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How to use make_arguments method in pytest-benchmark

Best Python code snippet using pytest-benchmark

tester.py

Source:tester.py

...140    msg.append('\n{}/{} test cases successful'141               .format(successful, len(outcomes)))142    msg.append('***************')143    return '\n'.join(msg)144def make_arguments(format, output,145                   pointers=None, pointer_type='glob', mode='document',146                   **kwargs):147    """Generates argument string to call the pipeline with"""148    args = dict(149        pointer_type=pointer_type,150        mode=mode,151        format=format,152        output=output,153        input=join(TESTFILES, format),154        termlist=TERMLIST,155        cache=CACHE.name,156        miscellaneous='',157        )158    args.update(kwargs)159    arguments = """160        -t {pointer_type}161        -m {mode}162        -f {format}163        -i {input}164        -o {output}165        -c termlist1_path {termlist}166        -c termlist_cache {cache}167        -c termlist_skip_header true168        -e {export}169        {miscellaneous}170        """.format(**args)171    if pointers is None and pointer_type == 'glob':172        pointers = '*'173    if pointers:174        arguments += '-- ' + pointers175    return arguments176def run_with_arguments(arguments_string):177    argument_list = shlex.split(arguments_string.strip())178    arguments = parameters.parse_cmdline(argument_list)179    run(**arguments)180def outdir(outputdir, *args):181    'Create an output directory name with datetime and test-case name.'182    # Get the name of the calling function.183    testcase = sys._getframe(1).f_code.co_name184    subcase = '_'.join((testcase,) + args)185    return join(outputdir, subcase)186##########################187# ACTUAL TESTING FUNCTIONS188##########################189def txt_directory(outputdir):190    for output_format in OUTPUT_FORMATS:191        testlogger.info('-> %s', output_format)192        output = join(outdir(outputdir), output_format)193        arguments = make_arguments(format='txt',194                                   output=output,195                                   export=output_format,196                                   pointers='*.txt')197        run_with_arguments(arguments)198    # It doesn't crash when there's an empty file,199    # or a file in a different format200    # but it crashes if the encoding is messed up201    # (this is why I added *.txt for testing)202def txt_id(outputdir):203    pointers = join(IDFILES, 'txt_ids.txt')204    for output_format in OUTPUT_FORMATS:205        testlogger.info('-> %s', output_format)206        output = join(outdir(outputdir), output_format)207        arguments = make_arguments(pointer_type='id',208                                   format='txt',209                                   output=output,210                                   export=output_format,211                                   pointers=pointers,212                                   miscellaneous='-b pubmed')213        run_with_arguments(arguments)214def txt_collection(outputdir):215    for output_format in OUTPUT_FORMATS:216        testlogger.info('-> %s', output_format)217        output = join(outdir(outputdir), output_format)218        arguments = make_arguments(format='txt',219                                   output=output,220                                   mode='collection',221                                   export=output_format,222                                   pointers='*.txt')223        run_with_arguments(arguments)224    # TODO output is just called 'None'225    # Is there a way to make that nicer?226def txt_json(outputdir):227    _multiple_outfmts(outdir(outputdir), 'txt_json')228def pubtator(outputdir):229    _multiple_outfmts(outdir(outputdir), 'pubtator')230def pubtator_fbk(outputdir):231    _multiple_outfmts(outdir(outputdir), 'pubtator_fbk')232def pxmlgz(outputdir):233    _multiple_outfmts(outdir(outputdir), 'pxml.gz')234def pxml_directory(outputdir):235    _multiple_outfmts(outdir(outputdir), 'pxml')236def _multiple_outfmts(outputdir, fmt):237    for mode in ['collection', 'document']:238        export = ' '.join(OUTPUT_FORMATS)239        testlogger.info('-> %s (%s mode)', export, mode)240        output = '_'.join((outputdir, mode))241        misc = '-c fn-format-out {fmt}/{id}.{ext}'242        arguments = make_arguments(format=fmt,243                                   output=output,244                                   mode=mode,245                                   export=export,246                                   miscellaneous=misc)247        run_with_arguments(arguments)248def pxml_id(outputdir):249    testlogger.info('-> tsv (ID pointers)')250    pointers = join(IDFILES, 'pxml_pmids.txt')251    arguments = make_arguments(format='pxml',252                               output=outdir(outputdir, 'pmid'),253                               pointers=pointers,254                               pointer_type='id',255                               export='tsv')256    run_with_arguments(arguments)257    # missing ids are downloaded258    testlogger.info('-> tsv (ID pointers, pubmed fallback)')259    pointers = join(IDFILES, 'pxml_pmids_dl.txt')260    arguments = make_arguments(format='pxml',261                               output=outdir(outputdir, 'pmid', 'dl'),262                               pointers=pointers,263                               pointer_type='id',264                               export='tsv',265                               miscellaneous='-b pubmed')266    run_with_arguments(arguments)267def bioc_xml(outputdir):268    output = join(outputdir, 'bioc_xml')269    arguments = make_arguments(format='bioc_xml',270                               output=output,271                               export='xml')272    run_with_arguments(arguments)273def bioc_json(outputdir):274    output = join(outputdir, 'bioc_json')275    arguments = make_arguments(format='bioc_json',276                               output=output,277                               export='pubtator')278    run_with_arguments(arguments)279def download_pubmed(outputdir):280    pointers = join(IDFILES, 'pubmed_pmids.txt')281    output = join(outputdir, 'pubmed')282    arguments = make_arguments(format='pubmed',283                               output=output,284                               pointers=pointers,285                               pointer_type='id',286                               export='odin')287    run_with_arguments(arguments)288def download_pmc(outputdir):289    # running with a PMCID we know works290    good_pmcids = join(IDFILES, 'good_pmcids.txt')291    output = join(outputdir, 'pmc')292    arguments = make_arguments(format='pmc',293                               output=output,294                               pointers=good_pmcids,295                               pointer_type='id',296                               export='xml')297    run_with_arguments(arguments)298def download_bad_pmc(outputdir):299    # some PMC articles do not allow DLing the whole article300    bad_pmcids = join(IDFILES, 'bad_pmcids.txt')301    output = join(outputdir, 'pmc')302    arguments = make_arguments(format='pmc',303                               output=output,304                               pointers=bad_pmcids,305                               pointer_type='id',306                               export='xml')307    run_with_arguments(arguments)308def download_fictious_pmc(outputdir):309    # running with PMCIDs that don't exist310    # raises a ValueError with a list of missed IDs.311    fictious_pmcids = join(IDFILES, 'fictious_pmcids.txt')312    output = join(outputdir, 'pmc')313    arguments = make_arguments(format='pmc',314                               output=output,315                               pointers=fictious_pmcids,316                               pointer_type='id',317                               export='xml')318    with open(fictious_pmcids) as f:319        ids = [i.strip() for i in f]320    try:321        run_with_arguments(arguments)322    except ValueError as e:323        if getattr(e, 'ids', None) != ids:324            raise325def download_random_pmc(outputdir):326    # generate random list of pmcids to be dowloaded327    # to make testing deterministic, this is commented328    # import random329    random_pmcids = join(IDFILES, 'random_pmcids.txt')330    # with open(random_pmcids, 'w+') as f:331    #    for r in random.sample(range(1, 5000000), 100):332    #        f.write(str(r) + "\n")333    output = join(outputdir, 'pmc')334    misc = '-c ignore-load-errors true'335    arguments = make_arguments(format='pmc',336                               output=output,337                               pointers=random_pmcids,338                               pointer_type='id',339                               export='xml',340                               miscellaneous=misc)...

