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How to use dpath method in tox

Best Python code snippet using tox_python

tests.py

Source:tests.py

...16if not which("snakemake"):17    raise Exception("snakemake not in PATH. For testing, install snakemake with "18                    "'pip install -e .'. You should do this in a separate environment "19                    "(via conda or virtualenv).")20def dpath(path):21    """get path to a data file (relative to the directory this22	test lives in)"""23    return os.path.realpath(join(os.path.dirname(__file__), path))24def md5sum(filename):25    data = open(filename, 'rb').read()26    return hashlib.md5(data).hexdigest()27def is_connected():28    try:29        urllib.request.urlopen("http://www.google.com", timeout=1)30        return True31    except urllib.request.URLError:32        return False33def run(path,34        shouldfail=False,35        needs_connection=False,36        snakefile="Snakefile",37        subpath=None,38        check_md5=True, cores=3, **params):39    """40    Test the Snakefile in path.41    There must be a Snakefile in the path and a subdirectory named42    expected-results.43    """44    if needs_connection and not is_connected():45        print("Skipping test because of missing internet connection",46              file=sys.stderr)47        return False48    results_dir = join(path, 'expected-results')49    snakefile = join(path, snakefile)50    assert os.path.exists(snakefile)51    assert os.path.exists(results_dir) and os.path.isdir(52        results_dir), '{} does not exist'.format(results_dir)53    with tempfile.TemporaryDirectory(prefix=".test", dir=os.path.abspath(".")) as tmpdir:54        config = {}55        if subpath is not None:56            # set up a working directory for the subworkflow and pass it in `config`57            # for now, only one subworkflow is supported58            assert os.path.exists(subpath) and os.path.isdir(59                subpath), '{} does not exist'.format(subpath)60            subworkdir = os.path.join(tmpdir, "subworkdir")61            os.mkdir(subworkdir)62            call('find {} -maxdepth 1 -type f -print0 | xargs -0 -I%% -n 1 cp %% {}'.format(63                quote(subpath), quote(subworkdir)),64                 shell=True)65            config['subworkdir'] = subworkdir66        call('find {} -maxdepth 1 -type f -print0 | xargs -0 -I%% -n 1 cp -r %% {}'.format(67            quote(path), quote(tmpdir)),68             shell=True)69        success = snakemake(snakefile,70                            cores=cores,71                            workdir=tmpdir,72                            stats="stats.txt",73                            config=config, **params)74        if shouldfail:75            assert not success, "expected error on execution"76        else:77            assert success, "expected successful execution"78            for resultfile in os.listdir(results_dir):79                if resultfile == ".gitignore" or not os.path.isfile(80                    os.path.join(results_dir, resultfile)):81                    # this means tests cannot use directories as output files82                    continue83                targetfile = join(tmpdir, resultfile)84                expectedfile = join(results_dir, resultfile)85                assert os.path.exists(86                    targetfile), 'expected file "{}" not produced'.format(87                        resultfile)88                if check_md5:89                    # if md5sum(targetfile) != md5sum(expectedfile):90                    #     import pdb; pdb.set_trace()91                    assert md5sum(targetfile) == md5sum(92                        expectedfile), 'wrong result produced for file "{}"'.format(93                            resultfile)94def test01():95    run(dpath("test01"))96def test02():97    run(dpath("test02"))98def test03():99    run(dpath("test03"), targets=['test.out'])100def test04():101    run(dpath("test04"), targets=['test.out'])102def test05():103    run(dpath("test05"))104def test06():105    run(dpath("test06"), targets=['test.bla.out'])106def test07():107    run(dpath("test07"), targets=['test.out', 'test2.out'])108def test08():109    run(dpath("test08"), targets=['test.out', 'test2.out'])110def test09():111    run(dpath("test09"), shouldfail=True)112def test10():113    run(dpath("test10"))114def test11():115    run(dpath("test11"))116def test12():117    run(dpath("test12"))118def test13():119    run(dpath("test13"))120def test14():121    run(dpath("test14"), snakefile="Snakefile.nonstandard", cluster="./qsub")122def