[med-svn] [Git][med-team/python-pairix][master] try autopkgtest

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / python-pairix


Commits:
a77b2ba9 by Andreas Tille at 2020-06-14T00:29:19+02:00
try autopkgtest

- - - - -


5 changed files:

- debian/control
- + debian/python3-pairix-examples.install
- debian/rules
- debian/tests/control
- debian/tests/run-unit-test


Changes:

=====================================
debian/control
=====================================
@@ -16,6 +16,7 @@ Homepage: https://github.com/4dn-dcic/pairix
 
 Package: python3-pairix
 Architecture: any
+Section: python
 Depends: ${shlib:Depends},
          ${python3:Depends},
          ${misc:Depends}
@@ -36,3 +37,27 @@ Description: 1D/2D indexing and querying with a pair of genomic coordinates
  read the Pairs file from beginning to end. Pairix creates an index and
  uses it to access the file from a relevant position by taking advantage
  of bgzf compression, allowing for a fast query on large files.
+
+Package: python3-pairix-examples
+Architecture: all
+Depends: ${misc:Depends}
+Enhances: python3-pairix
+Description: 1D/2D indexing and querying with a pair of genomic coordinates (examples)
+ Pairix is a tool for indexing and querying on a block-compressed text
+ file containing pairs of genomic coordinates.
+ .
+ Pairix is a stand-alone C program that was written on top of tabix as a
+ tool for the 4DN-standard pairs file format describing Hi-C data:
+ pairs_format_specification.md
+ .
+ However, Pairix can be used as a generic tool for indexing and querying
+ any bgzipped text file containing genomic coordinates, for either 2D- or
+ 1D- indexing and querying.
+ .
+ For example: given the custom text file below, you want to extract
+ specific lines from the Pairs file further below. An awk command would
+ read the Pairs file from beginning to end. Pairix creates an index and
+ uses it to access the file from a relevant position by taking advantage
+ of bgzf compression, allowing for a fast query on large files.
+ .
+ This package contains some example data to test the package.


=====================================
debian/python3-pairix-examples.install
=====================================
@@ -0,0 +1 @@
+test	usr/share/doc/python2-pairix/examples


=====================================
debian/rules
=====================================
@@ -4,5 +4,13 @@
 
 export PYBUILD_NAME=pairix
 
+export PYBUILD_BEFORE_TEST=cp -a $(CURDIR)/samples {build_dir}; cp -a $(CURDIR)/VERSION.txt {build_dir};
+
 %:
 	dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_installexamples:
+	dh_installexamples
+	mkdir -p debian/python3-$(PYBUILD_NAME)-examples/usr/share/doc/python3-$(PYBUILD_NAME)/examples
+	mv debian/python3-$(PYBUILD_NAME)/usr/lib/python3*/dist-packages/samples debian/python3-$(PYBUILD_NAME)-examples/usr/share/doc/python3-$(PYBUILD_NAME)/examples
+	mv debian/python3-$(PYBUILD_NAME)/usr/lib/python3*/dist-packages/VERSION.txt debian/python3-$(PYBUILD_NAME)-examples/usr/share/doc/python3-$(PYBUILD_NAME)/examples


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
 Tests: run-unit-test
-Depends: @
+Depends: @, python3-pytest
 Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,7 +1,7 @@
 #!/bin/bash
 set -e
 
-pkg=#PACKAGENAME#
+pkg=python3-pairix
 
 export LC_ALL=C.UTF-8
 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
@@ -16,4 +16,4 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
 
-#do_stuff_to_test_package#
+pytest-3



View it on GitLab: https://salsa.debian.org/med-team/python-pairix/-/commit/a77b2ba9c3d289a3cbddc456ce6763f766b09f37

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View it on GitLab: https://salsa.debian.org/med-team/python-pairix/-/commit/a77b2ba9c3d289a3cbddc456ce6763f766b09f37
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