[med-svn] [Git][med-team/pychopper][upstream] New upstream version 2.7.3

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Med / pychopper


Commits:
e8fe9efd by Pierre Gruet at 2023-06-18T14:19:43+02:00
New upstream version 2.7.3
- - - - -


3 changed files:

- CHANGELOG.md
- pychopper/__init__.py
- pychopper/scripts/pychopper.py


Changes:

=====================================
CHANGELOG.md
=====================================
@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v2.7.3]
+### Changed
+- Fixes for pandas v2 concat api changes
+- set default batchsize to 10,000
+
 ## [v2.7.2]
 ### Added
 - umi detection and extraction


=====================================
pychopper/__init__.py
=====================================
@@ -2,4 +2,4 @@
 
 __author__ = 'ONT Applications Group'
 __email__ = 'Apps at nanoporetech.com'
-__version__ = "2.7.2"
+__version__ = "2.7.3"


=====================================
pychopper/scripts/pychopper.py
=====================================
@@ -289,8 +289,8 @@ def main():
         '-t', metavar='threads', type=int, default=8,
         help="Number of threads to use (8).")
     parser.add_argument(
-        '-B', metavar='batch_size', type=int, default=1000000,
-        help="Maximum number of reads processed in each batch (1000000).")
+        '-B', metavar='batch_size', type=int, default=10000,
+        help="Maximum number of reads processed in each batch (10000).")
     parser.add_argument(
         '-D', metavar='read stats', type=str, default=None,
         help="Tab separated file with per-read stats (None).")
@@ -539,7 +539,7 @@ def main():
     if args.S is not None or args.r is not None:
         stdf = _process_stats(st)
         if tune_df is not None:
-            stdf = stdf.append(pd.DataFrame(tune_df))
+            stdf = pd.concat([stdf, pd.DataFrame(tune_df)])
 
     _detect_anomalies(st, config)
 



View it on GitLab: https://salsa.debian.org/med-team/pychopper/-/commit/e8fe9efdd432b0afd2a16973a7b8c037fd626b6c

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View it on GitLab: https://salsa.debian.org/med-team/pychopper/-/commit/e8fe9efdd432b0afd2a16973a7b8c037fd626b6c
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