[med-svn] [Git][med-team/q2-feature-classifier][master] 4 commits: add build dir to PYTHONPATH

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / q2-feature-classifier


Commits:
3229570c by Étienne Mollier at 2021-01-27T18:37:28+01:00
add build dir to PYTHONPATH

- - - - -
9068af8a by Étienne Mollier at 2021-01-27T19:48:43+01:00
add vsearch.patch

- - - - -
6fd52326 by Étienne Mollier at 2021-01-27T19:52:13+01:00
vsearch.patch dep3 header

- - - - -
bb5186c8 by Étienne Mollier at 2021-01-27T19:52:26+01:00
update changelog

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/series
- + debian/patches/vsearch.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -15,6 +15,10 @@ q2-feature-classifier (2020.11.1-1) UNRELEASED; urgency=medium
   * Build-Depends: q2-taxa
     Closes: #974839
 
+  [ Étienne Mollier ]
+  * Add build directory to PYTHONPATH for dh_auto_test.
+  * Add vsearch.patch to fix --search_exact invalid options.
+
  -- Liubov Chuprikova <chuprikovalv at gmail.com>  Sat, 07 Sep 2019 13:41:46 +0200
 
 q2-feature-classifier (2019.4.0-1) unstable; urgency=medium


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+vsearch.patch


=====================================
debian/patches/vsearch.patch
=====================================
@@ -0,0 +1,25 @@
+Description: fix failure to invoke vsearch --search_exact
+ TODO: confirm simply dropping options is the proper approach
+Author: Étienne Mollier <etienne.mollier at mailoo.org>
+Forwarded: no
+Last-Update: 2021-01-27
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- q2-feature-classifier.orig/q2_feature_classifier/_vsearch.py
++++ q2-feature-classifier/q2_feature_classifier/_vsearch.py
+@@ -50,6 +50,15 @@
+            '--threads', str(threads)]
+     if search_exact:
+         cmd[1] = '--search_exact'
++        # These options are not compatible with a --search_exact command.
++        cmd.remove('--id')
++        cmd.remove(str(perc_identity))
++        cmd.remove('--maxaccepts')
++        cmd.remove(str(maxaccepts))
++        cmd.remove('--maxrejects')
++        cmd.remove(str(maxrejects))
++        cmd.remove('--query_cov')
++        cmd.remove(str(query_cov))
+     if top_hits_only:
+         cmd.append('--top_hits_only')
+     if output_no_hits:


=====================================
debian/rules
=====================================
@@ -14,6 +14,7 @@ export PYBUILD_BEFORE_INSTALL=rm -rvf {build_dir}/q2-feature-classifier.egg-* \
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	PYTHONPATH=$(CURDIR) \
 	dh_auto_test -- -s custom --test-args="cd {build_dir}; py.test-3 --cov=q2_feature_classifier"
 endif
 



View it on GitLab: https://salsa.debian.org/med-team/q2-feature-classifier/-/compare/2a328d9d9885f043056ca7e7e22eb5c40ef10817...bb5186c8ce72d8ec8088db7f85246209950c38b5

-- 
View it on GitLab: https://salsa.debian.org/med-team/q2-feature-classifier/-/compare/2a328d9d9885f043056ca7e7e22eb5c40ef10817...bb5186c8ce72d8ec8088db7f85246209950c38b5
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