From 80eb1ad4c23d69bb11af7aa5a62e3801c512d876 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Mon, 21 Oct 2024 12:46:59 -0700
Subject: [PATCH 1/4] Add `pykofamsearch`

---
 recipes/pykofamsearch/meta.yaml | 49 +++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 recipes/pykofamsearch/meta.yaml

diff --git a/recipes/pykofamsearch/meta.yaml b/recipes/pykofamsearch/meta.yaml
new file mode 100644
index 0000000000000..5cd133ad4bec1
--- /dev/null
+++ b/recipes/pykofamsearch/meta.yaml
@@ -0,0 +1,49 @@
+{% set name = "pykofamsearch" %}
+{% set version = "2024.10.20" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/pykofamsearch-{{ version }}.tar.gz
+  sha256: f9455f343095327bab331a35010867d5d60f67b13bd5c2344d012e6801e48fad
+
+build:
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  number: 0
+  noarch: python
+  entry_points:
+    - pykofamsearch=pykofamsearch.pykofamsearch:main
+    - reformat_enzymes=pykofamsearch.reformat_enzymes:main
+    - reformat_pykofamsearch=pykofamsearch.reformat_pykofamsearch:main
+    - serialize_kofam_models=pykofamsearch.serialize_kofam_models:main
+    - subset_serialized_models=pykofamsearch.subset_serialized_models:main
+  run_exports:
+    - {{ pin_subpackage("pyhmmsearch", max_pin=None) }}
+
+requirements:
+  host:
+    - python
+    - pip
+  run:
+    - python
+    - pyhmmer >=0.10.12
+    - pandas >=2
+    - tqdm >=4
+
+test:
+  commands:
+    - pykofamsearch --help
+    - reformat_enzymes --help
+    - reformat_pykofamsearch --help
+    - serialize_kofam_models --help
+    - subset_serialized_models --helps
+
+about:
+  home: "https://github.com/jolespin/pykofamsearch"
+  summary: "Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer."
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  dev_url: "https://github.com/jolespin/pykofamsearch"

From 28a5e924d5cf2f4a5f2ed407d7b28e92b87a5561 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Mon, 21 Oct 2024 13:22:57 -0700
Subject: [PATCH 2/4] Fix run_exports

---
 recipes/pykofamsearch/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/pykofamsearch/meta.yaml b/recipes/pykofamsearch/meta.yaml
index 5cd133ad4bec1..860f678a20fba 100644
--- a/recipes/pykofamsearch/meta.yaml
+++ b/recipes/pykofamsearch/meta.yaml
@@ -20,7 +20,7 @@ build:
     - serialize_kofam_models=pykofamsearch.serialize_kofam_models:main
     - subset_serialized_models=pykofamsearch.subset_serialized_models:main
   run_exports:
-    - {{ pin_subpackage("pyhmmsearch", max_pin=None) }}
+    - {{ pin_subpackage("pykofamsearch", max_pin=None) }}
 
 requirements:
   host:

From 5c19018a6a6356ff226e8467f9326778ad5db45b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Mon, 21 Oct 2024 16:18:19 -0700
Subject: [PATCH 3/4] Remove `subset_serialized_models` test

---
 recipes/pykofamsearch/meta.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/recipes/pykofamsearch/meta.yaml b/recipes/pykofamsearch/meta.yaml
index 860f678a20fba..a43dd252f29bf 100644
--- a/recipes/pykofamsearch/meta.yaml
+++ b/recipes/pykofamsearch/meta.yaml
@@ -18,7 +18,6 @@ build:
     - reformat_enzymes=pykofamsearch.reformat_enzymes:main
     - reformat_pykofamsearch=pykofamsearch.reformat_pykofamsearch:main
     - serialize_kofam_models=pykofamsearch.serialize_kofam_models:main
-    - subset_serialized_models=pykofamsearch.subset_serialized_models:main
   run_exports:
     - {{ pin_subpackage("pykofamsearch", max_pin=None) }}
 

From 9198b144d253ea75c2350b40e7942be05b79cbf6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Tue, 22 Oct 2024 12:58:10 -0700
Subject: [PATCH 4/4] Fix `subset_serialized_models` test

---
 recipes/pykofamsearch/meta.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/recipes/pykofamsearch/meta.yaml b/recipes/pykofamsearch/meta.yaml
index a43dd252f29bf..2eae16bea7e77 100644
--- a/recipes/pykofamsearch/meta.yaml
+++ b/recipes/pykofamsearch/meta.yaml
@@ -18,6 +18,7 @@ build:
     - reformat_enzymes=pykofamsearch.reformat_enzymes:main
     - reformat_pykofamsearch=pykofamsearch.reformat_pykofamsearch:main
     - serialize_kofam_models=pykofamsearch.serialize_kofam_models:main
+    - subset_serialized_models=pykofamsearch.subset_serialized_models:main
   run_exports:
     - {{ pin_subpackage("pykofamsearch", max_pin=None) }}
 
@@ -37,7 +38,7 @@ test:
     - reformat_enzymes --help
     - reformat_pykofamsearch --help
     - serialize_kofam_models --help
-    - subset_serialized_models --helps
+    - subset_serialized_models --help
 
 about:
   home: "https://github.com/jolespin/pykofamsearch"