[med-svn] [Git][med-team/spades][master] 5 commits: d/m/coronaspades.1.adoc: add manual page for coronaspades.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / spades


Commits:
9304c2be by Étienne Mollier at 2022-07-24T13:35:19+02:00
d/m/coronaspades.1.adoc: add manual page for coronaspades.

- - - - -
446da7df by Étienne Mollier at 2022-07-24T16:05:29+02:00
d/t/run-upstreams-tests: update to current binaries.

Notably, the truspades command is deprecated, so don't make it's
self-test failure critical.

- - - - -
ccdca122 by Étienne Mollier at 2022-07-24T16:21:09+02:00
d/links: create link for coronaspades.py manual.

- - - - -
ed5eacb0 by Étienne Mollier at 2022-07-24T17:34:51+02:00
NEWS: drafted entry about truspades deprecation.

- - - - -
bb3eeb69 by Étienne Mollier at 2022-07-24T17:38:16+02:00
update changelog, with notice about finishing NEWS

- - - - -


5 changed files:

- + debian/NEWS
- debian/changelog
- debian/links
- + debian/man_src/coronaspades.1.adoc
- debian/tests/run-upstreams-tests


Changes:

=====================================
debian/NEWS
=====================================
@@ -0,0 +1,20 @@
+spades (3.15.5+dfsg-1) UNRELEASED; urgency=medium
+
+  Since version 3.15, the truspades command is deprecated.  According to
+  upstream[1], the technology behind truspades is a thing of the past:
+
+  > Thanks for the report. truSPAdes is not maintained anymore for many reasons
+  > (the technology is dead, etc.), so these issues will likely be fixed in
+  > radical way when truSPAdes will be deprecated and removed
+
+  [1]: https://github.com/ablab/spades/issues/560#issuecomment-675915841
+
+  It is quite possible that the truspades version still provided by Debian Med
+  is not working well anymore.  At least it has been noticed that it failed its
+  self-test since version 3.15.5.  The test fails by not outputting the
+  assemble scaffolds file then supposed to be processed by the `bwa` program in
+  the sample workflow.
+
+  The command truspades will probably not make it beyond spades version 3.16.
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 24 Jul 2022 16:05:54 +0200


=====================================
debian/changelog
=====================================
@@ -1,13 +1,19 @@
 spades (3.15.5+dfsg-1) UNRELEASED; urgency=medium
 
+ TODO: NEWS: drafted entry about truspades deprecation, need polishing.
   * New upstream version 3.15.5+dfsg
   * d/patches/:
     + fix-privacy-breaches.patch: update badges list.
     + python3.patch: refresh.
     + 0003_accept-system-bwa.patch: unfuzz.
     + yaml_load.patch: unfuzz.
+  * d/m/coronaspades.1.adoc: add manual page for coronaspades.
+  * d/links: create a link for coronaspades.py manual.
+  * d/t/run-upstreams-tests: add self tests for plasmidspades and coronaspades.
+    Also, the truspades command is deprecated, so don't make it's self-test
+    failure critical.
 
- -- Étienne Mollier <emollier at debian.org>  Sun, 24 Jul 2022 07:41:58 +0200
+ -- Étienne Mollier <emollier at debian.org>  Sun, 24 Jul 2022 17:35:37 +0200
 
 spades (3.15.4+dfsg-3) unstable; urgency=medium
 


=====================================
debian/links
=====================================
@@ -15,4 +15,5 @@ usr/share/man/man1/truspades.1.gz /usr/share/man/man1/truspades.py.1.gz
 usr/share/man/man1/metaspades.1.gz /usr/share/man/man1/metaspades.py.1.gz
 usr/share/man/man1/plasmidspades.1.gz /usr/share/man/man1/plasmidspades.py.1.gz
 usr/share/man/man1/rnaspades.1.gz /usr/share/man/man1/rnaspades.py.1.gz
+usr/share/man/man1/coronaspades.1.gz /usr/share/man/man1/coronaspades.py.1.gz
 usr/share/spades/VERSION usr/libexec/spades/VERSION


=====================================
debian/man_src/coronaspades.1.adoc
=====================================
@@ -0,0 +1,18 @@
+= coronaspades(1)
+
+## NAME
+
+coronaspades - SPAdes genome assembler (coronaSPAdes mode)
+
+## SYNOPSIS
+
+*coronaspades* [options] -o <output_dir>
+
+## DESCRIPTION
+
+*coronaspades* runs **SPAdes** in coronaSPAdes mode. All parameters are
+identical to the regular SPAdes.
+
+## SEE ALSO
+
+spades(1)


=====================================
debian/tests/run-upstreams-tests
=====================================
@@ -8,6 +8,17 @@ trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
 cd $WORKDIR
 
 spades --test
-truspades --test
+coronaspades --test
 metaspades --test
+plasmidspades --test
 rnaspades --test
+
+# truspades is deprecated in v3.15 and may fail its own test suite.
+if command -v truspades > /dev/null
+then
+	if ! truspades --test
+	then echo 'W: truspades failed its self-test suite.'
+	fi
+else
+	echo 'W: truspades is not provided upstream anymore.'
+fi



View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/fbfcea010aef8ce5bd51ae473a8e6e7bee66b7c9...bb3eeb69b86200c3762d00ed8db339f2fb782912

-- 
View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/fbfcea010aef8ce5bd51ae473a8e6e7bee66b7c9...bb3eeb69b86200c3762d00ed8db339f2fb782912
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