[med-svn] [Git][med-team/microbegps][master] Updated changelog
Israel Komolehin pushed to branch master at Debian Med / microbegps Commits: f2d714b2 by Komolehin Israel Timilehin at 2024-02-14T06:42:51+00:00 Updated changelog - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,3 +1,14 @@ +microbegps (1.0.0-6) UNRELEASED; urgency=medium + + [ Steffen Moeller ] + * d/u/metadata: yamllint + + [ Komolehin Israel Timilehin ] + * Created patch to include TkAgg backend from matplotlib + * Added autopkgtest (Closes: #1036480) + + -- Komolehin Israel Timilehin Wed, 14 Feb 2024 05:34:56 + + microbegps (1.0.0-5) unstable; urgency=medium * Port to PyQt5 View it on GitLab: https://salsa.debian.org/med-team/microbegps/-/commit/f2d714b2dadf1211fcc4968dad25074800d2b899 -- View it on GitLab: https://salsa.debian.org/med-team/microbegps/-/commit/f2d714b2dadf1211fcc4968dad25074800d2b899 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/microbegps][master] Install test as doc and a README.test on how to run the test
Israel Komolehin pushed to branch master at Debian Med / microbegps Commits: 679bbf7d by Komolehin Israel Timilehin at 2024-02-14T06:25:04+00:00 Install test as doc and a README.test on how to run the test - - - - - 2 changed files: - + debian/README.test - + debian/microbegps.docs 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. \ No newline at end of file = debian/microbegps.docs = @@ -0,0 +1,3 @@ +README +debian/tests/run-unit-test +debian/README.test \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/microbegps/-/commit/679bbf7d40dc1f5f0d3264692baa4c7ae8ada2b6 -- View it on GitLab: https://salsa.debian.org/med-team/microbegps/-/commit/679bbf7d40dc1f5f0d3264692baa4c7ae8ada2b6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/microbegps][master] Created patch to include TkAgg backend from matplotlib
Israel Komolehin pushed to branch master at Debian Med / microbegps Commits: c93a9993 by Komolehin Israel Timilehin at 2024-02-14T05:42:46+00:00 Created patch to include TkAgg backend from matplotlib - - - - - 1 changed file: - debian/patches/series Changes: = debian/patches/series = @@ -1,2 +1,3 @@ 2to3.patch PyQt5.patch +TkAgg.patch View it on GitLab: https://salsa.debian.org/med-team/microbegps/-/commit/c93a9993a83c828f42ab454fc705c245eacc0e23 -- View it on GitLab: https://salsa.debian.org/med-team/microbegps/-/commit/c93a9993a83c828f42ab454fc705c245eacc0e23 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/microbegps][master] Add salsa-ci file
Israel Komolehin pushed to branch master at Debian Med / microbegps Commits: df199eae by Komolehin Israel Timilehin at 2024-02-14T05:31:01+00:00 Add salsa-ci file - - - - - 1 changed file: - + debian/salsa-ci.yml Changes: = debian/salsa-ci.yml = @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/microbegps/-/commit/df199eae42b018a9a72cad0705c7fe8af8868508 -- View it on GitLab: https://salsa.debian.org/med-team/microbegps/-/commit/df199eae42b018a9a72cad0705c7fe8af8868508 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/microbegps][master] 2 commits: Created patch to include TkAgg backend from matplotlib
Israel Komolehin pushed to branch master at Debian Med / microbegps
Commits:
f25c074c by Komolehin Israel Timilehin at 2024-02-14T05:12:17+00:00
Created patch to include TkAgg backend from matplotlib
- - - - -
206ebdb0 by Komolehin Israel Timilehin at 2024-02-14T05:24:03+00:00
Added autopkgtest
- - - - -
3 changed files:
- + debian/patches/TkAgg.patch
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=
debian/patches/TkAgg.patch
=
@@ -0,0 +1,16 @@
+Description: Includes TkAgg backend
+ Running the package throws an Exception "ImportError: Cannot load backend
'TkAgg' which requires the 'tk' interactive framework, as 'qt' is currently
running"
+ This patch includes the TkAgg backend from matplotlib to fix the error.
+Author: Komolehin Israel
+Last-Update: Wed, 14 Feb 2024 04:40:53 +
+--- a/microbegps/gui.py
b/microbegps/gui.py
+@@ -11,6 +11,8 @@
+
+ from PyQt5 import QtGui, QtCore, QtWidgets
+
++import matplotlib
++matplotlib.use('Agg')
+ import matplotlib.pyplot as plt
+ from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as
FigureCanvas
+ import matplotlib_venn as venn
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Test-Command: xvfb-run -s "-screen 0 1024x768x24 -ac +extension GLX +render
-noreset" sh debian/tests/run-unit-test
+Depends: xvfb, xauth, microbegps
+Restrictions: allow-stderr, superficial
\ No newline at end of file
=
debian/tests/run-unit-test
=
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+pkg=microbegps
+
+
+if [ "$AUTOPKGTEST_TMP" = ""]; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
+
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+cd $AUTOPKGTEST_TMP
+
+# Start program
+
+echo "Starting MicrobeGPS"
+
+timeout 10s MicrobeGPS || true
+
+echo "Pass"
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/microbegps/-/compare/88f43526da9121813a099bd2aded0c0512595ad0...206ebdb0bc041d525ea081ec7abf0a69f07de764
--
View it on GitLab:
https://salsa.debian.org/med-team/microbegps/-/compare/88f43526da9121813a099bd2aded0c0512595ad0...206ebdb0bc041d525ea081ec7abf0a69f07de764
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[med-svn] [Git][med-team/terraphast][master] 2 commits: Revert changes on README.test
Israel Komolehin pushed to branch master at Debian Med / terraphast Commits: cdb12517 by Komolehin Israel Timilehin at 2024-01-30T05:14:38+00:00 Revert changes on README.test - - - - - 33019899 by Komolehin Israel Timilehin at 2024-01-30T05:15:09+00:00 Added README to the test - - - - - 2 changed files: - debian/README.test - + debian/tests/README.md Changes: = debian/README.test = @@ -3,8 +3,6 @@ Notes on how this package can be tested. This package can be tested by running the provided test: -`sh run-unit-test` +sh run-unit-test -in order to confirm its integrity. - -Data can be referenced [here](https://github.com/terraphast/terraphast/tree/master/terraphastI/data/data) +in order to confirm its integrity. \ No newline at end of file = debian/tests/README.md = @@ -0,0 +1,10 @@ +## 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. + +Data can be referenced [here](https://github.com/terraphast/terraphast/tree/master/terraphastI/data/data) \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/terraphast/-/compare/a746ba245beab0e98be1342ab61d946a776090b5...330198990cc587a5d9574c9de743b01c4131fe19 -- View it on GitLab: https://salsa.debian.org/med-team/terraphast/-/compare/a746ba245beab0e98be1342ab61d946a776090b5...330198990cc587a5d9574c9de743b01c4131fe19 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/terraphast][master] 4 commits: Added README.test
Israel Komolehin pushed to branch master at Debian Med / terraphast Commits: 6cc17d6f by Komolehin Israel Timilehin at 2024-01-30T05:04:59+00:00 Added README.test - - - - - c07ac9fb by Komolehin Israel Timilehin at 2024-01-30T05:05:30+00:00 Added run-unit-test and README.test to doc - - - - - d5d7deec by Komolehin Israel Timilehin at 2024-01-30T05:08:05+00:00 Updated test - - - - - a746ba24 by Komolehin Israel Timilehin at 2024-01-30T05:08:22+00:00 Updated changelog - - - - - 4 changed files: - + debian/README.test - debian/changelog - + debian/terraphast.doc - debian/tests/run-unit-test Changes: = debian/README.test = @@ -0,0 +1,10 @@ +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. + +Data can be referenced [here](https://github.com/terraphast/terraphast/tree/master/terraphastI/data/data) = debian/changelog = @@ -1,3 +1,9 @@ +terraphast (0.0+git20200413.8af2e4c+dfsg-3) UNRELEASED; urgency=medium + + * Added autopkgtest + + -- Komolehin Israel Timilehin Tue, 30 Jan 2024 05:06:12 + + terraphast (0.0+git20200413.8af2e4c+dfsg-2) unstable; urgency=medium * Team Upload. = debian/terraphast.doc = @@ -0,0 +1,2 @@ +debian/tests/run-unit-test +debian/README.test \ No newline at end of file = debian/tests/run-unit-test = @@ -16,4 +16,7 @@ wget https://raw.githubusercontent.com/terraphast/terraphast/master/terraphastI/ wget https://raw.githubusercontent.com/terraphast/terraphast/master/terraphastI/data/data/Meusemann.data # Enumerate terraces in phylogenetic tree space -terraphast Meusemann.nwk Meusemann.data \ No newline at end of file +terraphast Meusemann.nwk Meusemann.data + +# Remove data +rm Meusemann.* \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/terraphast/-/compare/41c27930a2a99012a3b2a87dc50e1cf40c719178...a746ba245beab0e98be1342ab61d946a776090b5 -- View it on GitLab: https://salsa.debian.org/med-team/terraphast/-/compare/41c27930a2a99012a3b2a87dc50e1cf40c719178...a746ba245beab0e98be1342ab61d946a776090b5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/terraphast][master] Added autopkgtest
Israel Komolehin pushed to branch master at Debian Med / terraphast
Commits:
41c27930 by Komolehin Israel Timilehin at 2024-01-30T04:50:21+00:00
Added autopkgtest
- - - - -
2 changed files:
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: wget, terraphast
+Restrictions: needs-internet, allow-stderr
\ No newline at end of file
=
debian/tests/run-unit-test
=
@@ -0,0 +1,19 @@
+#!/bin/sh
+
+pkg=terraphast
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
+ trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+cd $AUTOPKGTEST_TMP
+
+# Get data
+wget
https://raw.githubusercontent.com/terraphast/terraphast/master/terraphastI/data/data/Meusemann.nwk
+wget
https://raw.githubusercontent.com/terraphast/terraphast/master/terraphastI/data/data/Meusemann.data
+
+# Enumerate terraces in phylogenetic tree space
+terraphast Meusemann.nwk Meusemann.data
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/terraphast/-/commit/41c27930a2a99012a3b2a87dc50e1cf40c719178
--
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[med-svn] [Git][med-team/ghmm][master] 2 commits: Updated tests. Skipped two test executions due to segfault
Israel Komolehin pushed to branch master at Debian Med / ghmm Commits: 9ed18967 by Komolehin Israel Timilehin at 2024-01-26T14:34:02+00:00 Updated tests. Skipped two test executions due to segfault - - - - - 11fedf45 by Komolehin Israel Timilehin at 2024-01-26T14:34:55+00:00 Updated test documentation - - - - - 2 changed files: - debian/tests/README.md - debian/tests/autopkgtest.mk Changes: = debian/tests/README.md = @@ -2,16 +2,8 @@ Test in python can be referenced [here](https://ghmm.sourceforge.net/documentation.html) +## GHMM test in C -## Executed commands - - - Error - -# Missing files in installed libghmm. These missing files are blockers for some tests - -- `ghmm/matrix.h` -- `ghmm/matrixop.h` -- `ghmm_internals.h` -- `randvar.h` -- `mes.h` \ No newline at end of file +The following tests were skipped due to segfault: +- `test_mcmc` +- `test_chmm` \ No newline at end of file = debian/tests/autopkgtest.mk = @@ -3,7 +3,7 @@ CFLAGS=-I/usr/include/ghmm LDFLAGS=-lghmm -llapack -all: test_label_higher_order test_two_states_three_symbols test_libxml test_read_fa test_sequences +all: test_label_higher_order test_two_states_three_symbols test_libxml test_read_fa test_sequences test_chmm test_chmm_test test_coin_toss test_mcmc test_randvar test_label_higher_order: label_higher_order_test.o $(CC) $^ -o $@ $(LDFLAGS) -lm @@ -20,16 +20,35 @@ test_read_fa: read_fa.o test_sequences: sequences_test.o $(CC) $^ -o $@ $(LDFLAGS) +test_chmm: chmm.o + $(CC) $^ -o $@ $(LDFLAGS) + +test_chmm_test: chmm_test.o + $(CC) $^ -o $@ $(LDFLAGS) + +test_coin_toss: coin_toss_test.o + $(CC) $^ -o $@ $(LDFLAGS) + +test_mcmc: mcmc.o + $(CC) $^ -o $@ $(LDFLAGS) + +test_randvar: randvar_test.o + $(CC) $^ -o $@ $(LDFLAGS) + %.o: %.c $(CC) -c $< -o $@ $(CFLAGS) clean: - rm -f *.o test_label_higher_order test_two_sates_three_symbols test_libxml test_read_fa test_sequences + rm -f *.o test_* words.txt run: all ./test_label_higher_order ./test_two_states_three_symbols ./test_libxml ./test_sequences + ./test_chmm_test + ./test_coin_toss + ./test_randvar # read_fa needs seqence and model to be passed as arguments - # ./test_read_fa \ No newline at end of file + # ./test_read_fa + # ./test_chmm and ./test_mcmc returns SEGFAULT \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/0d8be32b72169d46487056adbb3416643031dd55...11fedf4559b5a26d4b3c5a4d53ce7fc126da9e4d -- View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/0d8be32b72169d46487056adbb3416643031dd55...11fedf4559b5a26d4b3c5a4d53ce7fc126da9e4d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/clonalframeml][master] Added reference to test documentation
Israel Komolehin pushed to branch master at Debian Med / clonalframeml Commits: ecf0b447 by Komolehin Israel Timilehin at 2024-01-24T09:50:13+00:00 Added reference to test documentation - - - - - 1 changed file: - debian/tests/README.md Changes: = debian/tests/README.md = @@ -5,4 +5,6 @@ This package can be tested by running the provided test: Note! This is a real-world example, and requires around 12 hours of run time. -`sh run-unit-test` \ No newline at end of file +`sh run-unit-test` + +Test documentation can be referenced [here](https://github.com/xavierdidelot/clonalframeml/wiki) \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/clonalframeml/-/commit/ecf0b44773a6c6be04243e28c0deb2c5fec2b234 -- View it on GitLab: https://salsa.debian.org/med-team/clonalframeml/-/commit/ecf0b44773a6c6be04243e28c0deb2c5fec2b234 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/clonalframeml][master] 2 commits: Added test for the package analysis
Israel Komolehin pushed to branch master at Debian Med / clonalframeml
Commits:
c89d193c by Komolehin Israel Timilehin at 2024-01-24T09:40:40+00:00
Added test for the package analysis
- - - - -
bac98550 by Komolehin Israel Timilehin at 2024-01-24T09:41:35+00:00
Added README to document how to run the test and test observation
- - - - -
2 changed files:
- + debian/tests/README.md
- + debian/tests/run-unit-test
Changes:
=
debian/tests/README.md
=
@@ -0,0 +1,8 @@
+## Notes on how this package can be tested.
+
+
+This package can be tested by running the provided test:
+
+ Note! This is a real-world example, and requires around 12 hours of run
time.
+
+`sh run-unit-test`
\ No newline at end of file
=
debian/tests/run-unit-test
=
@@ -0,0 +1,23 @@
+#!/bin/bash -e
+
+pkg=clonalframeml
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
+ trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+cd "$AUTOPKGTEST_TMP"/
+
+# Download data
+wget -O clmf.tgz https://figshare.com/ndownloader/files/34861005
+
+# Unzip data
+tar -xzvf clmf.tgz
+
+cd ClonalFrameML
+
+# Run the standard ClonalFrameML analysis as follows. Note! This is a
real-world example, and requires around 12 hours of run time.
