Shruti Sridhar pushed to branch master at Debian Med / prime-phylo
Commits: 98d3cc33 by Shruti Sridhar at 2021-05-20T16:35:31+05:30 Add test data - - - - - 840c7d69 by Shruti Sridhar at 2021-05-20T16:37:01+05:30 Add autopkgtests - - - - - 1539fc00 by Shruti Sridhar at 2021-05-20T16:38:17+05:30 Install docs - - - - - f14fb466 by Shruti Sridhar at 2021-05-20T16:50:08+05:30 Update changelog - - - - - 10 changed files: - + debian/README.test - debian/changelog - + debian/docs - + debian/examples - + debian/tests/control - + debian/tests/data/gse - + debian/tests/data/hostfile - + debian/tests/data/seqfile - + debian/tests/data/treefile - + debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,14 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +This package can be tested by running the provided test: + + sh run-unit-test + +in order to confirm its integrity. + +Notes on the files used for testing +──────────────────────────────────────── +Files: debian/tests/data/* +Source: https://github.com/arvestad/jprime/tree/master/sample_data + ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +prime-phylo (1.0.11-9) UNRELEASED; urgency=medium + + * Add test data + * Add autopkgtests + * Install docs + + -- Shruti Sridhar <[email protected]> Thu, 20 May 2021 16:46:36 +0530 + prime-phylo (1.0.11-9) unstable; urgency=medium * Team Upload. ===================================== debian/docs ===================================== @@ -0,0 +1,3 @@ +README +debian/README* +debian/tests/run-unit-test \ No newline at end of file ===================================== debian/examples ===================================== @@ -0,0 +1 @@ +debian/tests/data/* \ No newline at end of file ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/data/gse ===================================== @@ -0,0 +1,11 @@ +Oryctolagus_cuniculus_1 Oryctolagus_cuniculus +Cavia_porcellus_1 Cavia_porcellus +Cavia_porcellus_2 Cavia_porcellus +Mus_musculus_1 Mus_musculus +Oryctolagus_cuniculus_2 Oryctolagus_cuniculus +Cavia_porcellus_3 Cavia_porcellus +Mus_musculus_2 Mus_musculus +Equus_caballus_1 Equus_caballus +Felis_catus_1 Felis_catus +Felis_catus_2 Felis_catus +Canis_lupus_1 Canis_lupus ===================================== debian/tests/data/hostfile ===================================== @@ -0,0 +1 @@ +(((Oryctolagus_cuniculus:89.9, (Cavia_porcellus:78.3,Mus_musculus:78.3):11.6):11.8, (Equus_caballus:80.8, (Felis_catus:55.7, Canis_lupus:55.7):25.1):20.9)):41.0; ===================================== debian/tests/data/seqfile ===================================== @@ -0,0 +1,22 @@ +>Canis_lupus_1 +LVCRFITVIFDLYDDFNNFLDILKAYKGMFSNDYCYNMLLQRRGVRFAIPGNSQHLVNWLKLIGARVEPAASSVFHASTSWDQRKTSIGKGHGIYYEYGNVLSDAMAVQCEILGGHADLTYQKDGIGNRVLITVVRYMDRYAADNLRSWQVEALDGGQLTDMCAVICGYEDEGTCRKALPNLDRKATGEDLFKVKSSRRFTTNVMSFFHQTSERTETTIVEVPDLNCVCPDITVGLLQTPSMEIWAPTRIPGSIMKGEASSNSKDMSVWDGIIATTQLVGDNNCYFLEARKALPNPSAFP +>Cavia_porcellus_1 +VLCRFLTVIFALYDDFNRFLDILKAYKGMFSNCYCYNMLVTRRGVRFAIPGNSQHLVNWLKTIGGRVEPAAANVFEANTSWDQRKTSIGKDHGIYYEYGNTTPVAMAVQCDILGDHAGLTYQQDGIGNRVNITVLGYMDRYAVDTLLVWQVQIFDGGQYTDMCAVVCGYSDEYTCRKTLPNLDRKASGEDVFKAKVSRRFTINVMSFFHQTSERTKTVGVEVPDLNCVCSGTTAGLLQTPSMEKWAPTKMSSAIMKGEGGSNKSDMSVGVVIVATLQLTGDANCYFLETRKVLLNPSAFP +>Cavia_porcellus_2 +TLCRFMTVIFNAYDDFNRFLDILISYKGMFADRYCLNMLLTRRGVRFTLPGNSQHLVNWLKTIGGRVKPRANSIFEANTSWDQRKTSIGKDHGIYYEYGNKVSVAMAVQCEILGEHADLTYQRDGIGNRISITVMPYMDRYAIDALRSWQVKIFDGTQYTEMCVVVCGYGDEYTCRKTLPNLDRVASAEDVFKSKLSARFFINSMSLFHQTSKRTETTGVEVPDLNCVCSGTTVGLLQTPSMEKWAPVKIGSAIMQGEAGSNTSDMSVVVAIVVTPQLTGDANCYFLQTRKVLLNPSAFP +>Cavia_porcellus_3 +VLCRFITTIFALYGDFNRFLDVVRAYKGMFSNCYCYNMLLTRQALRFGIPGNSQHLVGWLKTIGGRVEPVASSAFEANTSWDQRKTSIGKDHGIYYEYGNTVSVTMAVQCDILGDHADLTYQKDGIGNRVSITVLGYMDQYAIDRLRSWQVQIFDGGQYADMCSVVCGYTDNNTCRKILPNVDRKASGEDVFKSKKSRRFTPNVMSFFHQTSERAETVGVEMPDLNCVCSGATAGLLQTPSMEKWAPNKISSAIMKGEAGSNTSDMVVGAGIVATLQLTGDANCYFVEGRKVLPNPSSFP +>Equus_caballus_1 +IVCRFMTVIFALYDDFNSFLGILKVYKGMFGNCYCFNMLLKRQSVRFGISGNSQHLVNWLKRIGGRVEPAASNVFEGVTSWDQRKTSIGKDHGIYYEYGNQKNVAMAVQCDLLGDHAGLTYQREGIGDRVSITVRRYMDRYAVDGLRSWQVRLMAGGQFADMCAVVCGYTDEYSCRKTLPNTDRNATGENVFKVRNSRRFSSNVMSFFHQASEDTESNGAEVPDLNCVCSGTTAGLLQTPTMEKWTPIKMVSAIMKGEAGVNSKDMSIGDGIIATIQLLGDSNRYSLETREVLPNPSVFP +>Felis_catus_1 +LTCRFVTVIFDLYDDFNNFLDILKAYKGMFSNCYCYNMLLQRRSVRFAIPGNSQHLVNWLKLIGGRVEPAASSVFAASTSWDQRKTSIGKGHGIYYEYGNNVGDAMAVQCDILGGHADLTYQKDGIGNRVLITVLRYMDRYAADGLRSWAVLVLDGGQFTDECAIVCGYADECTCRETLPNLDRKASGEDLFKIKSSRQFTTNVMSFFHQSSERQETSGVEVPDLNCVCSDDTAGLLQTPSMEIWAPTRIPGSIMKLEAGKNAKGMSVWDGIIATLQLVGDTNCYFLEARKALPNPSAFP +>Felis_catus_2 +LTCRFVTVIFDLYDDFNNFLDILKAYKGMFSNCYCYNMLLQRRSVRFAIPGNSQHLVNWLKLIGGRVEPAASSVFAASTSWDQRKTSIGKGHGIYYEYGNNVGDVMAVQCDILGGHADLTYQKDGIGNRVLITVLRYMDRYAADGLRSWAVLVLDGGQFTDECAIVCGYADECTCRETLPNLDRKASGEDLFKIKSSRQFTTNVMSFFHQSSERQETSGVEVPDLNCVCSDNTAGLLQTPSMEIWAPTRIPGSIMKLEAGKNAKGMSVWDGIIATLQLVGDTNCYFLEARKALPNPSAFP +>Mus_musculus_1 +VLCRFISVIFALYDDFSRFLDILKLYKGMFSNCYCYNMLLTRRGVRFGIPGNSQHLVNWLKTIGGRVEPAAASVFEANTSWDQRKTSIGKDHGIYYEYGNTISVAMAVQCDILGDHADLTYRKDGIGNRVSITIVGYMDRYAVDRLRVWQVQIFDGGQYTEICSVVCGYTDEYTCRKPLPKLDRKASGEALFKAKVSRRFTTNVMSFFHQASNRTETVGVEDPDLNCVCSGTTAGLLQTPSMEKWAPTKIVSAIMKGDAVSNTSNMTVGSVIIATLQLTADANCYFVDARKVLLNPSAFP +>Mus_musculus_2 +VLCRFITAIFALFEDFNRFLDILRAYKGMFSNCYCYNMVLTRQGIRFRIRGNSDHLVGWLKTIGGRVEPTASSVFQANTSWDQRKTSIGKDHGIYYEYGNAISVTMAVQCDILGDDADLTYQKDGIGNRVSITVARYMDRYAVDPLRSWQVQVFDGGQYVDMCVVVCGYTDEDTCRHILPNVERKATGENVFKGKKSRRFTTNAMSFFHQTSDRTETSGVEMPDLNCVCSVATGGVLQTPSMEKWAPTKITSAIMKGEAGTNPSDMVVGDLITATLQWTGDANCYFLETRKVLPNPSSFP +>Oryctolagus_cuniculus_1 +TLCRFISVIFALYADFNRFLEILKVYVGMISNDYCYNMLLTRQVLRFGIPGNSQHLVNWLKTIGTRVEPGASSVFEADTSWDERKTSIGKDHGVYYEYGNTVSVAMSVQCDILGDHADLTYQKDGIGNRVSTNDLRYMDRYAVDQLRSWQVGMFDGGNYTEMNSVVCGYFDGYTCRVALPNMNRAASGEDVFRAKASRFFTANVMSFFHQTSERTETIGVEVPDLNCACSGTLTGLLQTPSMEVWARTNISSAIMKGQSGSNISDMSVGVTIVATLQLTADANCYFLETRVLLVNRSAFP +>Oryctolagus_cuniculus_2 +DVCRFITVIFALYDDFNRFLNIERAYKGMFSNCYCYNMLLTRQGVRFGIPGNSQHLVGWLKTIGVRVDAVAVSAFEANTSWDQRKTSIGKDHGIYYEYANTVSVTMAVQCDILGDHADLTYQRDGIGNLVSITVVSYMDRYKVDRLRSWQVQIFDGGQLSDMCAVVCGYNDEDKCRKILPNVDRKASGENMFKVKRLRRFTANVMSFFHQTSERTETVRVEMPDLNCVCPGATAGLLQTPSMEVWAAQKISSAIMKGETARNTSDMSVGVSIVATLQLSGDANCYFIETRKVLPNPSSFP ===================================== debian/tests/data/treefile ===================================== @@ -0,0 +1 @@ +((A,B),(C,D)) ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,32 @@ +#!/bin/bash +set -e + +pkg=prime-phylo + +export LC_ALL=C.UTF-8 +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}" + +treesize treefile > treesize_output +echo "48a24b70a0b376535542b996af517398 treesize_output" >> checksums + +tree2leafnames treefile > leaf_names +echo "13c9f6064385b0e429d9c42e8ce1ccfd leaf_names" >> checksums + +showtree treefile > show_tree +echo "d517fa198ef97a8d42a3af5f493326c1 show_tree" >> checksums + +md5sum --check checksums + +primeDLRS -i 1 seqfile hostfile gse + +#Since the output is not consistent, it cannot be compared with a reference. + + + View it on GitLab: https://salsa.debian.org/med-team/prime-phylo/-/compare/5ff243814c071c70bef2e4854dbe668eb1efc233...f14fb466c775cc58fdabf83b89505e3761559d37 -- View it on GitLab: https://salsa.debian.org/med-team/prime-phylo/-/compare/5ff243814c071c70bef2e4854dbe668eb1efc233...f14fb466c775cc58fdabf83b89505e3761559d37 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
