badexperiment

Convert Index of Terms to LinkML YAML.

TODOs:

convert to actual LinkML artifcats after that
convert to DataHarmonizer template

Many moving parts = bad experiment.

Development or use within the repo requires Poetry

Usage within this environment

poetry run becli

Publishing

Don't forget to update version in [tool.poetry]

Note the use of initial whitespace for keeping the PyPI password out of the zsh history. There are similar tricks for other shells like Bash.

setopt HIST_IGNORE_SPACE
export pypi_user='mamillerpa'
 export pypi_pw='<SECRET>'
poetry build
poetry publish --username $pypi_user --password $pypi_pw

Installation outside of this repo

Aggressive cleanup?

# assume we're inside a venv virtual environment
deactivate
rm -rf venv
# purge under what circumstances?
python3.9 -m pip cache purge
python3.9 -m venv venv
source venv/bin/activate
python3.9 -m pip install --upgrade pip
pip install wheel
# check status of package under development
# don't continue with installation when
pip index versions badexperiment
# installation of pandas is slow
#   platform dependent? M1 MBA
pip install badexperiment

Usage outside of this repo

becli --help

Concerns

How to create, modify and save a LinkML schema?

Preferably with schemaview
Otherwise direct linkml methods
Otherwise dict -> yaml file

Poetry autocomplete

Values trying to be set on a copy of a slice from a DataFrame

/Users/mark/sandbox/venv/lib/python3.9/site-packages/pandas/core/indexing.py:1667: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy self.obj[key] = value

/Users/mark/sandbox/venv/lib/python3.9/site-packages/badexperiment/sheet2yaml.py:119: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy slot_to_pack[coalesced] = slot_to_pack[repaired_col_name]

/Users/mark/sandbox/venv/lib/python3.9/site-packages/pandas/core/indexing.py:1732: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy self._setitem_single_block(indexer, value, name)

turbomam/badexperiment