diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..03bbf03
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,2 @@
+tests/data/icesat-2-ATL06/ATL06_20230816161508_08782002_006_02.h5 filter=lfs diff=lfs merge=lfs -text
+tests/data/icesat-2-ATL06/ATL06_20230816234629_08822013_006_01.h5 filter=lfs diff=lfs merge=lfs -text
diff --git a/.github/workflows/reusable_run_tests.yml b/.github/workflows/reusable_run_tests.yml
index e970e9b..96037d0 100644
--- a/.github/workflows/reusable_run_tests.yml
+++ b/.github/workflows/reusable_run_tests.yml
@@ -22,6 +22,8 @@ jobs:
name: Python ${{ matrix.python-version }} tests
steps:
- uses: actions/checkout@v4
+ with:
+ lfs: 'true'
- name: Set up Python
uses: actions/setup-python@v5
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0486047..1a97089 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed
- Code readability and CPU branching improvements [Time/Location stamp: Ursynow, Warsaw at 15:23 21/12/2024 UTC] ([#264](https://github.com/nasa/ncompare/pull/264)) ([**@kokroo**](https://github.com/kokroo))
+### Added
+- Enable comparison of HDF files ([#281](https://github.com/nasa/ncompare/pull/281)) ([**@danielfromearth**](https://github.com/danielfromearth))
+
## [1.12.0] - 2024-12-20
### Changed
diff --git a/README.md b/README.md
index 3233110..f5a6b17 100644
--- a/README.md
+++ b/README.md
@@ -32,8 +32,13 @@ _____
-Compare the structure of two NetCDF files at the command line or via Python.
-`ncompare` generates a view of the matching and non-matching groups and variables between two NetCDF datasets.
+Compare the structure of two [netCDF](https://www.unidata.ucar.edu/software/netcdf) files
+at the command line or via Python. `ncompare` generates a view of the matching and
+non-matching groups and variables between two netCDF datasets.
+
+Allthough tailored for netCDF files, `ncompare`
+also works with some [HDF5](https://www.hdfgroup.org/solutions/hdf5/) files
+(see [notes and known limitations](#notes-and-known-limitations)).
## Installing
@@ -75,13 +80,8 @@ ncompare S001G01.nc S001G01_SUBSET.nc --file-text subset_comparison.txt
```python
from ncompare import compare
-total_number_of_differences = compare(
- "",
- "",
- only_diffs=True,
- show_attributes=True,
- show_chunks=True,
-)
+total_number_of_differences = compare("", "", only_diffs=True,
+ show_chunks=True, show_attributes=True)
```
@@ -139,7 +139,7 @@ poetry run ncompare
## Why ncompare?
The `cdo` (climate data operators) tool
-[does not support NetCDF4 groups](https://code.mpimet.mpg.de/boards/2/topics/12073).
+[does not support netCDF4 groups](https://code.mpimet.mpg.de/boards/2/topics/12073).
Moreover, `nco` operators' `ncdiff` function computes value differences, but
--- as far as the developers of this tool are aware ---
`nco` does not have a simple function to show structural differences between NetCDF4 datasets.
@@ -150,8 +150,11 @@ and can generate report files formatted for other applications. However, note th
`h5diff` provides comparison of some otherwise "hidden" hdf5 properties, such as _Netcdf4Dimid or _Netcdf4Coordinates,
which are not currently assessed by `ncompare`.
-## Known limitations
+## Notes and known limitations
+- `ncompare` works successfully with select HDF5 files,
+ although it has not been tested extensively; therefore,
+ it would not be surprising to find additional limitations with other HDF files.
- `ncompare` uses `xarray` to access the root-level dimensions.
