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Added routine to return correct storage string and test #216

Merged
merged 28 commits into from
Feb 6, 2020
Merged

Added routine to return correct storage string and test #216

merged 28 commits into from
Feb 6, 2020

Commits on Jan 9, 2020

  1. Added routine to return correct storage string and test

    @aidanheerdegen
    aidanheerdegen committed Jan 9, 2020
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Commits on Jan 10, 2020

  1. Changed find_mounts to return set. 

    Updated tests.

PEP8 fixes.
    @aidanheerdegen
    aidanheerdegen committed Jan 10, 2020
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Commits on Jan 13, 2020

  1. Moved all PBS related code from cli to scheduler/pbs.py 

    Made PBS call testable by returning string for cli to execute.

Added test for generate_command routine. Used argparse to facilitate
checking.

Moved all PBS related tests to a new test script.
    @aidanheerdegen
    aidanheerdegen committed Jan 13, 2020
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Commits on Jan 14, 2020

  1. Monkey patch PBS init so tests run without error

    @aidanheerdegen
    aidanheerdegen committed Jan 14, 2020
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  2. PEP8 cleanup

    @aidanheerdegen
    aidanheerdegen committed Jan 14, 2020
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  3. More PEP8 fixes

    @aidanheerdegen
    aidanheerdegen committed Jan 14, 2020
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  4. Insist there is no module support available in test

    @aidanheerdegen
    aidanheerdegen committed Jan 14, 2020
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  5. Added verbosity to module init for debugging

    @aidanheerdegen
    aidanheerdegen committed Jan 14, 2020
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  6. Set pytest to not capture output

    @aidanheerdegen
    aidanheerdegen committed Jan 14, 2020
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  7. Fixed typo

    @aidanheerdegen
    aidanheerdegen committed Jan 14, 2020
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  8. More debugging

    @aidanheerdegen
    aidanheerdegen committed Jan 14, 2020
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  9. Fixed faulty logic in module detection

    @aidanheerdegen
    aidanheerdegen committed Jan 14, 2020
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Commits on Jan 16, 2020

  1. Rearranged pbs code to make it more testable/monkey-patchable. 

    Created two separate routines, encode_mount and make_mount_string,
and wrote tests.

pbs.generate_command now takes an optional python interpreter
path to allow arbitrary paths to be passed for testing.

Changed to a regular expression to parse mounts in find_mounts.
Explicitly do not support mount paths that have no subdirectories
under project code, or no trailing slash.
    @aidanheerdegen
    aidanheerdegen committed Jan 16, 2020
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  2. Removed old tests that had been moved to test_pbs

    @aidanheerdegen
    aidanheerdegen committed Jan 16, 2020
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Commits on Jan 17, 2020

  1. Removed dependence on passing experiment object to manifest

    @aidanheerdegen
    aidanheerdegen committed Jan 17, 2020
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Commits on Jan 20, 2020

  1. Split manifest load from setup to allow this to be called separately. 

    Made get_all_fullpaths to Manifest to access all fullpaths. Required
to support checking paths for storage flags using PBS at NCI.
    @aidanheerdegen
    aidanheerdegen committed Jan 20, 2020
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  2. Fixed call to get_all_fullpaths

    @aidanheerdegen
    aidanheerdegen committed Jan 20, 2020
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Commits on Jan 29, 2020

  1. Major reorganisation of manifest code. 

    Made separate load method that will load whatever manifests are
available.

Logic for checking for reproduce consistency is all contained in
setup.

Create separate init_mf method for initialising submanifests and
use this to zero off other manifests when loaded versions not
required.

Streamlined code in manifest init
    @aidanheerdegen
    aidanheerdegen committed Jan 29, 2020
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  2. Isolated code to make config files in a function.

    @aidanheerdegen
    aidanheerdegen committed Jan 29, 2020
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  3. Added storage flag check for laboratory and shortpath

    @aidanheerdegen
    aidanheerdegen committed Jan 29, 2020
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  4. Change code comment

    @aidanheerdegen
    aidanheerdegen committed Jan 29, 2020
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Commits on Feb 5, 2020

  1. Removed debugging statements

    @aidanheerdegen
    aidanheerdegen committed Feb 5, 2020
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  2. Changed call to Manifest init in run_cmd to be compatible with 

    changed API
    @aidanheerdegen
    aidanheerdegen committed Feb 5, 2020
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  3. Added tests for storage flag extraction from laboratory and shortpath

    @aidanheerdegen
    aidanheerdegen committed Feb 5, 2020
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  4. PEP8 fixes, and removed redundant code in storage search

    @aidanheerdegen
    aidanheerdegen committed Feb 5, 2020
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  5. PEP8 cleanup

    @aidanheerdegen
    aidanheerdegen committed Feb 5, 2020
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Commits on Feb 6, 2020

  1. PEP8 cleanup

    @aidanheerdegen
    aidanheerdegen committed Feb 6, 2020
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  2. PEP8 cleanup

    @aidanheerdegen
    aidanheerdegen committed Feb 6, 2020
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