From 20c204265aeebec1169c6833b7a33d264709ea6a Mon Sep 17 00:00:00 2001
From: Oliver Schwengers <oliver.schwengers@computational.bio.uni-giessen.de>
Date: Wed, 30 Oct 2024 13:34:44 +0100
Subject: [PATCH] bump pyrodigal dependency to v3.5.0

---
 bakta/utils.py  | 2 +-
 environment.yml | 2 +-
 setup.py        | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/bakta/utils.py b/bakta/utils.py
index 5b4f65a..8b11c64 100644
--- a/bakta/utils.py
+++ b/bakta/utils.py
@@ -42,7 +42,7 @@ def print_version(self):
 DEPENDENCY_ARAGORN = (Version(1, 2, 41), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Aragorn', ('aragorn', '-h'), ['skip-tmrna'])
 DEPENDENCY_CMSCAN = (Version(1, 1, 4), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'CMscan', ('cmscan', '-h'), ['--skip-rrna', '--skip-ncrna', '--skip-ncrna-region'])
 DEPENDENCY_PILERCR = (Version(1, 6), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'PilerCR', ('pilercr', '-options'), ['--skip-crispr'])
-DEPENDENCY_PYRODIGAL = (Version(3, 1, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyrodigal', (sys.executable, '-c', 'import pyrodigal; print(pyrodigal.__version__)'), ['--skip-cds'])
+DEPENDENCY_PYRODIGAL = (Version(3, 5, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyrodigal', (sys.executable, '-c', 'import pyrodigal; print(pyrodigal.__version__)'), ['--skip-cds'])
 DEPENDENCY_PYHMMER = (Version(0, 10, 4), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyhmmer', (sys.executable, '-c', 'import pyhmmer; print(pyhmmer.__version__)'), ['--skip-cds', '--skip-sorf'])
 DEPENDENCY_DIAMOND = (Version(2, 1, 10), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Diamond', ('diamond', 'help'), ['--skip-cds', '--skip-sorf'])
 DEPENDENCY_DEEPSIG = (Version(1, 2, 5), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'DeepSig', ('deepsig', '--version'), ['--gram ?'])
diff --git a/environment.yml b/environment.yml
index 3aba4a1..7baa0fd 100644
--- a/environment.yml
+++ b/environment.yml
@@ -9,7 +9,7 @@ dependencies:
   - requests>=2.25.1
   - alive-progress>=3.0.1
   - pyyaml>=6.0
-  - pyrodigal>=3.1.0
+  - pyrodigal>=3.5.0
   - trnascan-se>=2.0.11
   - aragorn>=1.2.41
   - infernal>=1.1.4
diff --git a/setup.py b/setup.py
index 60b347d..6fab4de 100644
--- a/setup.py
+++ b/setup.py
@@ -31,7 +31,7 @@
         'requests >= 2.25.1',
         'alive-progress >= 3.0.1',
         'PyYAML >= 6.0',
-        'pyrodigal >= 3.1.0',
+        'pyrodigal >= 3.5.0',
         'pyhmmer >= 0.10.15'
     ],
     entry_points={