Linting and pre-commit #15
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afrubin
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Feb 6, 2025
* define specific CRUD functions * add imports * create class inheriting base client, add doc strings, define get_experiment * initial get_experiment docstring * return experiment model instance * define get_scoreset * return scoreset model instance * define post_experiment and post_scoreset, docstring and return for post_experiment * return confirmation of post scoreset * delete duplicated code * instantiate base client object * update get_experiment function signature * update get_experiment docstring * edit parameter named in get_experiment docstring * edit return value for get_experiment * update variable name in return statement * update get_scoreset function signature * update get_scoreset docstring description * edit get_scoreset docstring parameters * edit get_scoreset docstring return value * update parameters passed in return statement * update create_experiment method signature * update create_experiment docstring description * update parameters in docstring * change variable name in return statement * update create_scoreset function signature * update create_scoreset docstring description * update create_scoreset docstring parameters * change variable name in return statement * add docstring to BaseClient * add docstring to Client object * reformat * delete unused imports * edit return type * error is defined in self * add init file * delete redundant code files * edit return type * edit variable names to match json dict keys from API response * edit variable names and mark new variables TODO, see where they should go * mark new variables TODO, see where they should go * edit variable names * edit variable names, comment out variables not seen in json API response * edit variable names to align with key values in json API response * mark variable TODO as potentially optional * edit arguments * edit docstring parameters * edit docstring returns * set model urn * edit return value and function parameters * edit method docstring parameters and return values * set model url * add note to include mavecore validation * fix typo * edit request * note where to include next request * edit return type * delete imports * edit method return values * edit method docstring parameters and return values * edit method docstring parameters and return values * edit method return values * edit method return values * change function signature * fix typo * delete output * fix typo * change base url * edit method call * change print type * change version * delete output * edit base url * change method call * edit print type * change version * fix typo * clear output * edit import * change base url * edit experiment format * post experiment * change version * update function signatures to be more readable * update docstrings to reflect changes to function signatures * update docstrings to reflect changes to function signatures * update return description within docstrings * change instance_url * document additional error handling * change error message * set urn to None * handle case where scores_df should not be None * update request to reflect changes in API * set urn after post request * add additional request for data files to reflect changes in API * log a successful request * return urn * import logging * change method called * change method called * note where validation should occur and change method called * edit function signature to be more readable * edit docstring to reflect changes to function signature * document added error handling * add error handling and note where validation should occur * set file_upload as dictionary * create async client * simple create dataset * simple get dataset * delete file * create scoreset easy * get scoreset easy * get experiment easy * create experiment easy * edit title * edit text inaccuracies * edit imports * edit url * add detail to markdown * remove redundant comment * delete cell * remove comment * add markdown cell * edit print statement * change function called in code block * edit title * edit imports * remove cells * edit client instantiation * edit markdown text * create scoreset client * reset cells * edit import * edit imports * edit markdown * delete cells * edit client instantiation * mak markdown text more readable * make docstring more readable * edit imports * add session attribute to client * define async functions * edit exceptions * configure requests for asyncio * edit docstring to be more readable * edit imports * define functions as asynchronous * add init file * create client async notebooks * change session instantiation * delete methods, add await to return * edit imports * add await to return * define and implement get_scoresets and run methods with new client sessions * add await to return * add await to return * edit imports * edit test urn * call async methods * print results * define and implement get experiments * define and implement create experiments * define and implement create scoresets * correct saving of URN * change argument name * update async client documentation * update base url * dont exit when error occurs * update base url * dont exit when error occurs * add note * automatically set base url in easy api * update jupyter notebooks for creating multiple experiments * update jupyter notebooks for easy api create experiment * update jupyter notebooks for easy api get experiment * update jupyter notebooks for easy api create scoreset * update jupyter notebooks for easy api get scoreset * update jupyter notebooks for getting multiple scoresets * update jupyter notebooks for getting multiple experiments * update jupyter notebooks for creating multiple scoresets * dont require base url in easy api * update urn * rename python notebooks * edit imports * edit url to reflect changes in API * update requests to httpx, add debugging print statements, mark TODO to resolve requests error * reformat * resolve timeout error, change requests to httpx * remove debugging print statements * change requests to httpx * edit imports * display errors in understandable way, remove requests module comments * set ssl context for async requests * set ssl context to resolve certificate error * update imports * add async requests to easy api * add async POST requests to easy api * edit imports * edit imports * update url to reflect changes in API * reformat files * display errors in readable way * Release/0.3.0 (#12) * Upload API convenience fixes (#9) (#10) * return the HTTP response when posting a model * drop internal MaveDB attributes * make virtual method explicit * update authors * update version * update version * use pyproject.toml * drop local validators * fix deps * API client rewrite (#13) * drop local validators * fix deps * remove non-async client * add missing deps * remove BaseClient class in favor of a single Client class * read the API url from an environment variable if not passed in * minor syntax changes to deal with warnings * update test case since rna isn't supported * deduplication fix and test fixes * add mavedb requirement * refactor of API client creation and get method * refactor dataset submission by POST * delete thin wrapper functions * allow get operations for private datasets * make record type checking accept camel or snake case * drop the basic wrappers that create a client for each call * added local validation for dataframes * add docstring * Linting and pre-commit (#15) * drop local validators * fix deps * add pre-commit hooks and linting options * black formatting * bump version * delete old models that are now imported from mavedb-api * delete old examples and data * undo bump version * clean up docs for removed code * update to new API naming convention for score sets * updates to imports to match latest mavedb version * change to src/ layout * use pyproject for flake8 * remove some locally maintained utility functions * remove outdated/redundant functions * minor refactor and remove unused tests * clean up old enrich seqid conversion code * add coverage to dev requirements * drop unused import * update codon sub to create a variant object instead of a string * update infer_record_type for field name change * remove local df validation until it can be updated * don't use http keepalive to avoid disconnect errors * add trailing slashes to urls * add project.license * update copyright * add missing dependencies * clean up docs for new version * update badges * update pre-commit versions * add required server dependencies for validation * add version check function * add isort to precommit * run isort * add isort options to pyproject.toml * add flake8-bugbear * remove Enrich2-only tests from base * flake8 cleanup * flake8 compliance * documentation updates for new version --------- Co-authored-by: harmatt <79935163+harmatt@users.noreply.github.com>
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