+ClonalFrameML Saureus.phyML.newick Saureus.fasta example.output -kappa
4.967695 -emsim 100 -ignore_user_sites Saureus.non-core-sites.txt > example.log
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/clonalframeml/-/compare/0e8c95683dc9cb0b3a778bc588084cd087f8f284...bac98550596e087efba2ec01ec024e83eee2c4c7
--
View it on GitLab:
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[med-svn] [Git][med-team/ska][master] Documented how to run the test in README
Israel Komolehin pushed to branch master at Debian Med / ska Commits: 6b6c6fef by Komolehin Israel Timilehin at 2024-01-22T06:41:33+00:00 Documented how to run the test in README - - - - - 1 changed file: - + debian/tests/README.md Changes: = debian/tests/README.md = @@ -0,0 +1,7 @@ +## Notes on how this package can be tested. + + +This package can be tested by running the provided test: + +`sh run-unit-test` + View it on GitLab: https://salsa.debian.org/med-team/ska/-/commit/6b6c6fefb5cd8c62bc2f9f55ceb770d4fb0f83eb -- View it on GitLab: https://salsa.debian.org/med-team/ska/-/commit/6b6c6fefb5cd8c62bc2f9f55ceb770d4fb0f83eb You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ska][master] Updated changelog
Israel Komolehin pushed to branch master at Debian Med / ska Commits: 7a81ed3c by Komolehin Israel Timilehin at 2024-01-22T06:37:41+00:00 Updated changelog - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,3 +1,9 @@ +ska (1.0+dfsg-4) UNRELEASED; urgency=medium + + * Added autopkgtest + + -- Komolehin Israel Timilehin Mon, 22 Jan 2024 06:36:19 + + ska (1.0+dfsg-3) unstable; urgency=medium * Cleanup after testing View it on GitLab: https://salsa.debian.org/med-team/ska/-/commit/7a81ed3c0cdc5331b135ebbfee7fd241db60fd3c -- View it on GitLab: https://salsa.debian.org/med-team/ska/-/commit/7a81ed3c0cdc5331b135ebbfee7fd241db60fd3c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ska][master] 4 commits: Added autopkgtest
Israel Komolehin pushed to branch master at Debian Med / ska
Commits:
b35dffd1 by Komolehin Israel Timilehin at 2024-01-21T15:51:06+00:00
Added autopkgtest
- - - - -
6aaae159 by Komolehin Israel Timilehin at 2024-01-21T15:52:08+00:00
Install files to build test
- - - - -
7e6f30b0 by Komolehin Israel Timilehin at 2024-01-21T15:52:33+00:00
Install test as examples
- - - - -
60798836 by Komolehin Israel Timilehin at 2024-01-21T17:07:28+00:00
Updated test depends
- - - - -
4 changed files:
- + debian/ska.docs
- + debian/ska.examples
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=
debian/ska.docs
=
@@ -0,0 +1 @@
+debian/tests/run-unit-test
\ No newline at end of file
=
debian/ska.examples
=
@@ -0,0 +1,5 @@
+src/DNA.*
+src/general.*
+src/kmers.*
+src/gzstream.h
+tests/*
\ No newline at end of file
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, build-essential, zlib1g-dev, googletest, libgtest-dev
+Restrictions: allow-stderr
\ No newline at end of file
=
debian/tests/run-unit-test
=
@@ -0,0 +1,37 @@
+#!/bin/sh
+
+pkg=ska
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
+ trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd $AUTOPKGTEST_TMP
+
+sed -i 's+#include "../src/\(.*\)"+#include "\1"+' general_unittest.cpp
kmers_unittest.cpp DNA_unittest.cpp
+
+# Build google test
+ln -s /usr/src/googletest/googletest
+g++ -Igoogletest -std=c++14 -Wall -Wextra -pthread -c
googletest/src/gtest-all.cc
+g++ -Igoogletest -std=c++14 -Wextra -pthread -c googletest/src/gtest_main.cc
+ar rv gtest_main.a gtest-all.o gtest_main.o
+
+
+# Build tests
+g++ -std=c++14 -Wall -Wextra -pthread -c general.cpp
+g++ -std=c++14 -Wextra -pthread -lpthread general.o general_unittest.cpp
gtest_main.a -o general_unittest -lz
+
+g++ -std=c++14 -Wextra -pthread -c kmers.cpp
+g++ -std=c++14 -Wextra -pthread -c DNA.cpp
+
+
+g++ -std=c++14 -Wextra -pthread -lpthread kmers.o DNA.o general.o
kmers_unittest.cpp gtest_main.a -o kmers_unittest -lz
+g++ -std=c++14 -Wextra -pthread -lpthread DNA.o DNA_unittest.cpp gtest_main.a
-o DNA_unittest -lz
+
+# Run built tests
+./general_unittest && ./kmers_unittest && ./DNA_unittest
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/ska/-/compare/2043fb52617bff74ef40b6a8ca4b6a24dec0b218...607988364fd5b387f3aaf90d7f3532416ec0111d
--
View it on GitLab:
https://salsa.debian.org/med-team/ska/-/compare/2043fb52617bff74ef40b6a8ca4b6a24dec0b218...607988364fd5b387f3aaf90d7f3532416ec0111d
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[med-svn] [Git][med-team/ghmm][master] 3 commits: Updated ghmm.examples
Israel Komolehin pushed to branch master at Debian Med / ghmm
Commits:
8a0fc06b by Komolehin Israel Timilehin at 2024-01-18T18:54:28+00:00
Updated ghmm.examples
- - - - -
fe239153 by Komolehin Israel Timilehin at 2024-01-18T18:55:19+00:00
Used custom name for the makefile to avoid auto deletion
- - - - -
4b731563 by Komolehin Israel Timilehin at 2024-01-18T18:56:52+00:00
Updated autopkgtest
- - - - -
3 changed files:
- debian/ghmm.examples
- debian/tests/Makefile → debian/tests/autopkgtest.mk
- debian/tests/run-unit-test
Changes:
=
debian/ghmm.examples
=
@@ -1,2 +1,3 @@
debian/tests/*.py
+debian/tests/autopkgtest.mk
tests/*.c
=
debian/tests/Makefile → debian/tests/autopkgtest.mk
=
=
debian/tests/run-unit-test
=
@@ -10,10 +10,9 @@ if [ "$AUTOPKGTEST_TMP" = "" ]; then
fi
cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-cp -a debian/tests/Makefile "${AUTOPKGTEST_TMP}"
cd $AUTOPKGTEST_TMP
-make run
+make -f autopkgtest.mk run
python3 ghmm_test.py
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/ghmm/-/compare/f7306d7fc95f7d5dba68ed001f04d055c6bd3c30...4b7315639467debeee94abec285d40858b973bb3
--
View it on GitLab:
https://salsa.debian.org/med-team/ghmm/-/compare/f7306d7fc95f7d5dba68ed001f04d055c6bd3c30...4b7315639467debeee94abec285d40858b973bb3
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[med-svn] [Git][med-team/ghmm][master] Updated clean command
Israel Komolehin pushed to branch master at Debian Med / ghmm Commits: 960452fb by Komolehin Israel Timilehin at 2024-01-18T17:39:18+00:00 Updated clean command - - - - - 1 changed file: - debian/tests/Makefile Changes: = debian/tests/Makefile = @@ -24,7 +24,7 @@ test_sequences: sequences_test.o $(CC) -c $< -o $@ $(CFLAGS) clean: - rm -f *.o test_two_sates_three_symbols test_libxml + rm -f *.o test_label_higher_order test_two_sates_three_symbols test_libxml test_read_fa test_sequences run: all ./test_label_higher_order View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/commit/960452fb88dae318577fbab2e235e36780b6d195 -- View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/commit/960452fb88dae318577fbab2e235e36780b6d195 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ghmm][master] 3 commits: Added Makefile to run working upstream tests
Israel Komolehin pushed to branch master at Debian Med / ghmm
Commits:
05107096 by Komolehin Israel Timilehin at 2024-01-18T17:29:32+00:00
Added Makefile to run working upstream tests
- - - - -
5db04538 by Komolehin Israel Timilehin at 2024-01-18T17:31:03+00:00
Updated README with list of missing files in libghmm
- - - - -
7915b392 by Komolehin Israel Timilehin at 2024-01-18T17:34:25+00:00
Updated ghmm.examples
- - - - -
4 changed files:
- debian/ghmm.examples
- + debian/tests/Makefile
- debian/tests/README.md
- debian/tests/run-unit-test
Changes:
=
debian/ghmm.examples
=
@@ -1,3 +1,2 @@
-debian/tests/*.c
debian/tests/*.py
-
+tests/*.c
=
debian/tests/Makefile
=
@@ -0,0 +1,35 @@
+CC=gcc
+CFLAGS=-I/usr/include/ghmm
+LDFLAGS=-lghmm -llapack
+
+
+all: test_label_higher_order test_two_states_three_symbols test_libxml
test_read_fa test_sequences
+
+test_label_higher_order: label_higher_order_test.o
+ $(CC) $^ -o $@ $(LDFLAGS) -lm
+
+test_two_states_three_symbols: two_states_three_symbols.o
+ $(CC) $^ -o $@ $(LDFLAGS)
+
+test_libxml: libxml-test.o
+ $(CC) $^ -o $@ $(LDFLAGS)
+
+test_read_fa: read_fa.o
+ $(CC) $^ -o $@ $(LDFLAGS)
+
+test_sequences: sequences_test.o
+ $(CC) $^ -o $@ $(LDFLAGS)
+
+%.o: %.c
+ $(CC) -c $< -o $@ $(CFLAGS)
+
+clean:
+ rm -f *.o test_two_sates_three_symbols test_libxml
+
+run: all
+ ./test_label_higher_order
+ ./test_two_states_three_symbols
+ ./test_libxml
+ ./test_sequences
+ # read_fa needs seqence and model to be passed as arguments
+ # ./test_read_fa
\ No newline at end of file
=
debian/tests/README.md
=
@@ -2,10 +2,16 @@
Test in python can be referenced
[here](https://ghmm.sourceforge.net/documentation.html)
-## Executed command
-`python3 ghmm_test.py`
- NameError: name 'IntegerRange' is not defined
+## Executed commands
+ Error
+# Missing files in installed libghmm. These missing files are blockers for
some tests
+
+- `ghmm/matrix.h`
+- `ghmm/matrixop.h`
+- `ghmm_internals.h`
+- `randvar.h`
+- `mes.h`
\ No newline at end of file
=
debian/tests/run-unit-test
=
@@ -10,11 +10,10 @@ if [ "$AUTOPKGTEST_TMP" = "" ]; then
fi
cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-cd $AUTOPKGTEST_TMP
+cp -a debian/tests/Makefile "${AUTOPKGTEST_TMP}"
-gcc -c ghmm_test.c -o ghmm_test.o -I/usr/include/ghmm
-gcc ghmm_test.o -o ghmm_test -lghmm -llapack
+cd $AUTOPKGTEST_TMP
-./ghmm_test
+make run
-python3 ghmm_test.py
+python3 ghmm_test.py
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/ghmm/-/compare/2845f134775c316423398c158fc93f842709a179...7915b392555252ac5ff82bb01fe3e81549ab2c0f
--
View it on GitLab:
https://salsa.debian.org/med-team/ghmm/-/compare/2845f134775c316423398c158fc93f842709a179...7915b392555252ac5ff82bb01fe3e81549ab2c0f
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[med-svn] [Git][med-team/ghmm][master] ghmm python attributes and methods can't be found
Israel Komolehin pushed to branch master at Debian Med / ghmm Commits: f1691f8f by Komolehin Israel Timilehin at 2024-01-16T12:36:04+00:00 ghmm python attributes and methods can't be found - - - - - 2 changed files: - debian/tests/README.md - debian/tests/ghmm_test.py Changes: = debian/tests/README.md = @@ -9,7 +9,8 @@ Test in python can be referenced [here](https://ghmm.sourceforge.net/documentati ## Executed command `python3 ghmm_test.py` -- `ModuleNotFoundError: No module named 'ghmm'` +- `ghmm import works fine` +- `Attributes and methods are not found` ## GHMM test in C = debian/tests/ghmm_test.py = @@ -1,3 +1,3 @@ -import ghmm +from ghmm import * -help(ghmm) \ No newline at end of file +sigma = IntegerRange(1,7) \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/commit/f1691f8f85c66e0c1d3e03f85f22d3fec6ab26c5 -- View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/commit/f1691f8f85c66e0c1d3e03f85f22d3fec6ab26c5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/cat-bat][master] Updated Tests
Israel Komolehin pushed to branch master at Debian Med / cat-bat Commits: 42353863 by Komolehin Israel Timilehin at 2024-01-11T08:53:18+00:00 Updated Tests - - - - - 1 changed file: - debian/tests/control Changes: = debian/tests/control = @@ -1,3 +1,3 @@ -Tests: run-bat-unit-test, run-cat-unit-test +Tests: run-unit-test Depends: cat-bat Restrictions: allow-stderr \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/commit/423538633ca6d0cf9f280e4befa5afbdd3cdef41 -- View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/commit/423538633ca6d0cf9f280e4befa5afbdd3cdef41 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/cat-bat][master] 2 commits: Run CAT and BAT test in a single file
Israel Komolehin pushed to branch master at Debian Med / cat-bat
Commits:
8ce616af by Komolehin Israel Timilehin at 2024-01-11T08:04:13+00:00
Run CAT and BAT test in a single file
- - - - -
c9329b6b by Komolehin Israel Timilehin at 2024-01-11T08:04:47+00:00
Added examples
- - - - -
3 changed files:
- + debian/examples
- − debian/tests/run-bat-unit-test
- debian/tests/run-cat-unit-test → debian/tests/run-unit-test
Changes:
=
debian/examples
=
@@ -0,0 +1 @@
+tests/data
\ No newline at end of file
=
debian/tests/run-bat-unit-test deleted
=
@@ -1,44 +0,0 @@
-#!/bin/bash
-
-CUR_DIR=`pwd`
-
-if [ "$AUTOPKGTEST_TMP" = "" ]; then
-
- AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
- trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
-
-fi
-
-mkdir -p "$AUTOPKGTEST_TMP"/data
-
-# Copy tests data
-cp -a "${CUR_DIR}"/tests/data/* "$AUTOPKGTEST_TMP"/data
-
-# Change directory into data
-cd "$AUTOPKGTEST_TMP"/data/
-
-# Extract fasta
-gunzip prepare/small.fa.gz
-
-# Prepare CAT database
-CAT prepare \
---db_fasta ./prepare/small.fa \
---names ./prepare/names.dmp \
---nodes ./prepare/nodes.dmp \
---acc2tax ./prepare/prot2acc.txt \
---db_dir ./output_db
-
-# Run BAT on single MAG
-CAT bins -b prepare/small.fa \
- -d output_db/db \
- -t output_db/tax
-
-# Check final classification files (output files)
-if [ -f "out.BAT.ORF2LCA.txt" ] && [ -f "out.BAT.bin2classification.txt" ];
then
-echo "Final Classification Files Generated"
-rm -rf *
-else
-echo "One or both classification files not generated"
-rm -rf *
-exit 1
-fi
\ No newline at end of file
=
debian/tests/run-cat-unit-test → debian/tests/run-unit-test
=
@@ -1,6 +1,7 @@
#!/bin/bash
CUR_DIR=`pwd`
+pkg=cat-bat
if [ "$AUTOPKGTEST_TMP" = "" ]; then
@@ -12,11 +13,13 @@ fi
mkdir -p "$AUTOPKGTEST_TMP"/data
# Copy tests data
-cp -a "${CUR_DIR}"/tests/data/* "$AUTOPKGTEST_TMP"/data
+cp -a /usr/share/doc/"${pkg}"/examples/data/* "$AUTOPKGTEST_TMP"/data
+
# Change directory into data
cd "$AUTOPKGTEST_TMP"/data/
+
# Extract fasta
gunzip prepare/small.fa.gz
@@ -37,9 +40,24 @@ CAT contigs \
# Check final classification files (output files)
if [ -f "out.CAT.ORF2LCA.txt" ] && [ -f "out.CAT.contig2classification.txt" ];
then
echo "Final Classification Files Generated"
-rm -rf *
+rm -rf out.*
+else
+echo "One or both classification files not generated"
+rm -rf out.*
+exit 1
+fi
+
+# Run BAT on single MAG
+CAT bins -b prepare/small.fa \
+ -d output_db/db \
+ -t output_db/tax
+
+# Check final classification files (output files)
+if [ -f "out.BAT.ORF2LCA.txt" ] && [ -f "out.BAT.bin2classification.txt" ];
then
+echo "Final Classification Files Generated"
+rm -rf out.*
else
echo "One or both classification files not generated"
-rm -rf *
+rm -rf out.*
exit 1
fi
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/cat-bat/-/compare/446fb2f7966393f2e3a6346921fcb95960ab8fe1...c9329b6bb448cd2f54e3448118aeb03581a18a54
--
View it on GitLab:
https://salsa.debian.org/med-team/cat-bat/-/compare/446fb2f7966393f2e3a6346921fcb95960ab8fe1...c9329b6bb448cd2f54e3448118aeb03581a18a54
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[med-svn] [Git][med-team/hinge][master] 2 commits: Updated restrictions
Israel Komolehin pushed to branch master at Debian Med / hinge Commits: d71cb31d by Komolehin Israel Timilehin at 2024-01-10T12:29:15+00:00 Updated restrictions - - - - - 2dbe3b42 by Komolehin Israel Timilehin at 2024-01-10T12:29:39+00:00 Allow test to fail - - - - - 2 changed files: - debian/tests/control - debian/tests/run-demo Changes: = debian/tests/control = @@ -1,3 +1,3 @@ Tests: run-demo Depends: wget, hinge, seqtk -Restrictions: superficial, allow-stderr \ No newline at end of file +Restrictions: allow-stderr, needs-internet \ No newline at end of file = debian/tests/run-demo = @@ -52,4 +52,4 @@ hinge layout --db ecoli --las ecoli.las -x ecoli --config nominal.ini -o ecoli # Run postprocessing ( networkx version needs to be downgraded to 1.x ) -# hinge clip ecoli.edges.hinges ecoli.hinge.list demo \ No newline at end of file +hinge clip ecoli.edges.hinges ecoli.hinge.list demo \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/hinge/-/compare/451960c27c6076e34523832af4ea6ae0490f3d1d...2dbe3b422f155efee99196d521a7bc99fd6083c3 -- View it on GitLab: https://salsa.debian.org/med-team/hinge/-/compare/451960c27c6076e34523832af4ea6ae0490f3d1d...2dbe3b422f155efee99196d521a7bc99fd6083c3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/hinge][master] Updated autopkgtest
Israel Komolehin pushed to branch master at Debian Med / hinge
Commits:
d800f7c4 by Komolehin Israel Timilehin at 2024-01-09T19:07:27+00:00
Updated autopkgtest
- - - - -
1 changed file:
- debian/tests/run-demo
Changes:
=
debian/tests/run-demo
=
@@ -11,8 +11,8 @@ fi
mkdir -p "$AUTOPKGTEST_TMP"/tests
+# Copy configuration file
cp -a "${CUR_DIR}"/utils/nominal.ini "$AUTOPKGTEST_TMP"/tests
-cp -a "${CUR_DIR}"/debian/tests/reads.fasta "$AUTOPKGTEST_TMP"/tests
cd "$AUTOPKGTEST_TMP"/tests/
@@ -50,6 +50,6 @@ hinge maximal --db ecoli --las ecoli.las -x ecoli --config
nominal.ini
hinge layout --db ecoli --las ecoli.las -x ecoli --config nominal.ini -o ecoli
-# Run postprocessing ( networkx version used is deprecated )
+# Run postprocessing ( networkx version needs to be downgraded to 1.x )
-# hinge clip ecoli.edges.hinges ecoli.hinge.list demo
+# hinge clip ecoli.edges.hinges ecoli.hinge.list demo
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/hinge/-/commit/d800f7c4a742587d8a258527be31901429228873
--
View it on GitLab:
https://salsa.debian.org/med-team/hinge/-/commit/d800f7c4a742587d8a258527be31901429228873
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[med-svn] [Git][med-team/hinge][master] 9 commits: Added Autopkgtest
Israel Komolehin pushed to branch master at Debian Med / hinge
Commits:
432b0f8e by Komolehin Israel Timilehin at 2024-01-08T08:27:01+00:00
Added Autopkgtest
- - - - -
155c77aa by Komolehin Israel Timilehin at 2024-01-08T09:20:00+00:00
Updated depends
- - - - -
81c55097 by Komolehin Israel Timilehin at 2024-01-09T14:37:28+00:00
Replicate upstream demo
- - - - -
c174ee0b by Komolehin Israel Timilehin at 2024-01-09T15:07:46+00:00
Updated autopkgtest
- - - - -
f1ddc368 by Komolehin Israel Timilehin at 2024-01-09T16:24:44+00:00
Updated autopkgtest
- - - - -
a22052b4 by Komolehin Israel Timilehin at 2024-01-09T16:56:14+00:00
Added superficial restriction
- - - - -
8a678ceb by Komolehin Israel Timilehin at 2024-01-09T17:34:40+00:00
Added README to document error
- - - - -
840be992 by Komolehin Israel Timilehin at 2024-01-09T17:50:59+00:00
Updated readme
- - - - -
ee7a7986 by Komolehin Israel Timilehin at 2024-01-09T18:01:42+00:00
Updated readme
- - - - -
3 changed files:
- + debian/tests/README.md
- + debian/tests/control
- + debian/tests/run-demo
Changes:
=
debian/tests/README.md
=
@@ -0,0 +1,6 @@
+## Hinge Autopkgtest
+
+- The test breaks at line 55 of `run-demo` due to `networkx` with the
following error:
+- **AttributeError: 'DiGraph' object has no attribute 'node'. Did you mean:
'_node'?**
+- Suggestions on resolving the error can be found
[here](https://github.com/victorlei/smop/issues/165)
+
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Tests: run-demo
+Depends: wget, hinge, seqtk
+Restrictions: superficial, allow-stderr
\ No newline at end of file
=
debian/tests/run-demo
=
@@ -0,0 +1,55 @@
+#!/bin/bash
+
+CUR_DIR=`pwd`
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
+
+ trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+mkdir -p "$AUTOPKGTEST_TMP"/tests
+
+cp -a "${CUR_DIR}"/utils/nominal.ini "$AUTOPKGTEST_TMP"/tests
+cp -a "${CUR_DIR}"/debian/tests/reads.fasta "$AUTOPKGTEST_TMP"/tests
+
+cd "$AUTOPKGTEST_TMP"/tests/
+
+
+# Download Data
+wget http://gembox.cbcb.umd.edu/mhap/raw/ecoli_p4_filtered.fastq.gz
+
+# Extract Data
+gunzip ecoli_p4_filtered.fastq.gz
+
+seqtk seq -a ecoli_p4_filtered.fastq > reads.fasta
+hinge correct-head reads.fasta reads.pb.fasta map.txt
+
+fasta2DB ecoli reads.fasta
+DBsplit -x500 -s100 ecoli
+HPC.daligner -t5 ecoli | bash -v
+
+LAmerge ecoli.las ecoli.[1-5].las
+
+rm ecoli.*.las
+DAScover -v -H1 -mrepeat_mask ecoli.db ecoli.las
+DASqv -c100 ecoli ecoli.las
+
+# Run filter
+
+mkdir log
+hinge filter --db ecoli --las ecoli.las -x ecoli --config nominal.ini
+
+# Get maximal reads
+
+hinge maximal --db ecoli --las ecoli.las -x ecoli --config nominal.ini
+
+# Run layout
+
+hinge layout --db ecoli --las ecoli.las -x ecoli --config nominal.ini -o ecoli
+
+
+# Run postprocessing ( networkx version used is deprecated )
+
+# hinge clip ecoli.edges.hinges ecoli.hinge.list demo
View it on GitLab:
https://salsa.debian.org/med-team/hinge/-/compare/1d7b155a759d8060ce76dd7ab63150d4dd9d41de...ee7a79860b1275f8e789d029936401adb09b5ee1
--
View it on GitLab:
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[med-svn] [Git][med-team/hinge][master] Removed installation error log
Israel Komolehin pushed to branch master at Debian Med / hinge Commits: 1d7b155a by Komolehin Israel Timilehin at 2024-01-07T18:01:05+00:00 Removed installation error log - - - - - 1 changed file: - − debian/tests/README.md Changes: = debian/tests/README.md deleted = @@ -1,39 +0,0 @@ -## Installation Errors - -During the installation process `sudo apt-get install libboost-graph-dev --fix-missing`, the following errors occurred: - -- **Err:1** http://deb.debian.org/debian sid/main amd64 libboost-nowide1.83.0 amd64 1.83.0-1+b1 - - **404 Not Found [IP: 151.101.174.132 80] -- **Err:2** http://deb.debian.org/debian sid/main amd64 libboost-nowide1.83-dev amd64 1.83.0-1+b1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:3** http://deb.debian.org/debian sid/main amd64 libboost-numpy1.83.0 amd64 1.83.0-1+b1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:4** http://deb.debian.org/debian sid/main amd64 libboost-numpy-dev amd64 1.83.0.1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:5** http://deb.debian.org/debian sid/main amd64 libboost-numpy1.83-dev amd64 1.83.0-1+b1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:6** http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:7** http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-1+b1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:8** http://deb.debian.org/debian sid/main amd64 libboost-tools-dev amd64 1.83.0.1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:9** http://deb.debian.org/debian sid/main amd64 libboost1.83-tools-dev amd64 1.83.0-1+b1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:10** http://deb.debian.org/debian sid/main amd64 libboost-graph1.83.0 amd64 1.83.0-1+b1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:11** http://deb.debian.org/debian sid/main amd64 libboost-regex1.83.0 amd64 1.83.0-1+b1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:12** http://deb.debian.org/debian sid/main amd64 libboost-regex1.83-dev amd64 1.83.0-1+b1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:13** http://deb.debian.org/debian sid/main amd64 libboost-serialization1.83-dev amd64 1.83.0-1+b1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:14** http://deb.debian.org/debian sid/main amd64 libboost-test1.83.0 amd64 1.83.0-1+b1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:15** http://deb.debian.org/debian sid/main amd64 libboost-test1.83-dev amd64 1.83.0-1+b1 - - **404** Not Found [IP: 151.101.174.132 80] -- **Err:16** http://deb.debian.org/debian sid/main amd64 libboost-graph-dev amd64 1.83.0.1 - - **404** Not Found [IP: 151.101.174.132 80] -- Unable to correct missing packages. - - View it on GitLab: https://salsa.debian.org/med-team/hinge/-/commit/1d7b155a759d8060ce76dd7ab63150d4dd9d41de -- View it on GitLab: https://salsa.debian.org/med-team/hinge/-/commit/1d7b155a759d8060ce76dd7ab63150d4dd9d41de You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/seqan-needle][master] 2 commits: Added Autopkgtest
Israel Komolehin pushed to branch master at Debian Med / seqan-needle
Commits:
47a7ef7c by Komolehin Israel Timilehin at 2024-01-07T16:38:54+00:00
Added Autopkgtest
- - - - -
7a327d54 by Komolehin Israel Timilehin at 2024-01-07T16:41:01+00:00
Updated debian changelog
- - - - -
3 changed files:
- debian/changelog
- + debian/tests/control
- + debian/tests/run-unit-tests
Changes:
=
debian/changelog
=
@@ -3,6 +3,9 @@ seqan-needle (1.0.2+ds-2) UNRELEASED; urgency=medium
* d/clean: remove HTML build of the documentation. Closes: #1048377
* corrected some patch metadata.
+ [ Komolehin Israel Timilehin ]
+ * Added Autopkgtest
+
-- Michael R. Crusoe Fri, 15 Sep 2023 15:08:23 +0200
seqan-needle (1.0.2+ds-1) unstable; urgency=medium
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Tests: run-unit-tests
+Depends: build-essential, cmake, libseqan3-dev, libgtest-dev, libcereal-dev
+Restrictions: allow-stderr
\ No newline at end of file
=
debian/tests/run-unit-tests
=
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
+
+ trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+# Create test build directory
+mkdir build-tests
+cd build-tests
+
+# Generate build files
+cmake ..
+
+# Run test
+make test
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/seqan-needle/-/compare/118793436a6b4993f1d4bfedd9c9b3cbe9e8dc0d...7a327d54e794d55010b03fd95a1e652e1718cc75
--
View it on GitLab:
https://salsa.debian.org/med-team/seqan-needle/-/compare/118793436a6b4993f1d4bfedd9c9b3cbe9e8dc0d...7a327d54e794d55010b03fd95a1e652e1718cc75
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[med-svn] [Git][med-team/hinge][master] Document dependency installation errors
Israel Komolehin pushed to branch master at Debian Med / hinge Commits: 87291122 by Komolehin Israel Timilehin at 2024-01-04T13:27:14+00:00 Document dependency installation errors - - - - - 1 changed file: - + debian/tests/README.md Changes: = debian/tests/README.md = @@ -0,0 +1,39 @@ +## Installation Errors + +During the installation process `sudo apt-get install libboost-graph-dev --fix-missing`, the following errors occurred: + +- **Err:1** http://deb.debian.org/debian sid/main amd64 libboost-nowide1.83.0 amd64 1.83.0-1+b1 + - **404 Not Found [IP: 151.101.174.132 80] +- **Err:2** http://deb.debian.org/debian sid/main amd64 libboost-nowide1.83-dev amd64 1.83.0-1+b1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:3** http://deb.debian.org/debian sid/main amd64 libboost-numpy1.83.0 amd64 1.83.0-1+b1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:4** http://deb.debian.org/debian sid/main amd64 libboost-numpy-dev amd64 1.83.0.1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:5** http://deb.debian.org/debian sid/main amd64 libboost-numpy1.83-dev amd64 1.83.0-1+b1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:6** http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:7** http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-1+b1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:8** http://deb.debian.org/debian sid/main amd64 libboost-tools-dev amd64 1.83.0.1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:9** http://deb.debian.org/debian sid/main amd64 libboost1.83-tools-dev amd64 1.83.0-1+b1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:10** http://deb.debian.org/debian sid/main amd64 libboost-graph1.83.0 amd64 1.83.0-1+b1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:11** http://deb.debian.org/debian sid/main amd64 libboost-regex1.83.0 amd64 1.83.0-1+b1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:12** http://deb.debian.org/debian sid/main amd64 libboost-regex1.83-dev amd64 1.83.0-1+b1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:13** http://deb.debian.org/debian sid/main amd64 libboost-serialization1.83-dev amd64 1.83.0-1+b1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:14** http://deb.debian.org/debian sid/main amd64 libboost-test1.83.0 amd64 1.83.0-1+b1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:15** http://deb.debian.org/debian sid/main amd64 libboost-test1.83-dev amd64 1.83.0-1+b1 + - **404** Not Found [IP: 151.101.174.132 80] +- **Err:16** http://deb.debian.org/debian sid/main amd64 libboost-graph-dev amd64 1.83.0.1 + - **404** Not Found [IP: 151.101.174.132 80] +- Unable to correct missing packages. + + View it on GitLab: https://salsa.debian.org/med-team/hinge/-/commit/872911223a10b345b8b38ea335fd1f547e2024ae -- View it on GitLab: https://salsa.debian.org/med-team/hinge/-/commit/872911223a10b345b8b38ea335fd1f547e2024ae You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/pymia][master] Updated README
Israel Komolehin pushed to branch master at Debian Med / pymia Commits: 931b45db by Komolehin Israel Timilehin at 2024-01-03T12:41:11+00:00 Updated README - - - - - 1 changed file: - debian/tests/README.md Changes: = debian/tests/README.md = @@ -4,30 +4,21 @@ running `sudo apt-get install libmia-2.4-dev --fix-missing` generates the follow -Err:1 http://deb.debian.org/debian sid/main amd64 libboost-nowide1.83.0 amd64 1.83.0-1+b1 - 404 Not Found [IP: 151.101.174.132 80] -Err:2 http://deb.debian.org/debian sid/main amd64 libboost-nowide1.83-dev amd64 1.83.0-1+b1 - 404 Not Found [IP: 151.101.174.132 80] -Err:3 http://deb.debian.org/debian sid/main amd64 libboost-numpy1.83.0 amd64 1.83.0-1+b1 - 404 Not Found [IP: 151.101.174.132 80] -Err:4 http://deb.debian.org/debian sid/main amd64 libboost-numpy-dev amd64 1.83.0.1 - 404 Not Found [IP: 151.101.174.132 80] -Err:5 http://deb.debian.org/debian sid/main amd64 libboost-numpy1.83-dev amd64 1.83.0-1+b1 - 404 Not Found [IP: 151.101.174.132 80] -Err:6 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.1 - 404 Not Found [IP: 151.101.174.132 80] -Err:7 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-1+b1 - 404 Not Found [IP: 151.101.174.132 80] -Err:8 http://deb.debian.org/debian sid/main amd64 libboost-tools-dev amd64 1.83.0.1 - 404 Not Found [IP: 151.101.174.132 80] -Err:9 http://deb.debian.org/debian sid/main amd64 libboost1.83-tools-dev amd64 1.83.0-1+b1 - 404 Not Found [IP: 151.101.174.132 80] -Err:10 http://deb.debian.org/debian sid/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-1+b1 - 404 Not Found [IP: 151.101.174.132 80] -Err:11 http://deb.debian.org/debian sid/main amd64 libboost-test1.83.0 amd64 1.83.0-1+b1 - 404 Not Found [IP: 151.101.174.132 80] -Err:12 http://deb.debian.org/debian sid/main amd64 libboost-test1.83-dev amd64 1.83.0-1+b1 - 404 Not Found [IP: 151.101.174.132 80] -Err:13 http://deb.debian.org/debian sid/main amd64 libboost-test-dev amd64 1.83.0.1 - 404 Not Found [IP: 151.101.174.132 80] -Unable to correct missing packages. +While attempting to install `sudo apt-get install libmia-2.4-dev --fix-missing`, the system encountered 404 Not Found errors: + +1. **libboost-nowide1.83.0** amd64 1.83.0-1+b1 +2. **libboost-nowide1.83-dev** amd64 1.83.0-1+b1 +3. **libboost-numpy1.83.0** amd64 1.83.0-1+b1 +4. **libboost-numpy-dev** amd64 1.83.0.1 +5. **libboost-numpy1.83-dev** amd64 1.83.0-1+b1 +6. **libboost-dev** amd64 1.83.0.1 +7. **libboost1.83-dev** amd64 1.83.0-1+b1 +8. **libboost-tools-dev** amd64 1.83.0.1 +9. **libboost1.83-tools-dev** amd64 1.83.0-1+b1 +10. **libboost-filesystem1.83.0** amd64 1.83.0-1+b1 +11. **libboost-test1.83.0** amd64 1.83.0-1+b1 +12. **libboost-test1.83-dev** amd64 1.83.0-1+b1 +13. **libboost-test-dev** amd64 1.83.0.1 + +The URLs provided for these packages returned 404 Not Found errors, indicating that the packages could not be found at the specified location. + View it on GitLab: https://salsa.debian.org/med-team/pymia/-/commit/931b45dbf26acb1ee85f104fcd16b7f9bb81c270 -- View it on GitLab: https://salsa.debian.org/med-team/pymia/-/commit/931b45dbf26acb1ee85f104fcd16b7f9bb81c270 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/pymia][master] Added readme for libmia-2.4-dev installation problem
Israel Komolehin pushed to branch master at Debian Med / pymia Commits: f162438e by Komolehin Israel Timilehin at 2024-01-03T12:25:51+00:00 Added readme for libmia-2.4-dev installation problem - - - - - 1 changed file: - + debian/tests/README.md Changes: = debian/tests/README.md = @@ -0,0 +1,33 @@ +## Installing libmia-2.4-dev + +running `sudo apt-get install libmia-2.4-dev --fix-missing` generates the following error: + + + +Err:1 http://deb.debian.org/debian sid/main amd64 libboost-nowide1.83.0 amd64 1.83.0-1+b1 + 404 Not Found [IP: 151.101.174.132 80] +Err:2 http://deb.debian.org/debian sid/main amd64 libboost-nowide1.83-dev amd64 1.83.0-1+b1 + 404 Not Found [IP: 151.101.174.132 80] +Err:3 http://deb.debian.org/debian sid/main amd64 libboost-numpy1.83.0 amd64 1.83.0-1+b1 + 404 Not Found [IP: 151.101.174.132 80] +Err:4 http://deb.debian.org/debian sid/main amd64 libboost-numpy-dev amd64 1.83.0.1 + 404 Not Found [IP: 151.101.174.132 80] +Err:5 http://deb.debian.org/debian sid/main amd64 libboost-numpy1.83-dev amd64 1.83.0-1+b1 + 404 Not Found [IP: 151.101.174.132 80] +Err:6 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.1 + 404 Not Found [IP: 151.101.174.132 80] +Err:7 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-1+b1 + 404 Not Found [IP: 151.101.174.132 80] +Err:8 http://deb.debian.org/debian sid/main amd64 libboost-tools-dev amd64 1.83.0.1 + 404 Not Found [IP: 151.101.174.132 80] +Err:9 http://deb.debian.org/debian sid/main amd64 libboost1.83-tools-dev amd64 1.83.0-1+b1 + 404 Not Found [IP: 151.101.174.132 80] +Err:10 http://deb.debian.org/debian sid/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-1+b1 + 404 Not Found [IP: 151.101.174.132 80] +Err:11 http://deb.debian.org/debian sid/main amd64 libboost-test1.83.0 amd64 1.83.0-1+b1 + 404 Not Found [IP: 151.101.174.132 80] +Err:12 http://deb.debian.org/debian sid/main amd64 libboost-test1.83-dev amd64 1.83.0-1+b1 + 404 Not Found [IP: 151.101.174.132 80] +Err:13 http://deb.debian.org/debian sid/main amd64 libboost-test-dev amd64 1.83.0.1 + 404 Not Found [IP: 151.101.174.132 80] +Unable to correct missing packages. View it on GitLab: https://salsa.debian.org/med-team/pymia/-/commit/f162438e4ccbe6136edb8f1add98d7d46297d951 -- View it on GitLab: https://salsa.debian.org/med-team/pymia/-/commit/f162438e4ccbe6136edb8f1add98d7d46297d951 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/xpore][master] Updated Copyright
Israel Komolehin pushed to branch master at Debian Med / xpore Commits: d3cb5348 by Komolehin Israel Timilehin at 2023-12-31T20:39:48+00:00 Updated Copyright - - - - - 1 changed file: - debian/copyright Changes: = debian/copyright = @@ -15,6 +15,7 @@ License: Expat Files: debian-tests-data/demo.tar.gz Copyright: Zenodo Source: wget https://zenodo.org/record/5162402/files/demo.tar.gz +Comment: https://zenodo.org/records/5162402 Licence: CC-BY-4.0 License: Expat View it on GitLab: https://salsa.debian.org/med-team/xpore/-/commit/d3cb5348b28f04445659e2b5c2e832a1c2104602 -- View it on GitLab: https://salsa.debian.org/med-team/xpore/-/commit/d3cb5348b28f04445659e2b5c2e832a1c2104602 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/xpore][master] Added readme for the test data reference and to run the test
Israel Komolehin pushed to branch master at Debian Med / xpore Commits: c2c02c00 by Komolehin Israel Timilehin at 2023-12-30T17:22:34+00:00 Added readme for the test data reference and to run the test - - - - - 1 changed file: - + debian/tests/README.md Changes: = debian/tests/README.md = @@ -0,0 +1,11 @@ +Test for Xpore +=== + +The data for the test has been referenced from: +https://zenodo.org/records/5162402 + +To download the test data and generate tarball: + run `./get-test-data` + +To run the test, run the test from the project root: + run `sh ./debian/tests/run-data-preprocess-test` \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/xpore/-/commit/c2c02c00d35c0a339aa4903edfb7511ac97eb854 -- View it on GitLab: https://salsa.debian.org/med-team/xpore/-/commit/c2c02c00d35c0a339aa4903edfb7511ac97eb854 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/xpore][master] Added script to fetch test data
Israel Komolehin pushed to branch master at Debian Med / xpore
Commits:
abb28516 by Komolehin Israel Timilehin at 2023-12-30T17:08:01+00:00
Added script to fetch test data
- - - - -
1 changed file:
- + debian/tests/get-test-data
Changes:
=
debian/tests/get-test-data
=
@@ -0,0 +1,7 @@
+#!/bin/sh
+
+wget https://zenodo.org/record/5162402/files/demo.tar.gz
+tar -xvf demo.tar.gz
+tarball=$(dpkg-parsechangelog --file ../changelog | awk '/^Source:/ {print
$2}')_$(dpkg-parsechangelog --file ../changelog | awk '/^Version:/ {print $2}'
| cut -f1 -d-).orig-debian-tests-data.tar.gz
+tar --owner=root --group=root --mode=a+rX -caf $tarball demo
+rm -rf demo.tar.gz demo/
View it on GitLab:
https://salsa.debian.org/med-team/xpore/-/commit/abb28516eeeaba4f670aa46986707f4ffe339891
--
View it on GitLab:
https://salsa.debian.org/med-team/xpore/-/commit/abb28516eeeaba4f670aa46986707f4ffe339891
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[med-svn] [Git][med-team/xpore][master] 3 commits: Removed trailing whitespace
Israel Komolehin pushed to branch master at Debian Med / xpore Commits: e9810ce3 by Komolehin Israel Timilehin at 2023-12-29T09:08:29+00:00 Removed trailing whitespace - - - - - 5be9b6c9 by Komolehin Israel Timilehin at 2023-12-29T09:09:46+00:00 Updated Copyright - - - - - 90e43dc9 by Komolehin Israel Timilehin at 2023-12-29T09:13:02+00:00 Updated Changelog - - - - - 3 changed files: - debian/changelog - debian/copyright - debian/tests/run-data-preprocess-test Changes: = debian/changelog = @@ -1,3 +1,9 @@ +xpore (2.1-2) UNRELEASED; urgency=medium + + * Added Autopkgtest (Closes: #1035276) + + -- Komolehin Israel Timilehin Fri, 29 Dec 2023 09:10:47 + + xpore (2.1-1) unstable; urgency=medium * Team Upload. = debian/copyright = @@ -12,6 +12,11 @@ Files: debian/* Copyright: 2021 Steffen Moeller License: Expat +Files: debian-tests-data/demo.tar.gz +Copyright: Zenodo +Source: wget https://zenodo.org/record/5162402/files/demo.tar.gz +Licence: CC-BY-4.0 + License: Expat Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal @@ -30,3 +35,42 @@ License: Expat LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +License: CC-BY-4.0 + Creative Commons public licenses provide a standard set of terms and + conditions that creators and other rights holders may use to share + original works of authorship and other material subject to copyright + and certain other rights specified in the public license below. The + following considerations are for informational purposes only, are not + exhaustive, and do not form part of our licenses. + . + Considerations for licensors: Our public licenses are + intended for use by those authorized to give the public + permission to use material in ways otherwise restricted by + copyright and certain other rights. Our licenses are + irrevocable. Licensors should read and understand the terms + and conditions of the license they choose before applying it. + Licensors should also secure all rights necessary before + applying our licenses so that the public can reuse the + material as expected. Licensors should clearly mark any + material not subject to the license. This includes other CC- + licensed material, or material used under an exception or + limitation to copyright. More considerations for licensors: + wiki.creativecommons.org/Considerations_for_licensors + . + Considerations for the public: By using one of our public + licenses, a licensor grants the public permission to use the + licensed material under specified terms and conditions. If + the licensor's permission is not necessary for any reason--for + example, because of any applicable exception or limitation to + copyright--then that use is not regulated by the license. Our + licenses grant only permissions under copyright and certain + other rights that a licensor has authority to grant. Use of + the licensed material may still be restricted for other + reasons, including because others have copyright or other + rights in the material. A licensor may make special requests, + such as asking that all changes be marked or described. + Although not required by our licenses, you are encouraged to + respect those requests where reasonable. More considerations + for the public: + wiki.creativecommons.org/Considerations_for_licensees = debian/tests/run-data-preprocess-test = @@ -37,4 +37,4 @@ else echo "Output Directory Not Generated" exit 1 -fi +fi \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/xpore/-/compare/dcb319beede899a6ca30a6e15486fe230ad5083a...90e43dc99752835594e9055a6d7393e1525b6cf5 -- View it on GitLab: https://salsa.debian.org/med-team/xpore/-/compare/dcb319beede899a6ca30a6e15486fe230ad5083a...90e43dc99752835594e9055a6d7393e1525b6cf5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/xpore][pristine-tar] 2 commits: pristine-tar data for xpore_2.1.orig-debian-tests-data.tar.gz
Israel Komolehin pushed to branch pristine-tar at Debian Med / xpore Commits: 3be419e0 by Komolehin Israel Timilehin at 2023-12-28T05:48:47+00:00 pristine-tar data for xpore_2.1.orig-debian-tests-data.tar.gz - - - - - cd6e986f by Komolehin Israel Timilehin at 2023-12-28T05:48:48+00:00 pristine-tar data for xpore_2.1.orig.tar.gz - - - - - 4 changed files: - + xpore_2.1.orig-debian-tests-data.tar.gz.delta - + xpore_2.1.orig-debian-tests-data.tar.gz.id - xpore_2.1.orig.tar.gz.delta - xpore_2.1.orig.tar.gz.id Changes: = xpore_2.1.orig-debian-tests-data.tar.gz.delta = Binary files /dev/null and b/xpore_2.1.orig-debian-tests-data.tar.gz.delta differ = xpore_2.1.orig-debian-tests-data.tar.gz.id = @@ -0,0 +1 @@ +861cbf99e47818107f193c7463276e7733009838 = xpore_2.1.orig.tar.gz.delta = Binary files a/xpore_2.1.orig.tar.gz.delta and b/xpore_2.1.orig.tar.gz.delta differ = xpore_2.1.orig.tar.gz.id = @@ -1 +1 @@ -102b2278c2c0a76f48769b9a3cc39a5fb18de6b6 +856fbaa119edbffeace6784bfb3fab6776185cd9 View it on GitLab: https://salsa.debian.org/med-team/xpore/-/compare/76b23c61749efc6853527cd832bb57d062e09a37...cd6e986f9156c76ea145a2c6c234ef0f6dc93605 -- View it on GitLab: https://salsa.debian.org/med-team/xpore/-/compare/76b23c61749efc6853527cd832bb57d062e09a37...cd6e986f9156c76ea145a2c6c234ef0f6dc93605 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-iow][master] Updated changelog
Israel Komolehin pushed to branch master at Debian Med / python-iow Commits: 2626efcc by Komolehin Israel Timilehin at 2023-12-23T17:38:15+00:00 Updated changelog - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,3 +1,10 @@ +python-iow (1.0.6-4) UNRELEASED; urgency=medium + + * Added patch to fix tests + * Added Autopkgtest (Closes: #1035258) + + -- Komolehin Israel Timilehin Sat, 23 Dec 2023 17:04:39 + + python-iow (1.0.6-3) unstable; urgency=medium * Team upload View it on GitLab: https://salsa.debian.org/med-team/python-iow/-/commit/2626efcc22fbf3332929cf8ca738a5291973896d -- View it on GitLab: https://salsa.debian.org/med-team/python-iow/-/commit/2626efcc22fbf3332929cf8ca738a5291973896d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-iow][master] 4 commits: Added patch to fix tests
Israel Komolehin pushed to branch master at Debian Med / python-iow
Commits:
2e0a7534 by Komolehin Israel Timilehin at 2023-12-23T16:35:31+00:00
Added patch to fix tests
- - - - -
62a65de7 by Komolehin Israel Timilehin at 2023-12-23T16:36:25+00:00
Added Autopkgtest
- - - - -
609408d0 by Komolehin Israel Timilehin at 2023-12-23T16:56:39+00:00
Updated Patch
- - - - -
e9a7d87f by Komolehin Israel Timilehin at 2023-12-23T17:21:01+00:00
Document test observation when run with python3.12
- - - - -
5 changed files:
- + debian/patches/fix_test.diff
- debian/patches/series
- + debian/tests/README.md
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=
debian/patches/fix_test.diff
=
@@ -0,0 +1,61 @@
+--- a/bp/tests/test_insert.py
b/bp/tests/test_insert.py
+@@ -1,5 +1,5 @@
+ import unittest
+-import pkg_resources
++import os
+ from bp import parse_jplace, insert_fully_resolved
+ import skbio
+ import pandas as pd
+@@ -8,15 +8,14 @@
+ class InsertTests(unittest.TestCase):
+ package = 'bp.tests'
+ def setUp(self):
+-self.jplacedata_multiple = \
+-open(self.get_data_path('300/placement_mul.jplace')).read()
++with open(self.get_data_path('300/placement_mul.jplace'), 'r') as
file:
++self.jplacedata_multiple = file.read()
+ self.final_multiple_fully_resolved = \
+
skbio.TreeNode.read(self.get_data_path('300/placement.full_resolve.newick'))
+
+ def get_data_path(self, filename):
+-# adapted from qiime2.plugin.testing.TestPluginBase
+-return pkg_resources.resource_filename(self.package,
+- 'data/%s' % filename)
++current_directory = os.getcwd()
++return current_directory + "/tests/data/" + filename
+
+ def test_insert_fully_resolved(self):
+ exp = self.final_multiple_fully_resolved
+--- a/bp/tests/test_io.py
b/bp/tests/test_io.py
+@@ -4,7 +4,7 @@
+ import json
+ import pandas as pd
+ import pandas.testing as pdt
+-import pkg_resources
++import os
+ import skbio
+ import io
+ import numpy as np
+@@ -205,16 +205,15 @@
+ package = 'bp.tests'
+
+ def setUp(self):
+-self.jplacedata = open(self.get_data_path('200/placement.jplace'))
+-self.jplacedata = self.jplacedata.read()
++with open(self.get_data_path('200/placement.jplace'), 'r') as file:
++self.jplacedata = file.read()
+ no_edge_numbers = re.sub(r"{\d+}", '',
+ json.loads(self.jplacedata)['tree'])
+ self.tree = skbio.TreeNode.read([no_edge_numbers])
+
+ def get_data_path(self, filename):
+-# adapted from qiime2.plugin.testing.TestPluginBase
+-return pkg_resources.resource_filename(self.package,
+- 'data/%s' % filename)
++current_directory = os.getcwd()
++return current_directory + "/tests/data/" + filename
+
+ def test_place_jplace_square_braces(self):
+ self.jplacedata = json.loads(self.jplacedata)
=
debian/patches/series
=
@@ -1 +1,2 @@
no-runtime-cython.patch
+fix_test.diff
=
debian/tests/README.md
=
@@ -0,0 +1,10 @@
+## Run Tests
+
+`sh ./debian/tests/run-unit-test`
+
+## Observation with Python3.12
+Test fails when run with python3.12. The error appears to be from pandas with
the following exception.
+
+`File "/usr/lib/python3/dist-packages/pandas/_libs/__init__.py", line 13, in
`
+`from pandas._libs.interval import Interval`
+`ModuleNotFoundError: No module named 'pandas._libs.interval'`
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: python3-iow
+Restrictions: allow-stderr
=
debian/tests/run-unit-test
=
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+CUR_DIR=`pwd`
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
+
+ trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+mkdir -p "$AUTOPKGTEST_TMP"/tests
+
+cp -a "${CUR_DIR}"/bp/* "$AUTOPKGTEST_TMP"/tests
+
+cd "$AUTOPKGTEST_TMP"/tests/
+
+
+for py in $(py3versions -s 2> /dev/null)
+
+do
+
+# Run upstream tests
+$py -m unittest
+
+
+done
View it on GitLab:
https://salsa.debian.org/med-team/python-iow/-/compare/a12fccb9097fb21084c336330f8647acef0cb45c...e9a7d87f19b9e6903a888ef0056acb5947737632
--
View it on GitLab:
https://salsa.debian.org/med-team/python-iow/-/compare/a12fccb9097fb21084c336330f8647acef0cb45c...e9a7d87f19b9e6903a888ef0056acb5947737632
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deb
[med-svn] [Git][med-team/nitime][master] Updated Autopkgtest
Israel Komolehin pushed to branch master at Debian Med / nitime
Commits:
52d88fab by Komolehin Israel Timilehin at 2023-12-21T07:38:02+00:00
Updated Autopkgtest
- - - - -
2 changed files:
- debian/tests/control
- debian/tests/run-unit-test
Changes:
=
debian/tests/control
=
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: cython3, python3-nitime, python3-setuptools, python3-pytest
-Restrictions: allow-stderr, needs-root
\ No newline at end of file
+Depends: python3-nitime, python3-pytest
+Restrictions: allow-stderr
\ No newline at end of file
=
debian/tests/run-unit-test
=
@@ -1,23 +1,30 @@
#!/bin/bash
-if [ "$AUTOPKGTEST_TMP" = ""]; then
+CUR_DIR=`pwd`
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
fi
+cd $AUTOPKGTEST_TMP
+
+
+# Copy Upstream tests
+cp -a ${CUR_DIR}/nitime/algorithms/tests/ $AUTOPKGTEST_TMP
+cp -a ${CUR_DIR}/nitime/analysis/ $AUTOPKGTEST_TMP
+cp -a ${CUR_DIR}/nitime/fmri/ $AUTOPKGTEST_TMP
+cp -a ${CUR_DIR}/nitime/tests/ $AUTOPKGTEST_TMP
+
for py in $(py3versions -s 2> /dev/null)
do
-# Build the package
-$py setup.py install
# Run upstream tests
-$py -m pytest ./nitime/algorithms/
-$py -m pytest ./nitime/analysis/
-$py -m pytest ./nitime/fmri/
-$py -m pytest ./nitime/tests/
+$py -m pytest
+
done
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/nitime/-/commit/52d88fabb992a12aab75046371f0581929104432
--
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[med-svn] [Git][med-team/nitime][master] Updated debian/tests/control
Israel Komolehin pushed to branch master at Debian Med / nitime Commits: 1a7c02f4 by Komolehin Israel Timilehin at 2023-12-20T13:12:52+00:00 Updated debian/tests/control - - - - - 1 changed file: - debian/tests/control Changes: = debian/tests/control = @@ -1,3 +1,3 @@ Tests: run-unit-test -Depends: cython3, python3-nitime +Depends: cython3, python3-nitime, python3-setuptools, python3-pytest Restrictions: allow-stderr, needs-root \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/nitime/-/commit/1a7c02f4a2d22cde86f8e0064f846fc43acb2005 -- View it on GitLab: https://salsa.debian.org/med-team/nitime/-/commit/1a7c02f4a2d22cde86f8e0064f846fc43acb2005 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/nitime][master] 3 commits: Added autopkgtest
Israel Komolehin pushed to branch master at Debian Med / nitime
Commits:
44dabd52 by Komolehin Israel Timilehin at 2023-12-20T12:18:17+00:00
Added autopkgtest
- - - - -
013fe4e8 by Komolehin Israel Timilehin at 2023-12-20T12:18:45+00:00
Documented test observation
- - - - -
6e538d94 by Komolehin Israel Timilehin at 2023-12-20T12:22:08+00:00
Updated changelog. closes #1058705
- - - - -
4 changed files:
- debian/changelog
- + debian/tests/README.md
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=
debian/changelog
=
@@ -1,3 +1,9 @@
+nitime (0.10.2-2) UNRELEASED; urgency=medium
+
+ * Added autopkgtest (Closes: #1058705)
+
+ -- Komolehin Israel Timilehin Wed, 20 Dec 2023
12:19:23 +
+
nitime (0.10.2-1) unstable; urgency=medium
[ Andreas Tille ]
=
debian/tests/README.md
=
@@ -0,0 +1,13 @@
+## To run the test:
+
+`sh run-unit-test`
+
+The package needs be built from scratch to run the upstream test.
+
+Upstream test can be run with:
+
+`$py -m pytest`
+
+However, this will popup two GUIS which needs to be closed before tests run.
+
+The path to each test folder was specified to circumvent the GUI popup.
\ No newline at end of file
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: cython3, python3-nitime
+Restrictions: allow-stderr, needs-root
\ No newline at end of file
=
debian/tests/run-unit-test
=
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+if [ "$AUTOPKGTEST_TMP" = ""]; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
+
+ trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+
+for py in $(py3versions -s 2> /dev/null)
+
+do
+# Build the package
+$py setup.py install
+
+# Run upstream tests
+$py -m pytest ./nitime/algorithms/
+$py -m pytest ./nitime/analysis/
+$py -m pytest ./nitime/fmri/
+$py -m pytest ./nitime/tests/
+
+done
\ No newline at end of file
View it on GitLab:
https://salsa.debian.org/med-team/nitime/-/compare/44079317d6c26e906f47a008a6c6cf44dff9c45c...6e538d948376f2afae0a5f8ad664bc2baf3a464b
--
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[med-svn] [Git][med-team/busco][master] Created a separate Tests entry for busco analysis
Israel Komolehin pushed to branch master at Debian Med / busco Commits: 6192e3ce by Komolehin Israel Timilehin at 2023-12-19T15:09:14+00:00 Created a separate Tests entry for busco analysis - - - - - 2 changed files: - debian/tests/control - debian/tests/run-unit-test-2 → debian/tests/run-busco-analysis Changes: = debian/tests/control = @@ -1,3 +1,7 @@ -Tests: run-unit-test, run-unit-test-2 +Tests: run-unit-test Depends: @, python3-all, quilt -Restrictions: allow-stderr, needs-root, needs-internet +Restrictions: allow-stderr + +Tests: run-busco-analysis +Depends: @, python3-all +Restrictions: allow-stderr, needs-internet \ No newline at end of file = debian/tests/run-unit-test-2 → debian/tests/run-busco-analysis = @@ -38,6 +38,3 @@ else fi - - - View it on GitLab: https://salsa.debian.org/med-team/busco/-/commit/6192e3cee8dfceee3416af7a8cc2157a2d85b961 -- View it on GitLab: https://salsa.debian.org/med-team/busco/-/commit/6192e3cee8dfceee3416af7a8cc2157a2d85b961 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/busco][master] Clear busco_downloads folder
Israel Komolehin pushed to branch master at Debian Med / busco
Commits:
cdc3976f by Komolehin Israel Timilehin at 2023-12-19T12:44:09+00:00
Clear busco_downloads folder
- - - - -
1 changed file:
- debian/tests/run-unit-test-2
Changes:
=
debian/tests/run-unit-test-2
=
@@ -21,8 +21,8 @@ cp -a /usr/share/doc/${pkg}/examples/genome.fna .
# Busco will automatically download and version the dataset for the specified
lineage
$pkg -m genome -i genome.fna -o test_bacteria -l bacteria_odb10
-
-ls
+# Clear busco downloaded data after test
+rm -rf busco_downloads
# Check output directory
if [ -d "./test_bacteria" ]; then
View it on GitLab:
https://salsa.debian.org/med-team/busco/-/commit/cdc3976fea89070c15e21ceef3cbdd35f69fe8fe
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[med-svn] [Git][med-team/busco][master] Removed dataset tarball import
Israel Komolehin pushed to branch master at Debian Med / busco
Commits:
2b2747db by Komolehin Israel Timilehin at 2023-12-19T12:28:33+00:00
Removed dataset tarball import
- - - - -
1 changed file:
- debian/tests/run-unit-test-2
Changes:
=
debian/tests/run-unit-test-2
=
@@ -15,13 +15,8 @@ fi
cd $AUTOPKGTEST_TMP
# Copy data
-cp -a ${CUR_DIR}/debian/tests/data/* .
cp -a /usr/share/doc/${pkg}/examples/genome.fna .
-
-# Extract lineage
-
-
# This test requires Prodigal and HMMER
# Busco will automatically download and version the dataset for the specified
lineage
$pkg -m genome -i genome.fna -o test_bacteria -l bacteria_odb10
View it on GitLab:
https://salsa.debian.org/med-team/busco/-/commit/2b2747dbf9897711ee7daa2328360d59d6b95068
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[med-svn] [Git][med-team/busco][master] 4 commits: Added README
Israel Komolehin pushed to branch master at Debian Med / busco
Commits:
172a98c3 by Komolehin Israel Timilehin at 2023-12-15T17:08:56+00:00
Added README
- - - - -
5eeb0913 by Komolehin Israel Timilehin at 2023-12-15T17:09:31+00:00
Updated copyright
- - - - -
04b10cc9 by Komolehin Israel Timilehin at 2023-12-15T17:12:17+00:00
Updated changelog
- - - - -
2119ef11 by Komolehin Israel Timilehin at 2023-12-15T17:52:23+00:00
Updated copyright
- - - - -
3 changed files:
- debian/changelog
- debian/copyright
- + debian/tests/data/README.md
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+busco (5.5.0-2) UNRELEASED; urgency=medium
+
+
+ * Added autopkgtest to check hmmer and prodigal integration (Closes:
#1010653)
+ * Updated copyright
+
+ -- Komolehin Israel Timilehin Fri, 15 Dec 2023
17:09:43 +
+
busco (5.5.0-1) unstable; urgency=medium
* New upstream version
=
debian/copyright
=
@@ -10,6 +10,11 @@ Files: debian/*
Copyright: 2020 Andreas Tille
License: MIT
+Files: debian/tests/data/*
+Copyright: Busco
+Source: wget
https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz
+Licence: CC-BY-ND-4.0
+
License: MIT
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
@@ -28,3 +33,73 @@ License: MIT
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
+
+Licence: CC-BY-ND-4.0
+ Creative Commons Corporation ("Creative Commons") is not a law firm and
+ does not provide legal services or legal advice. Distribution of
+ Creative Commons public licenses does not create a lawyer-client or
+ other relationship. Creative Commons makes its licenses and related
+ information available on an "as-is" basis. Creative Commons gives no
+ warranties regarding its licenses, any material licensed under their
+ terms and conditions, or any related information. Creative Commons
+ disclaims all liability for damages resulting from their use to the
+ fullest extent possible.
+ .
+ Using Creative Commons Public Licenses
+ .
+ Creative Commons public licenses provide a standard set of terms and
+ conditions that creators and other rights holders may use to share
+ original works of authorship and other material subject to copyright
+ and certain other rights specified in the public license below. The
+ following considerations are for informational purposes only, are not
+ exhaustive, and do not form part of our licenses.
+ .
+ Considerations for licensors: Our public licenses are
+ intended for use by those authorized to give the public
+ permission to use material in ways otherwise restricted by
+ copyright and certain other rights. Our licenses are
+ irrevocable. Licensors should read and understand the terms
+ and conditions of the license they choose before applying it.
+ Licensors should also secure all rights necessary before
+ applying our licenses so that the public can reuse the
+ material as expected. Licensors should clearly mark any
+ material not subject to the license. This includes other CC-
+ licensed material, or material used under an exception or
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+ wiki.creativecommons.org/Considerations_for_licensors
+ .
