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Amandine PERRIN
pipeline_annotation
Commits
e9312e35
Commit
e9312e35
authored
Aug 02, 2021
by
Amandine PERRIN
Browse files
report for all tests now working!
parent
fb98ef92
Pipeline
#62573
passed with stages
in 7 minutes and 1 second
Changes
2
Pipelines
3
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.gitlab-ci.yml
View file @
e9312e35
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@@ -21,7 +21,6 @@ build-from-ubuntu:
-
pip3 install -r requirements-dev.txt
-
py.test test/test_install/test_make_ubuntu.py -xv
build-from-barrnap
:
image
:
registry-gitlab.pasteur.fr/aperrin/pipeline_annotation/install-ubuntu-barrnaponly
stage
:
build
...
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@@ -32,7 +31,6 @@ build-from-barrnap:
-
pip3 install -r requirements-dev.txt
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py.test test/test_install/test_make_barrnap.py -xv
build-from-prokka-quicktree
:
image
:
registry-gitlab.pasteur.fr/aperrin/pipeline_annotation/install-ubuntu-annote-quicktree
stage
:
build
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@@ -43,7 +41,6 @@ build-from-prokka-quicktree:
-
pip3 install -r requirements-dev.txt
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py.test test/test_install/test_make_prokka-quicktree.py -xv
build-from-prodigal
:
image
:
registry-gitlab.pasteur.fr/aperrin/pipeline_annotation/install-prodigal
stage
:
build
...
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@@ -54,7 +51,6 @@ build-from-prodigal:
-
pip3 install -r requirements-dev.txt
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py.test test/test_install/test_make_prodigal.py -xv
build-from-test-image
:
stage
:
build
only
:
...
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@@ -64,6 +60,7 @@ build-from-test-image:
-
pip3 install -r requirements-dev.txt
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py.test test/test_install/test_make_all-installed.py -xv
unit-test-ubuntu
:
stage
:
test
except
:
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@@ -87,7 +84,7 @@ unit-test-ubuntu:
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py.test test/test_unit/test_annotate/test_format* -v -x
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py.test test/test_unit/test_pangenome -vx
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py.test test/test_unit/test_corepers -vx
#
- py.test test/test_unit/test_align -vx
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py.test test/test_unit/test_align -vx
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py.test test/test_unit/test_tree -xv
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coverage report
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mv .coverage .coverage.unit
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@@ -108,17 +105,16 @@ func-test-ubuntu:
-
./make
script
:
-
pwd
# - py.test test/test_functional/test_pangenome.py -vx
# - py.test test/test_functional/test_pangenome-parser.py -vx
# - py.test test/test_functional/test_corepers* -vx
# - py.test test/test_functional/test_align-parser.py -vx
# - py.test test/test_functional/test_align.py -vx
# - py.test test/test_functional/test_tree* -vx
# - py.test test/test_functional/test_annote-parser.py -vx
# - py.test test/test_functional/test_annote.py -xv
# - py.test test/test_functional/test_all* -vx
# - py.test test/test_functional/test_prepare* -vx
-
py.test test/test_unit/test_align -vx
-
py.test test/test_functional/test_pangenome.py -vx
-
py.test test/test_functional/test_pangenome-parser.py -vx
-
py.test test/test_functional/test_corepers* -vx
-
py.test test/test_functional/test_align-parser.py -vx
-
py.test test/test_functional/test_align.py -vx
-
py.test test/test_functional/test_tree* -vx
-
py.test test/test_functional/test_annote-parser.py -vx
-
py.test test/test_functional/test_annote.py -xv
-
py.test test/test_functional/test_all* -vx
-
py.test test/test_functional/test_prepare* -vx
-
coverage report
-
mv .coverage .coverage.functional
artifacts
:
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@@ -127,6 +123,7 @@ func-test-ubuntu:
-
htmlcov/index.html
expire_in
:
1 hour
coverage
:
stage
:
coverage
except
:
...
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@@ -142,8 +139,8 @@ coverage:
script
:
-
pwd
-
coverage combine .coverage.unit .coverage.functional
-
coverage report
-i
-
coverage html
-i
-
coverage report
-
coverage html
# test coverage parsing: \d+\%\s*$
# or pytest-cov (Python): ^TOTAL.+?(\d+\%)$
artifacts
:
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setup.cfg
View file @
e9312e35
...
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@@ -20,9 +20,12 @@ exclude_lines =
pragma: no cover
[coverage:run]
# use relative paths in .coverage generated file.
# Useful when .coverage is used to generate a report from a different directory than the one it was generated
# (like, for gitlab-ci tests).
# see https://github.com/nedbat/coveragepy/issues/597
relative_files = True
[build_sphinx]
source-dir = doc_sources/
build-dir = doc/
...
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