Andreas Tille pushed to branch master at Debian Med / phyx
Commits: 8ab2c63e by Andreas Tille at 2019-09-11T19:21:16Z Add changelog entry - - - - - 54631f6a by Andreas Tille at 2019-09-11T19:21:51Z debhelper-compat 12 - - - - - aae7183c by Andreas Tille at 2019-09-11T19:21:56Z Standards-Version: 4.4.0 - - - - - 18d4d890 by Andreas Tille at 2019-09-11T19:49:46Z Add autopkgtest - - - - - 5 changed files: - debian/changelog - − debian/compat - debian/control - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,25 @@ +phyx (0.999+ds-2) UNRELEASED; urgency=medium + + * Team upload + + [ Steffen Möller ] + * Add new d/u/metadata file + + [ Afif Elghraoui ] + * Remove myself from Uploaders + + [ Shayan Doust ] + * Port couple of python files from python2 to python3 + Closes: #937285 + * Set debhelper 12 from 11 + + [ Andreas Tille ] + * debhelper-compat 12 + * Standards-Version: 4.4.0 + * Add autopkgtest + + -- Shayan Doust <[email protected]> Wed, 11 Sep 2019 21:17:58 +0200 + phyx (0.999+ds-1) unstable; urgency=medium * New upstream version ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -12 ===================================== debian/control ===================================== @@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 12~), +Build-Depends: debhelper-compat (= 12), python3, liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, libatlas-cpp-0.6-dev, libarmadillo-dev -Standards-Version: 4.2.1 +Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/phyx Vcs-Git: https://salsa.debian.org/med-team/phyx.git Homepage: https://github.com/FePhyFoFum/phyx ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,93 @@ +#!/bin/bash +set -e + +pkg=phyx + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" + +cd pxaa2cdn_example && pxaa2cdn -a AA_Alignment.fa -n Unaligned_Nucleotide.fa -o CDN_aln.fa && cd .. + +cd pxbdfit_example && pxbdfit -t bd.tre -m yule && cd .. + +# cd pxbdsim_example && pxbdsim -e 100 -s -b 1 -d 0.5 -o output_tree_file && cd .. + +cd pxboot_example && pxboot -s Alignment -x 112233 -f 0.50 -o output_of_50_jackknife && cd .. + +cd pxboot_example && pxboot -s Alignment -p parts -o output_of_bootstrap && cd .. + +cd pxbp_example && pxbp -t Tree.tre -o bp_output && cd .. + +cd pxcat_example && pxcat -s *.fas *.fa *.phy -p Parts.txt -o Supermatrix.fa && cd .. + +cd pxclsq_example && pxclsq -s Alignment -p 0.6 && cd .. + +cd pxconsq_example && pxconsq -s Alignment && cd .. + +cd pxcontrates_example && pxcontrates -c contrates_file.txt -t contrates_tree.tre -a 1 && cd .. + +cd pxfqfilt_example && pxfqfilt -s fqfilt_test.fastq -m 10 && cd .. + +cd pxlog_example && pxlog -t *.trees -i && cd .. + +cd pxlog_example && pxlog -t *.trees -b 75 -n 2 -o some_output_filename && cd .. + +cd pxlssq_example && pxlssq -s Alignment && cd .. + +cd pxlstr_example && pxlstr -t Tree.tre && cd .. + +cd pxmrca_example && pxmrca -t mrca_test.tre -m mrca.txt && cd .. + +cd pxmrcacut_example && pxmrcacut -t tree -m mrca_file && cd .. + +cd pxmrcaname_example && pxmrcaname -t tree -m mrca_file && cd .. + +cd pxnj_example && pxnj -s Alignment.aln && cd .. + +cd pxnw_example && pxnw -s Alignment.aln && cd .. + +cd pxrecode_example && pxrecode -s Nucleotide.fa && cd .. + +cd pxrevcomp_example && pxrevcomp -s Nucleotide.fa && cd .. + +cd pxrls_example && pxrls -s SeqFile -c CurrentNames -n NewNames && cd .. + +cd pxrlt_example && pxrlt -t kingdoms.tre -c kingdoms.oldnames.txt -n kingdoms.newnames.txt && cd .. + +cd pxrms_example && pxrms -s Nucleotide.fa -f taxa_to_delete.txt && cd .. + +cd pxrmt_example && pxrmt -t rmt_test.tre -n s1,s6,s8 && cd .. + +cd pxrr_example && pxrr -t rr_test.tre -g s1,s2 && cd .. + +cd pxs2fa_pxs2phy_pxs2nex_example && \ + pxs2fa -s Alignment && \ + pxs2phy -s Alignment && \ + pxs2nex -s Alignment && \ + cd .. + +cd pxseqgen_example && pxseqgen -t seqgen_test.tre && cd .. + +cd pxseqgen_example && pxseqgen -t tree_file -o output_alignment -m .33,.33,.33,.33,.33,.33,2,.3,.3,.2,.5,.4,.2 && cd .. + +cd pxsstat_example && pxsstat -s Alignment.fa && cd .. + +cd pxstrec_example && pxstrec -d test.data.narrow -t test.tre -c config_stmap && cd .. + +cd pxsw_example && pxsw -s Alignment.fa && cd .. + +cd pxt2new_example && pxt2new -t Tree.nex && cd .. + +cd pxtlate_example && pxtlate -s Sequence.fa && cd .. + +cd pxtscale_example && pxtscale -t Tree -s 2.0 && cd .. + +cd pxupgma_example && pxupgma -s drosophila.aln && cd .. + +cd pxvcf2fa_example && pxvcf2fa -s vcf_file && cd .. View it on GitLab: https://salsa.debian.org/med-team/phyx/compare/4536ab937063e79342452a3b54a043ec17934563...18d4d89037074256b3bc3c6ec8a5c6ec939b614f -- View it on GitLab: https://salsa.debian.org/med-team/phyx/compare/4536ab937063e79342452a3b54a043ec17934563...18d4d89037074256b3bc3c6ec8a5c6ec939b614f You're receiving this email because of your account on salsa.debian.org.
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