make.py

Source:make.py

1"""Extension providing the :ref:`command-zebra_make` command."""2import logging3from zaf.commands.command import CommandId4from zaf.component.decorator import requires5from zaf.config.options import ConfigOption, ConfigOptionId6from zaf.extensions.extension import AbstractExtension, FrameworkExtension7from zaf.messages.message import EndpointId, MessageId8from zebra.docker import docker9logger = logging.getLogger(__name__)10logger.addHandler(logging.NullHandler())11@requires(docker_run='DockerRun')12def make(application, docker_run):13    """14    Run make inside the container.15    The MAKE_ARGUMENTS variable will be forwarded to the make command.16    Example::17    \b18        zebra make -j8 <target>19        MAKE_ARGUMENTS='-j8' make <target>20    """21    make_arguments = application.config.get(MAKE_ARGUMENTS)22    make_command = docker.IMAGES[docker_run.docker_config.image].config.make_command23    application.messagebus.trigger_event(PRE_MAKE, MAKE_ENDPOINT, data=make_arguments)24    command_with_arguments = [make_command]25    command_with_arguments.extend(make_arguments)26    return docker_run.run_in_docker(command_with_arguments, forward_signals=False)27MAKE_ARGUMENTS = ConfigOptionId(28    'arguments',29    'The arguments to make.',30    multiple=True,31    namespace='make',32    argument=True,33)34MAKE_COMMAND = CommandId(35    'make',36    make.__doc__,37    make,38    config_options=[39        ConfigOption(MAKE_ARGUMENTS, required=True),40    ],41    allow_unknown_options=True,42)43MAKE_ENDPOINT = EndpointId('MAKE_ENDPOINT', 'Endpoint for the make command')44PRE_MAKE = MessageId('PRE_MAKE', 'Event triggered before make is executed.')45@FrameworkExtension(46    'makecommand', commands=[MAKE_COMMAND], endpoints_and_messages={47        MAKE_ENDPOINT: [PRE_MAKE]48    })49class MakeExtension(AbstractExtension):...

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