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typo fixes #530
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WalkthroughAdds Claude patterns to .gitignore; corrects Patch.mod to use elementwise modulo; makes BaseSpool.eq return False for unequal nested dicts; revises PatchAttrs deprecation wording; renames Changes
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## master #530 +/- ##
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Files 122 122
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⚠️ Outside diff range comments (2)
dascore/io/segy/utils.py (1)
165-169: Format string bug: {non_time} placeholder is not interpolated.
msgis composed of plain string literals;{non_time}will appear verbatim. Use an f-string to include the actual dimension name.- msg = ( - "Currently the segy writer only handles 'channel' as the non-time " - "dimension this results in a loss of the '{non_time}' dimension." - ) + msg = ( + f"Currently the segy writer only handles 'channel' as the non-time " + f"dimension; this results in a loss of the '{non_time}' dimension." + )dascore/proc/basic.py (1)
713-716: Bug: roll always operates on axis 0, ignoring selected dimension.
np.rollshould use the resolvedaxisfor the chosendim. As-is, rolling a non-leading dimension produces incorrect results.- roll_arr = np.roll(arr, value, axis=0) + roll_arr = np.roll(arr, value, axis=axis)
🧹 Nitpick comments (20)
dascore/io/segy/utils.py (1)
241-241: Typo: variable name ‘chanel_step’.Minor spelling nit; consider renaming to
channel_stepfor clarity, and update its single usage in the header dict.- chanel_step = channel.step + channel_step = channel.stepAnd below:
- segyio.su.offset: chanel_step, + segyio.su.offset: channel_step,tests/test_utils/test_hdf_utils.py (2)
34-36: Nit: class name typo.Consider renaming
TestGetHDF5Handlder→TestGetHDF5Handler.-class TestGetHDF5Handlder: +class TestGetHDF5Handler:
216-218: Nit: docstring typo.“attibute” → “attribute”.
- """A bad attibute should raise a KeyError.""" + """A bad attribute should raise a KeyError."""tests/test_io/test_dasdae/test_dasdae.py (2)
134-135: Nit: fix typos in docstring.“emtpy” → “empty”; “deserialize” → “be deserialized”.
- """Ensure an emtpy patch can be deserialize.""" + """Ensure an empty patch can be deserialized."""
127-128: Nit: path fragment spelling.Consistent naming helps grep: “dasedae_round_trip” → “dasdae_round_trip”.
- path = tmp_path_factory.mktemp("dasedae_round_trip") / "rt.h5" + path = tmp_path_factory.mktemp("dasdae_round_trip") / "rt.h5"dascore/transform/integrate.py (1)
102-104: Nit: parameter name consistency.“define” should be “definite”.
- If define is False, the shape of the patch is preserved and a + If definite is False, the shape of the patch is preserved and adascore/transform/differentiate.py (2)
110-118: Improve math text clarity (optional).You can keep LaTeX, but clean up spelling/grammar below to reduce friction for readers.
- The second order first derivative, for an evenly spaced coordinate, + The second-order first derivative, for an evenly spaced coordinate, @@ - Where $\hat{f}(x)$ is the estiamted derivative of $f$ at $x$, $dx$ is + Where $\hat{f}(x)$ is the estimated derivative of $f$ at $x$, $dx$ is
80-99: Sweep remaining typos in differentiate docstring.Several misspellings remain (“centeral”, “diferences”, “accuarcy”, “possitive”, “integar”, “differention”). Suggested cleanup:
- Calculate first derivative along dimension(s) using centeral diferences. + Calculate the first derivative along dimension(s) using central differences. @@ - along edges are calculated with the same order (accuarcy) as centeral + Along edges, derivatives are calculated with the same order (accuracy) as central @@ - The order of the differentiation operator. Must be a possitive, even - integar. + The order of the differentiation operator. Must be a positive, even + integer. @@ - The number of columns/rows to skip for differention. + The number of columns/rows to skip for differentiation.dascore/transform/fourier.py (2)
132-137: Nit: minor typo fixes in params.“dimenson” → “dimension”; “peforming” → “performing”.
