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Merged
mfarragher merged 8 commits into from
Jun 25, 2025
Merged

np.nan fix #47

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f90d7d3
Merge pull request #29 from mfarragher/dev
mfarragher Jan 8, 2023
34c0dfe
Compatibility with current Numpy version
max-uho Aug 1, 2024
758da60
Update np.nan in test scripts
mfarragher Jun 25, 2025
ae3cd90
More recent Python versions for CI/CD
mfarragher Jun 25, 2025
cecdc93
typo
mfarragher Jun 25, 2025
cd9a902
3.12 for now
mfarragher Jun 25, 2025
700974f
Revert (not figured out config for 3.12+)
mfarragher Jun 25, 2025
ecfe77f
Revert properly (been a long night)
mfarragher Jun 25, 2025
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24 changes: 12 additions & 12 deletions obsidiantools/api.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -702,7 +702,7 @@ def __get_file_dicts_tuple(self, linked_files_list: list[str], *,
if short_path in set_files_existent_not_linked}
# nonexistent files:
nonexistent_files_by_short_path = {
short_path: np.NaN
short_path: np.nan
for short_path in shortest_names_nonexistent.keys()
if short_path in set_files_nonexistent_linked}

Expand Down Expand Up @@ -1161,28 +1161,28 @@ def get_note_metadata(self) -> pd.DataFrame:
def _create_note_metadata_columns(self,
df: pd.DataFrame) -> pd.DataFrame:
"""pipe func for mutating df"""
df['rel_filepath'] = [self._md_file_index.get(f, np.NaN)
df['rel_filepath'] = [self._md_file_index.get(f, np.nan)
for f in df.index.tolist()]
df['abs_filepath'] = np.where(df['rel_filepath'].notna(),
[self._dirpath / str(f)
for f in df['rel_filepath'].tolist()],
np.NaN)
np.nan)
df['note_exists'] = np.where(df['rel_filepath'].notna(),
True, False)
df['n_backlinks'] = [len(self.get_backlinks(f)) for f in df.index]
df['n_wikilinks'] = np.where(df['note_exists'],
[len(self._wikilinks_index.get(f, []))
for f in df.index.tolist()],
np.NaN)
np.nan)
df['n_tags'] = np.where(df['note_exists'],
[len(self._tags_index.get(f, []))
for f in df.index.tolist()],
np.NaN)
np.nan)
df['n_embedded_files'] = np.where(df['note_exists'],
[len(self._embedded_files_index.get(
f, []))
for f in df.index.tolist()],
np.NaN)
np.nan)
df['modified_time'] = pd.to_datetime(
[f.lstat().st_mtime if not pd.isna(f)
else pd.NaT
Expand All @@ -1197,7 +1197,7 @@ def _clean_up_note_metadata_dtypes(self,
df['rel_filepath'] = np.where(df['rel_filepath'].notna(),
[Path(str(f))
for f in df['rel_filepath']],
np.NaN)
np.nan)
df['n_wikilinks'] = df['n_wikilinks'].astype(float) # for consistency
return df

Expand Down Expand Up @@ -1237,12 +1237,12 @@ def get_media_file_metadata(self) -> pd.DataFrame:
def _create_media_file_metadata_columns(self,
df: pd.DataFrame) -> pd.DataFrame:
"""pipe func for mutating df"""
df['rel_filepath'] = [self._media_file_index.get(f, np.NaN)
df['rel_filepath'] = [self._media_file_index.get(f, np.nan)
for f in df.index.tolist()]
df['abs_filepath'] = np.where(df['rel_filepath'].notna(),
[self._dirpath / str(f)
for f in df['rel_filepath'].tolist()],
np.NaN)
np.nan)
df['file_exists'] = pd.Series(
np.logical_not(df.index.isin(self._nonexistent_media_files)),
index=df.index)
Expand Down Expand Up @@ -1291,20 +1291,20 @@ def get_canvas_file_metadata(self) -> pd.DataFrame:
def _create_canvas_file_metadata_columns(self,
df: pd.DataFrame) -> pd.DataFrame:
"""pipe func for mutating df"""
df['rel_filepath'] = [self._canvas_file_index.get(f, np.NaN)
df['rel_filepath'] = [self._canvas_file_index.get(f, np.nan)
for f in df.index.tolist()]
df['abs_filepath'] = np.where(df['rel_filepath'].notna(),
[self._dirpath / str(f)
for f in df['rel_filepath'].tolist()],
np.NaN)
np.nan)
df['file_exists'] = pd.Series(
np.logical_not(df.index.isin(self._nonexistent_canvas_files)),
index=df.index)
if self._attachments:
df['n_backlinks'] = (
self._get_backlink_counts_for_canvas_files_only())
else:
df['n_backlinks'] = np.NaN
df['n_backlinks'] = np.nan
df['modified_time'] = pd.to_datetime(
[f.lstat().st_mtime if not pd.isna(f)
else pd.NaT
Expand Down
102 changes: 51 additions & 51 deletions tests/test_api_vault_stub_connect_attachments_true.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,18 +28,18 @@ def expected_note_metadata_dict():
'Vulnera ubera': Path('lipsum/Vulnera ubera.md'),
'lipsum/Isolated note': Path('lipsum/Isolated note.md'),
'Causam mihi': Path('lipsum/Causam mihi.md'),
'American Psycho (film)': np.NaN,
'Tarpeia': np.NaN,
'Caelum': np.NaN,
'Vita': np.NaN,
'Aras Teucras': np.NaN,
'Manus': np.NaN,
'Bacchus': np.NaN,
'Amor': np.NaN,
'Virtus': np.NaN,
'Tydides': np.NaN,
'Dives': np.NaN,
'Aetna': np.NaN},
'American Psycho (film)': np.nan,
'Tarpeia': np.nan,
'Caelum': np.nan,
'Vita': np.nan,
'Aras Teucras': np.nan,
'Manus': np.nan,
'Bacchus': np.nan,
'Amor': np.nan,
'Virtus': np.nan,
'Tydides': np.nan,
'Dives': np.nan,
'Aetna': np.nan},
# abs_filepath would be here
'note_exists': {'Sussudio': True,
'Isolated note': True,
Expand Down Expand Up @@ -89,18 +89,18 @@ def expected_note_metadata_dict():
'Vulnera ubera': 3.0,
'lipsum/Isolated note': 0.0,
'Causam mihi': 4.0,
'American Psycho (film)': np.NaN,
'Tarpeia': np.NaN,
'Caelum': np.NaN,
'Vita': np.NaN,
'Aras Teucras': np.NaN,
'Manus': np.NaN,
'Bacchus': np.NaN,
'Amor': np.NaN,
'Virtus': np.NaN,
'Tydides': np.NaN,
'Dives': np.NaN,
'Aetna': np.NaN},
'American Psycho (film)': np.nan,
'Tarpeia': np.nan,
'Caelum': np.nan,
'Vita': np.nan,
'Aras Teucras': np.nan,
'Manus': np.nan,
'Bacchus': np.nan,
'Amor': np.nan,
'Virtus': np.nan,
'Tydides': np.nan,
'Dives': np.nan,
'Aetna': np.nan},
'n_tags': {'Sussudio': 5.0,
'Isolated note': 0.0,
'Brevissimus moenia': 0.0,
Expand All @@ -109,18 +109,18 @@ def expected_note_metadata_dict():
'Vulnera ubera': 0.0,
'lipsum/Isolated note': 0.0,
'Causam mihi': 0.0,
'American Psycho (film)': np.NaN,
'Tarpeia': np.NaN,
'Caelum': np.NaN,
'Vita': np.NaN,
'Aras Teucras': np.NaN,
'Manus': np.NaN,
'Bacchus': np.NaN,
'Amor': np.NaN,
'Virtus': np.NaN,
'Tydides': np.NaN,
'Dives': np.NaN,
'Aetna': np.NaN},
'American Psycho (film)': np.nan,
'Tarpeia': np.nan,
'Caelum': np.nan,
'Vita': np.nan,
'Aras Teucras': np.nan,
'Manus': np.nan,
'Bacchus': np.nan,
'Amor': np.nan,
'Virtus': np.nan,
'Tydides': np.nan,
'Dives': np.nan,
'Aetna': np.nan},
'n_embedded_files': {'Isolated note': 0.0,
'Sussudio': 2.0,
'Brevissimus moenia': 0.0,
Expand All @@ -129,26 +129,26 @@ def expected_note_metadata_dict():
'Vulnera ubera': 0.0,
'lipsum/Isolated note': 0.0,
'Causam mihi': 0.0,
'American Psycho (film)': np.NaN,
'Tarpeia': np.NaN,
'Caelum': np.NaN,
'Vita': np.NaN,
'Aras Teucras': np.NaN,
'Manus': np.NaN,
'Bacchus': np.NaN,
'Amor': np.NaN,
'Virtus': np.NaN,
'Tydides': np.NaN,
'Dives': np.NaN,
'Aetna': np.NaN}
'American Psycho (film)': np.nan,
'Tarpeia': np.nan,
'Caelum': np.nan,
'Vita': np.nan,
'Aras Teucras': np.nan,
'Manus': np.nan,
'Bacchus': np.nan,
'Amor': np.nan,
'Virtus': np.nan,
'Tydides': np.nan,
'Dives': np.nan,
'Aetna': np.nan}
}


