pymc3
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- pip
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- seaborn
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- matplotlib
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- numpy
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- scipy
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- pandas
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- tqdm
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- missingno
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- scikit-learn
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- nodejs
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- pyjanitor
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- xarray
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- pandoc
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- black
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- nbstripout
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- pylint
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- arviz
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- theano
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- ipykernel
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- hvplot
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- bokeh
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- holoviews
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- mkl
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- mkl-service
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- pre-commit
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- networkx
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- mamba
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- pyprojroot
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- faker
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- pip:
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- mkdocs
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- mkdocs-material
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- mknotebooks
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- daft
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# Need to add pip install from github for repo, so solutions can be executed.

‎data/.gitignore‎

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ice_cream_shop_hierarchical_posterior.nc

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