Merge branch 'bioconda:master' into instanovo_gpu

recipes/biobb_model/meta.yaml

@@ -1,8 +1,8 @@
 {% set name = "biobb_model" %}
-{% set version = "4.2.3" %}
+{% set version = "5.0.0" %}
 {% set file_ext = "tar.gz" %}
 {% set hash_type = "sha256" %}
-{% set hash_value = "8c4b87ef92331d060700e5b346cddb718b1cc27b79752b1c8ef3583e0dce0927" %}
+{% set hash_value = "6f0cf1302d1b39404a65199e6aa5b9e4435099c2cef7d948253d20837d03d415" %}
 
 package:
   name: '{{ name|lower }}'
@@ -21,15 +21,15 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
-    - biobb_structure_checking >=3.13.4
+    - biobb_common ==5.0.0
+    - biobb_structure_checking >=3.13.5
     - xmltodict
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
-    - biobb_structure_checking >=3.13.4
+    - python >=3.9
+    - biobb_common ==5.0.0
+    - biobb_structure_checking >=3.13.5
     - xmltodict
 test:
   imports:

recipes/biobb_pdb_tools/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "biobb_pdb_tools" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 025d968ba5a5cee692f03d756f0fc474d7dcdec10e2babf150ad10af205aae25
+  sha256: 46cf4312ab7da0bf9491b1bf89677daf6f1163a3163c41d111863cf1baa1bd9a
 
 build:
   number: 0

recipes/mess/meta.yaml

@@ -1,16 +1,16 @@
 {% set name = "MeSS" %}
-{% set version = "0.9.0" %}
+{% set version = "0.10.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: {{ version }}
 
 source:
   url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: a0bb9d8dc81548cfad1cc45d43c82d41b28a399dd8f6bad4c5588a8201196f1a
+  sha256: f328a3a00973a411ee87193003ec747e59a46980161739f11ce78e6a23419437
 
 build:
-  number: 2
+  number: 0
   noarch: python
   entry_points:
     - mess=mess.__main__:main

recipes/mzspeclib/meta.yaml

@@ -0,0 +1,54 @@
+{% set name = "mzspeclib" %}
+{% set version = "1.0.1" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mzspeclib-{{ version }}.tar.gz
+  sha256: 44ed541be54f08d68b89b71f5892bbfc7458c8243df70c60774e2b07a939aaa2
+
+build:
+  entry_points:
+    - mzspeclib = mzspeclib.tools.cli:main
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('mzspeclib', max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.8
+    - setuptools
+    - pip
+  run:
+    - python >=3.8
+    - sqlalchemy
+    - click
+    - psims >=1.3.4
+    - pyteomics >=4.5.3
+    - mzpaf
+
+test:
+  imports:
+    - mzspeclib
+  commands:
+    - pip check
+    - mzspeclib --help
+  requires:
+    - pip
+
+about:
+  summary: HUPO-PSI Spectral library format
+  home: https://github.com/HUPO-PSI/mzSpecLib
+  license: CC-BY-4.0
+  license_family: CC
+  license_file: docs/LICENSE.txt
+  doc_url: https://mzspeclib-py.readthedocs.io/en/latest/
+  dev_url: https://github.com/HUPO-PSI/mzspeclib-py
+
+extra:
+  recipe-maintainers:
+    - hechth

recipes/psmc/build.sh

@@ -1,8 +1,11 @@
 #!/bin/bash
+
+set -xe
+
 export LIBRARY_PATH="$PREFIX/lib"
 
 mkdir -p $PREFIX/bin
-make CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib"
+make -j"${CPU_COUNT}" CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib"
 cp psmc $PREFIX/bin
-cd utils && make CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib"
+cd utils && make -j"${CPU_COUNT}" CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib"
 cp * $PREFIX/bin

recipes/psmc/meta.yaml

@@ -1,7 +1,8 @@
+{% set name = "psmc" %}
 {% set version = "0.6.5" %} # Remember to update sha256 below
 
 package:
-  name: psmc
+  name: {{ name }}
   version: {{ version }}
 
 source:
@@ -10,7 +11,9 @@ source:
 
 
 build:
-  number: 2
+  number: 3
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
 
 requirements:
   build:
@@ -33,3 +36,8 @@ about:
 test:
   commands:
     - psmc -h 2>&1 | cat > /dev/null
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64

recipes/pycomo/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "pycomo" %}
-{% set version = "0.2.4" %}
+{% set version = "0.2.5" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pycomo-{{ version }}.tar.gz
-  sha256: 5da3c1e85f0f0ca7b0fda240a7badb9ed8a84d65ec338c4334a0895463b1fb49
+  sha256: 5d60b805c0ba3829353d314d23df5bfa21e7ba078a72b2bbfd4316796e8ece5f
 
 build:
   entry_points:

recipes/sprinter/meta.yaml

@@ -0,0 +1,56 @@
+{% set name = "sprinter" %}
+{% set version = "1.0.0" %}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  url: https://github.com/zaccaria-lab/SPRINTER/archive/v{{ version }}.zip
+  sha256: e205cc6888f87fc2f345dad698308bc6397f6292ae2f4122d4c82d72a836e706
+
+build:
+  noarch: python
+  number: 0
+  entry_points:
+    - sprinter = sprinter.bin.sprinter:main
+  script: |
+    set -ex
+    {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  host:
+    - python >=3.9
+    - pip
+    - setuptools
+  run:
+    - python >=3.9
+    - numpy >=1.22.0,<=1.26.4
+    - pandas >=1.3.0
+    - scipy >=1.7.0,<2.0.0
+    - statsmodels >=0.13.0
+    - hmmlearn >=0.2.7
+    - matplotlib-base >=3.5.0
+    - pybedtools >=0.8.0
+    - scikit-learn >=1.0.0,<2.0.0
+    - seaborn >=0.11.0
+    - numba >=0.55.0
+
+test:
+  imports:
+    - sprinter
+    - sprinter.bin
+  commands:
+    - sprinter -h
+
+about:
+  home: https://github.com/zaccaria-lab/SPRINTER
+  summary: Single-cell Proliferation Rate Inference in Non-homogeneous Tumours through Evolutionary Routes (SPRINTER)
+  license: ACADEMIC NON-COMMERCIAL SOFTWARE LICENSE
+  license_family: OTHER
+  license_file: LICENSE.txt
+  dev_url: https://github.com/zaccaria-lab/SPRINTER
+  doc_url: https://github.com/zaccaria-lab/SPRINTER/blob/v{{ version }}/README.md
+  description: SPRINTER is an algorithm that uses single-cell whole-genome DNA sequencing data to enable the accurate identification of actively replicating cells in both the S and G2 phases of the cell cycle and their assignment to distinct tumour clones, thus providing a proxy to estimate clone-specific proliferation rates.