@pytest.fixture
def expected_media_file_metadata_dict():
return {
'rel_filepath': {'1999.flac': np.NaN,
'Sussudio.mp3': np.NaN},
'rel_filepath': {'1999.flac': np.nan,
'Sussudio.mp3': np.nan},
# abs_filepath would be here
'file_exists': {'1999.flac': False,
'Sussudio.mp3': False},
Expand Down Expand Up @@ -288,7 +288,7 @@ def test_get_media_file_dicts_tuple(actual_connected_vault):
expected_tuple = (
{},
{},
{'Sussudio.mp3': np.NaN, '1999.flac': np.NaN})
{'Sussudio.mp3': np.nan, '1999.flac': np.nan})
assert actual_tuple == expected_tuple


Expand Down
96 changes: 48 additions & 48 deletions tests/test_api_vault_stub_connect_defaults_md.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,18 +24,18 @@ def expected_metadata_dict():
'Vulnera ubera': Path('lipsum/Vulnera ubera.md'),
'lipsum/Isolated note': Path('lipsum/Isolated note.md'),
'Causam mihi': Path('lipsum/Causam mihi.md'),
'American Psycho (film)': np.NaN,
'Tarpeia': np.NaN,
'Caelum': np.NaN,
'Vita': np.NaN,
'Aras Teucras': np.NaN,
'Manus': np.NaN,
'Bacchus': np.NaN,
'Amor': np.NaN,
'Virtus': np.NaN,
'Tydides': np.NaN,
'Dives': np.NaN,
'Aetna': np.NaN},
'American Psycho (film)': np.nan,
'Tarpeia': np.nan,
'Caelum': np.nan,
'Vita': np.nan,
'Aras Teucras': np.nan,
'Manus': np.nan,
'Bacchus': np.nan,
'Amor': np.nan,
'Virtus': np.nan,
'Tydides': np.nan,
'Dives': np.nan,
'Aetna': np.nan},
# abs_filepath would be here
'note_exists': {'Sussudio': True,
'Isolated note': True,
Expand Down Expand Up @@ -85,18 +85,18 @@ def expected_metadata_dict():
'Vulnera ubera': 3.0,
'lipsum/Isolated note': 0.0,
'Causam mihi': 4.0,
'American Psycho (film)': np.NaN,
'Tarpeia': np.NaN,
'Caelum': np.NaN,
'Vita': np.NaN,
'Aras Teucras': np.NaN,
'Manus': np.NaN,
'Bacchus': np.NaN,
'Amor': np.NaN,
'Virtus': np.NaN,
'Tydides': np.NaN,
'Dives': np.NaN,
'Aetna': np.NaN},
'American Psycho (film)': np.nan,
'Tarpeia': np.nan,
'Caelum': np.nan,
'Vita': np.nan,
'Aras Teucras': np.nan,
'Manus': np.nan,
'Bacchus': np.nan,
'Amor': np.nan,
'Virtus': np.nan,
'Tydides': np.nan,
'Dives': np.nan,
'Aetna': np.nan},
'n_tags': {'Sussudio': 5.0,
'Isolated note': 0.0,
'Brevissimus moenia': 0.0,
Expand All @@ -105,18 +105,18 @@ def expected_metadata_dict():
'Vulnera ubera': 0.0,
'lipsum/Isolated note': 0.0,
'Causam mihi': 0.0,
'American Psycho (film)': np.NaN,
'Tarpeia': np.NaN,
'Caelum': np.NaN,
'Vita': np.NaN,
'Aras Teucras': np.NaN,
'Manus': np.NaN,
'Bacchus': np.NaN,
'Amor': np.NaN,
'Virtus': np.NaN,
'Tydides': np.NaN,
'Dives': np.NaN,
'Aetna': np.NaN},
'American Psycho (film)': np.nan,
'Tarpeia': np.nan,
'Caelum': np.nan,
'Vita': np.nan,
'Aras Teucras': np.nan,
'Manus': np.nan,
'Bacchus': np.nan,
'Amor': np.nan,
'Virtus': np.nan,
'Tydides': np.nan,
'Dives': np.nan,
'Aetna': np.nan},
'n_embedded_files': {'Isolated note': 0.0,
'Sussudio': 2.0,
'Brevissimus moenia': 0.0,
Expand All @@ -125,18 +125,18 @@ def expected_metadata_dict():
'Vulnera ubera': 0.0,
'lipsum/Isolated note': 0.0,
'Causam mihi': 0.0,
'American Psycho (film)': np.NaN,
'Tarpeia': np.NaN,
'Caelum': np.NaN,
'Vita': np.NaN,
'Aras Teucras': np.NaN,
'Manus': np.NaN,
'Bacchus': np.NaN,
'Amor': np.NaN,
'Virtus': np.NaN,
'Tydides': np.NaN,
'Dives': np.NaN,
'Aetna': np.NaN}
'American Psycho (film)': np.nan,
'Tarpeia': np.nan,
'Caelum': np.nan,
'Vita': np.nan,
'Aras Teucras': np.nan,
'Manus': np.nan,
'Bacchus': np.nan,
'Amor': np.nan,
'Virtus': np.nan,
'Tydides': np.nan,
'Dives': np.nan,
'Aetna': np.nan}
}


Expand Down
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