plugins should live in plugins.py
#419
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donaldcampbelljr
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plugins.py? they were a bit hard for me to locate where they currently are.plugins.py
donaldcampbelljr
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Oct 10, 2023
donaldcampbelljr
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* added new config docs * Remove --toggle key. Add logic during fetch samples for toggle. Remove checking for toggle off during sample submission (redundant). #263 * Remove toggle key constants. Apply formatting. #263 * Remove toggle key property. Simplified logic for fetching samples. #263 * fix pephub failing tests * cleaned up more to help pass pytests * distutils.dir_util for shutil for python 3.12 * added divvy entry point inside looper * black format * another black reformat * added docs * clean up based on feedback * clean up based on feedback * removed redundancy * black fmt * added divvy inspect * black fmt * added sub cmd, docker args * added line break for inspect output * added divvy docs #343 * added divvy docs #343 * divvy docs fix * mkdocs fix * Fixed mkdocs error * Update requirements-doc.txt * updated reqs-doc * merge mistake fix * added divvy imgs * added new looper init * added to changlog, fix divvy imgs * divvy readme img fix * fixed initialization of generic piface * fixed initialization of generic piface * added tests * fixed main setup * Update how_to_define_looper_config.md * Update __init__.py * Update test_other.py * Ise * added changelog and minor naming changes * remove old logging function * dev version bump * fix typo in html_report and upgraded pandas requirements for pephubclient * fixed requirements * fixed docs requirements * added versioneer to doc requirements * added Cython to doc requirements * added readthedocs config * added looper to requirements docs * allow for using pipestat.summarize, align with pipestat 0.4.0 * clean up code, update usage doc * update doc requirements pephubclient * downgrade docs to 3.10 * adjust get_status to use proper sample_name if pipestat configured #326 * adjust conductor to retrieve pipestat manager variables with pipestat 0.4.0 refactoring. * Allows skipping some tests if run offline. Closes #370 * work on using test_args instead of subprocesses * Finish switching applicable tests away from subprocess * Lint and update doc string to test_args_expansion * Change return type. * lint * add test for var_templates #357, and clean up tests * attempt simple check to see if provided pipelines are callable #195 * minor adjustments, polished docstring * work on new peppy * update changelog * lint * update version to 1.5.0 * update changelog * update reqs and changelog to use pipestat v0.5.0 * more work on peppy without attmap * Refactoring for looper config * added looper config file argument * code fix * Added comment about deprecating for old looper specification * fixed looper init error * change logo for docs build tab icon * fix favicon * update docs and changelog for 1.5.0 release * - fix `looper table` failing without sample.protocol , update change log for point release * fix "--looper-config" * update version and changelog date * adjust pipestat requirement to be >=0.5.1 * lint * clarify message on rereun * dev version flag * version bump to 1.5.2-dev * fix indentation * fix message logic * improve rerun messaging * use f strings * default msg * fix error message. * clean up divvy docs. Fix #393 * add expanding paths in read_looper_config_file * Is this the fix for #398? * fix some item attr confusion * lint * Adjust dry run submission reporting * oops * more attr fixes * lint * initial poc for rewiriting classes to return dict for pytests * more test changes * test polish * use logmuse for all logging msgs * typo * reduce runp and collator tests * Skip Checker related tests until CheckerOld is deprecated * remove divvy dependence on attmap * expand submission paths correctly * Update requirements pephubclient * refactor CLI code * clean up imports * cli imports cleanup * final cli polish, linting * have self.debug use consts and clean up structure * add imports to cli_divvy * Add pipestat configuration exception to sub commands and tests * first pass at refactoring prj.pipestat_configured_project prj.pipestat_configured * fix utils import * fix tests, lint * add pipeline type for looper table * add sample_level stats for looper table * fixed relative path * fixed tests and updatd documentation * added docstring to test * remove unused code * tweak sample_level pipestat retrieval * remove CheckerOld * Fixed #410 * Fixed #395 * change destroy_summary to use pipestat configuration and pipestat functions * add --project default for destroy command and rename funcs for disambiguation * remove html_reports and update imports. * add pipestat compatible pep for pytesting and associated test. * adjust pytest fixture. * add new pytests for pipestat