pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 23.3.0
   hooks:
   - id: black
     args: [--safe, --quiet, --line-length=100]
@@ -12,7 +12,7 @@ repos:
   - id: check-yaml
   - id: debug-statements
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.5.0
+  rev: v2.8.0
   hooks:
   - id: pretty-format-yaml
     args: [--autofix, --indent, '2']
@@ -40,7 +40,7 @@ repos:
   hooks:
   - id: setup-cfg-fmt
 - repo: https://github.com/tdegeus/conda_envfile
-  rev: v0.4.1
+  rev: v0.4.2
   hooks:
   - id: conda_envfile_parse
     files: environment.yaml

GooseHDF5/__init__.py

@@ -40,7 +40,6 @@ class ExtendableList:
     """
 
     def __init__(self, file: h5py.File, key: str, dtype, chunk: int = 1000, **kwargs):
-
         assert key not in file
 
         self.chunk = chunk
@@ -74,7 +73,6 @@ def flush(self):
         self.dset.parent.file.flush()
 
     def __add__(self, data: ArrayLike):
-
         if isinstance(data, list):
             self.data += data
             self._flush()
@@ -86,7 +84,6 @@ def __add__(self, data: ArrayLike):
             return self
 
     def append(self, data: int | float):
-
         self.data.append(data)
         self._flush()
 
@@ -131,7 +128,6 @@ def _dict_iterategroups(data: dict, root: str = "/"):
     """
 
     for key in data.keys():
-
         item = data[key]
         path = join(root, key)
 
@@ -383,9 +379,7 @@ def _getpaths(file, root):
     # ---------------------------------------------
 
     def iterator(g, prefix):
-
         for key in g.keys():
-
             item = g[key]
             path = join(prefix, key)
 
@@ -413,9 +407,7 @@ def _getpaths_maxdepth(file, root, max_depth, fold_symbol):
     # ---------------------------------------------
 
     def iterator(g, prefix, max_depth):
-
         for key in g.keys():
-
             item = g[key]
             path = join(prefix, key)
 
@@ -452,9 +444,7 @@ def _getpaths_fold(file, root, fold, fold_symbol):
     # ---------------------------------------------
 
     def iterator(g, prefix, fold):
-
         for key in g.keys():
-
             item = g[key]
             path = join(prefix, key)
 
@@ -489,9 +479,7 @@ def _getpaths_fold_maxdepth(file, root, fold, max_depth, fold_symbol):
     # ---------------------------------------------
 
     def iterator(g, prefix, fold, max_depth):
-
         for key in g.keys():
-
             item = g[key]
             path = join(prefix, key)
 
@@ -555,7 +543,6 @@ def verify(file, datasets, error=False):
     ret = []
 
     for path in datasets:
-
         try:
             file[path][...]
         except:  # noqa: E722
@@ -772,7 +759,6 @@ def isnumeric(a):
 
 
 def _equal_value(a, b, close):
-
     import numpy as np
 
     if type(a) == str:
@@ -825,9 +811,7 @@ def _equal_value(a, b, close):
 
 
 def _equal(a, b, attrs, matching_dtype, shallow, close):
-
     if attrs:
-
         for key in a.attrs:
             if key not in b.attrs:
                 return False
@@ -978,7 +962,6 @@ def _compare_paths(
             paths_b = list(getdatasets(b, max_depth=max_depth, fold=fold, fold_symbol=symbol))
 
     if fold:
-
         fold = [join(f, symbol, root=True) for f in fold]
 
         for path in paths_a:
@@ -1089,7 +1072,6 @@ def _(
     list_folded: bool = False,
     close: bool = False,
 ) -> dict[list]:
-
     ret = {"<-": [], "->": [], "!=": [], "==": []}
     paths_a, paths_b, fold_a, fold_b = _compare_paths(
         a, b, paths_a, paths_b, False if only_datasets else attrs, max_depth, fold
@@ -1134,7 +1116,6 @@ def _(
     list_folded: bool = False,
     close: bool = False,
 ) -> dict[list]:
-
     with h5py.File(a, "r") as a_file, h5py.File(b, "r") as b_file:
         return compare(
             a_file,
@@ -1301,7 +1282,6 @@ def copy_dataset(source, dest, paths, compress=False, double_to_float=False):
         paths = list(paths)
 
     for path in paths:
-
         data = source[path][...]
 
         if data.size == 1 or not compress or not isnumeric(data):
@@ -1318,7 +1298,6 @@ def copy_dataset(source, dest, paths, compress=False, double_to_float=False):
 
 
 def _linktype2str(source: h5py.File | h5py.Group, path: str) -> str:
-
     dset = source.get(path, getlink=True)
 
     if isinstance(dset, h5py.SoftLink):
@@ -1415,7 +1394,6 @@ def print_attribute(source, paths: list[str]):
 
     for path in paths:
         if path in source:
-
             data = source[path]
 
             print(f'"{path}"')
@@ -1472,7 +1450,6 @@ def G5print(args: list[str]):
         np.set_printoptions(threshold=sys.maxsize)
 
     with h5py.File(args.source, "r") as source:
-
         if len(args.dataset) == 0:
             print_header = True
             datasets = list(
@@ -1500,7 +1477,6 @@ def G5print(args: list[str]):
                 return 1
 
         for i, dataset in enumerate(datasets):
-
             data = source[dataset]
 
             if args.info:
@@ -1574,7 +1550,6 @@ def G5list(args: list[str]):
         raise OSError(f'"{args.source}" does not exist')
 
     with h5py.File(args.source, "r") as source:
-
         if args.layer is not None:
             paths = sorted(join(args.layer, i, root=True) for i in source[args.layer])
         else:
@@ -1684,7 +1659,6 @@ def G5compare(args: list[str]):
         )
 
     def def_row(arg, colors):
-
         if colors == "none":
             if arg[1] == "!=":
                 return arg
@@ -1780,17 +1754,14 @@ def G5modify(args: list[str]):
         raise OSError(f'"{args.file}" does not exist')
 
     with h5py.File(args.file, "r+") as file:
-
         if args.path not in file:
-
             shape = [len(args.values)]
             if args.shape:
                 shape = [int(i) for i in args.shape.split(",")]
             assert np.prod(shape) == len(args.values)
             file.create_dataset(args.path, shape=shape, dtype=args.dtype)
 
         else:
-
             assert len(args.values) == file[args.path].size
 
         file[args.path][:] = np.array(args.values).reshape(file[args.path].shape)

GooseHDF5/cli/G5check.py

@@ -42,15 +42,13 @@ def check_isfile(fname):
 
 
 def read(filename, check):
-
     with h5py.File(filename, "r") as source:
         paths = getdatapaths(source)
         if check:
             verify(source, paths, error=True)
 
 
 def main():
-
     try:
 
         class Parser(argparse.ArgumentParser):
@@ -67,11 +65,9 @@ def print_help(self):
         read(args.source, not args.basic)
 
     except Exception as e:
-
         print(e)
         return 1
 
 
 if __name__ == "__main__":
-
     main()

GooseHDF5/cli/G5repack.py

@@ -46,7 +46,6 @@ def check_isfile(fname):
 
 
 def main():
-
     try:
 
         class Parser(argparse.ArgumentParser):
@@ -63,7 +62,6 @@ def print_help(self):
         tempname = next(tempfile._get_candidate_names())
 
         for filename in args.source:
-
             print(filename)
 
             check_isfile(filename)
@@ -75,11 +73,9 @@ def print_help(self):
             os.replace(tempname, filename)
 
     except Exception as e:
-
         print(e)
         return 1
 
 
 if __name__ == "__main__":
-
     main()

GooseHDF5/cli/G5repair.py

@@ -47,7 +47,6 @@ def check_isfile(fname):
 
 
 def main():
-
     try:
 
         class Parser(argparse.ArgumentParser):
@@ -68,18 +67,15 @@ def print_help(self):
                 sys.exit(1)
 
         with h5py.File(args.source, "r") as source:
-
             paths = verify(source, getdatapaths(source))
 
             with h5py.File(args.destination, "w") as dest:
                 copy(source, dest, paths)
 
     except Exception as e:
-
         print(e)
         return 1
 
 
 if __name__ == "__main__":
-
     main()

docs/examples/copy_modify-selection.py

@@ -4,13 +4,11 @@
 import GooseHDF5 as g5
 
 with h5py.File("foo.h5", "w") as file:
-
     file["/a"] = np.arange(5)
     file["/b/c"] = np.arange(5)
     file["/d/e/f"] = np.arange(5)
 
 with h5py.File("foo.h5", "r") as file:
-
     paths = list(g5.getdatasets(file))
     paths.remove("/d/e/f")
 

tests/cli/G5compare.py

@@ -13,7 +13,6 @@ def run(cmd):
 
 with h5py.File("a.hdf5", "w") as source:
     with h5py.File("b.hdf5", "w") as other:
-
         # NumPy array
 
         a = np.random.random(25)

tests/test_cli.py

@@ -22,13 +22,11 @@ class MyTests(unittest.TestCase):
 
     @classmethod
     def setUpClass(self):
-
         if not os.path.isdir(dirname):
             os.makedirs(dirname)
 
     @classmethod
     def tearDownClass(self):
-
         shutil.rmtree(dirname)
 
     def test_G5list(self):
@@ -109,5 +107,4 @@ def test_G5modify_depth(self):
 
 
 if __name__ == "__main__":
-
     unittest.main()