From 9e66b8160209bd7006215204c5a65415f01a2778 Mon Sep 17 00:00:00 2001
From: John Lees <lees.john6@gmail.com>
Date: Thu, 7 Nov 2024 16:31:59 +0000
Subject: [PATCH 1/3] Add M1 builds for PopPUNK (#50011)

* Add M1 builds for PopPUNK

* clean up recipe

* clean up recipe

* Update poppunk to v2.7.1

* Reset build to zero

* Add libfortran dep

* Add fortran compiler

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/poppunk/meta.yaml | 30 ++++++++++++++----------------
 1 file changed, 14 insertions(+), 16 deletions(-)

diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml
index 802e0ca68a124..b75e51baa76af 100644
--- a/recipes/poppunk/meta.yaml
+++ b/recipes/poppunk/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.7.0" %}
+{% set version = "2.7.1" %}
 {% set name = "PopPUNK" %}
 
 package:
@@ -7,12 +7,12 @@ package:
 
 source:
   url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz
-  sha256: bba7cb9fad5027abc78fd6761755169ae999d3d86a96bdfbfe577a360f907067
+  sha256: 7e6f7242b8c2150c7963fc5f4a95cfd7f2656b8a80317ff87bf97dc75f753788
 
 build:
   number: 0
-  skip: true  # [py < 38]
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
+  skip: True  # [py < 38]
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   entry_points:
     - poppunk = PopPUNK.__main__:main
     - poppunk_assign = PopPUNK.assign:main
@@ -27,13 +27,12 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - {{ compiler('fortran') }}
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux64]
     - cmake >=3.18
     - make
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
   host:
     # python
     - python
@@ -64,7 +63,6 @@ requirements:
     - treeswift
     - requests
     # C++ extension
-    - zlib
     # The xorg-* requirements are only used for gtk3 which is pulled in via graph-tool.
     - xorg-libxi
     - xorg-libxcursor
@@ -80,7 +78,6 @@ test:
   imports:
     - PopPUNK
     - poppunk_refine
-
   commands:
     - poppunk --help
     - poppunk_assign --help
@@ -92,16 +89,17 @@ test:
     - poppunk_lineages_from_strains --help
 
 about:
-  home: https://poppunk.bacpop.org/
-  license: Apache-2.0
+  home: "https://poppunk.bacpop.org"
+  license: "Apache-2.0"
   license_family: APACHE
+  license_file: LICENSE
   summary: 'PopPUNK (POPulation Partitioning Using Nucleotide Kmers)'
+  dev_url: "https://github.com/bacpop/PopPUNK"
+  doc_url: "https://poppunk.bacpop.org/index.html"
 
 extra:
   identifiers:
     - doi:10.1101/gr.241455.118
-  # enabling this would require arm64 packages for: mandrake, pp-sketchlib,
-  # rapidnj
-  # additional-platforms:
-  #  - linux-aarch64
-  #  - osx-arm64
+    - biotools:poppunk
+  additional-platforms:
+    - osx-arm64

From e85bcbece2d56b82440b5e32c9da96ef7d671e46 Mon Sep 17 00:00:00 2001
From: SHANG Jiayu <Kenneth.Shang@foxmail.com>
Date: Fri, 8 Nov 2024 00:32:32 +0800
Subject: [PATCH 2/3] Update PhaBOX to 2.1.5 (#51997)

---
 recipes/phabox/meta.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml
index 3941d9b1cf7c0..940dad736add2 100644
--- a/recipes/phabox/meta.yaml
+++ b/recipes/phabox/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "PhaBOX" %}
-{% set version = "2.1.4" %}
+{% set version = "2.1.5" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 963d71ac1e600f5a41cd8ff22a66a34921190e7b8afe449aa5ca3fd10fabba40
+  sha256: 875124cd1568fcb706662e7f86ff7e1ef79b38944156c8c5d0b1b329d983d73a
 
 build:
   number: 0
@@ -42,6 +42,7 @@ requirements:
     - blast >=2.16.0
     - diamond <=0.9.14
     - mcl >=22.282
+    - accelerate >=1.0.1
     
 test:
   commands:

From 3765eb5a7bfa094a87c499338c5d39bff6a7d1c9 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 7 Nov 2024 11:33:37 -0500
Subject: [PATCH 3/3] Update centrifuger to 1.0.5 (#51999)

---
 recipes/centrifuger/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/centrifuger/meta.yaml b/recipes/centrifuger/meta.yaml
index dccd1d4dbe4d6..196d36ed4e995 100644
--- a/recipes/centrifuger/meta.yaml
+++ b/recipes/centrifuger/meta.yaml
@@ -1,18 +1,18 @@
 {% set name = "centrifuger" %}
-{% set version = "1.0.4" %}
+{% set version = "1.0.5" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
 source:
   url: https://github.com/mourisl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 5261abcfb3b88126000ae7708702d07704a0ee19d6f54f9f89f0d2e195e24d1d
+  sha256: 1de388229d3ee6a65a58308b5521bef6cbfcdf92628064a39d6b70c7523d68de
 
 requirements:
   build: