[med-svn] [Git][med-team/trinculo][master] 2 commits: Add to maintainers

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / trinculo


Commits:
2a1004df by Pranav Ballaney at 2020-04-07T21:06:28+05:30
Add to maintainers

- - - - -
226a5ea8 by Pranav Ballaney at 2020-04-07T21:06:41+05:30
Add autopkgtests

- - - - -


2 changed files:

- debian/control
- debian/tests/run-unit-test


Changes:

=====================================
debian/control
=====================================
@@ -2,7 +2,7 @@ Source: trinculo
 Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>, Pranav Ballaney <ballaneypranav at gmail.com>
 Build-Depends: debhelper-compat (= 12),
                liblapack-dev
 Standards-Version: 4.5.0


=====================================
debian/tests/run-unit-test
=====================================
@@ -5,11 +5,11 @@ pkg=trinculo
 
 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 ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+ AUTOPKGTEST_TMP=$(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}"
@@ -17,4 +17,31 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
 cd "${AUTOPKGTEST_TMP}"
 
 #do_stuff_to_test_package#
-trinculo multinom --help
+echo "1. Testing frequentist association (plink)..."
+trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control
+echo "PASSED"
+echo "2. Testing frequentist association (dosage)..."
+trinculo multinom --dosage genotypes.dose --pheno phenos.txt --phenoname Pheno --basepheno Control 
+echo "PASSED"
+echo "3. Testing frequentist association (covariates)..."
+trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt 
+echo "PASSED"
+echo "4. Testing frequentist association (conditioning)..."
+echo "SNP1" > condfile[1]
+trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt --condition condfile[1] 
+echo "PASSED"
+echo "5. Testing Bayesian association..."
+trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt --normalize --defaultprior 
+echo "PASSED"
+echo "6. Testing Bayesian association (prior file)..."
+trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt --normalize --priors priors.txt 
+echo "PASSED"
+echo "7. Testing Bayesian model selection..."
+trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt --normalize --defaultprior --select 
+echo "PASSED"
+echo "8. Testing Bayesian model selection (empirical prior)..."
+trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control --covar pcs.txt --normalize --empiricalprior --select 
+echo "PASSED"
+echo "9. Testing ordinal regression..."
+trinculo ordinal --bfile genotypes --pheno phenos.txt --phenoname Order --covar pcs.txt
+echo "PASSED"



View it on GitLab: https://salsa.debian.org/med-team/trinculo/-/compare/51ae677bda3da7b75bded509c58e3642a595b714...226a5ea833ac0db3323dfc13ba0cc4ca3efa6fae

-- 
View it on GitLab: https://salsa.debian.org/med-team/trinculo/-/compare/51ae677bda3da7b75bded509c58e3642a595b714...226a5ea833ac0db3323dfc13ba0cc4ca3efa6fae
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