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Update sativa #44990

Merged
merged 137 commits into from
Jan 24, 2024
Merged

Update sativa #44990

merged 137 commits into from
Jan 24, 2024

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erikrikarddaniel
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Recipe for the Sativa package updated, including addition of a test.


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erikrikarddaniel and others added 30 commits December 12, 2023 14:13
* Update keggcharter to 1.0.2

* Update meta.yaml

Now put all TXTs and TSVs from "resources" folder into "share" folder.

---------

Co-authored-by: João Sequeira <maildosequeira@gmail.com>
* Update conanfile.txt.patch

* Bump version
* add misha version 3.7.0 (history version)

* fix hash

* fix compiler settings

* use template variable to specify name

* add run_export to lock version
* add r-misha 3.7.1 (history version)

* fix: incorrect commit and hash
* Update viguno to 0.2.0

* run_exports

---------

Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk>
* Update recognizer to 1.10.0

* Update meta.yaml

No more build.sh file

* Update meta.yaml

Forgot about the other TSV files

* Removed build.sh

---------

Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
* genoflu version 1.02

* Update meta.yaml

* Update meta.yaml

* https://spdx.org/licenses/GPL-3.0-or-later.html

---------

Co-authored-by: Thanh Lee <thanh.le-viet@quadram.ac.uk>
* Update chromhmm to 1.25

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

---------

Co-authored-by: Christian Brueffer <christian@brueffer.io>
* Update ColabFold to 1.5.4

* Use 1.5.5 instead, 1.5.4 had a bug

* OpenMM 8.1 causes issues
* Update expam to 1.2.2.4

* add run_exports

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>
Co-authored-by: João Sequeira <maildosequeira@gmail.com>
multiple binaries and a wrapper scripts depending on available instruction sets.
* add strainscan recipes

* add annosine2 recipes

* Delete recipes/strainscan/meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml
* a round of fixes and build-skips

* add some build failures

* correct version for bioconductor-data-packages

* add build failure for STdeconvolve

* [ci run] trigger bulk run

* run_exports on bioconductor-data-packages

* [ci run] trigger bulk run

* build failure for omnipathr

* [ci run] trigger bulk run

* Build important packages first

* [ci run] trigger bulk run

* revert to full build

* [ci run] trigger bulk run

* build failure files

* skip iclusterplus

* skip bioconductor-lpsymphony

* bump bioconda-repodata-patches build number

* [ci run]

* build failures

* next round of high priority packages

* [ci run] trigger bulk run

* [ci run] add dependency

* [ci run] finish priority packages

* re-enable full bulk

* [ci run] trigger bulk run

* build failures

* [ci run] trigger bulk run

* next round of high priority packages

* [ci run] trigger bulk run

* build more high priority packages

* [ci run] test local channel fix

* [ci run] increase workers

* Try building bioconductor-geoquery (bioconda#44726)

* Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml

* Update meta.yaml

* try fixing parsing error

* [ci run] try rebuilding bioconductor-coregx (bioconda#44727)
* try rebuilding bioconductor-coregx
* Update meta.yaml

* add opencl loading libraries - will this work

* [ci run] remove a few build failure files

* [ci run] Bioconductor graph (bioconda#44733)

* remove build failure file
* trigger build
* Update meta.yaml
* add patch back
[ci run]

