Update version files to 1.0.2

bin/checkm2

@@ -105,15 +105,15 @@ if __name__ == '__main__':
     predict_arguments.add_argument('--tmpdir', action=ChangeTempAction,
                                    help="specify an alternative directory for temporary files")
 
-    predict_arguments.add_argument('--force', action='store_true', help='overwrite output directory [default: not set]', default=False)
+    predict_arguments.add_argument('--force', action='store_true', help='overwrite output directory [default: do not overwrite]', default=False)
     predict_arguments.add_argument('--resume', action='store_true', help='Reuse Prodigal and DIAMOND results found in output directory [default: not set]', default=False)
     predict_arguments.add_argument('--threads', '-t', type=int, metavar='num_threads', help='number of CPUS to use [default: %i]' % num_threads, default=num_threads)
     predict_arguments.add_argument('--stdout', action='store_true', help='Print results to stdout [default: write to file]', default=False)
     predict_arguments.add_argument('--remove_intermediates', action='store_true', help="Remove all intermediate files (protein files, diamond output) [default: don't]", default=False)
     predict_arguments.add_argument('--ttable', type=int, metavar='ttable', help="Provide a specific progidal translation table for bins [default: automatically determine either 11 or 4]", default=None)
     predict_arguments.add_argument('--database_path', help="Provide a location for the CheckM2 database for a given predict run [default: use either internal path set via <checkm2 database> or CHECKM2DB environmental variable]", default=None)
 
-    predict_arguments.add_argument('--dbg_cos', action='store_true', help="DEBUG: write cosing similarity values to file [default: don't]", default=False)
+    predict_arguments.add_argument('--dbg_cos', action='store_true', help="DEBUG: write cosine similarity values to file [default: don't]", default=False)
     predict_arguments.add_argument('--dbg_vectors', action='store_true', help="DEBUG: dump pickled feature vectors to file [default: don't]", default=False)
 
 

checkm2/version.py

@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.2"

setup.py

@@ -2,13 +2,13 @@
 
 setup(
     name='CheckM2',
-    version='1.0.1',
+    version='1.0.2',
     packages=find_packages(),
     data_files=[('data', ['checkm2/data/feature_ordering.json', 'checkm2/data/kegg_path_category_mapping.json',
                           'checkm2/data/min_ref_rsdata_v1.npz', 'checkm2/data/module_definitions.json']),
                 ('models', ['checkm2/models/specific_model_COMP.hd5', 'checkm2/models/cosine_table.pkl', 
                             'checkm2/models/model_CONT.gbm', 'checkm2/models/general_model_COMP.gbm', 'checkm2/models/scaler.sav']),
-                ('version', ['checkm2/version/diamond_path.json', 'checkm2/version/version_hashes_1.0.1.json']),
+                ('version', ['checkm2/version/diamond_path.json', 'checkm2/version/version_hashes_1.0.2.json']),
                 ('testrun', ['checkm2/testrun/TEST1.tst', 'checkm2/testrun/TEST2.tst', 'checkm2/testrun/TEST3.tst'])],
     include_package_data=True,
     url='https://github.com/chklovski/CheckM2',