Fix PyYAML yaml.load(input) Deprecation - Githubissues

Clinical-Genomics / demultiplexing

To keep scripts associated with execution of the Illumina demultiplexing pipeline

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Fix PyYAML yaml.load(input) Deprecation #105

Closed barrystokman closed 4 years ago

barrystokman commented 4 years ago

This PR fixes PyYAML yaml.load(input) Deprecation

How to prepare for test:

[x] ssh to thamalus as hiseq.clinical
[x] install on stage: bash servers/resources/clinical-preproc.scilifelab.se/update-demux-stage.sh yaml-load

How to test:

[x] login to thalamus
[x] source activate stage
[x] run demux sheet --help

Expected test outcome:

[x] check that the warning YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. context.obj = yaml.load(config) if config else {} does not appear
[x] Take a screenshot and attach or copy/paste the output.

Review:

[x] code approved by @barrystokman
[x] tests executed by @barrystokman
[x] "Merge and deploy" approved by @barrystokman Thanks for filling in who performed the code review and the test!

This version is a:

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

barrystokman commented 4 years ago

Old code:

New code: :heavy_check_mark: