[med-svn] [Git][med-team/pychopper][master] 7 commits: New upstream version 2.7.3

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / pychopper


Commits:
e8fe9efd by Pierre Gruet at 2023-06-18T14:19:43+02:00
New upstream version 2.7.3
- - - - -
d41f5e67 by Pierre Gruet at 2023-06-18T14:22:30+02:00
Update upstream source from tag 'upstream/2.7.3'

Update to upstream version '2.7.3'
with Debian dir 1598aa681d0ca07ba55b038b8da50bd6cec7901a
- - - - -
61b5aefc by Pierre Gruet at 2023-06-18T14:23:27+02:00
Raising Standards version to 4.6.2 (no change)

- - - - -
b7aa8e71 by Pierre Gruet at 2023-06-18T14:29:05+02:00
Adding a note in d/README.source about the non-free license of future versions

- - - - -
2fff2e98 by Pierre Gruet at 2023-06-18T14:29:38+02:00
Updating changelog

- - - - -
b7111e06 by Pierre Gruet at 2023-06-18T15:22:12+02:00
Removing an unused Lintian override

- - - - -
f9e154ee by Pierre Gruet at 2023-06-18T15:22:26+02:00
Upload to unstable

- - - - -


7 changed files:

- CHANGELOG.md
- + debian/README.source
- debian/changelog
- debian/control
- − debian/lintian-overrides
- 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


=====================================
debian/README.source
=====================================
@@ -0,0 +1,13 @@
+Version 2.7.3 is the last one that is licensed under MPL-2.0. Upstream has
+switched to some license with restriction of use for "Research purposes" since
+version 2.7.4.
+
+See the discussion at
+    https://github.com/epi2me-labs/pychopper/issues/27
+and possibly follow-up documented on
+    https://wiki.debian.org/DebianMed/SoftwareLiberation
+
+If we want to keep pychopper in main, then we are stuck with version 2.7.3 for
+the moment.
+
+ -- Pierre Gruet <pgt at debian.org>  Sun, 18 Jun 2023 14:27:19 +0200


=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+pychopper (2.7.3-1) unstable; urgency=medium
+
+  * Team upload
+  * New upstream version 2.7.3
+  * Raising Standards version to 4.6.2 (no change)
+  * Adding a note in d/README.source about the non-free license of future
+    versions
+  * Removing an unused Lintian override
+
+ -- Pierre Gruet <pgt at debian.org>  Sun, 18 Jun 2023 15:22:18 +0200
+
 pychopper (2.7.2-1) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/control
=====================================
@@ -29,7 +29,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-hypothesis <!nocheck>,
                python3-pytest-mock <!nocheck>,
                xonsh <!nocheck>
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Homepage: https://github.com/epi2me-labs/pychopper
 Vcs-Browser: https://salsa.debian.org/med-team/pychopper
 Vcs-Git: https://salsa.debian.org/med-team/pychopper.git


=====================================
debian/lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-python3-pychopper: script-with-language-extension usr/bin/*.*


=====================================
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/-/compare/5dfca39215069474f8cd0136a501875bd31c915b...f9e154ee3ff687251f1998bac173c584c17ee17c

-- 
View it on GitLab: https://salsa.debian.org/med-team/pychopper/-/compare/5dfca39215069474f8cd0136a501875bd31c915b...f9e154ee3ff687251f1998bac173c584c17ee17c
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