From ae43cc30c1a8443e5cd5e76d12c2ffaac4185f9e Mon Sep 17 00:00:00 2001
From: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
Date: Mon, 18 Sep 2023 08:38:44 +0200
Subject: [PATCH] Update Pyrodigal to 3.0.0

---
 pyproject.toml       | 2 +-
 vamb/parsemarkers.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7ba16c5f..391162bb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ dependencies = [
     "torch == 1.13.1",
     "pycoverm == 0.6.0",
     "pyhmmer == 0.10.2",
-    "pyrodigal == 2.3.0",
+    "pyrodigal == 3.0.0",
     "networkx == 3.1",
     "scikit-learn == 1.2.2",
     "pandas == 2.0.0",
diff --git a/vamb/parsemarkers.py b/vamb/parsemarkers.py
index f83cb607..81ca7a00 100644
--- a/vamb/parsemarkers.py
+++ b/vamb/parsemarkers.py
@@ -242,7 +242,7 @@ def process_chunk(
     chunk: list[FastaEntry],
     hmms: list[pyhmmer.plan7.HMM],
     name_to_id: dict[MarkerName, MarkerID],
-    finder: pyrodigal.OrfFinder,
+    finder: pyrodigal.GeneFinder,
 ) -> list[tuple[ContigID, np.ndarray]]:
     # We temporarily store them as sets in order to deduplicate. While single contigs
     # may have duplicate markers, it makes no sense to count this as contamination,
@@ -288,7 +288,7 @@ def work_per_process(
     # allowing pyhmmer to scan multiple sequences at once for speed
     chunk: list[FastaEntry] = []
     result: list[tuple[ContigID, np.ndarray]] = []
-    finder = pyrodigal.OrfFinder(meta=True)
+    finder = pyrodigal.GeneFinder(meta=True)
     with open(contig_path, "rb") as file:
         for record in byte_iterfasta(file):
             chunk.append(record)