test15():123    run(dpath("test15"))124def test_ancient():125    run(dpath("test_ancient"), targets=['D'])126def test_report():127    run(dpath("test_report"), check_md5=False)128def test_dynamic():129    run(dpath("test_dynamic"))130def test_params():131    run(dpath("test_params"))132def test_same_wildcard():133    run(dpath("test_same_wildcard"))134def test_conditional():135    run(dpath("test_conditional"),136        targets="test.out test.0.out test.1.out test.2.out".split())137def test_unpack_dict():138    run(dpath("test_unpack_dict"))139def test_unpack_list():140    run(dpath("test_unpack_list"))141def test_shell():142    run(dpath("test_shell"))143def test_temp():144    run(dpath("test_temp"),145        cluster="./qsub",146        targets="test.realigned.bam".split())147def test_keyword_list():148    run(dpath("test_keyword_list"))149def test_subworkflows():150    run(dpath("test_subworkflows"), subpath=dpath("test02"))151def test_globwildcards():152    run(dpath("test_globwildcards"))153def test_local_import():154    run(dpath("test_local_import"))155def test_ruledeps():156    run(dpath("test_ruledeps"))157def test_persistent_dict():158    try:159        import pytools160        run(dpath("test_persistent_dict"))161    except ImportError:162        pass163def test_url_include():164    run(dpath("test_url_include"), needs_connection=True)165def test_touch():166    run(dpath("test_touch"))167def test_config():168    run(dpath("test_config"))169def test_update_config():170    run(dpath("test_update_config"))171def test_wildcard_keyword():172    run(dpath("test_wildcard_keyword"))173def test_benchmark():174    run(dpath("test_benchmark"), check_md5=False)175def test_temp_expand():176    run(dpath("test_temp_expand"))177def test_wildcard_count_ambiguity():178    run(dpath("test_wildcard_count_ambiguity"))179def test_cluster_dynamic():180    run(dpath("test_cluster_dynamic"), cluster="./qsub")181def test_dynamic_complex():182    run(dpath("test_dynamic_complex"))183def test_srcdir():184    run(dpath("test_srcdir"))185def test_multiple_includes():186    run(dpath("test_multiple_includes"))187def test_yaml_config():188    run(dpath("test_yaml_config"))189# TODO reenable once S3Mocked works with boto3190# def test_remote():191#     try:192#         import moto193#         import boto3194#         import filechunkio195#196#         # only run the remote file test if the dependencies197#         # are installed, otherwise do nothing198#         run(dpath("test_remote"), cores=1)199#     except ImportError:200#         pass201def test_cluster_sync():202    run(dpath("test14"),203        snakefile="Snakefile.nonstandard",204        cluster_sync="./qsub")205def test_symlink_temp():206    run(dpath("test_symlink_temp"), shouldfail=True)207def test_empty_include():208    run(dpath("test_empty_include"))209def test_script():210    run(dpath("test_script"))211def test_shadow():212    run(dpath("test_shadow"))213def test_until():214    run(dpath("test_until"),215        until=["leveltwo_first", # rule name216               "leveltwo_second.txt", # file name217               "second_wildcard"]) # wildcard rule218def test_omitfrom():219    run(dpath("test_omitfrom"),220        omit_from=["leveltwo_first", # rule name221                   "leveltwo_second.txt", # file name222                   "second_wildcard"]) # wildcard rule223def test_nonstr_params():224    run(dpath("test_nonstr_params"))225def test_delete_output():226    run(dpath("test_delete_output"), cores=1)227def test_input_generator():228    run(dpath("test_input_generator"))229def test_symlink_time_handling():230    #See Snakefile for notes on why this fails on some systems231    if os.utime in os.supports_follow_symlinks:232        run(dpath("test_symlink_time_handling"))233def test_issue328():234    try:235        import pytools236        run(dpath("test_issue328"), forcerun=["split"])237    except ImportError:238        # skip test if import fails239        pass240def test_conda():241    if conda_available():242        run(dpath("test_conda"), use_conda=True)243def test_conda_custom_prefix():244    if conda_available():245        run(dpath("test_conda_custom_prefix"),246            use_conda=True, conda_prefix="custom")247def test_wrapper():248    if conda_available():249        run(dpath("test_wrapper"), use_conda=True)250def conda_available():251    return which("conda")252def test_get_log_none():253    run(dpath("test_get_log_none"))254def test_get_log_both():255    run(dpath("test_get_log_both"))256def test_get_log_stderr():257    run(dpath("test_get_log_stderr"))258def