neuropoly / spinalcordtoolbox / 10745
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DEFAULT BRANCH: master
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Jobs 3
Files 2253
Run time 9min
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travis-ci

jcohenadad 
First pass at also supporting pip installations (#1996)

* scripts: remove __init__.py (not a package)

* Travis: add environment for pip setup, refactor

- pip: download data
- refactor unit tests execution
- install pytest & pytest.cov
- don't source launcher
- remove MPLBACKEND envar
- no need to set PYTHONPATH for sct_testing
- run unit tests before integration tests

* add generic requirements.txt

* install_sct: update to piggy-back on pip install and more

- add anaconda-client
- don't install SCT from static requirements, use our setup.py
- run "sct_check_dependencies"
- add conda-forge source
- remove usage of update_bin script to create bins
- adjust paths without sct_env
- create launchers after install
- remove sentry DSN, write a sentry module

* add launcher for scripts

* sct_utils: add special case for SCT binaries (WIP)

* flag is_sct_binary in isct_* calls

* sct_utils: download binaries

* install: directly call scripts now they are reachable

* move the best parts of sct_utils into spinalcordtoolbox.utils

* launcher: force scripts to not use graphical output (#2005)

* documentation: sphinx: introduce the pip install

* setup: handle full install (except data & binaries) with pip

* launcher: handle MPI, ITK # threads

* sct_check_dependencies: fixup failing MPLBACKEND thing

* use __sct_dir__, __data_dir__

* sct_utils move logger

* documentation: sphinx: command-line: don't call python scripts as is, call the command

* unit_testing: deepseg_gm: fixup pytest.approx spec

* conda: explicit scipy installation

* requirements: simplify requirements (conda/pip), the specs are already constraining because of pyqt/sklearn

- dependencies versions are minimally fixated
- mpi option via setup

* is_sct_binary

* sct_check_dependencies: rework dependency checks

- Look at Conda requirements
- Look at pip requirements

* sct_utils: is_sct_binary

* install: remove obs... (continued)

119354 of 445546 relevant lines covered (26.79%)

0.31 hits per line

Jobs
ID Job ID Ran Files Coverage
1 10745.1 0
26.76
 Travis Job 10745.1
2 10745.2 (SCT_MINICONDA=2) 0
66.58
 Travis Job 10745.2
3 10745.3 (SCT_MINICONDA=2) 0
67.89
 Travis Job 10745.3
Source Files on build 10745
Detailed source file information is not available for this build.