FIX: reprozip #153
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FIX: reprozip #153
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added 30 commits
April 18, 2018 14:44
added 20 commits
April 18, 2018 19:22
kaczmarj
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Apr 26, 2018
* add: generic installation instructions
* ref: split programs into individual yaml files
* remove minc top-level key
* fix curl and tar options
* mv generics to specs
* refactor interface classes to yaml
* update for refactor to yaml
* update interface for yaml
* update yaml specs
* add debian-based deps
* minor fixes
* fix formatting
* update dcm2niix to yaml
* updates
* attempt to use jinja2
* use macro to install apt packages
* update ants yml
* update afni yml
* rename specs dir to templates for jinja compatibility
* updates
* remove trailing slashes
* update yaml templates
* first try at subclassed objects
* misc updates
* load templates in neurodocker.interfaces
* update import
* remove individual interfaces files
* updates
* all: template updates
* fixes matlab mcr and imports
* rename matlab yaml file
* make tar calls consistent
* add first pass at dockerfile generation
* use str.splitlines() instead of str.split('\n')
* add slash to pipe curl output to tar
* add methods to generate singularity and docker files
* update templates
* clean up
* begin removing unnecessary methods
* add init file
* update to achieve initial working status
* create generate docker subparser
* remove check_urls
* add singularity subparser + fixes
* remove ropeproject
* install deps in header
* fix indent method
* add makefile with clean command
* fix header template
* fix version in template
* add header
* add header
* do not render options for header
* update templates
* show more helpful error message
* install matlabmcr with spm12
* append matlabmcr ldlibpath
* fix spm unzip
* add matlab 2010a
* add latest url
* fix: entrypoint bash script
* remove generate.py + transfer methods to utils
* use new-style class for specs parser
* define common options once
* add options common to docker and singularity
* add user option
* make users a set
* update miniconda installation
* add version 1.9.15
* remove verbosity from entrypoint script
* fix: paths and PATH variable
* add neurodocker entrypoint
* add entrypoint to common opts
* add jinja2
* upgrade to alpine 3.7
* ignore Dockerfile
* fix parser logic
* add general build tests
* fix version keys
* add option to exclude freesurfer paths
* add option to exclude freesurfer paths
* use build functions
* fix path var
* update tests with new api
* minor fixes
* remove tests because module no longer exists
* change `.cmd` to `.render()`
* second pass at tests
* add circleci config and Dockerfile
* minor fixes
* add files
* install pytest-cov, reperozip
* fix general test
* attempt to get testing working
* fix formatting
* install openssh
* further testing ...
* fix: make checkout a mapping
* change checkout path
* change checkout path
* fix paths
* remove object inheritance from users
* do not show help message on all errors
* fix installation method
* minor fixes
* add env var to prevent pushing docker images
* raise version of dockerpy
* use docker base image
* copy shell scripts into container
* use `volumes_from` for circleci compat
* fix syntax error
* docker cp does not support wildcards
* set version='auto' in client creation
* fix: comply with docker-py 3.x codebase
* fix style
* copy dir contents, not dir
* add test for matlabmcr
* add url to curl call
* minor fixes
* test out whether user issue is ubuntu 16.04 specific
* deepcopy specs dict
* import copy
* use python3.6 in reprozip trace wrapper script
* use machine instead of docker
The machine executor allows us to bind mount directories, which is required for some tests (reprozip interfaces).
* do not use `setup_remote_docker` step
* remove working dir
* use python3.5.2 by default
* bind mount volumes + do not use volume container
* upgrade pip
* improve logging messages
* remove dropbox/dockerhub memory from testing
* temporarily add docker image tag
* fix install path in tar cmd
* add methods to simply container tests
* tmp test
* simplify testing
* tmp test three files
* debugging tests
* revert testing cmd
* clear Users memory on each init
* simplify testing
* fixes
* symlink gsl2 to gsl0
* update path var
* add version 5.0.11
* remove eddy from test
* use multi-line if
* add matlab 2018a
* set entrypoint in dockerfiles
* add entrypoint to singularity files
* fix bash syntax error
* minor fixes
* add wget + do not install quietly
* test 5.0.10
* update conda if running latest; related to #144
* tmp: only test docker building methods
* use circle workflows
* do not prepend v to version
* fix curl url
* update tests
* add env_name option
* fix config syntax
* fix miniconda test
* assert that tests end with "passed"
* add noninteractive frontend
* add -f to curl opts
* add neurodebian methods
* prune utils
* FIX: reprozip (#153)
* 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
* ENH: add singularity builds to CI tests (#154)
* 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
* Patches (#155)
* 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
* 0.4.0rc0 (#156)
* 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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Fixes reprozip support and conforms to most recent dockerpy api.