| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| setup.patch | Do not check existence of third party tools since these are removed. We are using Debian packaged tools | Andreas Tille <tille@debian.org> | not-needed | 2020-05-24 | ||
| use_debian_packaged_guppy_from_pplacer.patch | Use Debian packaged guppy and hmm* An if statement is added because copy_tool_to_lib is also called for the jar that is generated before the Python part of the build. |
Andreas Tille <tille@debian.org> | not-needed | 2020-08-19 | ||
| change_java_version_for_ant.patch | More recent version of Java suppresses some warnings | Pierre Gruet <pgt@debian.org> | not-needed | https://lists.debian.org/debian-med/2020/08/msg00104.html | 2021-09-25 | |
| java_build.patch | Adapting the build.xml file of ant to Debian policy There are no embedded jars to include. The classpath thus has to be changed to include Debian-packaged jars. The .java files should not be included in the target jars. |
Pierre Gruet <pgt@debian.org> | not-needed | 2021-09-25 | ||
| configuration_files_in_etc_and_per_user.patch | using configuration files that are in /etc or in ~/.sepp | Pierre Gruet <pgt@debian.org> | not-needed | 2020-10-08 | ||
| deactivating_log_test.patch | deactivating minor test relative to log verbosity level | Pierre Gruet <pgt@debian.org> | yes | 2020-10-05 | ||
| using_python3_interpreter.patch | Marking the Python interpreter as python3 This is to conform to Debian Python policy. | Pierre Gruet <pgt@debian.org> | yes | https://www.debian.org/doc/packaging-manuals/python-policy/programs.html#interpreter-directive | 2021-09-25 | |
| hmmbuild_path_for_testUPP.patch | use Debian path of hmmbuild in testUPP | Pierre Gruet <pgt@debian.org> | not-needed | 2021-09-26 | ||
| py310_collections_import.patch | fix collections import In python 3.10[1] deprecated aliases to Collections Abstract Base Classes from the collections module have been removed. These imports must be done from collections.abc. . 1. https://docs.python.org/3/whatsnew/3.10.html diff --git a/sepp/alignment.py b/sepp/alignment.py index ada5de8..61e9adb 100644 |
Andreas Hasenack <andreas@canonical.com> | yes | debian upstream | 2022-02-03 | |
| open-U-obsolete.patch | Drop obsolete "U" mode passed to open() The "U" mode has been deprecated in python since python3 and has had no effect. In python 3.11, it is now disallowed. Drop this mode flag that causes runtime failures. |
Steve Langasek <steve.langasek@ubuntu.com> | yes | 2023-01-24 |