configurations, re-implement Check tests * change LOGGER.warn to LOGGER.warning due to deprecation * change function name for copyfile, remove todos. * attempt to change the way looper gets pipestat configuration, tests broken * fix broken tests and file path issues * fix config_file namespace and pep-config issue * add plugin * Pipestat polish (#412) * fix pep-config issue * pass output_dir to pipestat #411 and # 390 * adjust building looper namespace * revert to using pipestat config path, tests broken * fix tests by reverting some changes * allow sample name to be passed during config check, raise value error if no pipestat config * pass sample name only * resolve schema path based on pipestat config * clean test and allow pipestat namespace to include config_file path * remove unnecessary pipestat namespace key value pairs * Attempt constructing a pipestat config file from looper config and piface and then writing to file. Tests broken. * fix tests * general clean up * remove sample name during pipestat creation * remove redundancy * lint * clean up comments * fix runp for pipestat and add to pytest * add information to looper's pipestat documentation. * Update changelog * 406 relative path (#408) * Changed relative path to project config * lint * fixed failing test * fixed failing test * merge from dev and fix conflicts --------- Co-authored-by: nsheff <[email protected]> Co-authored-by: Donald Campbell <[email protected]> * add info on looper report and point to pepatac example #41 * update looper to reflect pipestat's refactor from sample_name to record_identifier * use pipestat to set status to 'waiting' if rerunning a failed sample. #169 * update pipestat and yacman versions to alpha and dev versions in requirements. * update yacman to be released v0.9.2 * resolve pipestat module imports * update eido 0.2.1 and peppy to pre-release version * skip test failing on GitHub for now. * modify test skip to include entire class. * lint * revert change per discussion: #420 * change naming of generated pipeline_interface.yaml #417 * add clarification in docs for accessing sample.sample_yaml_path and sample.sample_yaml_cwl #421 * move plugins to `plugins.py` #419 * Added writing output_schema and count_lines.sh when initializing a pipeline interface #418 * begin work on looper link #72 * continue looper link, now functional #72 * allow access for looper.pep_config #424 * fix accessing looper.pep_config #424, add building out looper namespace based on config file #423 * add better error message for #397 * fix pipestat import * remove sample_name and project_name from pipestat_namespace in favor of record_identifier * update pipestat req * update pipestat req for newest alpha release * update changelog.md * update project definition docs * update pipeline-interface-specification.md * update parameterizing-pipelines.md and initialize.md * misc documentation corrections * update usage.md * update hello-world example * 2nd pass on docs * add clarification for sample_modifiers and configuring project * fix for #427 * implement path expansion during pipestat configuration check * print link directory to terminal after using looper link * print report directory to terminal after using looper report * change schema_path to output_schema for pipestat config * update docs schema_path to output_schema for pipestat config * fix key error with populate_sample_paths * allow rewriting looper config even if it exists * only pass sample_name as record_identifier if it is given * add default_project_record_identifier if using {record_identifier} in pipestat config * fix #428 * fix pep_config not populating during runp * remove redundant pep_config arg * fix bug with path expansion during config read * pass looper's samples to pipestat summarize * WIP attempt at selector-flag #126 * more progress, works for selection #126 * Add tests, both selection and exclusion based on flags now works #126 * fix path issue for items with underscores #126 * ignore flags if slecting on flags, change sel and exc to have nargs="*" * update docs * add more tests for selecting attributes in tandem with flags #126 * fix project typo in docs * version bump for prerelease 1.6.0a1 and add pipestat req v0.6.0a9 * 2nd attempt add pipestat req v0.6.0a9 * bump to 1.6.0a2 * fixes #430 and adds corresponding tests * Updates for new peppy * lint * basic tab completion for initial commands #422 * polish docs for tab completion #422 * lint * potential fix pepkit/peppy#459 * Revert "potential fix pepkit/peppy#459" This reverts commit 281cef4. * version 1.6.0a3 pre-release * v1.6.0 release prep --------- Co-authored-by: Khoroshevskyi <[email protected]> Co-authored-by: Donald C <[email protected]> Co-authored-by: ayobi <[email protected]>
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should plugins live in
plugins.py? they were a bit hard for me to locate where they currently are.The text was updated successfully, but these errors were encountered: