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BioHPC
clair-singularity
Commits
a292329c
Commit
a292329c
authored
Aug 25, 2017
by
David Trudgian
Browse files
Hopefully last testing fixes for now
parent
ab72e4ad
Changes
5
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.travis.yml
View file @
a292329c
...
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@@ -8,7 +8,11 @@ python:
-
"
3.4"
-
"
3.5"
-
"
3.6"
install
:
before_install
:
-
wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
-
sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
-
sudo apt-get -qq update
-
sudo apt-get install -y singularity-container
-
pip install flake8 pytest pytest-cov pytest-flake8 python-coveralls
script
:
-
build_scripts/travis_tests.sh
README.md
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a292329c
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@@ -106,7 +106,27 @@ report returned by Clair use the `--jsoon-output` option.
## Development / Testing
Tests are run using using pytest inside a docker container, via a script that will bring up a clair instance and run
clair-singularity within a correctly linked container:
Tests can are run in 3 different ways:
__Local - no access to Clair__
Runs all tests that don't depend on access to a Clair server, using the local Python.
$ build_scripts/noclair_local_tests.sh
__Local - dockerized with Clair__
Starts a Clair service with local docker, builds clair-singularity into a docker container, with Python 3.5, and
runs tests in this docker container.
$ build_scripts/docker_local_tests.sh
__TravisCI__
Travis CI automated testing will test non-Clair dependent code using Python 2.7, 3.4, 3.5, 3.6.
Clair dependent code will be tested only in the 3.5 environment, by building the docker container, starting a Clair
service, and running tests in the docker container.
./docker_local_tests.sh
build_scripts/docker_local_tests.sh
View file @
a292329c
#!/bin/sh
set
-e
set
-u
docker pull arminc/clair-db:2017-08-21
docker run
-d
--name
db arminc/clair-db:2017-08-21
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...
build_scripts/noclair_local_tests.sh
View file @
a292329c
#!/bin/bash
set
-e
set
-u
pytest tests/
-v
-m
"not needs_clair"
--cov
clair_singularity
--cov-report
term-missing
build_scripts/travis_tests.sh
View file @
a292329c
#!/bin/bash
set
-e
set
-u
echo
"Running setup.py install"
python setup.py
install
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