Commit 62dab795 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'feature-a/release' into 'dev'

Release 2021.04

Closes #4109

See merge request !939
parents 06d738f2 f96d7e87
Pipeline #243037 failed with stages
in 10 minutes and 43 seconds
......@@ -18,7 +18,6 @@ stages:
- test_shouldvdj
- test_functional_external
- coverage
- prepare_release
- tgz_release
- valgrind_unit
- valgrind_functional
......@@ -135,13 +134,6 @@ release_valgrind_functional:
only:
- /^feature-.*a.*\/release$/
prepare_release:
stage: prepare_release
script: make -C algo release RELEASE_TAG='rc'
when: manual
only:
- /^feature-.*a.*\/.*$/
tgz_release:
stage: tgz_release
script: make -C algo release RELEASE_TAG=`cat algo/release`
......
......@@ -17,7 +17,6 @@ https://gitlab.inria.fr/vidjil/vidjil/pipelines/XXXXX
(if tests passed on different pipelines, indicate below the relevant pipelines)
Usual tests should pass, but also:
* [ ] prepare_release
* [ ] valgrind_unit
* [ ] valgrind_functional
* [ ] multiple_tests
......
......@@ -277,7 +277,7 @@ RELEASE_ALGO = src/
RELEASE_TOOLS = $(wildcard ../tools/*.py)
RELEASE_MAKE = ../tools/tests/Makefile ../doc/Makefile
RELEASE_TESTS = ../doc/vidjil-format.md $(wildcard ../doc/analysis-example.vidjil) $(wildcard ../tools/tests/*.should_get) ../tools/should.py ../tools/diff_json.sh ../demo/get-sequences ../demo/Demo-X5.fa ../demo/Makefile
RELEASE_GERMLINES = ../germline/Makefile ../germline/germline_id ../germline/get-saved-germline ../germline/get-germline ../germline/split-from-imgt.py $(wildcard ../germline/*.g) ../germline/revcomp-fasta.py ../germline/fasta.py ../germline/homo-sapiens/IKZF*fa ../germline/homo-sapiens/ERG*fa
RELEASE_GERMLINES = ../germline/Makefile ../germline/germline_id ../germline/get-saved-germline ../germline/get-germline ../germline/split-germlines.py $(wildcard ../germline/*.g) ../germline/revcomp-fasta.py ../germline/fasta.py ../germline/homo-sapiens/IKZF*fa ../germline/homo-sapiens/ERG*fa
RELEASE_HELP = ../doc/vidjil-algo.md ../doc/locus.md ../doc/tools.md ../doc/vidjil-format.md ../doc/should-vdj.md ../doc/quality.md ../doc/credits.md ../doc/CHANGELOG ../doc/LICENSE ../README.md ../INSTALL.md
RELEASE_FILES = $(RELEASE_TOOLS) $(RELEASE_TESTS) $(RELEASE_MAKE) $(RELEASE_GERMLINES) $(RELEASE_HELP)
......
......@@ -24,7 +24,7 @@ VALGRIND_OUTPUT_XML=--xml=yes --xml-file='$(REPORTS_PATH)/valgrind.xml.%p'
VALGRIND_OUTPUT=--error-exitcode=1
SHOULD_TIMEOUT=140
SHOULD_TIMEOUT_VALGRIND=300
SHOULD_TIMEOUT_VALGRIND=500
ifeq ($(XML_OUTPUT), 1)
VALGRIND_OUTPUT=$(VALGRIND_OUTPUT_XML)
......
......@@ -40,13 +40,13 @@ BENCHS = OrderedDict([
('filter', LIMIT2e5 + FILTER + MULTI + L4),
('igh-0', LIMIT1e5 + IGH + L4 + CONSENSUS_NO),
('multi-0', LIMIT1e5 + MULTI + L4 + CONSENSUS_NO),
('multi-1', LIMIT1e5 + MULTI + L4 + CONSENSUS_ALL),
('multi-y', LIMIT1e5 + MULTI + L4 + CONSENSUS_ALL),
('multi-a', LIMIT1e3 + MULTI + L4 + DESIGNATIONS + '-z 1000'),
('igh-0', LIMIT1e5 + IGH + S22 + CONSENSUS_NO),
('igh-1', LIMIT1e5 + IGH + S22 + CONSENSUS_ALL),
('igh-a', LIMIT1e3 + IGH + S22 + DESIGNATIONS),
('S22-y', LIMIT1e3 + IGH + S22 + CONSENSUS_ALL),
('S22-a', LIMIT1e3 + IGH + S22 + DESIGNATIONS),
])
COMPATIBILITY = [
......@@ -58,7 +58,8 @@ INFOS = {
'2019.03': 'Aho by default',
'2018.07': '--analysis-filter (always 3)',
'2018.10': '--analysis-filter 1',
'2020.04': '#4287',
'2020.04': 'Report info only when not null #4287',
'2021.04': 'Update germlines (~ +50% IGH) !885',
}
# Simple colored output
......
!LAUNCH: $VIDJIL_DIR/$EXEC -c clones -z 2 -2 -r 1 -g $VIDJIL_DIR/germline/homo-sapiens.g ../should-vdj-tests/Demo-X5.should-vdj.fa > /dev/null ; cat out/Demo-X5.should-vdj.tsv
!OUTPUT_FILE: out/Demo-X5.should-vdj.tsv
!LAUNCH: $VIDJIL_DIR/$EXEC -c clones -z 2 -2 -r 1 -g $VIDJIL_DIR/germline/homo-sapiens.g ../should-vdj-tests/Demo-X5.should-vdj.fa
$ There are 15 = 1 + 14 lines, all with tabs
15:
......
This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil platform.
2021-04-28 The Vidjil Team
* New unproductivity cause, reporting IGH sequences without a {WP}GxG pattern !935
* Updated germlines from IMGT/GENE-DB, as well with 60bp up/downstream !885 !892
* Included Sus Scrofa and Gallus Gallus germlines !478 !839
* JUNCTION/CDR3 analysis by default, deprecating -3 option !947
* Smaller --max-consensus output, without debug information, new advanced option --out-details !724
* Updated outputs (e-values, affects) !932
* New and updated documentation and online help
2021-02-18 The Vidjil Team
* New preset --filter-reads to filter potentially huge datasets (vidjil.cpp) #4681
* Better --gz option, outputting also .fa.gz and .affects.gz files (vidjil.cpp) #4692
......
# vidjil-algo 2021.02.2
# vidjil-algo 2021.04
**Command-line manual**
*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Tatiana and Rayan)*
......@@ -63,11 +63,11 @@ Vidjil-algo is open-source, released under GNU GPLv3+ license.
Vidjil-algo is systematically tested with the following compilers :
- gcc/g++ 4.8, 5.3, 6.3, 7.3, 8.4, 9.3, 10.1
- clang 3.4, 4.0, 6.0, 7.0
- clang 3.4, 4.0, 6.0, 7.0, 11.0
These compilers are available on recent OS X and on the following Linux distributions:
- CentOS 7, 8
- Debian Jessie 8.0, Stretch 9.0, Buster 10.0
- Debian Jessie 8.0, Stretch 9.0, Buster 10.0, Bullseye 11
- FreeBSD 9.2, 10, 11, 12
- Ubuntu 16.04 LTS, 18.04 LTS, 20.04 LTS
......
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