+ Considerations for the public: By using one of our public
+ licenses, a licensor grants the public permission to use the
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+ the licensor's permission is not necessary for any reason--for
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+ public licenses is dedicated to the public domain under the CC0 Public
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+ material is shared under a Creative Commons public license or as
+ otherwise permitted by the Creative Common
[med-svn] [Git][med-team/busco][master] 3 commits: Inclued path to test dataset
Israel Komolehin pushed to branch master at Debian Med / busco
Commits:
d59409af by Komolehin Israel Timilehin at 2023-12-15T12:43:03+00:00
Inclued path to test dataset
- - - - -
2f2d6e73 by Komolehin Israel Timilehin at 2023-12-15T12:44:20+00:00
Added autopkgtest for hmmer and prodigal integration
- - - - -
214aaa52 by Komolehin Israel Timilehin at 2023-12-15T12:45:04+00:00
Added lineage tarball to source
- - - - -
5 changed files:
- debian/examples
- + debian/source/include-binaries
- debian/tests/control
- + debian/tests/data/bacteria_odb10.2020-03-06.tar.gz
- + debian/tests/run-unit-test-2
Changes:
=
debian/examples
=
@@ -1 +1,2 @@
config/*
+test_data/bacteria/genome.fna
=
debian/source/include-binaries
=
@@ -0,0 +1 @@
+debian/tests/data/bacteria_odb10.2020-03-06.tar.gz
=
debian/tests/control
=
@@ -1,3 +1,3 @@
-Tests: run-unit-test
+Tests: run-unit-test, run-unit-test-2
Depends: @, python3-all, quilt
-Restrictions: allow-stderr
+Restrictions: allow-stderr, needs-root, needs-internet
=
debian/tests/data/bacteria_odb10.2020-03-06.tar.gz
=
Binary files /dev/null and b/debian/tests/data/bacteria_odb10.2020-03-06.tar.gz
differ
=
debian/tests/run-unit-test-2
=
@@ -0,0 +1,44 @@
+#!/bin/bash
+
+set -e
+
+pkg='busco'
+CUR_DIR=`pwd`
+
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XX`
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+
+cd $AUTOPKGTEST_TMP
+
+# Copy data
+cp -a ${CUR_DIR}/debian/tests/data/* .
+cp -a /usr/share/doc/${pkg}/examples/genome.fna .
+
+
+# Extract lineage
+tar -xzf bacteria_odb10.2020-03-06.tar.gz
+
+# This test requires Prodigal and HMMER
+$pkg -m genome -i genome.fna -o test_bacteria -l ./bacteria_odb10
+
+# Check output directory
+if [ -d "./test_bacteria" ]; then
+
+echo "Output Directory Generated"
+echo "PASS"
+
+else
+
+echo "Output Directory Not Generated"
+exit 1
+
+fi
+
+
+
+
+
View it on GitLab:
https://salsa.debian.org/med-team/busco/-/compare/3fc8e694c4d83dfe7384a71ec619a40859f3ae6d...214aaa52c49bdab08e37432ee4a4bb2413868eb8
--
View it on GitLab:
https://salsa.debian.org/med-team/busco/-/compare/3fc8e694c4d83dfe7384a71ec619a40859f3ae6d...214aaa52c49bdab08e37432ee4a4bb2413868eb8
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[med-svn] [Git][med-team/pique][master] 4 commits: Added patch to fix smartpca command
Israel Komolehin pushed to branch master at Debian Med / pique
Commits:
fe7a3237 by Komolehin Israel Timilehin at 2023-12-12T16:43:02+00:00
Added patch to fix smartpca command
- - - - -
74b00c1c by Komolehin Israel Timilehin at 2023-12-12T16:44:40+00:00
Added autopkgtest
- - - - -
91c94c60 by Komolehin Israel Timilehin at 2023-12-12T17:01:16+00:00
Close Bug
- - - - -
bb78acdb by Komolehin Israel Timilehin at 2023-12-12T17:05:34+00:00
Updated debian/tests/control
- - - - -
6 changed files:
- debian/changelog
- + debian/patches/series
- + debian/patches/smartpca_fix.diff
- − debian/tests/_control_
- + debian/tests/control
- − debian/tests/run-unit-test
Changes:
=
debian/changelog
=
@@ -1,3 +1,10 @@
+pique (1.0-7) UNRELEASED; urgency=medium
+
+ * Added patch to fix smartpca command
+ * Added autopkgtest (Closes: #986194)
+
+ -- Komolehin Israel Timilehin Tue, 12 Dec 2023
16:57:46 +
+
pique (1.0-6) unstable; urgency=medium
* Team upload.
=
debian/patches/series
=
@@ -0,0 +1 @@
+smartpca_fix.diff
=
debian/patches/smartpca_fix.diff
=
@@ -0,0 +1,11 @@
+--- a/bin/pique-input
b/bin/pique-input
+@@ -838,7 +838,7 @@
+ must_close($par_fh);
+
+ # run smartpca
+-run("smartpca -p $par_file > $out-smartpca.log");
++run("/usr/lib/eigensoft/smartpca -p $par_file > $out-smartpca.log");
+
+ # tidy up
+ if ( !$opt_d ) {
=
debian/tests/_control_ deleted
=
@@ -1,3 +0,0 @@
-Tests: run-unit-test
-Depends: @
-Restrictions: allow-stderr
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Test-command: cd test && make
+Depends: pique, pique-doc, wget, r-cran-hmisc
+Restrictions: allow-stderr, needs-internet
=
debian/tests/run-unit-test deleted
=
@@ -1,15 +0,0 @@
-#!/bin/bash
-set -e
-
-pkg=pique
-
-if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
- AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XX)
- trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-
-cd "${AUTOPKGTEST_TMP}"
-
-make
View it on GitLab:
https://salsa.debian.org/med-team/pique/-/compare/d7cf8f68d7573bd2e9c6c1ae8dea3f26d1b32485...bb78acdbb21aaa147e24b47b32134b1575a8b0bd
--
View it on GitLab:
https://salsa.debian.org/med-team/pique/-/compare/d7cf8f68d7573bd2e9c6c1ae8dea3f26d1b32485...bb78acdbb21aaa147e24b47b32134b1575a8b0bd
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[med-svn] [Git][med-team/nipy][master] 3 commits: Added autopkgtest
Israel Komolehin pushed to branch master at Debian Med / nipy Commits: 10c532d7 by Komolehin Israel Timilehin at 2023-12-11T12:20:44+00:00 Added autopkgtest - - - - - f085d32f by Komolehin Israel Timilehin at 2023-12-11T12:42:21+00:00 Updated tests/control - - - - - 1c4d195b by Komolehin Israel Timilehin at 2023-12-11T12:44:16+00:00 Updated changelog - - - - - 3 changed files: - debian/changelog - + debian/tests/control - + debian/tests/nipy_test.py Changes: = debian/changelog = @@ -1,5 +1,6 @@ nipy (0.5.0-9) UNRELEASED; urgency=medium + [ Andreas Tille ] * Team upload. * Add alternatives liblapack-dev | liblapack.so, @@ -7,7 +8,11 @@ nipy (0.5.0-9) UNRELEASED; urgency=medium * Switch to cython3-legacy Closes: #1056823 - -- Andreas Tille Wed, 29 Nov 2023 10:17:22 +0100 + [ Komolehin Israel Timilehin ] + * Added autopkgtest + + + -- Komolehin Israel Timilehin Mon, 11 Dec 2023 12:43:32 + nipy (0.5.0-8) unstable; urgency=medium = debian/tests/control = @@ -0,0 +1,3 @@ +Test-Command: cd debian/tests && python3 -m pytest nipy_test.py +Depends: python3-nipy, python3-nipy-lib, python-nipy-doc +Restrictions: allow-stderr \ No newline at end of file = debian/tests/nipy_test.py = @@ -0,0 +1,35 @@ +import pytest +import numpy as np +from nipy.testing import anatfile +from nipy import load_image +from nipy import save_image +from nipy.core.api import Image, vox2mni + +# Reference for nipy example usage, visit official documentation +# https://nipy.org/nipy/users/basic_io.html + +# fixture +@pytest.fixture +def image_from_disk(): +return load_image(anatfile) + +# Load Image from File +def test_loaded_image_shape(image_from_disk): +assert image_from_disk.shape == (33, 41, 25) + +# Access Data into an Array +def test_loaded_image_dimension(image_from_disk): +assert image_from_disk.ndim == 3 + +# Save image to a File +def test_image_save_to_file(tmp_path, image_from_disk): +output_file = tmp_path / 'newimagefile.nii' +newimg = save_image(image_from_disk, str(output_file)) +assert output_file.is_file() + + +# Create Image from an Array +def test_create_image_from_array(): +rawarray = np.zeros((43,128,128)) +arr_img = Image(rawarray, vox2mni(np.eye(4))) +assert arr_img.shape == (43,128,128) \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/nipy/-/compare/c31d2d2f861afb2c3bf6fdcb7cae8548e63fed01...1c4d195ba0460890d92a7d1959e484c657bffa41 -- View it on GitLab: https://salsa.debian.org/med-team/nipy/-/compare/c31d2d2f861afb2c3bf6fdcb7cae8548e63fed01...1c4d195ba0460890d92a7d1959e484c657bffa41 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/qcumber][master] Added check for AUTOPKGTEST_TMP
Israel Komolehin pushed to branch master at Debian Med / qcumber
Commits:
8002d013 by Komolehin Israel Timilehin at 2023-12-09T06:14:08+00:00
Added check for AUTOPKGTEST_TMP
- - - - -
1 changed file:
- debian/tests/run-unit-test
Changes:
=
debian/tests/run-unit-test
=
@@ -1,6 +1,13 @@
#!/bin/bash
+if [ "$AUTOPKGTEST_TMP" = ""]; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
+
+ trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
cd test
# Generate test_yaml file
View it on GitLab:
https://salsa.debian.org/med-team/qcumber/-/commit/8002d013441795c82bc4dd048e82600de7dbc974
--
View it on GitLab:
https://salsa.debian.org/med-team/qcumber/-/commit/8002d013441795c82bc4dd048e82600de7dbc974
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[med-svn] [Git][med-team/qcumber][master] Updated control
Israel Komolehin pushed to branch master at Debian Med / qcumber Commits: 7cff860d by Komolehin Israel Timilehin at 2023-12-08T21:20:48+00:00 Updated control - - - - - 1 changed file: - debian/tests/control Changes: = debian/tests/control = @@ -1,3 +1,3 @@ Test-Command: sh debian/tests/run-unit-test Depends: dwgsim, python3-pandas, snakemake, wget -Restrictions: allow-stderr \ No newline at end of file +Restrictions: allow-stderr, needs-internet \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/commit/7cff860dacbf2d95c69fb6aefc12eade9ffb64ac -- View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/commit/7cff860dacbf2d95c69fb6aefc12eade9ffb64ac You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/qcumber][master] Updated control file
Israel Komolehin pushed to branch master at Debian Med / qcumber Commits: c3bdb534 by Komolehin Israel Timilehin at 2023-12-08T20:55:16+00:00 Updated control file - - - - - 1 changed file: - debian/tests/control Changes: = debian/tests/control = @@ -1,3 +1,3 @@ Test-Command: sh debian/tests/run-unit-test -Depends: dwgsim, python3-pandas, snakemake +Depends: dwgsim, python3-pandas, snakemake, wget Restrictions: allow-stderr \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/commit/c3bdb53477f11a1e0cefa513409ee16c8298d122 -- View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/commit/c3bdb53477f11a1e0cefa513409ee16c8298d122 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/qcumber][master] 2 commits: Added Autopkgtest
Israel Komolehin pushed to branch master at Debian Med / qcumber Commits: f256af5e by Komolehin Israel Timilehin at 2023-12-08T20:36:38+00:00 Added Autopkgtest - - - - - b8a21d7d by Komolehin Israel Timilehin at 2023-12-08T20:43:37+00:00 Updated changelog - - - - - 3 changed files: - debian/changelog - + debian/tests/control - + debian/tests/run-unit-test Changes: = debian/changelog = @@ -1,10 +1,15 @@ qcumber (2.3.0-3) UNRELEASED; urgency=medium + [ Andreas Tille ] * Recommends: dwgsim, kraken * Replace yaml.load() by yaml.safe_load() * Fix debian/get-minikrakendb + * bowtie2 which is not available on i386 + + [ Komolehin Israel Timilehin ] + * Added Autopkgtest - -- Andreas Tille Tue, 05 Apr 2022 10:16:12 +0200 + -- Komolehin Israel Timilehin Fri, 08 Dec 2023 20:43:19 + qcumber (2.3.0-2) unstable; urgency=medium = debian/tests/control = @@ -0,0 +1,3 @@ +Test-Command: sh debian/tests/run-unit-test +Depends: dwgsim, python3-pandas, snakemake +Restrictions: allow-stderr \ No newline at end of file = debian/tests/run-unit-test = @@ -0,0 +1,10 @@ +#!/bin/bash + + +cd test + +# Generate test_yaml file +./test_qcumber2.py gen_test_yaml + +# Run upstream test +./test_qcumber2.py \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/compare/8b2f03469da0bfac963471af31546c4951960abe...b8a21d7d757754f1b3b6081acac1537587363d00 -- View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/compare/8b2f03469da0bfac963471af31546c4951960abe...b8a21d7d757754f1b3b6081acac1537587363d00 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/amide][master] 2 commits: Added autopkgtest
Israel Komolehin pushed to branch master at Debian Med / amide
Commits:
93cf7c02 by Komolehin Israel Timilehin at 2023-12-05T19:38:22+00:00
Added autopkgtest
- - - - -
7faf5985 by Komolehin Israel Timilehin at 2023-12-05T19:39:58+00:00
Updated changelog
- - - - -
3 changed files:
- debian/changelog
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=
debian/changelog
=
@@ -1,3 +1,9 @@
+amide (1.0.6-3) UNRELEASED; urgency=medium
+
+ * Added autopkgtest
+
+ -- Komolehin Israel Timilehin Tue, 05 Dec 2023
19:39:39 +
+
amide (1.0.6-2) unstable; urgency=medium
* d/control: remove libxml-parser-perl from build dependencies.
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Test-Command: xvfb-run -s "-screen 0 1024x768x24 -ac +extension GLX +render
-noreset" sh debian/tests/run-unit-test
+Depends: xvfb, xauth, amide
+Restrictions: allow-stderr
=
debian/tests/run-unit-test
=
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+pkg=amide
+
+
+if [ "$AUTOPKGTEST_TMP" = ""]; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.`
+
+ trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+# Start amide
+timeout 10s amide || true
+
+echo "Amide Started"
+echo "Pass"
+
View it on GitLab:
https://salsa.debian.org/med-team/amide/-/compare/032e109e5b18ccc33c0b610c79db22eae43f59c4...7faf5985894fe0a7933008f08da0f451b9babc91
--
View it on GitLab:
https://salsa.debian.org/med-team/amide/-/compare/032e109e5b18ccc33c0b610c79db22eae43f59c4...7faf5985894fe0a7933008f08da0f451b9babc91
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[med-svn] [Git][med-team/orthanc-dicomweb][master] 3 commits: Added list of files to be installed
Israel Komolehin pushed to branch master at Debian Med / orthanc-dicomweb
Commits:
d290d1b3 by Komolehin Israel Timilehin at 2023-11-01T17:07:02+00:00
Added list of files to be installed
- - - - -
2d8dd009 by Komolehin Israel Timilehin at 2023-11-01T17:07:51+00:00
Added autopkgtest
- - - - -
fb974c12 by Komolehin Israel Timilehin at 2023-11-01T17:08:06+00:00
Updated changelog
- - - - -
4 changed files:
- debian/changelog
- + debian/examples
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=
debian/changelog
=
@@ -1,3 +1,10 @@
+orthanc-dicomweb (1.15+dfsg-2) UNRELEASED; urgency=medium
+
+ * Added autopkgtest
+ * Added list of files to be installed
+
+ -- Komolehin Israel Timilehin Wed, 01 Nov 2023
16:08:06 +
+
orthanc-dicomweb (1.15+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
=
debian/examples
=
@@ -0,0 +1,6 @@
+Build/AUTOGENERATED/*
+Plugin/Configuration.*
+Plugin/DicomWebServers.*
+Resources/Orthanc/Plugins/OrthancPluginCppWrapper.*
+Resources/Orthanc/Plugins/OrthancPluginException.h
+UnitTestsSources/UnitTestsMain.cpp
=
debian/tests/control
=
@@ -0,0 +1,12 @@
+Tests: run-unit-test
+Restrictions: allow-stderr
+Depends: @,
+build-essential,
+cmake,
+debhelper-compat (= 13),
+libgtest-dev,
+liborthancframework-dev,
+orthanc-dev (>= 1.10.1),
+unzip,
+uuid-dev
+
=
debian/tests/run-unit-test
=
@@ -0,0 +1,54 @@
+#!/bin/bash
+set -e
+
+pkg=orthanc-dicomweb
+upstream_version=1.15
+
+CPP=g++
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+# Create folder for the test sources
+mkdir -p "${AUTOPKGTEST_TMP}"/UnitTestsSources
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"/UnitTestsSources
+
+cd "${AUTOPKGTEST_TMP}"
+
+cd UnitTestsSources
+
+# Update relative import
+sed -i 's/..\/Resources\/Orthanc\/Plugins\///' DicomWebServers.h
Configuration.cpp
+
+sed -i 's/..\/Plugin\///' UnitTestsMain.cpp
+
+
+
+# Build target object files for UnitTests
+for cpp in $(find . -name "*.cpp") ; do
+
+ ${CPP} -DHAS_ORTHANC_EXCEPTION=1
-DORTHANC_DICOM_WEB_VERSION=\"${upstream_version}\"
-DORTHANC_ENABLE_LOGGING_PLUGIN=1 -DORTHANC_STANDALONE=1
-DOrthancDicomWeb_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 \
+-I/usr/include/jsoncpp -I/usr/include/orthanc-framework
-I/usr/src/gtest -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -Wall
-Wno-long-long \
+-Wno-variadic-macros -c -o O$(basename ${cpp} .cpp).o ${cpp}
+
+done
+
+# Build target object file for UnitTests
+${CPP} -DHAS_ORTHANC_EXCEPTION=1 -DORTHANC_DICOM_WEB_VERSION=\"1.15\"
-DORTHANC_ENABLE_LOGGING_PLUGIN=1 -DORTHANC_STANDALONE=1 \
+-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -I/usr/include/jsoncpp
-I/usr/include/orthanc-framework -I/usr/src/gtest -g -O2 \
+-fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG
-Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long \
+-Wno-variadic-macros -c -o gtest-all.cc.o /usr/src/gtest/src/gtest-all.cc
+
+# Linking files for UnitTests executable
+${CPP} -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-DNDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -Wall \
+-Wno-long-long -Wno-variadic-macros -Wl,-z,relro -Wl,-z,now
-Wl,--as-needed *.o -o UnitTests -lpthread -lrt -ldl \
+-Wl,-Bstatic -lOrthancFramework -Wl,-Bdynamic -lboost_filesystem
-lboost_iostreams -lboost_locale -lboost_regex -lboost_thread -ljsoncpp
-lpugixml -luuid -lsqlite3 \
+-ldcmdata -ldcmjpeg -ldcmjpls -lofstd -ldcmimage -lz -lrt -ldl
-Wl,-Bstatic -lOrthancFramework -Wl,-Bdynamic -lboost_filesystem
-lboost_iostreams -lboost_locale -lboost_regex \
+-lboost_thread -ljsoncpp -lpugixml -luuid -lsqlite3 -ldcmdata
-ldcmjpeg -ldcmjpls -lofstd -ldcmimage -lz
+
+
+# Execute UnitTests
+./UnitTests
+
View it on GitLab:
https://salsa.debian.org/med-team/orthanc-dicomweb/-/compare/c5f9d769023eea24265a1600c0a05ba90e0b1f26...fb974c123c1a4ff43480a719098d61b1844a9d38
--
View it on GitLab:
https://salsa.debian.org/med-team/orthanc-dicomweb/-/compare/c5f9d769023eea24265a1600c0a05ba90e0b1f26...fb974c123c1a4ff43480a719098d61b1844a9d38
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[med-svn] [Git][med-team/orthanc-wsi][master] Updated copyright
Israel Komolehin pushed to branch master at Debian Med / orthanc-wsi Commits: cefa6e88 by Komolehin Israel Timilehin at 2023-10-27T10:13:32+00:00 Updated copyright - - - - - 1 changed file: - debian/copyright Changes: = debian/copyright = @@ -137,7 +137,7 @@ License: CC0-1.0 THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER. . - On Debian systems, the full text of the GNU General Public License - version 3 can be found in the file + On Debian systems, the full text of the License + version 1 can be found in the file `/usr/share/common-licenses/CC0-1.0'. View it on GitLab: https://salsa.debian.org/med-team/orthanc-wsi/-/commit/cefa6e887a46fbf2e4594ffee76655e5d8d3ec3e -- View it on GitLab: https://salsa.debian.org/med-team/orthanc-wsi/-/commit/cefa6e887a46fbf2e4594ffee76655e5d8d3ec3e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/orthanc-wsi][master] Updated copyright
Israel Komolehin pushed to branch master at Debian Med / orthanc-wsi Commits: 51c57769 by Komolehin Israel Timilehin at 2023-10-27T10:00:46+00:00 Updated copyright - - - - - 1 changed file: - debian/copyright Changes: = debian/copyright = @@ -23,6 +23,7 @@ License: BSD-2-clause Files: debian-tests-data/CMU-1-Small-Region.tiff Copyright: Openslide +Source: wget https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1-Small-Region.svs License: CC0-1.0 View it on GitLab: https://salsa.debian.org/med-team/orthanc-wsi/-/commit/51c57769a9839dcccb5c3c023ec99702b355238c -- View it on GitLab: https://salsa.debian.org/med-team/orthanc-wsi/-/commit/51c57769a9839dcccb5c3c023ec99702b355238c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/orthanc-wsi][master] Updated copyright
Israel Komolehin pushed to branch master at Debian Med / orthanc-wsi
Commits:
4ff9b126 by Komolehin Israel Timilehin at 2023-10-27T09:31:58+00:00
Updated copyright
- - - - -
1 changed file:
- debian/copyright
Changes:
=
debian/copyright
=
@@ -21,6 +21,10 @@ Files: debian/JS/openlayers-3.19.0/*
Copyright: 2005-2016 OpenLayers Contributors. All rights reserved.
License: BSD-2-clause
+Files: debian-tests-data/CMU-1-Small-Region.tiff
+Copyright: Openslide
+License: CC0-1.0
+
License: AGPL-3.0+
This program is free software: you can redistribute it and/or
@@ -97,3 +101,42 @@ License: BSD-2-clause
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License: CC0-1.0
+ The laws of most jurisdictions throughout the world automatically confer
+ exclusive Copyright and Related Rights (defined below) upon the creator
+ and subsequent owner(s) (each and all, an "owner") of an original work of
+ authorship and/or a database (each, a "Work").
+ .
+ Certain owners wish to permanently relinquish those rights to a Work for
+ the purpose of contributing to a commons of creative, cultural and
+ scientific works ("Commons") that the public can reliably and without fear
+ of later claims of infringement build upon, modify, incorporate in other
+ works, reuse and redistribute as freely as possible in any form whatsoever
+ and for any purposes, including without limitation commercial purposes.
+ These owners may contribute to the Commons to promote the ideal of a free
+ culture and the further production of creative, cultural and scientific
+ works, or to gain reputation or greater distribution for their Work in
+ part through the use and efforts of others.
+ .
+ For these and/or other purposes and motivations, and without any
+ expectation of additional consideration or compensation, the person
+ associating CC0 with a Work (the "Affirmer"), to the extent that he or she
+ is an owner of Copyright and Related Rights in the Work, voluntarily
+ elects to apply CC0 to the Work and publicly distribute the Work under its
+ terms, with knowledge of his or her Copyright and Related Rights in the
+ Work and the meaning and intended legal effect of CC0 on those rights.
+ .
+ CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE
+ LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN
+ ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS
+ INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES
+ REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS
+ PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM
+ THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED
+ HEREUNDER.
+ .
+ On Debian systems, the full text of the GNU General Public License
+ version 3 can be found in the file
+ `/usr/share/common-licenses/CC0-1.0'.
+
View it on GitLab:
https://salsa.debian.org/med-team/orthanc-wsi/-/commit/4ff9b126888d2d1ebd8bc5074622974af8dc1267
--
View it on GitLab:
https://salsa.debian.org/med-team/orthanc-wsi/-/commit/4ff9b126888d2d1ebd8bc5074622974af8dc1267
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[med-svn] [Git][med-team/orthanc-webviewer][master] 7 commits: Updated test by building upstream test
Israel Komolehin pushed to branch master at Debian Med / orthanc-webviewer
Commits:
d2fd755d by Komolehin Israel Timilehin at 2023-10-23T21:06:15+00:00
Updated test by building upstream test
- - - - -
db854761 by Komolehin Israel Timilehin at 2023-10-23T21:09:24+00:00
Removed built upstream executable
- - - - -
2f49736e by Komolehin Israel Timilehin at 2023-10-24T08:26:54+00:00
Updated debian/tests/control
- - - - -
02693709 by Komolehin Israel Timilehin at 2023-10-24T08:27:25+00:00
Replace versions with wildcard *
- - - - -
00833bce by Komolehin Israel Timilehin at 2023-10-24T08:29:16+00:00
Removed UnitTests path
- - - - -
ea935904 by Komolehin Israel Timilehin at 2023-10-24T08:52:10+00:00
Updated changelog
- - - - -
9e4a35b7 by Komolehin Israel Timilehin at 2023-10-24T08:53:09+00:00
Updated comment
- - - - -
6 changed files:
- debian/changelog
- debian/source.lintian-overrides
- debian/source/include-binaries
- − debian/tests/UnitTests
- debian/tests/control
- debian/tests/run-upstream-test
Changes:
=
debian/changelog
=
@@ -12,8 +12,14 @@ orthanc-webviewer (2.8-3) UNRELEASED; urgency=medium
* Updated source/include-binaries
* Fixed mismatched overrides warning
* Fixed source missing error
+ * Updated test by building upstream test within test
+ * Removed prebuilt upstream executable test
+ * Updated debian/tests/control
+ * Replace versions with wildcard *
+ * Removed UnitTests path from source
+ * Updated test comment
- -- Komolehin Israel Timilehin Mon, 23 Oct 2023
10:46:17 +
+ -- Komolehin Israel Timilehin Tue, 24 Oct 2023
08:34:29 +
orthanc-webviewer (2.8-2) unstable; urgency=medium
=
debian/source.lintian-overrides
=
@@ -5,4 +5,3 @@ orthanc-webviewer source: source-is-missing
[debian/JS/cornerstone-0.11.0/corner
orthanc-webviewer source: source-is-missing
[debian/JS/jsPanel-2.3.3/mobile-detect.js]
orthanc-webviewer source: source-is-missing
[debian/JS/pako-0.2.5/pako_inflate.js]
orthanc-webviewer source: source-is-missing
[debian/JS/jquery-ui-1.11.3/jquery-ui.js]
-orthanc-webviewer source: source-is-missing [debian/tests/UnitTests]
\ No newline at end of file
=
debian/source/include-binaries
=
@@ -19,4 +19,3 @@ debian/JS/cornerstone-0.11.0/cornerstone.js
debian/JS/jquery-ui-1.11.3/jquery-ui.js
debian/JS/jsPanel-2.3.3/mobile-detect.js
debian/JS/pako-0.2.5/pako_inflate.js
-debian/tests/UnitTests
\ No newline at end of file
=
debian/tests/UnitTests deleted
=
Binary files a/debian/tests/UnitTests and /dev/null differ
=
debian/tests/control
=
@@ -1,2 +1,3 @@
Tests: run-upstream-test
Restrictions: allow-stderr
+Depends: @, cmake, libboost-all-dev, libgtest-dev,
libjpeg-dev,libjs-jquery-ui, libjs-jquery-ui-theme-base, libjsoncpp-dev,
liborthancframework-dev, libpng-dev, libsqlite3-dev, orthanc-dev (>= 0.9.5),
unzip, uuid-dev,yui-compressor, zlib1g-dev, build-essential
\ No newline at end of file
=
debian/tests/run-upstream-test
=
@@ -11,13 +11,42 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
fi
-cp ${CUR_DIR}/debian/tests/UnitTests* -a "${AUTOPKGTEST_TMP}"
+# cp ${CUR_DIR}/debian/tests/UnitTests* -a "${AUTOPKGTEST_TMP}"
+cp ${CUR_DIR}/* -a "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
-# Run upstream executable test
-./UnitTests
+# Set JS dependencies for build
+
+mkdir -p Build/javascript-libs/fonts
+mkdir -p Build/javascript-libs/images
+cp /usr/share/javascript/jquery/jquery.min.js Build/javascript-libs/jquery.js
+yui-compressor debian/JS/jquery-ui-*/jquery-ui.js >
Build/javascript-libs/jquery-ui.min.js
+yui-compressor debian/JS/jquery-ui-*/jquery-ui.css >
Build/javascript-libs/jquery-ui.min.css
+yui-compressor debian/JS/jquery-ui-*/jquery-ui.theme.css >
Build/javascript-libs/jquery-ui.theme.min.css
+cp debian/JS/jquery-ui-*/images/* Build/javascript-libs/images
+cp debian/JS/cornerstone-0.11.0/cornerstone.js
Build/javascript-libs/cornerstone.min.js
+cp debian/JS/cornerstone-0.11.0/cornerstone.css
Build/javascript-libs/cornerstone.css
+yui-compressor debian/JS/jsPanel-*/jquery.jspanel.js >
Build/javascript-libs/jquery.jspanel.min.js
+yui-compressor debian/JS/jsPanel-*/jquery.jspanel.css >
Build/javascript-libs/jquery.jspanel.min.css
+yui-compressor debian/JS/jsPanel-*/jquery.ui.touch-punch.js >
Build/javascript-libs/jquery.ui.touch-punch.min.js
+yui-compressor debian/JS/jsPanel-*/mobile-detect.js >
Build/javascript-libs/mobile-detect.min.js
+cp debian/JS/jsPanel-*/images/* Build/javascript-libs/images/
+cp debian/JS/jsPanel-*/fonts/* Build/javascript-libs/fonts/
+yui-compressor debian
[med-svn] [Git][med-team/orthanc-webviewer][master] 11 commits: Configured control file for autopkgtest
Israel Komolehin pushed to branch master at Debian Med / orthanc-webviewer
Commits:
93b13f7e by Komolehin Israel Timilehin at 2023-10-23T08:47:10+00:00
Configured control file for autopkgtest
- - - - -
1a8d5d6c by Komolehin Israel Timilehin at 2023-10-23T08:48:05+00:00
Set upstream test executable from build result
- - - - -
1d89e50e by Komolehin Israel Timilehin at 2023-10-23T08:49:32+00:00
Setup autopkgtest for upstream executable test
- - - - -
3e0d9e1e by Komolehin Israel Timilehin at 2023-10-23T09:52:12+00:00
Added salsa-ci file
- - - - -
7457fe82 by Komolehin Israel Timilehin at 2023-10-23T10:06:36+00:00
Added debian/tests/UnitTests source
- - - - -
9e824b68 by Komolehin Israel Timilehin at 2023-10-23T10:08:38+00:00
Updated changelog
- - - - -
257a6906 by Komolehin Israel Timilehin at 2023-10-23T10:20:41+00:00
Updated test comment
- - - - -
0fb39f50 by Komolehin Israel Timilehin at 2023-10-23T10:41:55+00:00
Updated source/include-binaries
- - - - -
a163e9c3 by Komolehin Israel Timilehin at 2023-10-23T10:42:36+00:00
Fixed mismatched overrides warning
- - - - -
fe4ee8d4 by Komolehin Israel Timilehin at 2023-10-23T10:43:18+00:00
Fixed source missing error
- - - - -
bca07280 by Komolehin Israel Timilehin at 2023-10-23T10:47:01+00:00
Updated changelog
- - - - -
7 changed files:
- debian/changelog
- + debian/salsa-ci.yml
- debian/source.lintian-overrides
- debian/source/include-binaries
- + debian/tests/UnitTests
- + debian/tests/control
- + debian/tests/run-upstream-test
Changes:
