1.0.13

- Made GenMine to export version with --version option
Changwanseo · May 17, 2024 · 646a59d · 646a59d
1 parent 477e878
commit 646a59d
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Showing 6 changed files with 36 additions and 12 deletions.
diff --git a/GenMine/GenMine.py b/GenMine/GenMine.py
@@ -1,6 +1,7 @@
 from Bio import Entrez
 from Bio import SeqIO
-from Bio.Blast.Applications import NcbiblastnCommandline
+
+# from Bio.Blast.Applications import NcbiblastnCommandline
 from Bio.Blast import NCBIXML
 from Bio.Seq import Seq
 import time
@@ -21,6 +22,8 @@
 
 log_file = None
 
+__version__ = "1.0.13"
+
 
 # Logging Functions
 def Time_now():
@@ -1160,12 +1163,14 @@ def Build_DB(DB_fasta, out):
     os.system(cmd)
 
 
+"""
 def BLASTn(query, db, evalue, out):
     blastn_cline = ncbiblastnCommandline(
         query=query, db=db, evalue=evalue, outfmt=7, out=out
     )
     Mes("BLAST: " + str(blastn_cline))
     blastn_cline()
+"""
 
 
 def classifier(json_in, out):

diff --git a/GenMine/__pycache__/GenMine.cpython-311.pyc b/GenMine/__pycache__/GenMine.cpython-311.pyc
diff --git a/GenMine/__pycache__/__init__.cpython-311.pyc b/GenMine/__pycache__/__init__.cpython-311.pyc
diff --git a/GenMine/command.py b/GenMine/command.py
@@ -1,5 +1,7 @@
 # GenMine_pypi/GenMine/command.py
+import sys
 import argparse
+from importlib.metadata import version
 
 
 class CommandParser:
@@ -10,28 +12,46 @@ def __init__(self) -> None:
         )
 
     def get_args(self) -> argparse.Namespace:
-
         self.parser.add_argument(
             "--email", "-e", help="Entrez Email, required", type=str, required=True
         )
         self.parser.add_argument(
-            "--genus", "-g", nargs="*", help="List of genus to find | File with genera in each line", type=str
+            "--genus",
+            "-g",
+            nargs="*",
+            help="List of genus to find | File with genera in each line",
+            type=str,
         )
         self.parser.add_argument(
-            "--accession", "-c", nargs="*", help="List of accessions to get | File with accessions in each line", type=str
+            "--accession",
+            "-c",
+            nargs="*",
+            help="List of accessions to get | File with accessions in each line",
+            type=str,
         )
         self.parser.add_argument(
             "--additional", "-a", nargs="*", help="additional terms", type=str
         )
-        self.parser.add_argument("--out", "-o", help="Out file path. Use previous result directory name for continue run", type=str)
+        self.parser.add_argument(
+            "--out",
+            "-o",
+            help="Out file path. Use previous result directory name for continue run",
+            type=str,
+        )
         self.parser.add_argument(
             "--max",
             "-m",
             help="Maximum length of sequence to search, in order to remove genomic sequences",
             type=int,
         )
-
-        '''
+
+        self.parser.add_argument(
+            "--version",
+            action="version",
+            version=f"GenMine {version('GenMine')}",
+        )
+
+        """
         self.parser.add_argument(
             "--start",
             "-s",
@@ -44,7 +64,6 @@ def get_args(self) -> argparse.Namespace:
             help="Final date of finding records, as term of YYYY-MM-DD",
             type=str,
         )
-        '''
-
+        """
 
         return self.parser.parse_args()
diff --git a/GenMine/meta.yaml b/GenMine/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "GenMine" %}
-{% set version = "1.0.12" %}
+{% set version = "1.0.13" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/GenMine-{{ version }}.tar.gz
-  sha256: 70208c1d8a311b9c4fa698ca69817a5ab147d29b30422e13564ec8d727a2f4b1
+  sha256: 091e9e4fe06864b26a3b5d36b87c76ad3df92c63a286366682b6f63e14f9cc80
 
 build:
   entry_points:

diff --git a/setup.py b/setup.py
@@ -3,7 +3,7 @@
 
 setup(
     name="GenMine",
-    version="1.0.12",
+    version="1.0.13",
     description="GenBank data miner for fungal taxonomists",
     author="Changwan Seo",
     author_email="[email protected]",