[med-svn] [Git][med-team/pplacer][master] 5 commits: Remove test data & use multi-orig tarball instead

Mon Apr 11 11:45:57 BST 2022


Mohd  Bilal pushed to branch master at Debian Med / pplacer


Commits:
deac3c82 by Mohammed Bilal at 2022-04-11T10:05:08+00:00
Remove test data & use multi-orig tarball instead

- - - - -
e397eff6 by Mohammed Bilal at 2022-04-11T10:05:58+00:00
d/t/run-unit-test : Update tests

- - - - -
b2a6c01d by Mohammed Bilal at 2022-04-11T10:06:22+00:00
New upstream version 1.1~alpha19
- - - - -
d18e2b21 by Mohammed Bilal at 2022-04-11T10:06:34+00:00
Update upstream source from tag 'upstream/1.1_alpha19'

Update to upstream version '1.1~alpha19'
with Debian dir 76cd5e5f9192bb4b4e67de9fbceacce88a3c70e8
- - - - -
64f705d8 by Mohammed Bilal at 2022-04-11T16:11:46+05:30
Add script to fetch test data

- - - - -


25 changed files:

- − .gitignore
- − .gitmodules
- debian/tests/data/src/docco.css → debian-tests-data/src/docco.css
- debian/tests/data/src/p1z1r2.jplace → debian-tests-data/src/p1z1r2.jplace
- debian/tests/data/src/p1z1r34.jplace → debian-tests-data/src/p1z1r34.jplace
- debian/tests/data/src/p1z2r19.jplace → debian-tests-data/src/p1z2r19.jplace
- debian/tests/data/src/p4z1r2.jplace → debian-tests-data/src/p4z1r2.jplace
- debian/tests/data/src/p4z1r36.fasta → debian-tests-data/src/p4z1r36.fasta
- debian/tests/data/src/p4z2r22.jplace → debian-tests-data/src/p4z2r22.jplace
- debian/tests/data/vaginal_16s.refpkg/CONTENTS.json → debian-tests-data/vaginal_16s.refpkg/CONTENTS.json
- debian/tests/data/vaginal_16s.refpkg/RAxML_info.bv_refs_aln → debian-tests-data/vaginal_16s.refpkg/RAxML_info.bv_refs_aln
- debian/tests/data/vaginal_16s.refpkg/RAxML_result.bv_refs_aln → debian-tests-data/vaginal_16s.refpkg/RAxML_result.bv_refs_aln
- debian/tests/data/vaginal_16s.refpkg/bacteria16S_508_mod5.cm → debian-tests-data/vaginal_16s.refpkg/bacteria16S_508_mod5.cm
- debian/tests/data/vaginal_16s.refpkg/bv_refdata.csv → debian-tests-data/vaginal_16s.refpkg/bv_refdata.csv
- debian/tests/data/vaginal_16s.refpkg/bv_refs.sto → debian-tests-data/vaginal_16s.refpkg/bv_refs.sto
- debian/tests/data/vaginal_16s.refpkg/bv_refs_aln.fasta → debian-tests-data/vaginal_16s.refpkg/bv_refs_aln.fasta
- debian/tests/data/vaginal_16s.refpkg/phylo_model.json → debian-tests-data/vaginal_16s.refpkg/phylo_model.json
- debian/tests/data/vaginal_16s.refpkg/tax_table.csv → debian-tests-data/vaginal_16s.refpkg/tax_table.csv
- − debian/examples
- + debian/gbp.conf
- + debian/tests/README
- + debian/tests/get-test-data
- debian/tests/run-unit-test
- − docs/generated_rst/.gitignore
- − pam_src/.gitignore


Changes:

=====================================
.gitignore deleted
=====================================
@@ -1,23 +0,0 @@
-/_build
-TAGS
-*.mltop
-*.top
-*.native
-*.swp
-*.byte
-*.annot
-.ocamlinit
-.toplevel_history
-.latest-upload
-top_tests
-bin
-common_src/install_common_pprs.txt
-common_src/version.ml
-makefile
-docs/generated_rst/
-docs/_build/doctrees/
-wiki
-Session.vim
-_builds
-_projects
-_steps


=====================================
.gitmodules deleted
=====================================
@@ -1,3 +0,0 @@
-[submodule "docs/_build/html"]
-	path = docs/_build/html
-	url = git at github.com:matsen/pplacer.git


=====================================
debian/tests/data/src/docco.css → debian-tests-data/src/docco.css
=====================================


=====================================
debian/tests/data/src/p1z1r2.jplace → debian-tests-data/src/p1z1r2.jplace
=====================================


=====================================
debian/tests/data/src/p1z1r34.jplace → debian-tests-data/src/p1z1r34.jplace
=====================================


=====================================
debian/tests/data/src/p1z2r19.jplace → debian-tests-data/src/p1z2r19.jplace
=====================================


=====================================
debian/tests/data/src/p4z1r2.jplace → debian-tests-data/src/p4z1r2.jplace
=====================================


=====================================
debian/tests/data/src/p4z1r36.fasta → debian-tests-data/src/p4z1r36.fasta
=====================================


