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
poetry run becli
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
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
becli --help
- Preferably with schemaview
- Otherwise direct linkml methods
- Otherwise dict -> yaml file
/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)