From 0a3a7419cedc59a8b56b94539ac8349012c5da85 Mon Sep 17 00:00:00 2001
From: Jon Palmer <nextgenusfs@gmail.com>
Date: Sun, 3 Nov 2024 22:22:09 -0800
Subject: [PATCH] clean some more bump version

---
 buscolite/__init__.py       |  4 +++-
 buscolite/__main__.py       |  2 +-
 buscolite/__version__.py    |  3 ---
 buscolite/busco.py          | 11 ++++++++---
 buscolite/help_formatter.py |  2 +-
 buscolite/utilities.py      | 11 +++++++++--
 pyproject.toml              |  2 +-
 7 files changed, 23 insertions(+), 12 deletions(-)
 delete mode 100755 buscolite/__version__.py

diff --git a/buscolite/__init__.py b/buscolite/__init__.py
index e9c9ef4..340ab3c 100755
--- a/buscolite/__init__.py
+++ b/buscolite/__init__.py
@@ -1 +1,3 @@
-from .__version__ import __version__
\ No newline at end of file
+import importlib.metadata
+
+__version__ = importlib.metadata.version("buscolite")
diff --git a/buscolite/__main__.py b/buscolite/__main__.py
index 9d80fc9..19805bc 100755
--- a/buscolite/__main__.py
+++ b/buscolite/__main__.py
@@ -4,7 +4,7 @@
 import os
 import argparse
 import json
-from .__version__ import __version__
+from .__init__ import __version__
 from .help_formatter import MyParser, MyHelpFormatter
 from .busco import runbusco
 from .utilities import summary_writer
diff --git a/buscolite/__version__.py b/buscolite/__version__.py
deleted file mode 100755
index 83c22d4..0000000
--- a/buscolite/__version__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-VERSION = (24, 7, 29)
-
-__version__ = ".".join(map(str, VERSION))
diff --git a/buscolite/busco.py b/buscolite/busco.py
index 8602f2e..9188a46 100755
--- a/buscolite/busco.py
+++ b/buscolite/busco.py
@@ -1,11 +1,10 @@
-
 import os
 import tempfile
 import concurrent.futures
 from natsort import natsorted
 import pyhmmer
 import pyfastx
-from .__version__ import __version__
+from .__init__ import __version__
 from .log import startLogging
 from .search import (
     hmmer_search_single,
@@ -408,7 +407,13 @@ def runbusco(
         for b in CutOffs.keys():
             if b not in b_results:
                 missing.append(b)
-        stats = {"total": 0, "single-copy": 0, "fragmented": 0, "duplicated": 0, "missing": len(missing)}
+        stats = {
+            "total": 0,
+            "single-copy": 0,
+            "fragmented": 0,
+            "duplicated": 0,
+            "missing": len(missing),
+        }
         for k, v in natsorted(b_results.items()):
             stats["total"] += 1
             if (
diff --git a/buscolite/help_formatter.py b/buscolite/help_formatter.py
index 16741dc..622c8f7 100755
--- a/buscolite/help_formatter.py
+++ b/buscolite/help_formatter.py
@@ -2,7 +2,7 @@
 import os
 import argparse
 import shutil
-from .__version__ import __version__
+from .__init__ import __version__
 import textwrap as _textwrap
 
 
diff --git a/buscolite/utilities.py b/buscolite/utilities.py
index f453d0c..20c4b8d 100755
--- a/buscolite/utilities.py
+++ b/buscolite/utilities.py
@@ -4,7 +4,7 @@
 import os
 import errno
 from natsort import natsorted
-from .__version__ import __version__
+from .__init__ import __version__
 
 
 def summary_writer(result, missing, cmd, cfg, handle, mode="genome"):
@@ -33,7 +33,14 @@ def summary_writer(result, missing, cmd, cfg, handle, mode="genome"):
             if v["status"] == "missing":
                 handle.write(
                     "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(
-                        busco, v["status"], "", "", "", "", "", "", ""
+                        busco,
+                        v["status"],
+                        "",
+                        "",
+                        "",
+                        "",
+                        "",
+                        "",
                     )
                 )
             else:
diff --git a/pyproject.toml b/pyproject.toml
index b38bcdc..4e655cc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "buscolite"
-version = "24.7.29"
+version = "24.11.03"
 description = "busco analysis for gene predictions"
 readme = {file = "README.md", content-type = "text/markdown"}
 authors = [