How to run the Python code for the Statistical Rethinking book (Python / Jupyter / PyMC3)

kovachwt / tidytuesday

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How to run the Python code for the Statistical Rethinking book (Python / Jupyter / PyMC3) #1

Open kovachwt opened 4 years ago

kovachwt commented 4 years ago

Step 1. Download Anaconda from https://www.anaconda.com/ (click to enlarge the animated images)

1_download_anaconda

kovachwt commented 4 years ago

Step 2. Install Anaconda

2_install_anaconda

kovachwt commented 4 years ago

Step 3. Download the code from Github: https://github.com/pymc-devs/resources/archive/master.zip

3_download_from_github

kovachwt commented 4 years ago

Step 4. Unpack the downloaded zip file to your Documents folder

4_unpack_resources

kovachwt commented 4 years ago

Step 5. Setup the Anaconda environment:

copy the full path of the "Rethinking" folder which is a subfolder of "resources-master"
start a new Anaconda Prompt (Anaconda3)
type "cd " followed by the path that is in your clipboard (right click to paste) and press ENTER
type in the following command: conda env create -f environment.yml

5_setup_conda

kovachwt commented 4 years ago

Step 6. Looks like not everything got installed properly by the automatic process, so let's manually install the required Python packages:

start a new Anaconda Prompt (Anaconda3)
type the following command and press ENTER: conda activate stat-rethink-pymc3
type the following command and press ENTER: pip install pymc3 arviz

6_install_packages

kovachwt commented 4 years ago

Step 7. You should be able to launch Jupyter now and run the Python code for reach chapter in it.

Find "Jupyter Notebook (stat-rethink-pymc3)" in your Start Menu and launch it
Open the Documents > resources-master > Rethinking folder
Launch a chapter python notebook file (like Chp_02.ipynb)

7_launch_jupyter

kovachwt commented 4 years ago

Step 8. When you run the first chunk of code, your will probably get some Theano warnings, and the code will be slow. Here is how to resolve that:

first close the Jupyter process window
start a new Anaconda Prompt (Anaconda3)
type the following command and press ENTER: conda activate stat-rethink-pymc3
type the following command and press ENTER: conda install -y anaconda m2w64-toolchain libpython

8_speedup

kovachwt commented 4 years ago

That's it! Next time you launch Jupyter it should work without showing any warnings...

kovachwt commented 4 years ago

Update: You can install Visual Studio Code and run the Jupyter notebooks there. Download from here: https://code.visualstudio.com/ Install it, and after installing you will need the Python extension.

install_vscode_plugin