Merge pull request #57 from databio/dev

v0.2.0

Author: khoroshevskyi

README.md

@@ -19,8 +19,8 @@
 
 ---
 
-bedboss is a command-line pipeline that filters, standardizes, and calculates statistics for genomic interval data, 
-and enters the results into a BEDbase database. 
+BEDboss is a command-line management tool for BEDbase. It contains pipelines that filters, standardizes, and calculates statistics for genomic interval data, 
+functions that enters the results into a BEDbase database, deletes bed and bedsets from the database, and indexes the data to qdrant.
 
 ## Installation
 To install `bedboss` use this command: 

bedboss/__init__.py

@@ -5,18 +5,7 @@
 import logging
 
 
-# from bedboss.bedqc.bedqc import bedqc
-# from bedboss.bedmaker.bedmaker import BedMaker
-# from bedboss.bedstat.bedstat import bedstat
 from bedboss._version import __version__
-from bedboss.bedboss import (
-    run_all,
-    insert_pep,
-    bedqc,
-    bedstat,
-    run_bedbuncher,
-)
-from bedboss.bedmaker.bedmaker import BedMaker
 
 
 __package_name__ = "bedboss"
@@ -27,21 +16,14 @@
     "Ognen Duzlevski",
     "Jose Verdezoto",
     "Bingjie Xue",
+    "Donald Campbell",
 ]
 __email__ = "khorosh@virginia.edu"
 
 __all__ = [
     "__version__",
     "__package_name__",
     "__author__",
-    "bedboss",
-    "bedqc",
-    "bedmaker",
-    "BedMaker",
-    "bedstat",
-    "run_all",
-    "insert_pep",
-    "run_bedbuncher",
 ]
 
 _LOGGER = logmuse.init_logger("bedboss")

bedboss/__main__.py

@@ -1,15 +1,19 @@
 import sys
 import logmuse
 
-from bedboss.bedboss import main
-
+from bedboss.cli import app
 
 _LOGGER = logmuse.init_logger("bedboss")
 
 
+def main():
+    app(prog_name="bedboss")
+
+
 if __name__ == "__main__":
     try:
         main()
+
     except KeyboardInterrupt:
         print("Pipeline aborted.")
         sys.exit(1)

bedboss/_version.py

@@ -1 +1 @@
-__version__ = "0.1.0"
+__version__ = "0.2.0"