[med-svn] [Git][med-team/q2cli][master] 8 commits: More tests to run-unit-test
Étienne Mollier
gitlab at salsa.debian.org
Sat Dec 12 11:44:25 GMT 2020
Étienne Mollier pushed to branch master at Debian Med / q2cli
Commits:
b3e374b1 by Étienne Mollier at 2020-12-12T11:09:21+01:00
More tests to run-unit-test
- - - - -
6c15489a by Étienne Mollier at 2020-12-12T11:09:43+01:00
routine-update: New upstream version
- - - - -
392b6192 by Étienne Mollier at 2020-12-12T11:09:44+01:00
New upstream version 2020.11.1
- - - - -
b18ee1c7 by Étienne Mollier at 2020-12-12T11:09:45+01:00
Update upstream source from tag 'upstream/2020.11.1'
Update to upstream version '2020.11.1'
with Debian dir 8376effb30321c7d254e7a67d2711de25a1fd64d
- - - - -
3e6e6199 by Étienne Mollier at 2020-12-12T11:10:54+01:00
routine-update: Ready to upload to unstable
- - - - -
cacfaaac by Étienne Mollier at 2020-12-12T11:16:49+01:00
add myself to uploaders
- - - - -
11329dde by Étienne Mollier at 2020-12-12T11:19:14+01:00
Bump dependency on qiime (>= 2020.11.1)
- - - - -
31849e00 by Étienne Mollier at 2020-12-12T12:41:34+01:00
improved autopkgtest coverage
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/tests/control
- debian/tests/run-unit-test
- q2cli/_version.py
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+q2cli (2020.11.1-1) unstable; urgency=medium
+
+ * Added enough tests do drop the "superficial" marker. (Closes: #976271)
+ * Add myself to Uploaders.
+ * Bump dependency on qiime (>= 2020.11.1)
+
+ -- Étienne Mollier <etienne.mollier at mailoo.org> Sat, 12 Dec 2020 11:09:49 +0100
+
q2cli (2020.11.0-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
Source: q2cli
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Liubov Chuprikova <chuprikovalv at gmail.com>
+Uploaders: Liubov Chuprikova <chuprikovalv at gmail.com>,
+ Étienne Mollier <etienne.mollier at mailoo.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -8,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),
python3,
python3-pytest <!nocheck>,
python3-setuptools,
- qiime (>= 2020.11.0),
+ qiime (>= 2020.11.1),
python3-click,
python3-nose,
Standards-Version: 4.5.1
@@ -22,7 +23,7 @@ Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
- qiime,
+ qiime (>= 2020.11.1),
python3-setuptools,
python3-click
Description: Click-based command line interface for QIIME 2
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @
-Restrictions: allow-stderr, superficial
+Depends: @, q2-sample-classifier, q2-feature-table, file
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -11,6 +11,118 @@ cd "${AUTOPKGTEST_TMP}"
export HOME=${HOME:-$PWD}
-/usr/bin/qiime --help
+QZA_SAMPLE="/usr/lib/python3/dist-packages/q2_sample_classifier/tests/data/vaw.qza"
+if [ ! -r "$QZA_SAMPLE" ]
+then
+ cat >&2 <<-ERR
+ error: could not find sample data: $QZA_SAMPLE
+ Please install the following package:
+ - q2-sample-classifier
+ - q2-feature-table
+ ERR
+ exit 1
+fi
+
+# TODO: same tests but with recommended dependencies!
+# This is important since there is a huge change of behavior, and
+# extensions may potentially break the qiime command as I am seeing with
+# python3-sklearn at the moment.
+set -v
+# 0. the basics
+ qiime --version
+
+# 1. help messages
+ qiime --help
+ qiime info --help
+ qiime tools --help
+ qiime dev --help
+ qiime tools citations --help
+ qiime tools export --help
+ qiime tools extract --help
+ qiime tools import --help
+ qiime tools inspect-metadata --help
+ qiime tools peek --help
+ qiime tools validate --help
+ qiime tools view --help
+ qiime dev export-default-theme --help
+ qiime dev import-theme --help
+ qiime dev refresh-cache --help
+ qiime dev reset-theme --help
+
+# 2. info command
+ qiime info
+
+# 3. tools commands
+ qiime tools
+
+ qiime tools citations "$QZA_SAMPLE" > citations.bib
+ file citations.bib | grep -qi 'bibtex'
+
+ qiime tools export --input-path "$QZA_SAMPLE" --output-path .
+ file feature-table.biom | grep -qi 'Hierarchical Data Format'
+
+ qiime tools extract --input-path "$QZA_SAMPLE"
+ cd 861451cc-c250-43fc-818a-ddc2159dbe25
+ md5sum --check checksums.md5
+ cd -
+
+ qiime tools inspect-metadata "$QZA_SAMPLE" --tsv > metadata.tsv
+ qiime tools inspect-metadata "$QZA_SAMPLE" --no-tsv
+
+ qiime tools peek "$QZA_SAMPLE"
+
+ qiime tools import --show-importable-types
+ qiime tools import --show-importable-formats
+ qiime tools import \
+ --type 'FeatureTable[Frequency]' \
+ --input-path '861451cc-c250-43fc-818a-ddc2159dbe25/data' \
+ --output-path artifact.qza
+ file artifact.qza | grep -qi 'zip archive data'
+
+ qiime tools validate artifact.qza
+
+ # TODO test qiime tools view, missing Vizualization data at the moment,
+ # most likely available under the form of *.qvz files.
+
+# 4. dev commands
+ qiime dev
+ qiime dev export-default-theme --output-path file.theme
+ diff file.theme - <<-END
+ [option]
+ fg = blue
+
+ [type]
+ fg = green
+
+ [default_arg]
+ fg = magenta
+
+ [command]
+ fg = blue
+
+ [emphasis]
+ underline = True
+
+ [problem]
+ fg = yellow
+
+ [warning]
+ fg = yellow
+ bold = True
+
+ [error]
+ fg = red
+ bold = True
+
+ [required]
+ underline = True
+
+ [success]
+ fg = green
+
+ END
+ qiime dev import-theme --theme file.theme
+ qiime dev refresh-cache
+ yes | qiime dev reset-theme
echo "\nRESULTS: OK\n"
=====================================
q2cli/_version.py
=====================================
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
- git_refnames = " (HEAD -> master, tag: 2020.11.0)"
- git_full = "e09576b507ecee9df78ed142aacad6dd595654ca"
- git_date = "2020-11-25 17:13:09 +0000"
+ git_refnames = " (tag: 2020.11.1)"
+ git_full = "cf25aa05a20ac823fb1f447d244f6801d083a713"
+ git_date = "2020-12-05 20:44:48 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
View it on GitLab: https://salsa.debian.org/med-team/q2cli/-/compare/aef444bbfd5c9ac840367a8d6f2f9e221527c44b...31849e00479ac2300aa1e31e59b1870515379398
--
View it on GitLab: https://salsa.debian.org/med-team/q2cli/-/compare/aef444bbfd5c9ac840367a8d6f2f9e221527c44b...31849e00479ac2300aa1e31e59b1870515379398
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