- True, which means the last (possibly only) dimenson should have an + True, which means the last (possibly only) dimension should have an @@ - If True, pad patch before peforming dft along desired dimensions to + If True, pad patch before performing dft along desired dimensions to
287-289: Nit: broken link formatting.Use backticks consistently in the docstring reference.
- (e.g., with [select]('dascore.proc.basic.select`) otherwise idft won't + (e.g., with [select](`dascore.proc.basic.select`) otherwise idft won'tdascore/proc/basic.py (1)
609-612: Nit: typo in pad docs.“pading” → “padding”.
- the frequency domain by pading to the next fast fft length after + the frequency domain by padding to the next fast fft length afterdascore/proc/units.py (1)
7-9: Rename alias u_covert_units → u_convert_units for clarity.Minor readability nit; prevents confusing “covert” vs “convert.”
-from dascore.units import convert_units as u_covert_units +from dascore.units import convert_units as u_convert_units @@ - data = u_covert_units(patch.data, data_units, current_units) + data = u_convert_units(patch.data, data_units, current_units)Also applies to: 88-92
dascore/utils/hdf5.py (2)
177-183: Fix spelling: _column_decorders → _column_decoders (and its use).Purely cosmetic but improves code searchability.
- _column_decorders = FrozenDict( + _column_decoders = FrozenDict( @@ - for col, func in self._column_decorders.items(): + for col, func in self._column_decoders.items():Also applies to: 242-244
321-324: Remove redundant store.close() around context manager.The with-statement already closes the store; the extra closes are unnecessary.
- try: - with _HDF5Store(self.path, "r") as store: - out = store.get(self._meta_node) - store.close() + try: + with _HDF5Store(self.path, "r") as store: + out = store.get(self._meta_node) return out except (FileNotFoundError, ValueError, KeyError, OSError): - with suppress(UnboundLocalError): - store.close() self._ensure_meta_table_exists() return pd.read_hdf(self.path, self._meta_node)Also applies to: 326-329
dascore/proc/coords.py (6)
249-257: Fix drop_coords docstring: it describes update, not drop.Align text with behavior.
- Update the coordinates of a patch. + Drop one or more non-dimensional coordinates from a patch.
305-317: Fix make_broadcastable_to docstring: wrong summary.Reflects broadcasting intent.
- Update the coordinates of a patch. + Make the patch broadcastable to the given shape by adding/expanding + non-coordinate dimensions or, if allowed, dropping/updating coords.
373-375: Typo: “uess” → “uses”.- * This function uess linear extrapolation between the nearest two points + * This function uses linear extrapolation between the nearest two points
475-476: Typo in example keyword.“distace” → “distance”.
- >>> new_distance_3 = patch.select(distace=distance[1::2]) + >>> new_distance_3 = patch.select(distance=distance[1::2])
561-563: Typo: “diemsnions” → “dimensions”.- Can also include ... to indicate diemsnions that should be left + Can also include ... to indicate dimensions that should be left
721-726: Grammar: “All coordinate” → “All coordinates”.- "All coordinate must be associated with the same dimension to " + "All coordinates must be associated with the same dimension to "
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📒 Files selected for processing (14)
.gitignore(1 hunks)dascore/core/attrs.py(1 hunks)dascore/core/patch.py(2 hunks)dascore/core/spool.py(1 hunks)dascore/io/segy/utils.py(1 hunks)dascore/proc/basic.py(1 hunks)dascore/proc/coords.py(4 hunks)dascore/proc/units.py(1 hunks)dascore/transform/differentiate.py(2 hunks)dascore/transform/fourier.py(1 hunks)dascore/transform/integrate.py(1 hunks)dascore/utils/hdf5.py(1 hunks)tests/test_io/test_dasdae/test_dasdae.py(1 hunks)tests/test_utils/test_hdf_utils.py(1 hunks)
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dascore/core/patch.py (1)
dascore/proc/basic.py (1)
apply_ufunc(365-485)
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🔇 Additional comments (15)
dascore/io/segy/utils.py (1)
35-37: Docstring typo fix looks good..gitignore (1)
95-97: Claude ignores added — LGTM.These patterns are fine. If the
.claudedirectory may contain nested content, the single entry already ignores all within. No action needed.tests/test_utils/test_hdf_utils.py (1)
120-121: Docstring typo fix confirmed.“written” spelling correction is correct.
tests/test_io/test_dasdae/test_dasdae.py (1)
117-120: Docstring typo fix confirmed.dascore/transform/integrate.py (1)
100-101: Docstring wording fix — good.dascore/transform/differentiate.py (1)
100-102: Example wording tweak is fine.dascore/transform/fourier.py (1)
153-155: Docstring typo fix — good.dascore/proc/basic.py (1)
561-565: Docstring example spelling fixes — good.dascore/proc/units.py (1)
67-71: Docstring typo fix looks good."Perform" is correct; no behavioral change.
dascore/utils/hdf5.py (1)
392-401: Docstring typo fix confirmed.“written” spelling is correct.
dascore/proc/coords.py (1)
220-241: Docstring correction looks good.“Update the coordinates of a patch.” reads correctly now.
dascore/core/attrs.py (1)
167-169: Deprecation message typo fix looks good.“deprecated” is correct; behavior unchanged.
dascore/core/spool.py (1)
95-97: Fix ensures boolean False on nested dict inequality.Prevents None bubbling; equality now reliably returns bool.
dascore/core/patch.py (2)
52-53: Docstring formatting tweak looks good.Properly references PatchAttrs.
127-129: % operator now uses numpy.mod as expected.Correct semantic for elementwise modulo; consistent with other operators via apply_ufunc.
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Actionable comments posted: 1
🧹 Nitpick comments (4)
dascore/proc/rolling.py (1)
212-212: Docstring token mismatch prevents compose_docstring substitutionDecorator uses
sample_explanation, but the docstring placeholder is{sample_explination}. The token won’t be replaced.Apply this diff to align the placeholder:
-@compose_docstring(sample_explanation=samples_arg_description) +@compose_docstring(sample_explanation=samples_arg_description) @@ - {sample_explination} + {sample_explanation}Also applies to: 246-246
scripts/_render_api.py (3)
69-75: More tiny typo/grammar fixes aligned with PR intent.Low-risk copy edits to comments/docstrings.
def is_it_subclass(obj, cls): - """A more intelligent issubclass that doesn't through TypeErrors.""" + """A safer issubclass wrapper that returns False instead of raising TypeError.""" @@ def _deduplicate_list(seq): - """Return a list with duplicate removed, preserves order.""" + """Return a list with duplicates removed; preserves order.""" @@ - # parameters dont have spaces at the start + # parameters don't have spaces at the start @@ def to_quarto_code(code_lines): - """Class for parsing code (eg examples in docstrings) to quarto output.""" + """Function for parsing code (e.g., examples in docstrings) to Quarto output.""" @@ - Example blocks can be written in standard doc-test or quarto styles. + Example blocks can be written in standard doctest or Quarto styles. @@ - def _get_github_source(self, data): - """Get the github source url.""" + def _get_github_source(self, data): + """Get the GitHub source URL.""" @@ - # grab repo stuff from environment (on GH actions) or defaults + # Grab repo info from environment (on GitHub Actions) or defaults @@ def render_markdown(self, heading="##"): - """Convert numpy docstrings to markdown with some html styling.""" + """Convert NumPy docstrings to Markdown with some HTML styling.""" @@ def sha_256(path_or_str: Path | str) -> str: - """Get the Sha256 hash of a file or a string.""" + """Get the SHA-256 hash of a file or a string.""" @@ - # dont render non-target file if debugging + # don't render non-target file if debuggingAlso applies to: 77-81, 246-250, 315-317, 271-273, 441-444, 447-451, 496-499, 51-53, 551-552
523-527: Fix path joins (duplicate api_path) and normalize URLs for cross-platform builds.Avoid composing Paths with embedded “/” strings and ensure forward slashes in emitted URLs.
@@ - for obj_id, data in data_dict.items(): - sub_dir = api_path / "/".join(data["key"].split(".")[:-1]) - path = api_path / sub_dir / f"{data['name']}.qmd" - out[data["key"]] = f"/{path.relative_to(DOC_PATH)}" + for obj_id, data in data_dict.items(): + sub_dir = Path(*data["key"].split(".")[:-1]) + path = api_path / sub_dir / f"{data['name']}.qmd" + out[data["key"]] = "/" + path.relative_to(DOC_PATH).as_posix() @@ - sub_dir = api_path / "/".join(data["key"].split(".")[:-1]) - path = api_path / sub_dir / f"{data['name']}.qmd" + sub_dir = Path(*data["key"].split(".")[:-1]) + path = api_path / sub_dir / f"{data['name']}.qmd" @@ - api_relative = str(api_path.relative_to(doc_path)) - for path in DOC_PATH.rglob("*.qmd"): - path_relative = str(path.relative_to(parent_doc)) + api_relative = api_path.relative_to(doc_path).as_posix() + for path in doc_path.rglob("*.qmd"): + path_relative = path.relative_to(parent_doc).as_posix() @@ - value = "/" + str(path.relative_to(doc_path)) + value = "/" + path.relative_to(doc_path).as_posix()Also applies to: 543-545, 590-598, 597-601
83-141: Correct typo: renameunpact_annotationtounpack_annotationand add alias
- Update the function definition and all its calls in scripts/_render_api.py (lines 83, 105–106, 110–111, 114, 151–152, 188–189)
- Append
unpact_annotation = unpack_annotationat the end for backward compatibility
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dascore/core/coords.py(1 hunks)dascore/examples.py(2 hunks)dascore/io/febus/utils.py(1 hunks)dascore/io/segy/utils.py(4 hunks)dascore/io/tdms/utils.py(1 hunks)dascore/proc/basic.py(2 hunks)dascore/proc/correlate.py(1 hunks)dascore/proc/filter.py(5 hunks)dascore/proc/rolling.py(1 hunks)dascore/transform/fourier.py(2 hunks)dascore/viz/map_fiber.py(1 hunks)dascore/viz/waterfall.py(1 hunks)docs/notes/doc_strategy.qmd(1 hunks)docs/tutorial/coords.qmd(2 hunks)scripts/_render_api.py(1 hunks)tests/test_core/test_coordmanager.py(1 hunks)tests/test_proc/test_detrend.py(1 hunks)tests/test_utils/test_chunk.py(1 hunks)tests/test_utils/test_misc.py(1 hunks)
✅ Files skipped from review due to trivial changes (15)
- dascore/examples.py
- dascore/io/tdms/utils.py
- tests/test_core/test_coordmanager.py
- tests/test_proc/test_detrend.py
- tests/test_utils/test_misc.py
- dascore/core/coords.py
- docs/notes/doc_strategy.qmd
- tests/test_utils/test_chunk.py
- dascore/viz/waterfall.py
- dascore/io/febus/utils.py
- dascore/viz/map_fiber.py
- dascore/proc/correlate.py
- docs/tutorial/coords.qmd
- dascore/proc/filter.py
- dascore/transform/fourier.py
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- dascore/io/segy/utils.py
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dascore/proc/rolling.py (1)
dascore/utils/docs.py (1)
compose_docstring(45-97)
dascore/proc/basic.py (1)
dascore/core/coords.py (2)
values(942-946)values(1201-1216)
🔇 Additional comments (3)
dascore/proc/basic.py (2)
561-565: LGTM: typo fixes in examples“occurrences” corrections read well; no functional impact.
713-713: LGTM: roll data along the correct dimension axisUsing
axis=axisfor the data roll matches the targeted dim derived above.scripts/_render_api.py (1)
560-560: LGTM: typo fixed in comment.The “written” correction is good and keeps the comment clear.
dascore/proc/basic.py
Outdated
| roll_coord_arr = np.roll(coord.values, value, axis=axis) | ||
| new_coord = coord.update(values=roll_coord_arr) | ||
| patch = patch.update_coords(**{dim: new_coord}) |
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🧩 Analysis chain
Fix coord rolling: wrong axis and wrong kwarg to coord.update
coord.valuesis 1D; usingaxis=axiscan raise or roll along a non-existent axis. Roll the 1D array (axis 0) or omit axis.coord.updateelsewhere takesdata=...(see pad at Line 659), notvalues=.
