From f8d2c8e3da90d77d818d2a65bbb2e1324e89e2de Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 24 Oct 2023 12:43:44 -0600
Subject: [PATCH] Update pharokka to 1.5.0 (#43183)

* Update pharokka to 1.5.0

* Update meta.yaml

update pyrodigal and dnaapler  to support pyrodigal v3

* Update meta.yaml

* pip arguments for `pyrodigal-gv`

* Update meta.yaml to get `pyrodigal-gv` to work x2

* Update meta.yaml

* Update meta.yaml with `prodigal_gv` manually in build script

* Update meta.yaml spell `pyrodigal-gv` properly

* edit dependencies

---------

Co-authored-by: George Bouras <84495559+gbouras13@users.noreply.github.com>
Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com>
---
 recipes/pharokka/meta.yaml | 51 ++++++++++++++++++++++----------------
 1 file changed, 30 insertions(+), 21 deletions(-)

diff --git a/recipes/pharokka/meta.yaml b/recipes/pharokka/meta.yaml
index 5249f49815287..f6e34449cfafe 100644
--- a/recipes/pharokka/meta.yaml
+++ b/recipes/pharokka/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "1.4.1" %}
+{% set version = "1.5.0" %}
 {% set name = "pharokka" %}
-{% set sha256 = "6184c11ddf83f38388d3aff6c39ac3a2bc8e8385bb9da41d04392f049319a20a" %}
+{% set sha256 = "afb5d8ac68f1d1d48b0280096018c3c31eb6c4ed07d0a5ee78e7ff19c651a5da" %}
 {% set user = "gbouras13" %}
 
 package:
@@ -10,7 +10,7 @@ package:
 build:
   number: 0
   noarch: python
-  script: python -m pip install --no-deps --ignore-installed . 
+  script: "{{ PYTHON }} -m pip install . --no-build-isolation --use-pep517 --no-deps -vvv"
   run_exports:
     - {{ pin_subpackage('pharokka', max_pin='x') }}
 
@@ -19,24 +19,32 @@ source:
   sha256: {{ sha256 }}
 
 requirements:
- host:
-  - python
-  - pip
- run:
-  - bcbio-gff >=0.7.0
-  - biopython >=1.78
-  - phanotate >=1.5.0
-  - mmseqs2 ==13.45111
-  - trnascan-se >=2.0.9
-  - minced >=0.4.2
-  - aragorn >=1.2.41
-  - mash >=2.2
-  - dnaapler >=0.3.0
-  - pyrodigal >=2.0.1
-  - pycirclize >=0.3.1
-  - alive-progress >=3.0.1
-  - requests >=2.25.1
-  - pyhmmer >=0.10.0
+  host:
+    - python >=3.5
+    - pip
+  run:
+    - python >=3.5
+    - bcbio-gff >=0.7.0
+    - biopython >=1.78
+    - phanotate >=1.5.0
+    - mmseqs2 ==13.45111
+    - trnascan-se >=2.0.9
+    - minced >=0.4.2
+    - aragorn >=1.2.41
+    - mash >=2.2
+    - dnaapler >=0.3.2
+    - pyrodigal >=3.0.0
+    - pyrodigal-gv >=0.2.0
+    - pycirclize >=0.3.1
+    - alive-progress >=3.0.1
+    - requests >=2.25.1
+    - pyhmmer >=0.10.0
+    - loguru >=0.5.4
+    - pyyaml >=6.0
+    - black >=22.3.0
+    - isort >=5.10.1
+    - pytest >=6.2.5
+    - pytest-cov >=3.0.0
 
 test:
   commands:
@@ -47,6 +55,7 @@ test:
 about:
   home: https://github.com/gbouras13/pharokka
   license: MIT
+  license_family: MIT
   license_file: LICENSE
   summary: "Fast Phage Annotation Program"
   dev_url: https://github.com/gbouras13/pharokka