95 fix docstring for with columns #98
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giuliabaldini
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* Update to 3.8 because of numpy security update (#64) * Update to 3.8 because of numpy security update * Remove openpyxl because 3.7 is not supported anymore * 33 convert basic bundle collection to generator (#60) * Convert functions to return generators * Update readme * Add more tests * Remove pyrohealth from tests because it is currently not working * Add another type ignore for function * Remove all fhirpathpy import tries * Update example 4 * Change functions used in public tests * Fix problems with trade_rows_for_dataframe_with_ref and mypy issues * Update example 2 * Update example 1 * Fix tqdm text name * Update example 2&4 * Update example 3 * Re-add none case to reset empty lists in fhirpaths * Add history support (#74) * 8 add handling for dataframe functions using (#72) * Remove initial reference name in df_constraints if the search parameter is _id * Add error if there are None values in a DF constraint column * Bump up version because of incompatibility * Add pipe for system only if the first element of the df_contraints is a URL * Update README.md * Fix Error for Paging when the URL changes from HTTP to HTTPS (#78) * Fix the bug by introducing a new variable that contains the domain * Add forgotten regex group and add test * Update README.md * 75 allow specifying multiple query arguments in df contraints (#76) * Add option to have multiple values for df_contraints keys * Working now, I did not remember the structure that should be expected, which also explains why mypy was not happy with it * Fix error for history, since it always expected a string instead of a list of strings * Add conversion to string when adding identifiers * Add more tests * Make tests less time-consuming * Update README.md * Update README.md * Create CITATION.cff * Update CITATION.cff * Update CITATION.cff * Update README.md * Fix CITATION.cff * Add version attribute to init (#80) * Check for file existance and return a warning and none in fix_mapping_dataframe (#82) * Update pyproject.toml * Update CITATION.cff * Fix readme error due to changes in code * Update CITATION.cff * Update CITATION.cff * 83 allow turning off checks for dicom download (#85) * Add turn of checks option * Make the continue statement depend on the turn_off_checks variable * Add resource name to the TQDM description (#88) * 84 merge trade rows for dataframe and trade rows for dataframe with ref (#89) * Merge trade_rows_for_dataframe and trade_rows_for_dataframe_with_ref * Update version * Modify tests * Update notebooks * 86 allow addition of any column to the trade rows for dataframe result (#90) * Update version * Add the option of adding to the output DF of trade_rows_for_dataframe any input column * Add the option of renaming the columns * Add space in warning * Remove blank lines * Make pre-commit up to date with pyproject * Remove version 3.7 from automatic tests and add 3.10 * 91 add merge on option to steal bundles to dataframe (#92) * Add merge_on to all dataframe functions * Modify mypy command in github workflows * Add directory for mypy check * Fix file after wrong conflict resolving * Fix readme * Fix readme hyperlink * Fix consistency in README * Update CITATION.cff * Update pyproject.toml * Update authors in readme * Update CITATION.cff * Update poetry in github actions * 95 fix docstring for with columns (#98) * Fix link to part of readme * Add docstring about with_columns * Improve spacing in docstring * Test for mypy * Check if the error depends on 3.10 * Update packages and try again with 3.10 * Set 3.10.6 as py version * Add type ignores * Add type ignores * Update version * 100 force read action on (#101) * Force read request for IDs * Update the bundle processing to go through the resources * 96 add format options for dicomdownloader (#99) * Add the possibility to always save in the study folder * Add new formats to store the downloaded data * Update README.md * Update README.md * Convert logging.warn to warnings when appropriate (#105) * Standardize bundles for read and search (#106) * Update CITATION.cff * Update CITATION.cff * 104 smarter caching (#107) * First draft of http caching * Improve docstrings * Add a couple of todos * Add retry option and custom create_key parameter for caching * Sort request params to ensure same order for caching * Update CITATION.cff * 111 make current beta compatible with 010 (#112) * Bump up version * Add query_to_dataframe function to ensure compatibility with v0.1.0 * Fix text in examples * Fix parameter inconsistency in query_to_dataframe§ * Update tests with query_to_dataframe * Adjust tests * 94 efficiency problem with merge on (#113) * Remove the merge on parameter and return one dataframe per resource * Filter out none values directly from the returned records * Modify bundle_to_dataframe to take the union of all processed bundles per resource * Adjust tests * Different outputs for query_to_dataframe * Remove always return dict overwrite, that may kill everything * Update pyproject.toml * Make fhirpathpy input greedy (#116) Co-authored-by: Giulia Baldini <Giulia.Baldini@uk-essen.de> * Update pyproject.toml --------- Co-authored-by: Giulia Baldini <Giulia.Baldini@uk-essen.de>
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