[med-svn] [Git][med-team/sepp][master] 3 commits: Dropping U mode in open() invocations

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / sepp


Commits:
ade98c56 by Pierre Gruet at 2023-01-25T12:39:16+01:00
Dropping U mode in open() invocations

- - - - -
8dddfe94 by Pierre Gruet at 2023-01-25T12:40:42+01:00
routine-update: Standards-Version: 4.6.2

- - - - -
4ba8cab5 by Pierre Gruet at 2023-01-25T12:41:16+01:00
routine-update: Ready to upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/open-U-obsolete.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+sepp (4.5.1+really4.5.1+dfsg-5) unstable; urgency=medium
+
+  * Dropping "U" mode from open() invocations, thanks to Steve Langasek!
+    (Closes: #1029580)
+  * Standards-Version: 4.6.2 (routine-update)
+
+ -- Pierre Gruet <pgt at debian.org>  Wed, 25 Jan 2023 12:41:16 +0100
+
 sepp (4.5.1+really4.5.1+dfsg-4) unstable; urgency=medium
 
   * Updating d/watch after a change in the Github layout


=====================================
debian/control
=====================================
@@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 13),
                ncbi-blast+ <!nocheck>,
                pplacer <!nocheck>,
                hmmer <!nocheck>
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/sepp
 Vcs-Git: https://salsa.debian.org/med-team/sepp.git
 Homepage: https://github.com/smirarab/sepp/


=====================================
debian/patches/open-U-obsolete.patch
=====================================
@@ -0,0 +1,49 @@
+Description: 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.
+Author: Steve Langasek <steve.langasek at ubuntu.com>
+Forwarded: https://github.com/smirarab/sepp/issues/124
+Reviewed-by: Pierre Gruet <pgt at debian.org>
+Last-Update: 2023-01-24
+
+--- a/sepp/alignment.py
++++ b/sepp/alignment.py
+@@ -108,7 +108,7 @@
+     file_obj = None
+     if isinstance(src, str):
+         try:
+-            file_obj = open(src, "rU")
++            file_obj = open(src, "r")
+         except IOError:
+             print(("The file `%s` does not exist, exiting gracefully" % src))
+     elif isinstance(src, filetypes):
+@@ -291,7 +291,7 @@
+         If duplicate sequence names are encountered then the old name will
+         be replaced.
+         """
+-        file_obj = open(filename, 'rU')
++        file_obj = open(filename, 'r')
+         return self.read_file_object(file_obj, file_format=file_format)
+ 
+     def read_file_object(self, file_obj, file_format='FASTA'):
+@@ -582,7 +582,7 @@
+         columns. Labels insertion columns with special labels and labels the
+         rest of columns (i.e. original columns) sequentially.
+         """
+-        handle = open(path, 'rU')
++        handle = open(path, 'r')
+         insertions = None
+         if aformat.lower() == "stockholm":
+             insertions = self._read_sto(handle)
+--- a/sepp/tree.py
++++ b/sepp/tree.py
+@@ -314,7 +314,7 @@
+ 
+     def read_tree_from_file(self, treefile, file_format):
+         dataset = Dataset()
+-        dataset.read(open(treefile, 'rU'), schema=file_format)
++        dataset.read(open(treefile, 'r'), schema=file_format)
+         dendropy_tree = dataset.trees_blocks[0][0]
+         self._tree = dendropy_tree
+         self.n_leaves = self.count_leaves()


=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ deactivating_log_test.patch
 using_python3_interpreter.patch
 hmmbuild_path_for_testUPP.patch
 py310_collections_import.patch
+open-U-obsolete.patch



View it on GitLab: https://salsa.debian.org/med-team/sepp/-/compare/9117831622906a23e3aca4bbcc061530494c1de1...4ba8cab591159d6b61bf6566ba86d53c11f66b86

-- 
View it on GitLab: https://salsa.debian.org/med-team/sepp/-/compare/9117831622906a23e3aca4bbcc061530494c1de1...4ba8cab591159d6b61bf6566ba86d53c11f66b86
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