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Replace alchy with sqlservice and unfreeze SQLAlchemy

Open northwestwitch opened this issue 1 month ago • 1 comments

This PR adds | fixes:

  • Fix #251

How to prepare for test:

  • Install in a local conda env -> pip install -e . (I've tested it with python=3.8)

How to test:

  • chanjo init --auto demodata

  • Make sure it has created a directory demodata containing these 3 files: image

  • Link sample to stats -> chanjo --config demodata/chanjo.yaml link demodata/hgnc.grch37p13.exons.bed

  • Load config stats for sample1 ->chanjo --config demodata/chanjo.yaml load chanjo/init/demo-files/sample1.coverage.bed

Expected outcome:

  • [x] Get samples mean coverage -> chanjo --config demodata/chanjo.yaml calculate mean -s sample1

Review:

  • [x] Code approved by DN
  • [x] Tests executed by CR, DN
  • [ ] "Merge and deploy" approved by

This version is a:

  • [ ] MAJOR - when you make incompatible API changes
  • [ ] MINOR - when you add functionality in a backwards compatible manner
  • [ ] PATCH - when you make backwards compatible bug fixes or documentation/instructions

northwestwitch avatar May 17 '24 07:05 northwestwitch