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 = [email protected]: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 You're receiving this email because of your account on salsa.debian.org.
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