Apply this diff:
- roll_coord_arr = np.roll(coord.values, value, axis=axis)
- new_coord = coord.update(values=roll_coord_arr)
+ roll_coord_arr = np.roll(coord.values, value)
+ new_coord = coord.update(data=roll_coord_arr)
patch = patch.update_coords(**{dim: new_coord})Run to confirm no other call sites use the unsupported values= kwarg and to spot any remaining axis misuse:
🏁 Script executed:
#!/bin/bash
# Find coord.update calls using `values=`
rg -nP '\.update\s*\(\s*values\s*=' -g '!**/dist/**' -S
# Cross-check compose_docstring placeholders for "explination" typos
rg -n 'sample_explination' -S
# Sanity: show other coord.update data-arg usage for reference
rg -nP '\.update\s*\(\s*data\s*=' -SLength of output: 2915
🏁 Script executed:
#!/bin/bash
# Search for any coord.update calls using the unsupported `values=` kwarg
rg -nP '\.update\s*\(\s*values\s*=' -S
# Display context around the existing roll snippet to verify `axis` usage
sed -n '700,740p' dascore/proc/basic.pyLength of output: 1006
Fix coordinate rolling and update kwarg in dascore/proc/basic.py
Change lines 717–719 as follows:
- roll_coord_arr = np.roll(coord.values, value, axis=axis)
- new_coord = coord.update(values=roll_coord_arr)
+ roll_coord_arr = np.roll(coord.values, value)
+ new_coord = coord.update(data=roll_coord_arr)No other .update(values=…) calls remain.
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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| roll_coord_arr = np.roll(coord.values, value, axis=axis) | |
| new_coord = coord.update(values=roll_coord_arr) | |
| patch = patch.update_coords(**{dim: new_coord}) | |
| roll_coord_arr = np.roll(coord.values, value) | |
| new_coord = coord.update(data=roll_coord_arr) | |
| patch = patch.update_coords(**{dim: new_coord}) |
🤖 Prompt for AI Agents
In dascore/proc/basic.py around lines 717-719, change the coordinate update to
use the correct update kwarg: replace coord.update(values=roll_coord_arr) with
coord.update(value=roll_coord_arr) and keep patch = patch.update_coords(**{dim:
new_coord}); ensure you only change the .update call to use "value" (not
"values") so no .update(values=...) calls remain in the file.
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Actionable comments posted: 0
🧹 Nitpick comments (1)
dascore/core/attrs.py (1)
165-169: Nit: quote attribute names and tighten punctuation in the warning.
Improves readability in logs.- msg = f"{item} is deprecated, use {first}_{second} instead." + msg = f"'{item}' is deprecated; use '{first}_{second}' instead."
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🔇 Additional comments (1)
dascore/core/attrs.py (1)
167-167: LGTM: fixed “depreciated” → “deprecated”.
Accurate wording in the warning message.
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Actionable comments posted: 0
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⚠️ Outside diff range comments (1)
dascore/proc/basic.py (1)
301-303: Max-norm should use absolute values (per docstring).Docstring says “maximum of the absolute value,” but code uses raw max.
- norm_values = np.max(data, axis=axis) + norm_values = np.max(np.abs(data), axis=axis)
♻️ Duplicate comments (1)
dascore/proc/basic.py (1)
717-719: Bug: coord.update uses unsupported kwarg; use data= not values=.Current call likely errors or is ignored; other sites (e.g., pad) use data=. Apply:
- roll_coord_arr = np.roll(coord.values, value) - new_coord = coord.update(values=roll_coord_arr) + roll_coord_arr = np.roll(coord.values, value) + new_coord = coord.update(data=roll_coord_arr)Run to ensure no remaining
.update(values=...):#!/bin/bash rg -nP '\.update\s*\(\s*values\s*=' -S
🧹 Nitpick comments (1)
dascore/proc/basic.py (1)
608-611: Typo: “pading” → “padding”.Minor docstring cleanup.
- "correlate" - prepare the coordinate for correlation/convolution in - the frequency domain by pading to the next fast fft length after + "correlate" - prepare the coordinate for correlation/convolution in + the frequency domain by padding to the next fast fft length after
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🔇 Additional comments (2)
dascore/proc/basic.py (2)
561-564: Docstring typo fixes look good in fillna examples.Both “occurrences” lines read correctly now.
713-713: Correct axis used for data roll.Using axis derived from the requested dim fixes prior axis=0 assumption.
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Description
This PR fixes a bunch of typos.
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Bug Fixes
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