test_get_log_stdout():259    run(dpath("test_get_log_stdout"))260def test_get_log_complex():261    run(dpath("test_get_log_complex"))262def test_spaces_in_fnames():263    run(dpath("test_spaces_in_fnames"),264        # cluster="./qsub",265        targets=["test bam file realigned.bam"],266        verbose=True,267        printshellcmds=True)268# TODO deactivate because of problems with moto and boto3.269# def test_static_remote():270#     import importlib271#     try:272#         importlib.reload(boto3)273#         importlib.reload(moto)274#         # only run the remote file test if the dependencies275#         # are installed, otherwise do nothing276#         run(dpath("test_static_remote"), cores=1)277#     except ImportError:278#         pass279def test_remote_ncbi_simple():280    try:281        import Bio282        # only run the remote file test if the dependencies283        # are installed, otherwise do nothing284        run(dpath("test_remote_ncbi_simple"))285    except ImportError:286        pass287def test_remote_ncbi():288    try:289        import Bio290        # only run the remote file test if the dependencies291        # are installed, otherwise do nothing292        run(dpath("test_remote_ncbi"))293    except ImportError:294        pass295def test_deferred_func_eval():296    run(dpath("test_deferred_func_eval"))297def test_format_params():298    run(dpath("test_format_params"), check_md5=True)299def test_rule_defined_in_for_loop():300    # issue 257301    run(dpath("test_rule_defined_in_for_loop"))302def test_issue381():303    run(dpath("test_issue381"))304def test_format_wildcards():305    run(dpath("test_format_wildcards"))306def test_with_parentheses():307    run(dpath("test (with parentheses)"))308def test_dup_out_patterns():309    """Duplicate output patterns should emit an error310    Duplicate output patterns can be detected on the rule level311    """312    run(dpath("test_dup_out_patterns"), shouldfail=True)313def test_restartable_job_cmd_exit_1():314    """Test the restartable job feature on ``exit 1``315    The shell snippet in the Snakemake file will fail the first time316    and succeed the second time.317    """318    # Even two consecutive times should fail as files are cleared319    run(dpath("test_restartable_job_cmd_exit_1"), cluster="./qsub",320        restart_times=0, shouldfail=True)321    run(dpath("test_restartable_job_cmd_exit_1"), cluster="./qsub",322        restart_times=0, shouldfail=True)323    # Restarting once is enough324    run(dpath("test_restartable_job_cmd_exit_1"), cluster="./qsub",325        restart_times=1, printshellcmds=True)326def test_restartable_job_qsub_exit_1():327    """Test the restartable job feature when qsub fails328    The qsub in the sub directory will fail the first time and succeed the329    second time.330    """331    # Even two consecutive times should fail as files are cleared332    run(dpath("test_restartable_job_qsub_exit_1"), cluster="./qsub",333        restart_times=0, shouldfail=True)334    run(dpath("test_restartable_job_qsub_exit_1"), cluster="./qsub",335        restart_times=0, shouldfail=True)336    # Restarting once is enough337    run(dpath("test_restartable_job_qsub_exit_1"), cluster="./qsub",338        restart_times=1, shouldfail=False)339def test_threads():340    run(dpath("test_threads"), cores=20)341def test_dynamic_temp():342    run(dpath("test_dynamic_temp"))343# TODO this currently hangs. Has to be investigated (issue #660).344#def test_ftp_immediate_close():345#    try:346#        import ftputil347#348#        # only run the remote file test if the dependencies349#        # are installed, otherwise do nothing350#        run(dpath("test_ftp_immediate_close"))351#    except ImportError:352#        pass353def test_issue260():354   run(dpath("test_issue260"))355# TODO reenable once S3Mocked works again with boto3356# def test_default_remote():357#     run(dpath("test_default_remote"),358#         default_remote_provider="S3Mocked",359#         default_remote_prefix="test-remote-bucket")360def test_run_namedlist():361    run(dpath("test_run_namedlist"))362def test_remote_gs():363    run(dpath("test_remote_gs"))364def test_remote_log():365    run(dpath("test_remote_log"), shouldfail=True)366def test_profile():367    run(dpath("test_profile"))368# TODO reenable once we run tests in a VM instead of Docker (maybe go back to codeship)?369# def test_singularity():370#     run(dpath("test_singularity"), use_singularity=True)371def test_issue612():372    run(dpath("test_issue612"), dryrun=True)373if __name__ == '__main__':374    import nose...

