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build: create independent environment files #111

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build: create independent environment files #111

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@deliaBlue deliaBlue commented Sep 19, 2023 •
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This PR makes the following changes:

  • Create four independent environment files
  • Update README with the correct installation steps
  • Update CI to meet the changes
  • Update the gffutils micro-environment version
  • Add nodefaults channel in the environment files (to avoid the defaults channel included by GitHub)

@deliaBlue
build: set correct channel in environment.root.yml
a538d30 
The installation fails when the channel is `Bioconda` and the user has the `priority_channel` set to `strict`.
@deliaBlue deliaBlue requested a review from uniqueg September 19, 2023 10:35
@deliaBlue deliaBlue self-assigned this Sep 19, 2023
uniqueg
uniqueg requested changes Sep 19, 2023
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Better implement/refactor as discussed on Slack

@deliaBlue deliaBlue changed the title build: set correct channel in environment.root.yml build: create independent environment files Sep 22, 2023
@deliaBlue
ci: add environment display
2bca799
@deliaBlue
build: swap channels
70f1f0a
@deliaBlue
build: swap channels
9aca076
@deliaBlue
build: pin versions
a66e46c
@deliaBlue
ci: fix environment files directory
900d063
@deliaBlue
ci: split conda and singularity snakemake tests
5df8005
@deliaBlue
build: update gffutils version
0b257d3
@deliaBlue
build: disable channel
64e9143
@deliaBlue
build: disable 'defaults' channel
f64361d
@deliaBlue
ci: update tests with mamba options
fb5576f
@deliaBlue
build remove nondefualts channel
9791ed4
@deliaBlue
ci: specify installation channels
66b9448
@deliaBlue
ci: include Mambaforge as an installer
dd26a02
@deliaBlue
ci: fix static code analysis
abef37c
@deliaBlue
ci: fix static code analysis
4b46293
@deliaBlue
refactor: fix variable types
bdc8758
@deliaBlue
refactor: fix return type
e82a7c0
@deliaBlue
build: upgrade and pin dependency versions
a5a4380
@deliaBlue
merge with fix_static_code branch
f5add74
@deliaBlue
build: upgrade and pin dependecies versions
2063c38
@deliaBlue
merge dev branch
c178635
@deliaBlue deliaBlue marked this pull request as draft November 16, 2023 12:49
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@uniqueg uniqueg uniqueg requested changes

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