* build failures

* [ci run] high priority packages

* bulk wiki page

* [ci run] add missing packges

* build failure for bioconductor-sictools

* [ci run] missed one

* [ci run] full run

* Update build.sh

* [ci run] fix dexseq

* [ci run] next round of high priority packages

* [ci run] missing packages

* [ci run] high priority package

* [ci run] build all bioconductor-bsgenome

* [ci run] remove failures associated with bioconductor-bsgenome dependency

* full build

* use bioconda-common version

* build failures: test dev version of utils

* escape characters correctly

* build failure for bioconductor-pics

* use branch

* build failure for bioconductor-inspect

* try to fix build failure git range

* build failure for bioconductor-distinct

* use head branch

* trigger build failure wf

* [ci run] trigger bulk run

* build failures fetch depth

* build failure for biconductor-benchdamic

* build failures

* build failures with log

* don't run build failures if last commit has ci skip

* [ci skip] test build failure wiki

* test build failure wiki job

* [ci run] reenable record-build-failures

* re-add token for build failure updates

* build failures add category column

* trigger wiki update

* fix libsbml version for bioconductor-rsbml

* build failure updates

* fix bioconductor-glad

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-wppi

* [ci skip] add build failure record for recipe recipes/bioconductor-gars

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-metascope

* [ci skip] add build failure record for recipe recipes/bioconductor-biggr

* [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank

* [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader

* [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer

* [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr

* [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r

* [ci skip] add build failure record for recipe recipes/bioconductor-gesper

* [ci skip] add build failure record for recipe recipes/bioconductor-sctensor

* [ci skip] add build failure record for recipe recipes/bioconductor-seqcna

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-inpas

* [ci skip] add build failure record for recipe recipes/bioconductor-factr

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble

* [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile

* [ci skip] add build failure record for recipe recipes/bioconductor-extrachips

* [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank

* [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc

* [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats

* [ci skip] add build failure record for recipe recipes/bioconductor-chipqc

* [ci skip] add build failure record for recipe recipes/bioconductor-outsplice

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci skip] add build failure record for recipe recipes/bioconductor-circseqaligntk

* [ci skip] add build failure record for recipe recipes/bioconductor-ritan

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-vulcan

* [ci skip] add build failure record for recipe recipes/bioconductor-singlecelltk

* [ci skip] add build failure record for recipe recipes/bioconductor-scfeatures

* [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper

* [ci skip] add build failure record for recipe recipes/bioconductor-deconvr

* [ci skip] add build failure record for recipe recipes/bioconductor-ideal

* [ci skip] add build failure record for recipe recipes/bioconductor-esatac

* [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr

* [ci skip] add build failure record for recipe recipes/bioconductor-inetgrate

* [ci skip] add build failure record for recipe recipes/bioconductor-ataccogaps

* [ci skip] add build failure record for recipe recipes/bioconductor-lemur

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] add build failure record for recipe recipes/bioconductor-regionreport

* [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr

* [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-cageminer

* [ci skip] add build failure record for recipe recipes/bioconductor-multicrispr

* [ci skip] add build failure record for recipe recipes/bioconductor-xde

* [ci skip] add build failure record for recipe recipes/bioconductor-affycoretools

* [ci skip] add build failure record for recipe recipes/bioconductor-scpipe

* Rbowtie2 (bioconda#44856)

[ci run] fix rbowtie2 builds

* [ci run] remove build file

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-biggr

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] remove build failure record for recipe recipes/bioconductor-affycoretools

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh

* failure for bioconda-multirnaflow

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-proloc

* [ci skip] add build failure record for recipe recipes/bioconductor-rcas

* [ci skip] add build failure record for recipe recipes/bioconductor-guideseq

* [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign

* [ci skip] add build failure record for recipe recipes/bioconductor-fraser

* bioconductor-lpsymphony fix from master

* remove build failures for finished dependencies

* restore skip osx-64

* fix bioconductor-rawrr

* high priority packages

* [ci run] trigger bulk run

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] remove build failure record for recipe recipes/bioconductor-proloc

* fix bioconductor-chemmineob

* [ci run] remove failures for built dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci run] full build

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* remove easy build failures

* [ci run] next round of dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-pigengene

* [ci skip] add build failure record for recipe recipes/bioconductor-repitools

* [ci skip] add build failure record for recipe recipes/bioconductor-xde

* [ci skip] add build failure record for recipe recipes/bioconductor-sctensor

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* build failure updates

* [ci run] next batch of fixes

* [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci run] full build

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci run]remove failures for built dependencies

