How to use the signac.Collection.open function in signac

def test_read(self):
        c = Collection.open(self._fn_collection, mode='r')
        assert len(list(c)) == 10
        assert len(list(c)) == 10
        assert len(c.find()) == 10
        c.close()

def setUp(self, request):
        self._tmp_dir = TemporaryDirectory(prefix='signac_collection_')
        request.addfinalizer(self._tmp_dir.cleanup)
        self._fn_json = os.path.join(self._tmp_dir.name, 'test.json')
        self.c = Collection.open(filename=':memory:')
        docs = [dict(_id=str(i)) for i in range(10)]
        self.c.update(docs)
        self.c.flush()

def test_write_flush_and_reopen(self):
        docs = [dict(_id=str(i)) for i in range(10)]
        self.c.update(docs)
        self.c.flush()
        assert os.path.getsize(self._fn_collection) > 0

        with Collection.open(self._fn_collection) as c:
            assert len(c) == len(docs)
            for doc in self.c:
                assert doc['_id'] in c

def test_read(self):
        with Collection.open(self._fn_collection, mode='r') as c:
            assert len(list(c)) == 3
        with open(self._fn_collection, 'a') as file:
            file.write("{'a': 0}\n")      # ill-formed JSON (single quotes instead of double quotes)
        with pytest.raises(JSONParseError):
            with Collection.open(self._fn_collection, mode='r') as c:
                pass

def test_file_size(self):
        docs = [dict(_id=str(i)) for i in range(10)]

        with open(self._fn_collection) as f:
            assert len(list(f)) == 0
        with Collection.open(self._fn_collection) as c:
            c.update(docs)
        with open(self._fn_collection) as f:
            assert len(list(f)) == len(docs)
        with Collection.open(self._fn_collection) as c:
            assert len(c) == len(docs)
            for doc in docs:
                c.replace_one({'_id': doc['_id']}, doc)
        with Collection.open(self._fn_collection) as c:
            assert len(c) == len(docs)
        with open(self._fn_collection) as f:
            assert len(list(f)) == len(docs)

def read_benchmark(filename, filter=None, include_metadata=False):
    with signac.Collection.open(filename) as c:
        docs = list(c.find(filter))

    df_data = pd.DataFrame(
        {doc['_id']: dict(normalize(doc['data'], doc['meta']['N'])) for doc in docs}).T

    if include_metadata:
        df_meta = pd.DataFrame(
            {doc['_id']: doc['meta'] for doc in docs}).T
        return pd.concat([df_meta, df_data], axis=1)
    else:
        return df_data

def store_result(key, doc):
        if args.output == '-':
            if args.json:
                print(json.dumps(doc, indent=2))
            else:
                pprint(doc)
        else:
            with signac.Collection.open(args.output) as c:
                c.replace_one(key, doc, upsert=True)

def _log_operation(operation, error=None):
            if self.strict_git:
                if git.Repo(operation.job._project.root_directory()).is_dirty():
                    raise RuntimeError(
                        "Unable to reliably log operation, because the git repository in "
                        "the project root directory is dirty.\n\nMake sure to commit all "
                        "changes or ignore this warning by setting '{}(strict_git=False)'.".format(
                            type(self).__name__))
            metadata = collect_metadata(operation)

            # Add additional execution-related information to metadata.
            metadata['stage'] = stage
            metadata['error'] = None if error is None else str(error)

            # Write metadata to collection inside job workspace.
            with Collection.open(operation.job.fn(self._fn_logfile)) as logfile:
                logfile.insert_one(metadata)