=
debian/changelog
=
@@ -1,3 +1,20 @@
+orthanc-webviewer (2.8-3) UNRELEASED; urgency=medium
+
+ * Configured control file for autopkgtest
+ * Set upstream test executable from build result
+ * Setup autopkgtest for upstream executable test
+ * Configured control file for autopkgtest
+ * Set upstream test executable from build result
+ * Setup autopkgtest for upstream executable test
+ * Added salsa-ci file
+ * Added debian/tests/UnitTests source
+ * Updated test comment
+ * Updated source/include-binaries
+ * Fixed mismatched overrides warning
+ * Fixed source missing error
+
+ -- Komolehin Israel Timilehin Mon, 23 Oct 2023
10:46:17 +
+
orthanc-webviewer (2.8-2) unstable; urgency=medium
* Updated d/copyright
=
debian/salsa-ci.yml
=
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ -
https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=
debian/source.lintian-overrides
=
@@ -1,6 +1,8 @@
# The following files are wrongly interpreted as minimified
# JavaScript by lintian, which is not the case.
# cf. https://lists.debian.org/debian-med/2015/09/msg00135.html
-orthanc-webviewer source: source-is-missing
debian/JS/cornerstone-0.11.0/cornerstone.js
-orthanc-webviewer source: source-is-missing
debian/JS/jsPanel-2.3.3/mobile-detect.js
-orthanc-webviewer source: source-is-missing
debian/JS/pako-0.2.5/pako_inflate.js
+orthanc-webviewer source: source-is-missing
[debian/JS/cornerstone-0.11.0/cornerstone.js]
+orthanc-webviewer source: source-is-missing
[debian/JS/jsPanel-2.3.3/mobile-detect.js]
+orthanc-webviewer source: source-is-missing
[debian/JS/pako-0.2.5/pako_inflate.js]
+orthanc-webviewer source: source-is-missing
[debian/JS/jquery-ui-1.11.3/jquery-ui.js]
+orthanc-webviewer source: source-is-missing [debian/tests/UnitTests]
\ No newline at end of file
=
debian/source/include-binaries
=
@@ -15,3 +15,8 @@ debian/JS/jsPanel-2.3.3/images/icon-sprite-20x20.jpg
debian/JS/jsPanel-2.3.3/images/icon-sprite-32x32.jpg
debian/JS/jsPanel-2.3.3/images/resize-handle.png
debian/JS/jsPanel-2.3.3/images/ui-icons_454545_256x240.png
+debian/JS/cornerstone-0.11.0/cornerstone.js
+debian/JS/jquery-ui-1.11.3/jquery-ui.js
+debian/JS/jsPanel-2.3.3/mobile-detect.js
+debian/JS/pako-0.2.5/pako_inflate.js
+debian/tests/UnitTests
\ No newline at end of file
=
debian/tests/UnitTests
=
Binary files /dev/null and b/debian/tests/UnitTests differ
=
debian/tests/control
=
@@ -0,0 +1,2 @@
+Tests: run-upstream-test
+Restrictions: allow-stderr
=
debian/tests/run-upstream-test
=
@@ -0,0 +1,23 @@
+#!/bin/bash
+set -e
+
+pkg=orthanc-webviewer
+CUR_DIR=`pwd`
+
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+
+cp ${CUR_DIR}/debian/tests/UnitTests* -a "${AUTOPKGTEST_TMP}"
+
+
+cd "${AUTOPKGTEST_TMP}"
+
+# Run upstr
[med-svn] [Git][med-team/orthanc-wsi][pristine-tar] 2 commits: pristine-tar data for orthanc-wsi_2.0+dfsg.orig-debian-tests-data.tar.xz
Israel Komolehin pushed to branch pristine-tar at Debian Med / orthanc-wsi Commits: 07ae1b46 by Komolehin Israel Timilehin at 2023-10-18T17:27:09+00:00 pristine-tar data for orthanc-wsi_2.0+dfsg.orig-debian-tests-data.tar.xz - - - - - 5127564e by Komolehin Israel Timilehin at 2023-10-18T17:27:09+00:00 pristine-tar data for orthanc-wsi_2.0+dfsg.orig.tar.xz - - - - - 3 changed files: - + orthanc-wsi_2.0+dfsg.orig-debian-tests-data.tar.xz.delta - + orthanc-wsi_2.0+dfsg.orig-debian-tests-data.tar.xz.id - orthanc-wsi_2.0+dfsg.orig.tar.xz.delta Changes: = orthanc-wsi_2.0+dfsg.orig-debian-tests-data.tar.xz.delta = Binary files /dev/null and b/orthanc-wsi_2.0+dfsg.orig-debian-tests-data.tar.xz.delta differ = orthanc-wsi_2.0+dfsg.orig-debian-tests-data.tar.xz.id = @@ -0,0 +1 @@ +9d7e2a595b71afd353bfcc3801a18dc0a4dcb2da = orthanc-wsi_2.0+dfsg.orig.tar.xz.delta = Binary files a/orthanc-wsi_2.0+dfsg.orig.tar.xz.delta and b/orthanc-wsi_2.0+dfsg.orig.tar.xz.delta differ View it on GitLab: https://salsa.debian.org/med-team/orthanc-wsi/-/compare/69f336ea5755a8a638ece9f48f9368d544c173e2...5127564e7be405d3c57b2072f2b284576d3888f1 -- View it on GitLab: https://salsa.debian.org/med-team/orthanc-wsi/-/compare/69f336ea5755a8a638ece9f48f9368d544c173e2...5127564e7be405d3c57b2072f2b284576d3888f1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/orthanc-wsi][master] 7 commits: Configured gbp.conf for debian-tests-data
Israel Komolehin pushed to branch master at Debian Med / orthanc-wsi
Commits:
c7a23923 by Komolehin Israel Timilehin at 2023-10-18T17:26:05+00:00
Configured gbp.conf for debian-tests-data
- - - - -
3f123956 by Komolehin Israel Timilehin at 2023-10-18T17:27:07+00:00
New upstream version 2.0+dfsg
- - - - -
43e44f85 by Komolehin Israel Timilehin at 2023-10-18T17:27:09+00:00
Update upstream source from tag 'upstream/2.0+dfsg'
Update to upstream version '2.0+dfsg'
with Debian dir 957e42a328011b02021f50bfc623a16c4ed9352a
- - - - -
367a2263 by Komolehin Israel Timilehin at 2023-10-18T17:32:50+00:00
Configured tests/control for autopkgtest
- - - - -
bb1484d1 by Komolehin Israel Timilehin at 2023-10-18T17:35:01+00:00
Created test for dicom image transcode
- - - - -
e19062ba by Komolehin Israel Timilehin at 2023-10-18T17:35:37+00:00
Created test for sample dataset generation
- - - - -
e709e1f0 by Komolehin Israel Timilehin at 2023-10-18T17:39:46+00:00
Updated debian/changelog
- - - - -
6 changed files:
- + debian-tests-data/CMU-1-Small-Region.tiff
- debian/changelog
- + debian/gbp.conf
- + debian/tests/control
- + debian/tests/run-dicom-image-transcode-test
- + debian/tests/run-generate-dataset-test
Changes:
=
debian-tests-data/CMU-1-Small-Region.tiff
=
Binary files /dev/null and b/debian-tests-data/CMU-1-Small-Region.tiff differ
=
debian/changelog
=
@@ -1,3 +1,13 @@
+orthanc-wsi (2.0+dfsg-2) UNRELEASED; urgency=medium
+
+ * Configured gbp.conf for debian-tests-data
+ * New upstream version 2.0+dfsg
+ * Configured tests/control for autopkgtest
+ * Created test for dicom image transcode
+ * Created test for sample dataset generation
+
+ -- Komolehin Israel Timilehin Wed, 18 Oct 2023
17:39:06 +
+
orthanc-wsi (2.0+dfsg-1) unstable; urgency=medium
* New upstream version
=
debian/gbp.conf
=
@@ -0,0 +1,4 @@
+[DEFAULT]
+pristine-tar=True
+filter=[ '.gitignore', '.travis.yml', '.git*' ]
+component=['debian-tests-data']
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Tests: run-generate-dataset-test, run-dicom-image-transcode-test
+Depends: orthanc, orthanc-wsi
+Restrictions: needs-root, allow-stderr
=
debian/tests/run-dicom-image-transcode-test
=
@@ -0,0 +1,43 @@
+#!/bin/bash
+set -e
+
+pkg=orthanc-wsi
+CUR_DIR=`pwd`
+service_name=orthanc
+orthanc_server="http://localhost:8042";
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp ${CUR_DIR}/debian-tests-data/* -a "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+# Check if user 'orthanc' exists
+if getent passwd orthanc > /dev/null 2>&1; then
+echo "User 'orthanc' exists."
+else
+ adduser --system --group orthanc
+echo "User 'orthanc' added."
+fi
+
+
+# Start the orthanc service
+/etc/init.d/$service_name start
+
+if [ $? -eq 0 ]; then
+echo "Orthanc is active."
+else
+echo "Orthanc is not active."
+fi
+
+
+# Transcode data and push to server
+OrthancWSIDicomizer CMU-1-Small-Region.tiff --orthanc=$orthanc_server
+
+
+if [ $? -eq 0 ]; then
+echo "TIFF transcoded and pushed to Orthanc server"
+fi
\ No newline at end of file
=
debian/tests/run-generate-dataset-test
=
@@ -0,0 +1,32 @@
+#!/bin/bash
+
+pkg=orthanc-wsi
+filename="dataset.json"
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+ # create the tmp directory
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.X`
+
+ # clean the directory upon detection of any of these signals
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+
+fi
+
+# change working directory
+cd $AUTOPKGTEST_TMP
+
+# Generate sample dataset
+OrthancWSIDicomizer --sample-dataset > $filename
+
+# Check if $filename exists
+if [ -f "$filename" ]; then
+echo "$filename exists, proceeding to remove it..."
+rm "$filename"
+echo "$filename removed successfully."
+# Exit with success status
+exit 0
+else
+echo "$filename does not exist, script will exit with failure."
+# Exit with failure status
+ exit 1
+fi
View it on GitLab:
https://salsa.debian.org/med-team/orthanc-wsi/-/compare/7e364e52f711ccd0b8288087113b5a8ae5342868...e709e1f0ef7fc102af6e8e4d18b35dc3c7fa6a17
--
View it on GitLab:
https://salsa.debian.org/med-team/orthanc-wsi/-/compare/7e364e52f711ccd0b8288087113b5a8ae5342868...e709e1f0ef7fc102af6e8e4d18b35dc3c7fa6a17
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[med-svn] [Git][med-team/orthanc-wsi][upstream] New upstream version 2.0+dfsg
Israel Komolehin pushed to branch upstream at Debian Med / orthanc-wsi Commits: 3f123956 by Komolehin Israel Timilehin at 2023-10-18T17:27:07+00:00 New upstream version 2.0+dfsg - - - - - 1 changed file: - + debian-tests-data/CMU-1-Small-Region.tiff Changes: = debian-tests-data/CMU-1-Small-Region.tiff = Binary files /dev/null and b/debian-tests-data/CMU-1-Small-Region.tiff differ View it on GitLab: https://salsa.debian.org/med-team/orthanc-wsi/-/commit/3f123956263965383606b0aa077409c98430b695 -- View it on GitLab: https://salsa.debian.org/med-team/orthanc-wsi/-/commit/3f123956263965383606b0aa077409c98430b695 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/orthanc][master] Updated debian/changelog
Israel Komolehin pushed to branch master at Debian Med / orthanc Commits: 33d2d8fe by Komolehin Israel Timilehin at 2023-10-16T16:41:02+00:00 Updated debian/changelog - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -4,7 +4,7 @@ orthanc (1.12.1+dfsg-4) unstable; urgency=medium * Created debian/tests/control * Added autopkgtest test - -- Komolehin Israel Timilehin Mon, 16 Oct 2023 17:58:25 +0200 + -- Komolehin Israel Timilehin Mon, 16 Oct 2023 17:58:25 +0200 orthanc (1.12.1+dfsg-3) unstable; urgency=medium View it on GitLab: https://salsa.debian.org/med-team/orthanc/-/commit/33d2d8fe36ced8941066d6ded213bd3c51e4c596 -- View it on GitLab: https://salsa.debian.org/med-team/orthanc/-/commit/33d2d8fe36ced8941066d6ded213bd3c51e4c596 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/orthanc][master] 6 commits: Created tests/control
Israel Komolehin pushed to branch master at Debian Med / orthanc
Commits:
4f8dd6f5 by Komolehin Israel Timilehin at 2023-10-15T09:28:39+00:00
Created tests/control
- - - - -
da68bb4c by Komolehin Israel Timilehin at 2023-10-15T14:36:05+00:00
Created autopkgtest test script
- - - - -
dd924864 by Komolehin Israel Timilehin at 2023-10-15T18:02:20+00:00
Updated changelog
- - - - -
9f5017f0 by Komolehin Israel Timilehin at 2023-10-15T19:41:00+00:00
Updated debian/tests/control restriction
- - - - -
eb56f27f by Komolehin Israel Timilehin at 2023-10-15T19:41:42+00:00
Removed sudo occurrences
- - - - -
4d071c75 by Komolehin Israel Timilehin at 2023-10-16T08:43:57+00:00
Updated tests/control
- - - - -
3 changed files:
- debian/changelog
- + debian/tests/control
- + debian/tests/run-test
Changes:
=
debian/changelog
=
@@ -1,7 +1,12 @@
orthanc (1.12.1+dfsg-3) unstable; urgency=medium
+ [ Sebastien Jodogne ]
* Fix compatibility with big-endian architectures. (Closes: #1041813)
+ [ Komolehin Israel Timilehin ]
+ * Created debian/tests/control
+ * Added autopkgtest test
+
-- Sebastien Jodogne Wed, 16 Aug 2023 09:07:21 +0200
orthanc (1.12.1+dfsg-2) unstable; urgency=high
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Tests: run-test
+Depends: curl, orthanc
+Restrictions: needs-root
=
debian/tests/run-test
=
@@ -0,0 +1,54 @@
+#!/bin/bash
+
+set -e
+
+
+pkg=orthanc
+service_name=$pkg
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+ # create the tmp directory
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.X`
+
+ # clean the directory if any of these signal is detected
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cd $AUTOPKGTEST_TMP
+
+
+# Check if user 'orthanc' exists
+if getent passwd orthanc > /dev/null 2>&1; then
+echo "User 'orthanc' exists."
+else
+ adduser --system --group orthanc
+echo "User 'orthanc' added."
+fi
+
+
+/etc/init.d/$service_name start
+
+if [ $? -eq 0 ]; then
+echo "Orthanc is active."
+else
+echo "Orthanc is not active."
+fi
+
+URL="http://localhost:8042/app/explorer.html";
+
+status_code=$(curl -s -o /dev/null -w "%{http_code}" "$URL")
+
+# Check the status code
+if [ "$status_code" -eq 200 ]; then
+echo "Request successful (HTTP status code 200)"
+exit 0
+else
+echo "Request failed with HTTP status code $status_code"
+exit 1
+fi
+
+
+
+
+
+
View it on GitLab:
https://salsa.debian.org/med-team/orthanc/-/compare/6f7521aa614bd539598959ba97a148fe6512997b...4d071c75179b4ac1deff16cfe01a4ae782beb68c
--
View it on GitLab:
https://salsa.debian.org/med-team/orthanc/-/compare/6f7521aa614bd539598959ba97a148fe6512997b...4d071c75179b4ac1deff16cfe01a4ae782beb68c
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