ordered dictionary is not a dictionary

[PeterKamphuis]

I just tried to upgrade the pipeline which forced an update for the ruamel.yaml to 0.15.22 and now I get the following errors when I try to run the pipeline.

/installdir/Anaconda2/lib/python2.7/site-packages/scipy/sparse/lil.py:19: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from . import _csparsetools /installdir/Anaconda2/lib/python2.7/site-packages/scipy/sparse/csgraph/init.py:165: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._shortest_path import shortest_path, floyd_warshall, dijkstra,\ /installdir/Anaconda2/lib/python2.7/site-packages/scipy/sparse/csgraph/_validation.py:5: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._tools import csgraph_to_dense, csgraph_from_dense,\ /installdir/Anaconda2/lib/python2.7/site-packages/scipy/sparse/csgraph/init.py:167: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._traversal import breadth_first_order, depth_first_order, \ /installdir/Anaconda2/lib/python2.7/site-packages/scipy/sparse/csgraph/init.py:169: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._min_spanning_tree import minimum_spanning_tree /installdir/Anaconda2/lib/python2.7/site-packages/scipy/sparse/csgraph/init.py:170: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._reordering import reverse_cuthill_mckee, maximum_bipartite_matching, \ /installdir/Anaconda2/lib/python2.7/site-packages/scipy/linalg/basic.py:17: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._solve_toeplitz import levinson /installdir/Anaconda2/lib/python2.7/site-packages/scipy/linalg/init.py:207: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._decomp_update import /installdir/Anaconda2/lib/python2.7/site-packages/scipy/special/init.py:640: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._ufuncs import /installdir/Anaconda2/lib/python2.7/site-packages/scipy/special/_ellip_harm.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm /installdir/Anaconda2/lib/python2.7/site-packages/scipy/optimize/_trlib/init.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._trlib import TRLIBQuadraticSubproblem /installdir/Anaconda2/lib/python2.7/site-packages/scipy/optimize/_numdiff.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 from ._group_columns import group_dense, group_sparse No handlers could be found for logger "pykwalify.core" Traceback (most recent call last): File "/installdir/Anaconda2/bin/meerkathi", line 6, in meerkathi.main(sys.argv[1:]) File "/installdir/Anaconda2/lib/python2.7/site-packages/meerkathi/init.py", line 200, in main args = cp(argv).args File "/installdir/Anaconda2/lib/python2.7/site-packages/meerkathi/dispatch_crew/config_parser.py", line 250, in init file_config[key] = c.validate(raise_exception=True)[_key] File "/installdir/Anaconda2/lib/python2.7/site-packages/pykwalify/core.py", line 167, in validate error_msg=u'.\n - '.join(self.validation_errors))) pykwalify.errors.SchemaError: <SchemaError: error code 2: Schema validation failed:

• Value 'ordereddict([('data_path', '/rundir/'), ('prefix', 'meerkathi-pipeline'), ('msdir', '/rundir/'), ('input', '/rundir/GMRT_In'), ('output', '/rundir/GMRT_Out'), ('init_pipeline', True)])' is not a dict. Value path: '/general'.: Path: '/'>

I think the dtype errors were there before but it was still running.

[SpheMakh]

Let me try typecasting the odereddict into a dict before parsing the schema for validation

[PeterKamphuis]

Am I the only one having this problem though? It prevents me from running the pipeline.

[KshitijT]

@PeterKamphuis , I tried out the recent version of the pipeline and didn't encounter this.

[PeterKamphuis]

Strange so it would be something in my anaconda installation somehow. I'll try re-installing that.

[SpheMakh]

I'm getting it too. A workaround is to rollback ruamel,

pip install --force-reinstall -U ruamel.yaml==0.15.22 

I'm still working on solution

[SpheMakh]

This PR includes the above fix. I'll keep the issue open, because we need to do it properly at some point

https://github.com/ska-sa/meerkathi/pull/281