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 <[email protected]> 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 <[email protected]> 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__ = '[email protected]' -__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 You're receiving this email because of your account on salsa.debian.org.
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