Étienne Mollier pushed to branch master at Debian Med / python-pauvre
Commits:
487352f9 by Etienne Mollier at 2020-04-26T14:00:47+02:00
enabled synplot testing
duplicating test data into debian/ for the moment, as they are
hosted in another repository.
- - - - -
9 changed files:
- debian/README.test
- debian/bin/pauvre
- debian/rules
- + debian/tests/gff_files/Bf201706.gff
- + debian/tests/gff_files/JN392469.gff
- + debian/tests/gff_files/LN898113.gff
- + debian/tests/gff_files/LN898114.gff
- + debian/tests/gff_files/LN898115.gff
- + debian/tests/gff_files/NC016117.gff
Changes:
=====================================
debian/README.test
=====================================
@@ -6,3 +6,15 @@ This package can be tested by running the provided test:
sh run-unit-test
in order to confirm its integrity.
+
+
+Build time tests
+────────────────
+
+Test data are not readily available in upstream repository, but can be
+retrieved from another repository, from the same author, seemingly dedicated to
+test data:
+
+
https://github.com/conchoecia/beroe_forskalii_mitogenome/tree/master/gff_files
+
+Those are made available inside debian/tests/gff_files.
=====================================
debian/bin/pauvre
=====================================
@@ -1,5 +1,6 @@
#! /bin/bash
# pauvre reimplementation in shell: the test suite expects its availability in
-# the PATH. Appropriate python environment is expected to be set in d/rules.
+# the PATH.
set -ex
-exec python3 "$CURDIR/pauvre/pauvre_main.py" "$@"
+export PYTHONPATH="$BUILDDIR"
+exec python3 "$BUILDDIR/pauvre/pauvre_main.py" "$@"
=====================================
debian/rules
=====================================
@@ -22,8 +22,11 @@ include /usr/share/dpkg/default.mk
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- CURDIR="$(CURDIR)" \
- PATH="$(CURDIR)/debian/bin:$$PATH" \
- PYTHONPATH="$(CURDIR)" \
+ PYBUILDDIR="$$(echo "$(CURDIR)"/.pybuild/cpython3_3.*/build)" \
+ && mkdir -p "$${PYBUILDDIR}/pauvre/tests/testdata/alignments" \
+ "$${PYBUILDDIR}/pauvre/tests/testresults" \
+ && cp -r "$(CURDIR)/debian/tests/gff_files" \
+ "$${PYBUILDDIR}/pauvre/tests/testdata" \
+ && BUILDDIR="$${PYBUILDDIR}" PATH="$(CURDIR)/debian/bin:$$PATH" \
dh_auto_test
endif
=====================================
debian/tests/gff_files/Bf201706.gff
=====================================
@@ -0,0 +1,18 @@
+##gff-version 3
+##source-version geneious 9.0.2
+Bf201706_circ Geneious region 1 13338 . + 0
Is_circular=true
+Bf201706_circ Geneious rRNA 2256 3115 . + .
Name=16S
+Bf201706_circ Geneious rRNA 1880 2255 . + .
Name=12S
+Bf201706_circ Geneious gene 1 1524 . + .
Name=COX1
+Bf201706_circ Geneious gene 5981 7459 . + .
Name=ND5
+Bf201706_circ Geneious gene 4699 5781 . + .
Name=ND4
+Bf201706_circ Geneious gene 7608 8672 . + .
Name=URF1
+Bf201706_circ Geneious gene 10863 11918 . + .
Name=CYTB
+Bf201706_circ Geneious gene 11837 12751 . + .
Name=ND1
+Bf201706_circ Geneious gene 3308 4051 . + .
Name=COX3
+Bf201706_circ Geneious gene 10016 10744 . + .
Name=ND2
+Bf201706_circ Geneious gene 9200 9868 . + .
Name=URF2
+Bf201706_circ Geneious gene 12757 13320 . + .
Name=COX2
+Bf201706_circ Geneious gene 4324 4698 . + .
Name=ND3
+Bf201706_circ Geneious gene 3099 3302 . + .
Name=ND6
+Bf201706_circ Geneious gene 5781 5969 . + .
Name=ND4L
=====================================
debian/tests/gff_files/JN392469.gff
=====================================
@@ -0,0 +1,17 @@
+##gff-version 3
+##source-version geneious 9.0.2
+JN392469 Geneious region 1 11017 . + 0
Is_circular=true
+JN392469 Geneious source 1 11017 . + .
Name=source Pleurobrachia bachei
+JN392469 Geneious gene 1 1539 . + .
Name=COX1 gene
+JN392469 Geneious gene 1660 2241 . + .
Name=COX2 gene
+JN392469 Geneious rRNA 2518 3460 . + .
Name=16S rRNA
+JN392469 Geneious rRNA 3491 4053 . + .
Name=12S rRNA
+JN392469 Geneious gene 4054 4794 . + .
Name=COX3 gene
+JN392469 Geneious gene 4802 5470 . + .
Name=ND2 gene
+JN392469 Geneious gene 5521 5841 . + .
Name=ND3 gene
+JN392469 Geneious gene 5842 6912 . + .
Name=ND4 gene
+JN392469 Geneious gene 7074 8156 . + .
Name=CYTB gene
+JN392469 Geneious gene 8158 9672 . + .
Name=ND5 gene
+JN392469 Geneious gene 9672 10511 . + .
Name=ND1 gene
+JN392469 Geneious gene 10511 10708 . + .
Name=ND6 gene
+JN392469 Geneious gene 10803 11003 . + .
Name=ND4L gene
\ No newline at end of file
=====================================
debian/tests/gff_files/LN898113.gff
=====================================
@@ -0,0 +1,17 @@
+##gff-version 3
+##source-version geneious 9.0.2
+LN898113 Geneious region 1 11574 . + 0
Is_circular=true
+LN898113 Geneious source 1 11574 . + .
Name=source Coeloplana loyai
+LN898113 Geneious gene 1 1551 . + .
Name=COX1 gene
+LN898113 Geneious gene 1556 2131 . + .
Name=COX2 gene
+LN898113 Geneious gene 2136 3242 . + .
Name=ND4 gene
+LN898113 Geneious gene 3242 3982 . + .
Name=ND2 gene
+LN898113 Geneious rRNA 4707 5549 . + .
Name=16S rRNA
+LN898113 Geneious rRNA 5550 5962 . + .
Name=12S rRNA
+LN898113 Geneious gene 5963 6190 . + .
Name=ND4L gene
+LN898113 Geneious gene 6192 7484 . + .
Name=ND1 gene
+LN898113 Geneious gene 7488 8555 . + .
Name=CYTB gene
+LN898113 Geneious gene 8556 9314 . + .
Name=COX3 gene
+LN898113 Geneious gene 9314 9655 . + .
Name=ND3 gene
+LN898113 Geneious gene 9790 11307 . + .
Name=ND5 gene
+LN898113 Geneious gene 11309 11515 . + .
Name=ND6 gene
=====================================
debian/tests/gff_files/LN898114.gff
=====================================
@@ -0,0 +1,17 @@
+##gff-version 3
+##source-version geneious 9.0.2
+LN898114 Geneious region 1 11551 . + 0
Is_circular=true
+LN898114 Geneious source 1 11551 . + .
Name=source Coeloplana yulianicorum
+LN898114 Geneious gene 1 1551 . + .
Name=COX1 gene
+LN898114 Geneious gene 1561 2136 . + .
Name=COX2 gene
+LN898114 Geneious gene 2137 3243 . + .
Name=ND4 gene
+LN898114 Geneious gene 3243 3983 . + .
Name=ND2 gene
+LN898114 Geneious rRNA 4694 5540 . + .
Name=16S rRNA
+LN898114 Geneious rRNA 5541 5948 . + .
Name=12S rRNA
+LN898114 Geneious gene 5949 6221 . + .
Name=ND4L gene
+LN898114 Geneious gene 6235 7482 . + .
Name=ND1 gene
+LN898114 Geneious gene 7488 8555 . + .
Name=CYTB gene
+LN898114 Geneious gene 8556 9314 . + .
Name=COX3 gene
+LN898114 Geneious gene 9314 9655 . + .
Name=ND3 gene
+LN898114 Geneious gene 9785 11302 . + .
Name=ND5 gene
+LN898114 Geneious gene 11304 11510 . + .
Name=ND6 gene
=====================================
debian/tests/gff_files/LN898115.gff
=====================================
@@ -0,0 +1,17 @@
+##gff-version 3
+##source-version geneious 9.0.2
+LN898115 Geneious region 1 9961 . + 0
Is_circular=true
+LN898115 Geneious source 1 9961 . + .
Name=source Vallicula multiformis
+LN898115 Geneious gene 1 1533 . + .
Name=COX1 gene
+LN898115 Geneious gene 1523 2080 . + .
Name=COX2 gene
+LN898115 Geneious gene 2074 3126 . + .
Name=ND4 gene
+LN898115 Geneious rRNA 3127 3951 . + .
Name=16S rRNA
+LN898115 Geneious rRNA 3952 4306 . + .
Name=12S rRNA
+LN898115 Geneious gene 4307 5011 . + .
Name=ND2 gene
+LN898115 Geneious gene 5011 6048 . + .
Name=CYTB gene
+LN898115 Geneious gene 6032 6799 . + .
Name=COX3 gene
+LN898115 Geneious gene 6796 7119 . + .
Name=ND3 gene
+LN898115 Geneious gene 7124 8569 . + .
Name=ND5 gene
+LN898115 Geneious gene 8577 8792 . + .
Name=ND4L gene
+LN898115 Geneious gene 8792 9655 . + .
Name=ND1 gene
+LN898115 Geneious CDS 9751 9948 . + .
Name=ND6 CDS
=====================================
debian/tests/gff_files/NC016117.gff
=====================================
@@ -0,0 +1,17 @@
+##gff-version 3
+##source-version geneious 9.0.2
+NC_016117 Geneious region 1 10326 . + 0
Is_circular=true
+NC_016117 Geneious source 1 10326 . + .
Name=source Mnemiopsis leidyi
+NC_016117 Geneious rRNA 3521 4398 . + .
Name=16S rRNA
+NC_016117 Geneious rRNA 3153 3520 . + .
Name=12S rRNA
+NC_016117 Geneious gene 1 1524 . + .
Name=COX1 gene
+NC_016117 Geneious gene 6527 7933 . + .
Name=ND5 gene
+NC_016117 Geneious gene 4399 5493 . + .
Name=ND4 gene
+NC_016117 Geneious gene 8775 9860 . + .
Name=CYTB gene
+NC_016117 Geneious gene 7933 8802 . + .
Name=ND1 gene
+NC_016117 Geneious gene 1525 2250 . + .
Name=COX3 gene
+NC_016117 Geneious gene 5495 6220 . + .
Name=ND2 gene
+NC_016117 Geneious gene 2574 3152 . + .
Name=COX2 gene
+NC_016117 Geneious gene 2247 2573 . + .
Name=ND3 gene
+NC_016117 Geneious gene 9847 10050 . + .
Name=ND6 gene
+NC_016117 Geneious gene 6221 6418 . + .
Name=ND4L gene
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/python-pauvre/-/commit/487352f977a7917d9796f944c906a85203391437
--
View it on GitLab:
https://salsa.debian.org/med-team/python-pauvre/-/commit/487352f977a7917d9796f944c906a85203391437
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