Dev #62
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Dev #62
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* WIP DRY refactoring Goal is to refactor code so that there is minimal duplication, easily extensible to enable metatranscriptomics and future Assay types, and breakout all of the functionality from the main plugin function so they can be tested properly. * Forgot to add new Step files to DRY refactor. Some Additional modifications added. * Laying out new test classes * Added support for base Step tests * Ensure output_dir is created * bugfix * Temporarily set mg-scripts dependency to development version * .gitignore fix * First test w/pseudo job-submission added. * CI Fixes * Fix for CI * debug CI. test works as intended locally * debugging CI * ci debug * ci debug * ci debug * Added test for base QCJob * Added MetagenomicStep tests * Updated testing infrastructure * Added AmpliconStep tests * flake8 * setup now points to merged mg-scripts. * Updated code to create fake files in a searchable path. * Bugfix * flake8 * Easy updates based on feedback * Removed configuration.json Removed configuration.json. Additional updates based on testing and feedback. * Merged klp_util.py into Step and klp.py based on feedback * Removed test_klp_util.py * Updates based on testing * Updates based on feedback * Changes based on feedback * Add new file * Changes based on feedback * bugfix
* Updates based on testing on qiita-rc * Updates based on feedback * Updates based on feedback * Removed sn_tid_map_by_project as a constructor parameter for Step() * flake8 * Updates based on feedback * Added test for get_special_map() * Added test_get_tube_ids_from_qiita() * Split BaseStepTests into two halves. Tests in BaseStepTests were being inherited by child BaseStepTests and run two more times (one for Amplicon and one for Metagenomic). Partitioning out general tests into a new child class allows all children to inherit configuration, but not inherit tests. * Updates based on feedback * Updates based on feedback * Migrated pipeline calls into a single function Migrated pipeline calls into a single function to preserve their sequence, offer potential alternatives, and include a debug option to not update Qiita. * Adding coveralls to project * bugfix * test coveralls * Updating coveralls * Testing codecov integration * testing codecov * Testing codecov
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