Skip to content

failing tests #71

@sroet

Description

@sroet

Tests have been failing for a while (I just re-enabled the test to be run on this repo, but they have been failing for my personal fork for a while) due to NetCDF being a lot more verbose.

Instead of printing

"Storage @ '/tmp/tmpfqsyxkfk/setup.nc'"

it stores:

E             +  "<class 'openpathsampling.storage.storage.Storage'>",
E             +  'root group (NETCDF4 data model, file format HDF5):',
E             +  '    format: netcdf+',
E             +  '    ncplus_version: 1.5.2',
E             +  '    storage_format: openpathsampling',
E             +  '    storage_version: 1.5.2',
E             +  '    use_uuid: True',
E             +  '    dimensions(sizes): scalar(1), pair(2), stores(22), trajectories(1), '
E             +  'topologies(2), snapshots(7), snapshottype(1), samples(1), samplesets(1), '
E             +  'movechanges(0), steps(0), details(0), pathmovers(5), '
E             +  'shootingpointselectors(1), engines(2), pathsimulators(0), transitions(2), '
E             +  'networks(1), schemes(1), interfacesets(0), msouters(0), volumes(8), '
E             +  'ensembles(16), tag(1), attributes(1), snapshot0(7), snapshot0n_atoms(1), '
E             +  'snapshot0n_spatial(3)',
E             +  "    variables(dimensions): <class 'str'> stores_json(stores), <class 'str'> "
E             +  "stores_uuid(stores), <class 'str'> stores_name(stores), <class 'str'> "
E             +  "trajectories_json(trajectories), <class 'str'> "
E             +  "trajectories_uuid(trajectories), <class 'str'> "
E             +  "trajectories_snapshots(trajectories), <class 'str'> "
E             +  "topologies_json(topologies), <class 'str'> topologies_uuid(topologies), "
E             +  "<class 'str'> topologies_name(topologies), <class 'str'> "
E             +  "snapshots_uuid(snapshots), int32 snapshots_store(snapshots), <class 'str'> "
E             +  "snapshottype(snapshottype), <class 'str'> samples_uuid(samples), <class "
E             +  "'str'> samples_trajectory(samples), <class 'str'> samples_ensemble(samples), "
E             +  "int32 samples_replica(samples), <class 'str'> samples_parent(samples), "
E             +  "float32 samples_bias(samples), <class 'str'> samples_mover(samples), <class "
E             +  "'str'> samplesets_uuid(samplesets), <class 'str'> "
E             +  "samplesets_samples(samplesets), <class 'str'> "
E             +  "samplesets_movepath(samplesets), <class 'str'> "
E             +  "movechanges_uuid(movechanges), <class 'str'> "
E             +  "movechanges_details(movechanges), <class 'str'> "
E             +  "movechanges_mover(movechanges), <class 'str'> movechanges_cls(movechanges), "
E             +  "<class 'str'> movechanges_subchanges(movechanges), <class 'str'> "
E             +  "movechanges_samples(movechanges), <class 'str'> "
E             +  "movechanges_input_samples(movechanges), <class 'str'> steps_uuid(steps), "
E             +  "<class 'str'> steps_change(steps), <class 'str'> steps_active(steps), <class "
E             +  "'str'> steps_previous(steps), <class 'str'> steps_simulation(steps), int32 "
E             +  "steps_mccycle(steps), <class 'str'> details_json(details), <class 'str'> "
E             +  "details_uuid(details), <class 'str'> pathmovers_json(pathmovers), <class "
E             +  "'str'> pathmovers_uuid(pathmovers), <class 'str'> "
E             +  "pathmovers_name(pathmovers), <class 'str'> "
E             +  "shootingpointselectors_json(shootingpointselectors), <class 'str'> "
E             +  "shootingpointselectors_uuid(shootingpointselectors), <class 'str'> "
E             +  "shootingpointselectors_name(shootingpointselectors), <class 'str'> "
E             +  "engines_json(engines), <class 'str'> engines_uuid(engines), <class 'str'> "
E             +  "engines_name(engines), <class 'str'> pathsimulators_json(pathsimulators), "
E             +  "<class 'str'> pathsimulators_uuid(pathsimulators), <class 'str'> "
E             +  "pathsimulators_name(pathsimulators), <class 'str'> "
E             +  "transitions_json(transitions), <class 'str'> transitions_uuid(transitions), "
E             +  "<class 'str'> transitions_name(transitions), <class 'str'> "
E             +  "networks_json(networks), <class 'str'> networks_uuid(networks), <class "
E             +  "'str'> networks_name(networks), <class 'str'> schemes_json(schemes), <class "
E             +  "'str'> schemes_uuid(schemes), <class 'str'> schemes_name(schemes), <class "
E             +  "'str'> interfacesets_json(interfacesets), <class 'str'> "
E             +  "interfacesets_uuid(interfacesets), <class 'str'> "
E             +  "interfacesets_name(interfacesets), <class 'str'> msouters_json(msouters), "
E             +  "<class 'str'> msouters_uuid(msouters), <class 'str'> "
E             +  "msouters_name(msouters), <class 'str'> volumes_json(volumes), <class 'str'> "
E             +  "volumes_uuid(volumes), <class 'str'> volumes_name(volumes), <class 'str'> "
E             +  "ensembles_json(ensembles), <class 'str'> ensembles_uuid(ensembles), <class "
E             +  "'str'> ensembles_name(ensembles), <class 'str'> tag_json(tag), <class 'str'> "
E             +  "tag_uuid(tag), <class 'str'> tag_name(tag), <class 'str'> "
E             +  "attributes_json(attributes), <class 'str'> attributes_uuid(attributes), "
E             +  "<class 'str'> attributes_name(attributes), <class 'str'> "
E             +  "attributes_cache(attributes), <class 'str'> snapshot0_uuid(snapshot0), int32 "
E             +  'snapshot0_index(snapshot0), float32 snapshot0_velocities(snapshot0, '
E             +  'snapshot0n_atoms, snapshot0n_spatial), float32 '
E             +  'snapshot0_coordinates(snapshot0, snapshot0n_atoms, snapshot0n_spatial), '
E             +  "<class 'str'> snapshot0_engine(snapshot0)",
E             +  '    groups: '

which trips up the 'contents'.

There are 2 solutions to this:

  1. Fix the tests by not testing these first elements of the content
  2. Alter the stuff contents prints

@dwhswenson do you have any preference ?

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions