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Convert deprecated ruamel.yaml function calls to method calls #152

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merged 2 commits into from
May 1, 2023
Merged

Convert deprecated ruamel.yaml function calls to method calls #152

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8f2f4bd
safe_load is deprecated
berquist Jun 12, 2022
7bb0992
remove remaining yaml.safe_dump and yaml.dump calls
berquist Mar 13, 2023
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7 changes: 2 additions & 5 deletions exdir/core/attribute.py
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Original file line number Diff line number Diff line change
Expand Up @@ -166,12 +166,9 @@ def _set_data(self, attrs):
attribute_data_quoted = attrs

with self.filename.open("w", encoding="utf-8") as attribute_file:
yaml.dump(
yaml.YAML(typ="rt", pure=True).dump(
attribute_data_quoted,
attribute_file,
default_flow_style=False,
allow_unicode=True,
Dumper=yaml.RoundTripDumper
)

# TODO only needs filename, make into free function
Expand All @@ -180,7 +177,7 @@ def _open_or_create(self):
attrs = {}
if self.filename.exists(): # NOTE str for Python 3.5 support
with self.filename.open("r", encoding="utf-8") as meta_file:
attrs = yaml.safe_load(meta_file)
attrs = yaml.YAML(typ="safe", pure=True).load(meta_file)
return attrs

def __iter__(self):
Expand Down
9 changes: 6 additions & 3 deletions exdir/core/exdir_object.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,10 @@ def _create_object_directory(directory, metadata):
version=1
)
else:
metadata_string = yaml.dump(metadata)
from io import StringIO
with StringIO() as buf:
yaml.YAML(typ="safe", pure=True).dump(metadata, buf)
metadata_string = buf.getvalue()

try:
meta_file.write(metadata_string)
Expand Down Expand Up @@ -103,7 +106,7 @@ def is_nonraw_object_directory(directory):
if not meta_filename.exists():
return False
with meta_filename.open("r", encoding="utf-8") as meta_file:
meta_data = yaml.safe_load(meta_file)
meta_data = yaml.YAML(typ="safe", pure=True).load(meta_file)

if not isinstance(meta_data, dict):
return False
Expand Down Expand Up @@ -140,7 +143,7 @@ def root_directory(path):

meta_filename = path / META_FILENAME
with meta_filename.open("r", encoding="utf-8") as meta_file:
meta_data = yaml.safe_load(meta_file)
meta_data = yaml.YAML(typ="safe", pure=True).load(meta_file)
if EXDIR_METANAME not in meta_data:
path = path.parent
continue
Expand Down
2 changes: 1 addition & 1 deletion exdir/core/group.py
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Original file line number Diff line number Diff line change
Expand Up @@ -402,7 +402,7 @@ def __getitem__(self, name):

meta_filename = directory / exob.META_FILENAME
with meta_filename.open("r", encoding="utf-8") as meta_file:
meta_data = yaml.safe_load(meta_file)
meta_data = yaml.YAML(typ="safe", pure=True).load(meta_file)
if meta_data[exob.EXDIR_METANAME][exob.TYPE_METANAME] == exob.DATASET_TYPENAME:
return self._dataset(name)
elif meta_data[exob.EXDIR_METANAME][exob.TYPE_METANAME] == exob.GROUP_TYPENAME:
Expand Down
23 changes: 10 additions & 13 deletions tests/test_help_functions.py
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Expand Up @@ -114,7 +114,7 @@ def test_create_object_directory(setup_teardown_folder):
}

with file_path.open("r", encoding="utf-8") as meta_file:
metadata = yaml.safe_load(meta_file)
metadata = yaml.YAML(typ="safe", pure=True).load(meta_file)

assert metadata == compare_metadata

Expand All @@ -141,10 +141,9 @@ def test_is_nonraw_object_directory(setup_teardown_folder):
exob.EXDIR_METANAME: {
exob.VERSION_METANAME: 1}
}
yaml.safe_dump(metadata,
meta_file,
default_flow_style=False,
allow_unicode=True)
yaml.YAML(typ="safe", pure=True).dump(
metadata,
meta_file)

result = exob.is_nonraw_object_directory(setup_teardown_folder[2])
assert result is False
Expand All @@ -156,10 +155,9 @@ def test_is_nonraw_object_directory(setup_teardown_folder):
exob.TYPE_METANAME: "wrong_typename",
exob.VERSION_METANAME: 1}
}
yaml.safe_dump(metadata,
meta_file,
default_flow_style=False,
allow_unicode=True)
yaml.YAML(typ="safe", pure=True).dump(
metadata,
meta_file)

result = exob.is_nonraw_object_directory(setup_teardown_folder[2])
assert result is False
Expand All @@ -171,10 +169,9 @@ def test_is_nonraw_object_directory(setup_teardown_folder):
exob.TYPE_METANAME: exob.DATASET_TYPENAME,
exob.VERSION_METANAME: 1}
}
yaml.safe_dump(metadata,
meta_file,
default_flow_style=False,
allow_unicode=True)
yaml.YAML(typ="safe", pure=True).dump(
metadata,
meta_file)

result = exob.is_nonraw_object_directory(setup_teardown_folder[2])
assert result is True
Expand Down
2 changes: 1 addition & 1 deletion tests/test_object.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ def test_object_attrs(setup_teardown_file):
obj.attrs = "test value"

with (setup_teardown_file[1] / "test_object" / ATTRIBUTES_FILENAME).open("r", encoding="utf-8") as meta_file:
meta_data = yaml.safe_load(meta_file)
meta_data = yaml.YAML(typ="safe", pure=True).load(meta_file)
assert meta_data == "test value"


Expand Down