[med-svn] [Git][med-team/prime-phylo][master] 4 commits: Add test data

[Shruti Sridhar (@shruti_sridhar)]

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 <shruti.sridhar99 at gmail.com>  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
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