[med-svn] [Git][med-team/ltrsift][master] Create ltrsift-sample package containing upstream sample data to enable...

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / ltrsift


Commits:
f85747dc by Andreas Tille at 2026-10-20T14:00:20+02:00
Create ltrsift-sample package containing upstream sample data to enable running more decent autopkgtest and enable users verifying functionality easily

- - - - -


6 changed files:

- debian/README.test
- debian/changelog
- debian/control
- + debian/ltrsift-sample.install
- − debian/not-installed
- debian/tests/run-unit-test


Changes:

=====================================
debian/README.test
=====================================
@@ -3,6 +3,7 @@ Notes on how this package can be tested.
 
 This package can be tested by running the provided test:
 
+    sudo apt install ltrsift-sample
     sh run-unit-test
 
 in order to confirm its integrity.


=====================================
debian/changelog
=====================================
@@ -6,6 +6,9 @@ ltrsift (1.0.2-12) UNRELEASED; urgency=medium
   * Reflow Uploaders field (cme)
   * Port from GTK+ 2 to GTK+ 3. Closes: #967603
   * Add autopkgtest checking the GTK+ 3 port.
+  * Create ltrsift-sample package containing upstream sample data to enable
+    running more decent autopkgtest and enable users verifying functionality
+    easily
 
  -- Andreas Tille <tille at debian.org>  Tue, 20 Oct 2026 11:20:34 +0200
 


=====================================
debian/control
=====================================
@@ -29,3 +29,20 @@ Description: postprocessing and classification of LTR retrotransposons
  structure in a hierarchical fashion, allowing the user to "sift" through the
  sometimes large results of de novo prediction software. It also offers
  customizable filtering and classification functionality.
+
+Package: ltrsift-sample
+Architecture: all
+Depends:
+ ${misc:Depends},
+Enhances:
+ ltrsift,
+Description: postprocessing and classification of LTR retrotransposons (sample data)
+ LTRsift is a graphical desktop tool for semi-automatic postprocessing of de
+ novo predicted LTR retrotransposon annotations, such as the ones generated by
+ LTRharvest and LTRdigest. Its user-friendly interface displays LTR
+ retrotransposon candidates, their putative families and their internal
+ structure in a hierarchical fashion, allowing the user to "sift" through the
+ sometimes large results of de novo prediction software. It also offers
+ customizable filtering and classification functionality.
+ .
+ This package contains example data to test this package.


=====================================
debian/ltrsift-sample.install
=====================================
@@ -0,0 +1 @@
+usr/sample_data	usr/share/doc/ltrsift


=====================================
debian/not-installed deleted
=====================================
@@ -1 +0,0 @@
-usr/sample_data


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,5 +1,5 @@
 #!/bin/sh
-set -eu
+set -e
 
 pkg=ltrsift
 
@@ -10,7 +10,7 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
-# cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+cp -a /usr/share/doc/${pkg}/sample_data "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
 
@@ -29,6 +29,10 @@ EOF
 ltrsift_encode "$TMP/test.fa" "$TMP/index"
 test -f "$TMP/index.esq"
 
+# Run the example provided upstream
+cd sample_data/
+sh ./prepare_encseqs
+
 # Start the GUI under Xvfb and make sure it stays alive. A timeout means the
 # main loop is running, which is the expected outcome of this smoke test.
 set +e



View it on GitLab: https://salsa.debian.org/med-team/ltrsift/-/commit/f85747dc600cd295db75e7e190ee566fa1f7a594

-- 
View it on GitLab: https://salsa.debian.org/med-team/ltrsift/-/commit/f85747dc600cd295db75e7e190ee566fa1f7a594
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