[med-svn] [Git][med-team/quast][master] Working on lintian erros - tests seem fine

Wed Aug 25 00:16:47 BST 2021


Steffen Möller pushed to branch master at Debian Med / quast


Commits:
4ad40d3f by Steffen Moeller at 2021-08-25T01:16:16+02:00
Working on lintian erros - tests seem fine

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/quast.links
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,6 +1,21 @@
 quast (5.0.2+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #963618)
-  * Builds, but tests fail - see d/TODO
+  * Seems fine, only some Lintian errors for embedded JavaScript need to be
+    addressed:
+E: quast source: source-is-missing quast_libs/html_saver/static/bootstrap/bootstrap-tooltip-5px-lower.min.js
+E: quast source: source-is-missing quast_libs/html_saver/static/bootstrap/bootstrap.min.js
+E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.js line length is 2964 characters (>512)
+E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.navigate.js line length is 1984 characters (>512)
+E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.pie.js line length is 259 characters (>256)
+E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.resize.js line length is 863 characters (>512)
+E: quast source: source-is-missing quast_libs/html_saver/static/ie_html5.js line length is 2252 characters (>512)
+E: quast source: source-is-missing quast_libs/html_saver/static/jquery-1.7.2.min.js
+W: quast: embedded-javascript-library usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery.css please use libjs-jquery
+W: quast: no-manual-page usr/bin/icarus.py
+W: quast: no-manual-page usr/bin/metaquast.py
+W: quast: no-manual-page usr/bin/quast-lg.py
+W: quast: no-manual-page usr/bin/quast.py
+
 
  -- Andreas Tille <tille at debian.org>  Wed, 22 Apr 2020 15:30:18 +0200


=====================================
debian/control
=====================================
@@ -17,7 +17,6 @@ Build-Depends: debhelper-compat (= 13),
 #               hmmer,
 #               bwa,
 #               bedtools,
-#               busco,
 #               ncbi-blast+,
 #               sambamba
 Standards-Version: 4.5.0
@@ -45,7 +44,10 @@ Depends: ${shlibs:Depends},
          busco,
          tigr-glimmer,
          python-matplotlib,
-         python3-joblib
+         python3-joblib,
+         libjs-excanvas,
+         libjs-jquery,
+         libjs-jquery-ui
 Description: Quality Assessment Tool for Genome Assemblies
  QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST
  project.  It works both with and without a given reference genome.


=====================================
debian/quast.links
=====================================
@@ -0,0 +1,8 @@
+usr/share/javascript/excanvas/excanvas.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/excanvas.js
+usr/share/javascript/excanvas/excanvas.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/excanvas.min.js
+usr/share/javascript/jquery/jquery.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/jquery.js
+usr/share/javascript/jquery/jquery.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/jquery.min.js
+usr/share/javascript/jquery-ui/ui/jquery-1-7.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-1.7.2.min.js
+usr/share/javascript/jquery/jquery.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-1.8.2.js
+usr/share/javascript/jquery/jquery.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-1.8.2.min.js
+usr/share/javascript/jquery-ui/jquery-ui.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-ui.js


=====================================
debian/rules
=====================================
@@ -1,19 +1,10 @@
 #!/usr/bin/make -f
 
-# DH_VERBOSE := 1
+DH_VERBOSE := 1
 
 %:
 	dh $@ --with python3 --buildsystem=pybuild
 
-override_dh_auto_clean:
-	dh_auto_clean
-	rm -f quast_libs/busco/hmmsearch
-	find quast_libs -name "*.o" -delete
-	rm -f quast_libs/glimmer/glimmerhmm quast_libs/glimmer/src/make.err quast_libs/glimmer/src/make.log
-	rm -f quast_libs/version.py
-	# files generated while testing
-	rm -f quast_test_output/quast.log quast_test_output/quast_corrected_input/contigs_1.fasta quast_test_output/quast_corrected_input/contigs_2.fasta quast_test_output/quast_corrected_input/reference.fasta
-
 override_dh_install:
 	dh_install
 	find debian -name LICENSE.txt -delete
@@ -22,3 +13,22 @@ override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	PATH=$PATH:. ./setup.py test
 endif
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -rf quast_test_output
+	rm -f quast_libs/busco/hmmsearch
+	find quast_libs -name "*.o" -delete
+	rm -f quast_libs/glimmer/glimmerhmm quast_libs/glimmer/src/make.err quast_libs/glimmer/src/make.log
+	rm -f quast_libs/version.py
+	#$(MAKE) -C quast_libs/MUMmer/ clean >/dev/null 2>/dev/null
+	rm -f   quast_libs/MUMmer/make.*
+	#$(MAKE) -C quast_libs/glimmer/src/ clean >/dev/null 2>/dev/null
+	rm -f   quast_libs/glimmer/src/make.*
+	rm -f   *.pyc
+	rm -f   quast_libs/*.pyc
+	rm -f   quast_libs/html_saver/*.pyc
+	rm -f   quast_libs/site_packages/*/*.pyc
+	#$(MAKE) -C quast_libs/bwa clean >/dev/null 2>/dev/null
+	rm -rf  quast_libs/gridss*
+	rm -rf  quast_libs/blast



View it on GitLab: https://salsa.debian.org/med-team/quast/-/commit/4ad40d3fbf2fe943311d95ebb2b6c8c098763215

-- 
View it on GitLab: https://salsa.debian.org/med-team/quast/-/commit/4ad40d3fbf2fe943311d95ebb2b6c8c098763215
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