build.py

Source:build.py

1# Copyright (c) 2017-present, Facebook, Inc.2# All rights reserved.3# This source code is licensed under the BSD-style license found in the4# LICENSE file in the root directory of this source tree. An additional grant5# of patent rights can be found in the PATENTS file in the same directory.6# Download and build the data if it does not exist.7import parlai.core.build_data as build_data8import os9def buildImage(opt):10    dpath = os.path.join(opt['datapath'], 'COCO-IMG')11    version = '1'12    if not build_data.built(dpath, version_string=version):13        print('[building image data: ' + dpath + ']')14        if build_data.built(dpath):15            # An older version exists, so remove these outdated files.16            build_data.remove_dir(dpath)17        build_data.make_dir(dpath)18        # Download the image data.19        fname1 = 'train2014.zip'20        fname2 = 'val2014.zip'21        fname3 = 'test2015.zip'22        url = 'https://s3.amazonaws.com/fair-data/parlai/COCO-IMG/'23        build_data.download(url + fname1, dpath, fname1)24        build_data.download(url + fname2, dpath, fname2)25        build_data.download(url + fname3, dpath, fname3)26        build_data.untar(dpath, fname1)27        build_data.untar(dpath, fname2)28        build_data.untar(dpath, fname3)29        # Mark the data as built.30        build_data.mark_done(dpath, version_string=version)31def build(opt):32    dpath = os.path.join(opt['datapath'], 'VQA-v1')33    version = None34    if not build_data.built(dpath, version_string=version):35        print('[building data: ' + dpath + ']')36        if build_data.built(dpath):37            # An older version exists, so remove these outdated files.38            build_data.remove_dir(dpath)39        build_data.make_dir(dpath)40        # Download the data.41        fname1 = 'Questions_Train_mscoco.zip'42        fname2 = 'Questions_Val_mscoco.zip'43        fname3 = 'Questions_Test_mscoco.zip'44        fname4 = 'Annotations_Val_mscoco.zip'45        fname5 = 'Annotations_Train_mscoco.zip'46        url = 'http://visualqa.org/data/mscoco/vqa/'47        build_data.download(url + fname1, dpath, fname1)48        build_data.download(url + fname2, dpath, fname2)49        build_data.download(url + fname3, dpath, fname3)50        build_data.download(url + fname4, dpath, fname4)51        build_data.download(url + fname5, dpath, fname5)52        build_data.untar(dpath, fname1)53        build_data.untar(dpath, fname2)54        build_data.untar(dpath, fname3)55        build_data.untar(dpath, fname4)56        build_data.untar(dpath, fname5)57        # Mark the data as built....

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