REF+REWRITE: use yaml templates + generate singularity recipes #157
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added 30 commits
October 28, 2017 19:23
added 24 commits
April 6, 2018 15:20
REF: use yaml templates + generate Singularity recipes
* rm tests dir * ignore new scraper dir * update to current dockerpy api * update error message * split up tests * add steps to workflow * remove dependency on dockerpy wrappers * remove files from previous branch * remove dockerpy wrappers * fix tests * fix tests * put docker client in local namespace * put get_docker_client in higher namespace * remove generate * fix tests * first pass at caching docker builds * tmp: only test mrtrix3 * make dirs if they don't exist * update license to 2018 * update cache dir * only cache docker things for now * fix cache key * rm unused methods * add shell df cmd + add json footer * test all for docker * minor change, build should be quick * tmp: test only mrtrix * test all docker builds * revert minor changes * test mrtrix and miniconda * small change * show log output * minor changes * remove white space * use miniconda * fix bashrc paths * minor change * test singularity and others * minor change, should build quickly * standardize test names * install pip from pypi * add pyyaml * only run non-container tests * run previously skipped test and print log * skip test * fix for tests * install from conda-forge * use same commands as in test_trace * assert that rm is not present * run all tests
* add singularity client * add singularity build tests * minor fixes * add singularity cache * minor change * prepend sudo * use correct sudo invocation * add bash_test_file arg * mkdir for sing files * do not save in new dir * bind path to singularity exec test * fix tests for singularity * pip install quietly + always save cache * error on unset variables * use singularity run instead of exec * remove execute privileges * use a cache dir in tmp * fix runscript syntax * tmp only test miniconda * prepend miniconda to path * use local cache directory * use local cache * enh cache path * run all tests * suppress find warnings in singularity * only test miniconda * tmp minor change * tmp: fail miniconda test * fix path * revert changes * update new args * add todos * fix templates
* rm travis yml * add extras for testing reqs * update examples * rewrite setup with more setup args * only get git version if not release * minor json updates * update help * add json output * change c3d to convert3d * add codecov * ignore coverage artifacts * update badges * rm coverage shield * rm coverage shield * add petpvc support * minimize dockerfile * do not upload test artifacts * standardize values * fix petpvc tests * fix binary name * update examples * add workdir and add_to_entrypoint * fix typo * add freesurfer url 6.0.1 * rm todo * fix another typo
* exclude examples and circleci * increase version to 0.4.0rc0 * add missing comma * fix paths * test dev version * rm test for version * test dev on ubuntu 18.04 * rename spm test to spm12 * fix bash test path * guess docker base if no prefix
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This PR proposes the use of templates to define installation instructions and adds the ability to generate singularity recipes. Matlab Compiler Runtime can also be installed on its own.
The CLI is changed to: