Merge branch 'master' into aarch64-medaka

bioconda · May 13, 2024 · 0f60692 · 0f60692
2 parents bde756b + 957c6af
commit 0f60692
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -9,7 +9,7 @@ executors:
   linux-aarch64:
     machine:
       image: ubuntu-2204:current
-    resource_class: arm.large
+    resource_class: arm.medium
 
 jobs: # a basic unit of work in a run
   build_and_test:
@@ -53,12 +53,13 @@ jobs: # a basic unit of work in a run
       - run:
           name: Build and test
           command: |
+            . common.sh
             source /opt/mambaforge/etc/profile.d/conda.sh
             source /opt/mambaforge/etc/profile.d/mamba.sh
             mamba activate bioconda
             bioconda-utils build recipes config.yml \
                 --lint --docker --mulled-test \
-                --docker-base-image quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch) \
+                --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \
                 --git-range origin/master HEAD
 
       - run:
@@ -201,6 +202,7 @@ jobs: # a basic unit of work in a run
           name: Build and upload
           command: |
             set -e
+            . common.sh
             source /opt/mambaforge/etc/profile.d/conda.sh
             source /opt/mambaforge/etc/profile.d/mamba.sh
             mamba activate bioconda
@@ -211,7 +213,7 @@ jobs: # a basic unit of work in a run
             echo '============'
             bioconda-utils build recipes config.yml \
               --worker-offset << parameters.runner >> --n-workers 6 \
-              --docker --mulled-test --docker-base-image quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch) \
+              --docker --mulled-test --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \
               --anaconda-upload \
               --mulled-upload-target biocontainers \
               --record-build-failures \

diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -95,7 +95,6 @@ recipes/workspace
 recipes/wtforms-alchemy
 recipes/wtforms-components
 recipes/xmlbuilder
-recipes/yaggo
 
 # the following packages have open PRs labeled with "Move to conda-forge"
 recipes/perl-alien-build

diff --git a/recipes/allo/meta.yaml b/recipes/allo/meta.yaml
@@ -1,26 +1,27 @@
-{% set version = "1.0.5" %} 
+{% set name = "allo" %}
+{% set version = "1.1.1" %} 
 
 package:
-  name: allo
+  name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://files.pythonhosted.org/packages/45/65/e52455e8c4edb3bf93cb2b429f22ea36f54f2e6e21fe2789967d08cc390e/bio-allo-1.0.5.tar.gz
-  sha256: 0834fce916e3523af3e06c4c713f549c89cb846e08e3b74fe75cef4ad53dea26
+  url: https://pypi.io/packages/source/b/bio-{{ name }}/bio_allo-{{ version }}.tar.gz
+  sha256: b72bcbd900965e8b2fbbc17b174b44a8938994a4aeb8d532fb6f6a52b115b69e
 
 build:
   run_exports:
     - {{ pin_subpackage('allo', max_pin="x") }}
-  number: 0
+  number: 1
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
 
 requirements:
   host:
     - pip
-    - python >=3.8
+    - python >=3.10
   run:
-    - python >=3.8
+    - python >=3.10
     - numpy
     - joblib
     - tensorflow >=2.11
@@ -31,10 +32,12 @@ test:
     - allo --help
 
 about:
-  home: https://github.com/seqcode/allo
+  home: "https://github.com/seqcode/allo"
   license: MIT
-  license_file: LICENSE.txt
+  license_family: MIT
+  license_file: "LICENSE.txt"
   summary: "Multi-mapped read rescue strategy for gene regulatory analyses"
+  dev_url: "https://github.com/seqcode/allo"
 
 extra:
   recipe-maintainers:

diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml
@@ -1,18 +1,18 @@
-{% set version = "0.36.1" %}
+{% set version = "0.36.2" %}
 
 package:
   name: annonars
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   skip: True # [osx]
   run_exports:
     - {{ pin_subpackage("annonars", max_pin="x.x") }}
 
 source:
   url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 7aee8b87780956171a922b8fead5201c1506d5ec9cadc7ea33c009ce2f0b3816
+  sha256: 89b39a7e08ceb33ffc99364396222fffdda7e2fabd313bebf2976b365ed057c3
 
 requirements:
   build:
@@ -45,5 +45,6 @@ about:
 extra:
   recipe-maintainers:
     - holtgrewe
+    - tedil
   additional-platforms:
     - linux-aarch64
diff --git a/recipes/argnorm/meta.yaml b/recipes/argnorm/meta.yaml
@@ -1,17 +1,17 @@
 {% set name = "argnorm" %}
-{% set version = "0.2.0" %}
+{% set version = "0.3.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 8210aaa121272f2bd815498332bd076b9a5322b064c851dfb32d01486921a88c
+  sha256: 32ae41d1c099558b3257f88dd5ff34e70614646dec5bbf6fd7e0b30f816a5f57
 
 build:
   noarch: python
-  number: 1
+  number: 0
   entry_points:
     - argnorm=argnorm.cli:main
   script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation"

diff --git a/recipes/binchicken/meta.yaml b/recipes/binchicken/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "0.10.4" %}
+{% set version = "0.10.5" %}
 {% set name = "binchicken" %}
-{% set sha256 = "0a48da6e24e8c0b0d6746914d80991b1662180fcd58b987ae0925326d0007382" %}
+{% set sha256 = "687430f21caba05f654c6ebd26147c9130265de4cfc49d5233d0bcf9fcb07162" %}
 
