payu-org / payu / 420
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Added routine to return correct storage string and test (#216)

* Added routine to return correct storage string and test

* Changed find_mounts to return set.

Updated tests.

* 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.

* Monkey patch PBS init so tests run without error

* Insist there is no module support available in test

* Set pytest to not capture output

* Fixed faulty logic in module detection

* 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.

* Removed dependence on passing experiment object to manifest

* 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.

* 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

* Isolated code to make config files in a function.

* Added storage flag check for laboratory and shortpath

* Changed call to Manifest init in run_cmd to be compatible with
changed API

* Added tests for storage flag extraction f... (continued)

1080 of 3056 relevant lines covered (35.34%)

0.71 hits per line

Jobs
ID Job ID Ran Files Coverage
1 420.1 0
Travis Job 420.1
2 420.2 0
35.34
 Travis Job 420.2
3 420.3 0
35.34
 Travis Job 420.3
Source Files on build 420
Detailed source file information is not available for this build.