Update savana to 1.0.4 (Resolve errors by pinning scikit-learn to 1.2.x) #42859
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
helrick
changed the title
helrick
changed the title
|
@BiocondaBot please add label |
|
@BiocondaBot please update |
|
@BiocondaBot please fetch artifacts |
|
Package(s) built on Azure are ready for inspection:
You may also use Docker image(s) built (images are in the LinuxArtifacts zip file above):
|
dpryan79
approved these changes
Sep 11, 2023
helrick
commented
Sep 11, 2023
| @@ -25,7 +27,7 @@ requirements: | |||
| - pybedtools >=0.9.0 | |||
| - pysam >=0.20.0 | |||
| - cyvcf2 >=0.30.16 | |||
| - scikit-learn >=1.2.2 | |||
| - scikit-learn >=1.2.2,<1.3.0 | |||
There was a problem hiding this comment.
Hi @dpryan79 I've just tested installing the newly merged 1.0.4 version of savana, with both conda and mamba, but version 1.3.0 of scikit-learn is still being installed though I've tried to pin it below 1.3.0 in the meta.yaml here. Would you be able to advise how best to pin the version of a dependency? Many thanks.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Attempted fix for reported issue with scikit-learn minor version (>=1.2.2 specified but 1.3.0 breaks, see: cortes-ciriano-lab/savana#27)
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.