[med-svn] [Git][med-team/phyx][master] Redirect output of tests, just print test name, fix dirname

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / phyx


Commits:
c350e8b1 by Andreas Tille at 2019-09-11T20:05:20Z
Redirect output of tests, just print test name, fix dirname

- - - - -


1 changed file:

- debian/tests/run-unit-test


Changes:

=====================================
debian/tests/run-unit-test
=====================================
@@ -12,82 +12,82 @@ 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 pxaa2cdn_example && echo pxaa2cdn && pxaa2cdn -a AA_Alignment.fa -n Unaligned_Nucleotide.fa -o CDN_aln.fa >/dev/null && cd ..
 
-cd pxbdfit_example && pxbdfit -t bd.tre -m yule && cd ..
+cd pxbdfit_example && echo pxbdfit && pxbdfit -t bd.tre -m yule >/dev/null && cd ..
 
-# cd pxbdsim_example && pxbdsim -e 100 -s -b 1 -d 0.5 -o output_tree_file && cd ..
+# cd pxbdsim_example && echo pxbdsim && pxbdsim -e 100 -s -b 1 -d 0.5 -o output_tree_file >/dev/null && cd ..
 
-cd pxboot_example && pxboot -s Alignment -x 112233 -f 0.50 -o output_of_50_jackknife && cd ..
+cd pxboot_example && echo pxboot && pxboot -s Alignment -x 112233 -f 0.50 -o output_of_50_jackknife >/dev/null && cd ..
 
-cd pxboot_example && pxboot -s Alignment -p parts -o output_of_bootstrap && cd ..
+cd pxboot_example && echo pxboot && pxboot -s Alignment -p parts -o output_of_bootstrap >/dev/null && cd ..
 
-cd pxbp_example && pxbp -t Tree.tre -o bp_output && cd ..
+cd pxbp_example && echo pxbp && pxbp -t Tree.tre -o bp_output >/dev/null && cd ..
 
-cd pxcat_example && pxcat -s *.fas *.fa *.phy -p Parts.txt -o Supermatrix.fa && cd ..
+cd pxcat_example && echo pxcat && pxcat -s *.fas *.fa *.phy -p Parts.txt -o Supermatrix.fa >/dev/null && cd ..
 
-cd pxclsq_example && pxclsq -s Alignment -p 0.6 && cd ..
+cd pxclsq_example && echo pxclsq && pxclsq -s Alignment -p 0.6 >/dev/null && cd ..
 
-cd pxconsq_example && pxconsq -s Alignment && cd ..
+cd pxconsq_example && echo pxconsq && pxconsq -s Alignment >/dev/null && cd ..
 
-cd pxcontrates_example && pxcontrates -c contrates_file.txt -t contrates_tree.tre -a 1 && cd ..
+cd pxcontrates_example && echo pxcontrates && pxcontrates -c contrates_file.txt -t contrates_tree.tre -a 1 >/dev/null 2>/dev/null && cd ..
 
-cd pxfqfilt_example && pxfqfilt -s fqfilt_test.fastq -m 10 && cd ..
+cd pxfqfilt_example && echo pxfqfilt && pxfqfilt -s fqfilt_test.fastq -m 10 >/dev/null && cd ..
 
-cd pxlog_example && pxlog -t *.trees -i && cd ..
+cd pxlog_example && echo pxlog && pxlog -t *.trees -i >/dev/null && cd ..
 
-cd pxlog_example && pxlog -t *.trees -b 75 -n 2 -o some_output_filename && cd ..
+cd pxlog_example && echo pxlog && pxlog -t *.trees -b 75 -n 2 -o some_output_filename >/dev/null && cd ..
 
-cd pxlssq_example && pxlssq -s Alignment && cd ..
+cd pxlssq_example && echo pxlssq && pxlssq -s Alignment >/dev/null && cd ..
 
-cd pxlstr_example && pxlstr -t Tree.tre && cd ..
+cd pxlstr_example && echo pxlstr && pxlstr -t Tree.tre >/dev/null && cd ..
 
-cd pxmrca_example && pxmrca -t mrca_test.tre -m mrca.txt && cd ..
+cd pxmrca_example && echo pxmrca && pxmrca -t mrca_test.tre -m mrca.txt >/dev/null && cd ..
 
-cd pxmrcacut_example && pxmrcacut -t tree -m mrca_file && cd ..
+cd pxmrcacut_example && echo pxmrcacut && pxmrcacut -t tree -m mrca_file >/dev/null && cd ..
 
-cd pxmrcaname_example && pxmrcaname -t tree -m mrca_file && cd ..
+cd pxmrcaname_example && echo pxmrcaname && pxmrcaname -t tree -m mrca_file >/dev/null && cd ..
 
-cd pxnj_example && pxnj -s Alignment.aln && cd ..
+cd pxnj_example && echo pxnj && pxnj -s Alignment.aln >/dev/null && cd ..
 