=====================================
debian/tests/data/src/p4z2r22.jplace → debian-tests-data/src/p4z2r22.jplace
=====================================


=====================================
debian/tests/data/vaginal_16s.refpkg/CONTENTS.json → debian-tests-data/vaginal_16s.refpkg/CONTENTS.json
=====================================


=====================================
debian/tests/data/vaginal_16s.refpkg/RAxML_info.bv_refs_aln → debian-tests-data/vaginal_16s.refpkg/RAxML_info.bv_refs_aln
=====================================


=====================================
debian/tests/data/vaginal_16s.refpkg/RAxML_result.bv_refs_aln → debian-tests-data/vaginal_16s.refpkg/RAxML_result.bv_refs_aln
=====================================


=====================================
debian/tests/data/vaginal_16s.refpkg/bacteria16S_508_mod5.cm → debian-tests-data/vaginal_16s.refpkg/bacteria16S_508_mod5.cm
=====================================


=====================================
debian/tests/data/vaginal_16s.refpkg/bv_refdata.csv → debian-tests-data/vaginal_16s.refpkg/bv_refdata.csv
=====================================


=====================================
debian/tests/data/vaginal_16s.refpkg/bv_refs.sto → debian-tests-data/vaginal_16s.refpkg/bv_refs.sto
=====================================


=====================================
debian/tests/data/vaginal_16s.refpkg/bv_refs_aln.fasta → debian-tests-data/vaginal_16s.refpkg/bv_refs_aln.fasta
=====================================


=====================================
debian/tests/data/vaginal_16s.refpkg/phylo_model.json → debian-tests-data/vaginal_16s.refpkg/phylo_model.json
=====================================


=====================================
debian/tests/data/vaginal_16s.refpkg/tax_table.csv → debian-tests-data/vaginal_16s.refpkg/tax_table.csv
=====================================


=====================================
debian/examples deleted
=====================================
@@ -1 +0,0 @@
-debian/tests/data/*


=====================================
debian/gbp.conf
=====================================
@@ -0,0 +1,4 @@
+[DEFAULT]
+pristine-tar=True
+filter=[ '.gitignore', '.travis.yml', '.git*' ]
+component=['debian-tests-data']


=====================================
debian/tests/README
=====================================
@@ -0,0 +1,4 @@
+Tests for stringtie
+===================
+
+The data for tests has been referenced from: http://github.com/fhcrc/microbiome-demo


=====================================
debian/tests/get-test-data
=====================================
@@ -0,0 +1,12 @@
+#!/bin/sh
+
+git clone https://github.com/fhcrc/microbiome-demo.git data
+find . -name '.git*' | xargs rm -rf
+cd data
+rm -rf $(ls -A | grep -vE "(src)|(vaginal_16s.refpkg)")
+cd ..
+tarball=$(dpkg-parsechangelog --file ../changelog | awk '/^Source:/ {print $2}')_$(dpkg-parsechangelog --file ../changelog | awk '/^Version:/ {print $2}' | cut -f1 -d-).orig-debian-tests-data.tar.gz
+tar --owner=root --group=root --mode=a+rX -cvzSf $tarball data
+rm -rf data.zip data/
+echo "Now move $tarball next to the new upstream tarball and gbp import it as usual"
+


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,5 +1,5 @@
 #!/bin/bash
-set -e
+set -ex
 
 pkg=pplacer
 CUR_DIR=`pwd`
@@ -10,20 +10,10 @@ 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 ${CUR_DIR}/ $AUTOPKGTEST_TMP
+cp ${CUR_DIR}/debian-tests-data/* -a "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
 
-echo -e "\e[93m\e[1mTest 1\e[0m"   # Running test defined in Makefile
-cd src
-make test
-echo -e "\e[92m\e[1mPASS\e[0m"
-make clean
-
-cd -
-
 echo "127b8f054fc0e2cade75c7922f06e919  p4z1r36.xml" >> checksums
 echo "eb8193d86364a6c5687199f4cd1b2caf  dist_matrix" >> checksums
 echo "0e738fe4fccf66d29c349af393393e8b  cluster.tre" >> checksums
@@ -49,6 +39,3 @@ guppy squash -c vaginal_16s.refpkg --out-dir . src/*.jplace
 
 md5sum --check checksums
 echo -e "\e[92m\e[1mPASS\e[0m"
-
-#cleanup
-rm -rf $(ls -A | grep -v src)


=====================================
docs/generated_rst/.gitignore deleted
=====================================
@@ -1 +0,0 @@
-*
\ No newline at end of file


=====================================
pam_src/.gitignore deleted
=====================================
@@ -1,3 +0,0 @@
-pam.o
-pam
-.sconsign.dblite



View it on GitLab: https://salsa.debian.org/med-team/pplacer/-/compare/596fc62d6579a8db78da39fe7400c98e85bcb0e9...64f705d86af17a6f81a47ab331087f082bac45d9

-- 
View it on GitLab: https://salsa.debian.org/med-team/pplacer/-/compare/596fc62d6579a8db78da39fe7400c98e85bcb0e9...64f705d86af17a6f81a47ab331087f082bac45d9
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