chanjo
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Replace alchy with sqlservice and unfreeze SQLAlchemy
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: -
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