* [ci skip] add build failure record for recipe recipes/bioconductor-ihw

* [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony

* [ci skip] add build failure record for recipe recipes/bioconductor-rlseq

* [ci skip] add build failure record for recipe recipes/bioconductor-gatom

* [ci run] set failures to skip

* [ci run] reduce resources that are wasted

* [ci skip] add build failure record for recipe recipes/bioconductor-pd.barley1

* fix accidental reverts

* add GSL to bioconductor-pics

* add back fix from master for omnipathr

* remove build failure

* [ci run] skip root nodes to spread out builds

* [ci run] include more root nodes in blacklist

* update build failures

* [ci run] add more blacklist items and do osx build

* [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-ping

* [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes

* [ci skip] add build failure record for recipe recipes/bioconductor-mumosa

* [ci skip] add build failure record for recipe recipes/bioconductor-chromscape

* [ci skip] add build failure record for recipe recipes/bioconductor-scmerge

* [ci skip] add build failure record for recipe recipes/bioconductor-tadcompare

* fix build errors

* [ci run] more skipped builds

* [ci skip] add build failure record for recipe recipes/bioconductor-cghmcr

* [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper

* [ci skip] add build failure record for recipe recipes/bioconductor-ccpromise

* [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh

* [ci skip] add build failure record for recipe recipes/bioconductor-interactivedisplay

* [ci run] reduce workers

* [ci skip] add build failure record for recipe recipes/bioconductor-cepo

* [ci skip] add build failure record for recipe recipes/bioconductor-tbsignatureprofiler

* [ci run] manually distribute packages

* [ci skip] add build failure record for recipe recipes/bioconductor-cocoa

* [ci skip] add build failure record for recipe recipes/bioconductor-condiments

* [ci skip] add build failure record for recipe recipes/bioconductor-scclassify

* [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf

* [ci skip] add build failure record for recipe recipes/bioconductor-gcapc

* [ci skip] add build failure record for recipe recipes/bioconductor-cepo

* [ci skip] add build failure record for recipe recipes/bioconductor-traviz

* remove build failures

* remove colon that breaks yaml parsing

* remove temporary bioconductor bulk skips

* [ci run] remaining packages

* [ci skip] add build failure record for recipe recipes/bioconductor-distinct

* [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf

* [ci skip] add build failure record for recipe recipes/bioconductor-promise

* [ci skip] add build failure record for recipe recipes/bioconductor-otubase

* [ci skip] add build failure record for recipe recipes/bioconductor-cocoa

* [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes

* retry http error

* [ci run] full bulk build

* [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer

* [ci skip] remove build failure record for recipe recipes/bioconductor-meb

* [ci skip] add build failure record for recipe recipes/bioconductor-distinct

* [ci run] categorize failures

* add bioconductor-cdi

* remove old failure files

* update bioconductor-reusedata to 3.18

* remove failures for dependencies that have been built

* [ci run] build certain packages

* bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (bioconda#44986)

* update bioconductor-ccfindr with gsl

* update bioconductor-rjmcmcnucleosomes with gsl

* [ci run] build updated recipes

* [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr

* [ci skip] add build failure record for recipe recipes/bioconductor-reusedata

* remove temporary changes from workflows

* build got bumped in merge

* remove temp files

---------

Co-authored-by: Ryan Dale <ryan.dale@nih.gov>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com>
Co-authored-by: BiocondaBot <BiocondaBot@users.noreply.github.com>
* Update deeplc to 2.2.23

* Update deeplc to 2.2.24

* add pyopenms

* Update deeplc to 2.2.25

* Update deeplc to 2.2.26

* try extended base

* revert extended base

---------

Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
* Add recipe for CellBender v0.3.0

* add run_exports
@erikrikarddaniel
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@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Jan 10, 2024
@apeltzer apeltzer enabled auto-merge (squash) January 24, 2024 21:40
@apeltzer apeltzer merged commit e07b175 into bioconda:master Jan 24, 2024
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