Merge branch 'master' into biobb_chemistry

bioconda · Nov 8, 2024 · 3621e9c · 3621e9c
2 parents fe66799 + 41713ae
commit 3621e9c
Show file tree

Hide file tree

Showing 12 changed files with 36 additions and 142 deletions.
diff --git a/recipes/bioblend/meta.yaml b/recipes/bioblend/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "bioblend" %}
-{% set version = "1.3.0" %}
+{% set version = "1.4.0" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/b/bioblend/bioblend-{{ version }}.tar.gz
-  sha256: e72318e10c29a81c16281d25aaac00989a07fc2900be7479137964232cc4a507
+  sha256: 175d49d288e27d132ff59c870551c87cd95d7747be55ab94807c563291a3fa1d
 
 build:
   number: 0
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - requests >=2.20.0
@@ -66,7 +67,7 @@ test:
 about:
   home: "https://github.com/galaxyproject/bioblend"
   license: MIT
-  summary: 'A Python library for interacting with the Galaxy API'
+  summary: 'A Python library for interacting with the Galaxy API.'
   license_family: MIT
   license_file: LICENSE
   doc_url: "https://bioblend.readthedocs.org/"

diff --git a/recipes/gadma/meta.yaml b/recipes/gadma/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "gadma" %}
-{% set version = "2.0.0" %}
+{% set version = "2.0.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 1e891b87749261ce9c1866fd3e0ac389306096e3b940eb364101448efeca4cfd
+  sha256: f7b610d0d347e97afb30e6b5f9a814c19e479203838de31aa2e44f7427073db5
 
 build:
   number: 0
@@ -19,27 +19,31 @@ build:
     - gadma-get_confidence_intervals = gadma.get_confidence_intervals:main
     - gadma-get_confidence_intervals_for_ld = gadma.get_confidence_intervals_for_ld:main
     - gadma-precompute_ld_data = gadma.precompute_ld_data:main
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   noarch: python
   run_exports:
     - {{ pin_subpackage('gadma', max_pin="x") }}
 
 requirements:
   host:
-    - python >=3.6,<3.9
+    - python >=3.6
     - pip
     - setuptools-scm
+    - setuptools
   run:
-    - python >=3.6,<3.9
+    - python >=3.6
     - dadi
+    - demes
+    - demesdraw
+    - h5py ==3.10.0
     - matplotlib-base
     - mpmath
     - nlopt
     - numpy
-    - pandas
+    - pandas <=2.2.2
     - pillow
-    - ruamel.yaml
-    - scipy
+    - ruamel.yaml ==0.16.12
+    - scipy <1.14
     - networkx
     - moments
     - scikit-allel
@@ -69,6 +73,7 @@ about:
   license_file: LICENSE
   summary: "Genetic Algorithm for Demographic Inference"
   doc_url: https://gadma.readthedocs.io/en/latest/
+  dev_url: "https://github.com/ctlab/GADMA"
 
 extra:
   identifiers:

diff --git a/recipes/gnparser/meta.yaml b/recipes/gnparser/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.10.3" %}
-{% set sha256 = "899661ab88b716b7c1e3c4430bfb388997e510b28961e0246c361407f34cf0d2" %}
+{% set version = "1.10.4" %}
+{% set sha256 = "55e944b38dab4c680e96fd5b0effc2ccef300e91da1b6076cea4ad4e4e93fbcb" %}
 
 package:
   name: "gnparser"
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('gnparser', max_pin="x") }}
 

diff --git a/recipes/goldrush/meta.yaml b/recipes/goldrush/meta.yaml
@@ -11,7 +11,7 @@ source:
 
 build:
   skip: true  # [py < 38 or win or py > 39]
-  number: 0
+  number: 1
   run_exports: {{ pin_subpackage("goldrush", max_pin="x") }}
 
 requirements:
@@ -41,6 +41,7 @@ requirements:
     - gperftools
     - bc
     - snakemake
+    - numpy >=1.22.4
 
 test:
   commands:

diff --git a/recipes/k8/build_failure.linux-aarch64.yaml b/recipes/k8/build_failure.linux-aarch64.yaml
diff --git a/recipes/k8/build_failure.osx-64.yaml b/recipes/k8/build_failure.osx-64.yaml
diff --git a/recipes/regenie/meta.yaml b/recipes/regenie/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "regenie" %}
-{% set version = "3.6" %}
-{% set sha256 = "bb935b196da08ef7b37dad9736022030a686ae84539c47c106de6096d4612e09" %}
+{% set version = "4.0" %}
+{% set sha256 = "8f678d55bccf18ab70680637aca3cfd737060b3da291c803f3016d2ac3a07ccf" %}
 
 package:
   name: {{ name|lower }}

diff --git a/recipes/resistify/meta.yaml b/recipes/resistify/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "resistify" %}
-{% set version = "0.5.1" %}
-{% set sha256 = "d89d8d3553fd14c1ca4f6a7a995910a3244f1e70ccd06148be6c1278229183b5" %}
+{% set version = "0.5.2" %}
+{% set sha256 = "2c8e71e4ce52f014a62e5a5a5b32c04ed67af3651ddf9013f96953e711f4d234" %}
 
 package:
   name: "{{ name }}"
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: python
-  number: 1
+  number: 0
   entry_points:
     - resistify = resistify.main:main
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv "

diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "snakemake-executor-plugin-slurm" %}
-{% set version = "0.11.1" %}
+{% set version = "0.11.2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz
-  sha256: 293a951dcf829400bf6197705d6c602faed95aaaae9ad0d661d23b0184074134
+  sha256: fca29038d78387c237afb4ec2b04638e6128d2456940dd7b96ac4205f319d7f3
 
 build:
   noarch: python

diff --git a/recipes/strangepg/meta.yaml b/recipes/strangepg/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "strangepg" %}
-{% set version = "0.8.12" %}
+{% set version = "0.8.13" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/qwx9/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 323c161f3be6ec3c2d43cc7daeb7b139f75fb4ed70ec095f22e39d2450dd912c
+  sha256: b7dc45385297fa46458bf83931acd7dbc0fdbb594f63fe59db12d9a5080a95d8
 
 build:
   number: 0

diff --git a/recipes/sylph/build.sh b/recipes/sylph/build.sh
@@ -1,8 +1,4 @@
 #!/bin/bash -euo
 
-# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
-# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
-export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
-
 # build statically linked binary with Rust
 RUST_BACKTRACE=1 cargo install --verbose --path . --root $PREFIX
diff --git a/recipes/sylph/meta.yaml b/recipes/sylph/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.6.1" %}
+{% set version = "0.7.0" %}
 
 package:
   name: sylph
@@ -11,12 +11,12 @@ build:
 
 source:
   url: https://github.com/bluenote-1577/sylph/archive/v{{ version }}.tar.gz
-  sha256: 9f384ecf33d5eed57e518c1cc238ffb5ac68948dcf921731ba77ccbd02b57bdb
+  sha256: 8d0dd0c4b64de9b4c7402f6a44a019b2f54aae0626308a6b8831b3239640b609
 
 requirements:
   build:
     - {{ compiler("cxx") }}
-    - rust >=1.61
+    - {{ compiler("rust") }}
     - make
     - cmake >=3.12
 
@@ -27,10 +27,11 @@ test:
 about:
   home: https://github.com/bluenote-1577/sylph
   license: MIT
+  license_family: MIT
   summary: sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.  
   license_file: LICENSE
+  dev_url: https://github.com/bluenote-1577/sylph
 
 extra:
   recipe-maintainers:
     - bluenote-1577
-