-cd pxnw_example && pxnw -s Alignment.aln && cd ..
+cd pxnw_examples && echo pxnw && pxnw -s Alignment.aln >/dev/null && cd ..
 
-cd pxrecode_example && pxrecode -s Nucleotide.fa && cd ..
+cd pxrecode_example && echo pxrecode && pxrecode -s Nucleotide.fa >/dev/null && cd ..
 
-cd pxrevcomp_example && pxrevcomp -s Nucleotide.fa && cd ..
+cd pxrevcomp_example && echo pxrevcomp && pxrevcomp -s Nucleotide.fa >/dev/null && cd ..
 
-cd pxrls_example && pxrls -s SeqFile -c CurrentNames -n NewNames && cd ..
+cd pxrls_example && echo pxrls && pxrls -s SeqFile -c CurrentNames -n NewNames >/dev/null && cd ..
 
-cd pxrlt_example && pxrlt -t kingdoms.tre -c kingdoms.oldnames.txt -n kingdoms.newnames.txt && cd ..
+cd pxrlt_example && echo pxrlt && pxrlt -t kingdoms.tre -c kingdoms.oldnames.txt -n kingdoms.newnames.txt >/dev/null && cd ..
 
-cd pxrms_example && pxrms -s Nucleotide.fa -f taxa_to_delete.txt && cd ..
+cd pxrms_example && echo pxrms && pxrms -s Nucleotide.fa -f taxa_to_delete.txt >/dev/null && cd ..
 
-cd pxrmt_example && pxrmt -t rmt_test.tre -n s1,s6,s8 && cd ..
+cd pxrmt_example && echo pxrmt && pxrmt -t rmt_test.tre -n s1,s6,s8 >/dev/null && cd ..
 
-cd pxrr_example && pxrr -t rr_test.tre -g s1,s2 && cd ..
+cd pxrr_example && echo pxrr && pxrr -t rr_test.tre -g s1,s2 >/dev/null && cd ..
 
 cd pxs2fa_pxs2phy_pxs2nex_example && \
-   pxs2fa -s Alignment && \
-   pxs2phy -s Alignment && \
-   pxs2nex -s Alignment && \
+   echo pxs2fa && pxs2fa -s Alignment >/dev/null && \
+   echo pxs2phy && pxs2phy -s Alignment >/dev/null && \
+   echo pxs2nex && pxs2nex -s Alignment >/dev/null && \
    cd ..
 
-cd pxseqgen_example && pxseqgen -t seqgen_test.tre && cd ..
+cd pxseqgen_example && echo pxseqgen && pxseqgen -t seqgen_test.tre >/dev/null && 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 pxseqgen_example && echo pxseqgen && pxseqgen -t tree_file -o output_alignment -m .33,.33,.33,.33,.33,.33,2,.3,.3,.2,.5,.4,.2 >/dev/null && cd ..
 
-cd pxsstat_example && pxsstat -s Alignment.fa && cd ..
+cd pxsstat_example && echo pxsstat && pxsstat -s Alignment.fa >/dev/null && cd ..
 
-cd pxstrec_example && pxstrec -d test.data.narrow -t test.tre -c config_stmap && cd ..
+cd pxstrec_example && echo pxstrec && pxstrec -d test.data.narrow -t test.tre -c config_stmap >/dev/null && cd ..
 
-cd pxsw_example && pxsw -s Alignment.fa && cd ..
+cd pxsw_example && echo pxsw && pxsw -s Alignment.fa >/dev/null && cd ..
 
-cd pxt2new_example && pxt2new -t Tree.nex && cd ..
+cd pxt2new_example && echo pxt2new && pxt2new -t Tree.nex >/dev/null && cd ..
 
-cd pxtlate_example && pxtlate -s Sequence.fa && cd ..
+cd pxtlate_example && echo pxtlate && pxtlate -s Sequence.fa >/dev/null && cd ..
 
-cd pxtscale_example && pxtscale -t Tree -s 2.0 && cd ..
+cd pxtscale_example && echo pxtscale && pxtscale -t Tree -s 2.0 >/dev/null && cd ..
 
-cd pxupgma_example && pxupgma -s drosophila.aln && cd ..
+cd pxupgma_example && echo pxupgma && pxupgma -s drosophila.aln >/dev/null && cd ..
 
-cd pxvcf2fa_example && pxvcf2fa -s vcf_file && cd ..
+cd pxvcf2fa_example && echo pxvcf2fa && pxvcf2fa -s vcf_file >/dev/null && cd ..



View it on GitLab: https://salsa.debian.org/med-team/phyx/commit/c350e8b1125bdf3a4c1acf171030ac4efea31d0b

-- 
View it on GitLab: https://salsa.debian.org/med-team/phyx/commit/c350e8b1125bdf3a4c1acf171030ac4efea31d0b
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