__init__.py

# not sure if we need to include these
# from .classes import (
#     CWLEngine,
# )

from .cwlFile import (
    CWLFile,
)

from .cwlRunner import (
    CWLRunner,
)

from .mafio import (
    TableReader,
    MafWriter
)

from .plutoPreRunTestCase import (
    PlutoPreRunTestCase,
)

from .plutoTestCase import (
    PlutoTestCase,
)

from .run import (
    run_cwl,
    run_command,
    run_cwl_toil
)

from .serializer import (
    OFile,
    ODir,
    serialize_repr
)

from .settings import (
    ENABLE_LARGE_TESTS,
    ENABLE_INTEGRATION_TESTS,
    USE_LSF,
    CWL_ENGINE,
    CWL_DEFAULT_ENGINE,
    CWL_DIR,
    REF_DIR,
    EXAMPLES_DIR,
    TMP_DIR,
    KEEP_TMP,
    PRINT_COMMAND,
    PRINT_TESTNAME,
    TOIL_STATS,
    PRINT_STATS,
    SAVE_STATS,
    STATS_DIR,
    PRINT_STATS,
    CWL_ARGS,
    TOIL_ARGS,
    TOIL_CLEAN_SETTINGS,
)

from .util import (
    write_table,
    dicts2lines,
    clean_dicts,
    parse_header_comments,
    load_mutations,
    md5_file,
    md5_obj
)