Merge branch 'master' into master

recipes/amdirt/meta.yaml

@@ -1,54 +1,56 @@
 {% set name = "amdirt" %}
-{% set version = "1.6.2" %}
+{% set version = "1.6.5" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/AMDirT-{{ version }}.tar.gz
-  sha256: 9e7ac732ac9faca5900b18c42d2fee9528081d97614f629ae81c7e1052aac46e
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/amdirt-{{ version }}.tar.gz
+  sha256: 907c06035768dea2ee9d9ea4d681872880c30c064fdfb9ac173a68512203ce5b
 
 build:
   entry_points:
-    - AMDirT = AMDirT.cli:cli
+    - amdirt = amdirt.cli:cli
   noarch: python
-  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
   number: 0
   run_exports:
     - {{ pin_subpackage("amdirt", max_pin="x") }}
 
 requirements:
   host:
-    - pip
     - python >=3.9
+    - pip
+    - setuptools
   run:
+    - python >=3.9
     - click
-    - colorlog
-    - jsonschema
-    - defusedxml
-    - numpy
     - pandas
-    - python >=3.9
-    - requests
+    - tabulate
+    - jsonschema
     - rich
     - streamlit <=1.35.0
-    - streamlit-aggrid <=0.3.5
-    - tabulate
+    - streamlit-aggrid
+    - numpy
+    - requests
+    - colorlog
+    - protobuf <=3.20
 
 test:
   imports:
-    - AMDirT
-  #commands:
-    #- AMDirT --help
+    - amdirt
+  commands:
+    - pip check
+    - amdirt --help
+  requires:
+    - pip
 
 about:
-  home: https://github.com/SPAAM-community/AMDirT
-  summary: 'AMDirT: AncientMetagenomeDir Toolkit'
-  license: GPL-3.0-or-later
-  license_family: GPL3
+  home: https://github.com/SPAAM-community/amdirt
+  summary: 'amdirt: AncientMetagenomeDir Toolkit'
+  license: GPL-3.0
   license_file: LICENSE
-  dev_url: https://github.com/SPAAM-community/AMDirT
 
 extra:
   recipe-maintainers:

recipes/arborator/meta.yaml

@@ -12,7 +12,7 @@ source:
 
 
 build:
-  number: 1
+  number: 2
   noarch: python
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}

recipes/artic/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "artic" %}
-{% set version = "1.6.0" %}
-{% set sha256 = "9037ce813170e76ee2e37b94871b549e850faad26fffab201c04a2368ab81cfc" %}
+{% set version = "1.6.1" %}
+{% set sha256 = "f451eb93da7927a05c67bc77926ba42b5dceb8962940e5cc52a66b3c842da636" %}
 
 package:
   name: {{ name|lower }}

recipes/aspera-cli/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "aspera-cli" %}
-{% set version = "4.19.0" %}
+{% set version = "4.20.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   - url: https://github.com/IBM/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-    sha256: e4f9eb47510094132ff02960764254dfc322f1a16c9ad2b8abc60a54e5e21da1
+    sha256: d07d8ee94ab83159495b2c911fcb427975a26e7280085a80352c6390899b7a05
 
 build:
   noarch: generic

recipes/augur/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "27.1.0" %}
+{% set version = "27.2.0" %}
 
 package:
   name: augur
   version: {{ version }}
 
 source:
   url: https://github.com/nextstrain/augur/releases/download/{{ version }}/nextstrain_augur-{{ version }}.tar.gz
-  sha256: 1fc51fc8b58ce8757146ae4a99dcfb439e22d25fe2f964140c2632dad075432b
+  sha256: cb8917825c496d3f4e8c3864ab8d65ee6d0042c367d8939bdde94791baf84001
 
 build:
   number: 0

recipes/auspice/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "2.59.1" %}
+{% set version = "2.62.0" %}
 {% set name = "auspice" %}
 
 package:
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://registry.npmjs.org/{{ name }}/-/{{ name }}-{{ version }}.tgz
-  sha256: 828bc00e27ca3d403332686ab041dd3171c999a1a942b9fe89ba8256daedfecc
+  sha256: 23b78a713aa6197fbccfa528d1dd73fa120d350021688aedeb1c59abd12206d9
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 

recipes/autobigs-cli/meta.yaml

@@ -0,0 +1,50 @@
+{% set name = "autoBIGS.cli" %}
+{% set version = "0.4.2" %}
+
+package:
+  name: {{ name|lower|replace(".", "-") }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/autobigs_cli-{{ version }}.tar.gz
+  sha256: fc7bf6c604974796f5c8aae52fd9ab9924f5490f4f207a26be803217aae30c82
+
+build:
+  entry_points:
+    - autoBIGS = autobigs.cli.program:run
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage( name|lower|replace(".", "-"), max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.12
+    - setuptools >=64
+    - setuptools-scm >=8
+    - pip
+  run:
+    - python >=3.12
+    - autobigs-engine
+
+test:
+  imports:
+    - autobigs
+  commands:
+    - pip check
+    - autoBIGS --help
+    - autoBIGS info -h
+    - autoBIGS st -h
+  requires:
+    - pip
+
+about:
+  home: https://github.com/RealYHD/autoBIGS.cli
+  summary: A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases.
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - Harrison Deng

recipes/autobigs-engine/meta.yaml

@@ -0,0 +1,46 @@
+{% set name = "autoBIGS.engine" %}
+{% set version = "0.8.0" %}
+
+package:
+  name: {{ name|lower|replace(".", "-") }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/autobigs_engine-{{ version }}.tar.gz
+  sha256: 8d2a66aea26f0704f4be21b2882f4514011455bb2897d23f118fd02b75d5480c
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage( name|lower|replace(".", "-"), max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.12
+    - setuptools >=64
+    - setuptools-scm >=8
+    - pip
+  run:
+    - python >=3.12
+    - biopython
+    - aiohttp
+
+test:
+  imports:
+    - autobigs
+  commands:
+    - pip check
+  requires:
+    - pip
+
+about:
+  home: https://github.com/RealYHD/autoBIGS.engine
+  summary: A library to rapidly fetch fetch MLST profiles given sequences for various diseases.
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - Harrison Deng

recipes/aviary/meta.yaml

@@ -1,6 +1,6 @@
-{% set version = "0.10.0" %}
+{% set version = "0.11.0" %}
 {% set name = "aviary" %}
-{% set sha256 = "a7ff834830fcfa7c4754a3881530875d9a1210d4c532be6a8391b9747645742e" %}
+{% set sha256 = "3aa2a71a2b3cd6fd712b19eed09db8091c3c69cf463f3fbc491d016b8be3b3c8" %}
 
 package:
   name: aviary

recipes/bakta/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "1.10.3" %}
+{% set version = "1.10.4" %}
 
 package:
   name: bakta
   version: '{{ version }}'
 
 source:
   url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz
-  sha256: '99ee0bcf559fabcebb3c1e896638da537a0691312eb07fd41788f3cb79ef22ba'
+  sha256: 'cb9ae9d3d76cf02e3578986b05937eb1c9c70ab9a1660fabfd705fd5cae0d97e'
 
 build:
   noarch: python

recipes/bali-phy/meta.yaml

@@ -1,13 +1,13 @@
 package:
   name: bali-phy
-  version: '4.0beta16'
+  version: '4.0beta17'
 
 source:
-  url: https://github.com/bredelings/bali-phy/archive/4.0-beta16.tar.gz
-  sha256: f7819b0f68043abbadc3df19adc9a590d0bab6c2fbbf4ddb0feeb44165796c03
+  url: https://github.com/bredelings/bali-phy/archive/4.0-beta17.tar.gz
+  sha256: 024f736d70fc0e0b5f59d6b27dcaeb41e6e0aa7d2e8dbc0dd178d268c6413621
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('bali-phy', max_pin='x') }}
 

recipes/bayescode/meta.yaml

@@ -1,14 +1,15 @@
-{% set version = "1.3.2" %}
-{% set sha256 = "53febe5e4495bfb029da04b209c5722ee0de0c13db53ec98de277d571469d26f" %}
+{% set name = "bayescode" %}
+{% set version = "1.3.3" %}
+{% set sha256 = "040a87d139b4bfc2343ca6c9ae6a91b6941432de7d8a85de0e3fc877fdeaec74" %}
 
 package:
-  name: bayescode
+  name: {{ name }}
   version: {{ version }}
 
 build:
   number: 1
   run_exports:
-    - {{ pin_subpackage('bayescode', max_pin="x") }}
+    - {{ pin_subpackage(name, max_pin="x") }}
 
 source:
   url: https://github.com/ThibaultLatrille/bayescode/archive/refs/tags/v{{ version }}.tar.gz
@@ -50,3 +51,8 @@ about:
   license_family: MIT
   license_file: License.MD
   summary: Mutation-Selection phylogenetic codon models to detect site-specific adaptive evolution or to infer long-term effective population size
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64

recipes/bbmap/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "BBMap" %}
-{% set version = "39.13" %}
-{% set sha256 = "6920a94549d3fca129e031cc14e5306ae571a223410e1f116b0292e530c433de" %}
+{% set version = "39.15" %}
+{% set sha256 = "b6698469a2a90f4930537c575ff1f70332f88a933dd5e286c83ea0ff30802344" %}
 
 package:
   name: {{ name|lower }}
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x") }}
 
@@ -41,12 +41,12 @@ test:
     - bbnorm.sh --help 2>&1 | grep "BBNorm" > /dev/null
 
 about:
-  home: https://sourceforge.net/projects/bbmap
-  doc_url: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+  home: "https://sourceforge.net/projects/bbmap"
+  doc_url: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide"
   license: "UC-LBL license (see package)"
   license_file: "license.txt"
   summary: "BBMap is a short read aligner, as well as various other bioinformatic tools."
-  dev_url: https://sourceforge.net/projects/bbmap
+  dev_url: "https://sourceforge.net/projects/bbmap"
 
 extra:
   additional-platforms:

recipes/biobb_amber/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "biobb_amber" %}
-{% set version = "5.0.3" %}
+{% set version = "5.0.4" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 78dfd40a00c729549fee6f31f96a70dc93e532bd44f267e976cd85e7191e0835
+  sha256: c877f30528088a68c11db3879ef05fdc068da1c9ca061bea0268d686edf0ed13
 
 build:
   number: 0