[med-svn] [Git][med-team/seer][master] 2 commits: Add autopkgtests

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / seer


Commits:
21df148a by Pranav Ballaney at 2020-06-02T03:35:10+05:30
Add autopkgtests

- - - - -
304f82cc by Pranav Ballaney at 2020-06-02T03:35:41+05:30
Add docs

- - - - -


6 changed files:

- + debian/README.test
- debian/changelog
- + debian/docs
- debian/examples
- + debian/tests/control
- + debian/tests/run-unit-test


Changes:

=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+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.


=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+seer (1.1.4-3) UNRELEASED; urgency=medium
+
+  [ Steffen Moeller ]
+  * d/u/metadata: yamllint
+
+  [ Steffen Möller ]
+  * Update metadata with ref to conda
+
+  [ Pranav Ballaney ]
+  * Add autopkgtests
+  * Add docs
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com>  Tue, 02 Jun 2020 03:35:16 +0530
+
 seer (1.1.4-2) unstable; urgency=medium
 
   * debhelper 11


=====================================
debian/docs
=====================================
@@ -0,0 +1,2 @@
+debian/README*
+debian/tests/run-unit-test
\ No newline at end of file


=====================================
debian/examples
=====================================
@@ -1 +1,2 @@
 example_wrapper.py
+test/*
\ No newline at end of file


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,60 @@
+#!/bin/bash
+set -e
+
+pkg=seer
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  # Double quote below to expand the temporary directory variable now versus
+  # later is on purpose.
+  # shellcheck disable=SC2064
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+gunzip -r *
+gzip example_kmers
+#do_stuff_to_test_package#
+echo -e "\e[93m\e[1mTest 1: Basic Filters\e[0m"
+seer -k example_kmers.gz -p subset.pheno
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 2: Binary Phenotype Assocation\e[0m"
+seer -k example_kmers.gz -p subset.pheno --pval 1 --chisq 1
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 3:Print Output\e[0m"
+seer -k example_kmers.gz -p subset.pheno --pval 1 --chisq 1 --maf 0.1 --print_samples
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 4: Continuous Phenotype Assocation\e[0m"
+seer -k example_kmers.gz -p subset.cont.pheno --pval 1 --chisq 1 --maf 0.1
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 5: Assocation with Population Structure\e[0m"
+seer -k example_kmers.gz -p example.pheno --struct all_structure_new --pval 1 --chisq 1
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 6: Assocation with Covariates\e[0m"
+seer -k example_kmers.gz -p subset.pheno --covar_file covariates.txt --covar_list 2q,3 --pval 1 --chisq 1
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 7: Filter Output\e[0m"
+filter_seer -k filter_in.txt --pos_beta
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 8: Map k-mers\e[0m"
+map_back -k map_in.txt -r assembly_locations.txt --threads 1
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo



View it on GitLab: https://salsa.debian.org/med-team/seer/-/compare/46463ac8639232f5e7d97c739f57177d4448ffec...304f82cc695ae8ee30a0ba0637905389927748a1

-- 
View it on GitLab: https://salsa.debian.org/med-team/seer/-/compare/46463ac8639232f5e7d97c739f57177d4448ffec...304f82cc695ae8ee30a0ba0637905389927748a1
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