Python at Recursion

Installing a new python version

I get errors after a new pyenv install X that I don’t get on versions I’ve been using awhile (e.g. 3.9.15). This section is attempting to collect all the commands I ran over time to make new versions work.

1. Confirm new version is active with pyenv version

• If not, activate new version with pyenv local X or pyenv global X

2. Solve clang error…how?
3. Run pip install -U 'roadie[cli]'

Set up a new Python project on my laptop

1. Confirm desired pyenv version is active with pyenv version
2. Confirm roadie is installed and up-to-date with pip install -U 'roadie[cli]'
3. Create venv by running roadie venv

• or run my rv alias (which runs pip install -U 'roadie[cli]' && roadie venv, which creates new pyenv shell case)
• It’s safe to delete a project’s venv folder(s) + rerun the above steps anytime (e.g. if dependency-related issues come up and seem difficult to debug).
• The rv alias is safe to rerun anytime.

4. Update my venv, edit and run aliases to include cases for this project

Links:

• Developing Python at Recursion • recursionpharma/rxrx-python

Updating Python dependencies

• Update the lock file by running roadie lock or roadie lock -c to update everything

Pandas DataFrames

• Series = entire column
  • you can modify an entire column at once with a single expression (e.g. line 63 of phenoapp/plots/heatmap/__init__.py):
    • plot_value = plotdf.distance * COLOR_DARKENING_FACTOR — this multiplies every cell in the “distance” column by the darkening factor and returns the modified series (kind of like an Array.map)

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