 package:
   name: binchicken

diff --git a/recipes/biobb_io/meta.yaml b/recipes/biobb_io/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "biobb_io" %}
-{% set version = "4.1.0" %}
+{% set version = "4.1.1" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 074ea97a3682731e13d559b7f91b04e4a3f0f02ee798503089e4af79a730bf72
+  sha256: 2bccb966ab28bc6f63d1f09309c1a300392643fbfaf66ca690f8f7fad7abe516
 
 build:
   number: 0
@@ -45,7 +45,7 @@ about:
     \ building blocks that\ncreate new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest\
     \ API documentation](http://biobb_io.readthedocs.io/en/latest/).\n\
     \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\
-    \n\n* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\
+    \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\
     Licensed under the\n\
     [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\
     \n\

diff --git a/recipes/biobb_pytorch/meta.yaml b/recipes/biobb_pytorch/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "biobb_pytorch" %}
-{% set version = "4.1.2" %}
+{% set version = "4.1.3" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 2beb946b85e02f5907caf32a08bf38230d7dd1820a16416c08546118e423b268
+  sha256: 5ffce86986e458cc62f2f3695b58095d33636e35d8a29f8bc14a3c2ed1796061
 
 build:
   number: 0

diff --git a/recipes/biobb_vs/meta.yaml b/recipes/biobb_vs/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "biobb_vs" %}
-{% set version = "4.1.1" %}
+{% set version = "4.1.2" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 0be7e032922617797552024ee942cb3f99ecfb125cb767ba0f80a38f43402224
+  sha256: a0f8f09859ae547c7fbc33f637de6eb41546f175abe6274570c90467839b8dd5
 
 build:
   number: 0
@@ -22,12 +22,12 @@ requirements:
     - setuptools
     - biobb_common ==4.1.0
     - vina ==1.2.3
-    - fpocket >=3.1.4.2
+    - fpocket ==4.1
   run:
     - python >=3.8
     - biobb_common ==4.1.0
     - vina ==1.2.3
-    - fpocket >=3.1.4.2
+    - fpocket ==4.1
 
 test:
   imports:
@@ -45,7 +45,7 @@ about:
   description: "# biobb_vs\n\n### Introduction\nBiobb_vs is the Biobb module collection to perform virtual screening studies.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\
     \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb-vs.readthedocs.io/en/latest/).\n\
     \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\
-    \n\n* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\
+    \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\
     Licensed under the\n\
     [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\
     \n\

diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "bioconda-utils" %}
-{% set version = "2.15.0" %}
-{% set sha256 = "d4d0985220481fb2654e0f5743a2784befac1d59a52cc275ebebce52cee01fa4" %}
+{% set version = "2.15.1" %}
+{% set sha256 = "729f00c8ca5b3c7f469215edfc8122aa8617111b3151ed359081cc6a4b4f1a24" %}
 
 package:
   name: {{ name }}
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: python
-  number: 1
+  number: 0
   script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
   entry_points:
     - bioconda-utils = bioconda_utils.cli:main
@@ -30,6 +30,7 @@ requirements:
     - conda-libmamba-solver 24.1.*
     - conda-build 24.3.*
     - conda-index 0.4.*
+    - conda-package-streaming 0.9.*
     - mamba 1.5.*
     - boa 0.17.*
     - argh 0.31.*

diff --git a/recipes/bioconductor-acgh/meta.yaml b/recipes/bioconductor-acgh/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: 137af76dc5756a83094da18eb0bededa
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -42,11 +42,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-2
+  license: GPL-2.0-only
   summary: 'Classes and functions for Array Comparative Genomic Hybridization data'
   description: 'Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:acgh
     - doi:10.1093/bioinformatics/bti677

diff --git a/recipes/bioconductor-acme/meta.yaml b/recipes/bioconductor-acme/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: 6668a82e0a26ac03c9697e2cf22eb75e
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -37,11 +37,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: 'GPL (>= 2)'
+  license: 'GPL-3-only'
   summary: 'Algorithms for Calculating Microarray Enrichment (ACME)'
   description: 'ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment".  It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods.  It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:acme
   parent_recipe:

diff --git a/recipes/bioconductor-affy/meta.yaml b/recipes/bioconductor-affy/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: 09376016b32f86f707ff9b8f8cb8a1a5
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -47,11 +47,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: 'LGPL (>= 2.0)'
+  license: 'LGPL-3-only'
   summary: 'Methods for Affymetrix Oligonucleotide Arrays'
   description: 'The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. ''affy'' is fully functional without it.'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:affy
   parent_recipe:

diff --git a/recipes/bioconductor-affyio/meta.yaml b/recipes/bioconductor-affyio/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: 9bd1e4acedbf756386f96d4c1ebb21f3
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -36,11 +36,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: 'LGPL (>= 2)'
+  license: 'LGPL-3.0-or-later'
   summary: 'Tools for parsing Affymetrix data files'
   description: 'Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:affyio
     - doi:10.1038/nmeth.3252

diff --git a/recipes/bioconductor-bamsignals/meta.yaml b/recipes/bioconductor-bamsignals/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: e7b42351aa9651bdf7d429a6377143f5
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -48,11 +48,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-2
+  license: GPL-2.0-only
   summary: 'Extract read count signals from bam files'
   description: 'This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:bamsignals
     - doi:10.1038/nmeth.3252