In some cases, `xarray` will miss dimensions whose names do not also exist as variable names in the dataset
(also known as non-coordinate dimensions).
diff --git a/docs/example/ncompare-example-usage.ipynb b/docs/example/ncompare-example-usage.ipynb
index 689cf5b..e5e4954 100644
--- a/docs/example/ncompare-example-usage.ipynb
+++ b/docs/example/ncompare-example-usage.ipynb
@@ -40,7 +40,7 @@
"id": "6a145933-e57b-4e33-bed1-95b13800878d",
"metadata": {},
"source": [
- "***✍️ Syntax Note:*** Commands preceeded by an exclamation point \"!\" \n",
+ "***✍️ Syntax Note:*** Commands are preceded by an exclamation point \"!\"\n",
"(which is needed to [run shell commands in a Jupyter notebook](https://stackoverflow.com/a/48529220)) can be run from a terminal. \n",
"In a shell/terminal, the exclamation point should not be used."
]
@@ -785,8 +785,8 @@
" file_names[0],\n",
" file_names[2],\n",
" only_diffs=True,\n",
- " show_attributes=True,\n",
" show_chunks=True,\n",
+ " show_attributes=True,\n",
" column_widths=[33, 30, 30],\n",
")"
]
diff --git a/ncompare/Comparison.py b/ncompare/Comparison.py
new file mode 100644
index 0000000..aed32a9
--- /dev/null
+++ b/ncompare/Comparison.py
@@ -0,0 +1,481 @@
+from collections.abc import Iterator
+from typing import Union
+
+import h5py
+import netCDF4
+import numpy as np
+from colorama import Fore
+
+from ncompare.getters import (
+ get_and_check_variable_attributes,
+ get_and_check_variable_scale_factor,
+ get_root_dims,
+ get_root_groups,
+ get_subgroups,
+ get_variables,
+)
+from ncompare.printing import Outputter
+from ncompare.sequence_operations import common_elements, count_diffs
+from ncompare.utility_types import (
+ FileToCompare,
+ GroupPair,
+ SummaryDifferenceKeys,
+ SummaryDifferencesDict,
+ VarProperties,
+)
+
+
+class Comparison:
+ def __init__(
+ self,
+ file1: FileToCompare,
+ file2: FileToCompare,
+ out: Outputter,
+ show_chunks: bool,
+ show_attributes: bool,
+ ):
+ assert file1.type == file2.type
+ self.file1 = file1
+ self.file2 = file2
+ self.file_types = file1.type
+ self.out: Outputter = out
+ self.show_chunks: bool = show_chunks
+ self.show_attributes: bool = show_attributes
+
+ blank_difference_dict: SummaryDifferencesDict = {
+ "shared": 0,
+ "left": 0,
+ "right": 0,
+ "both": 0,
+ "difference_types": set(),
+ }
+ self.num_group_diffs: SummaryDifferencesDict = blank_difference_dict.copy()
+ self.num_var_diffs: SummaryDifferencesDict = blank_difference_dict.copy()
+ self.num_attribute_diffs: SummaryDifferencesDict = blank_difference_dict.copy()
+
+ self.open_file1 = None
+ self.open_file2 = None
+
+ def run_through_comparisons(self) -> int:
+ """Execute a series of comparisons between two netCDF or HDF files.
+
+ Returns
+ -------
+ int
+ total number of differences found (across variables, groups, and attributes)
+ """
+ self._print_root_dimensions()
+ self._print_root_groups()
+
+ # Run through all the rest of the groups and variables, tallying differences along the way.
+ self.out.print(Fore.LIGHTBLUE_EX + "\nAll variables:", add_to_history=True)
+ self.out.side_by_side(" ", "File A", "File B", force_display_even_if_same=True)
+
+ self._traverse_hierarchy()
+ self._print_summary()
+
+ # Return the total number of differences; zero indicates no differences were found.
+ total_diff_count = sum(
+ [
+ x["left"] + x["right"]
+ for x in [self.num_var_diffs, self.num_group_diffs, self.num_attribute_diffs]
+ ]
+ )
+
+ return total_diff_count
+
+ def _traverse_hierarchy(self):
+ self.out.side_by_side(
+ "All Variables", " ", " ", dash_line=False, force_display_even_if_same=True
+ )
+ self.out.side_by_side("-", "-", "-", dash_line=True, force_display_even_if_same=True)
+
+ # Determine how the files will be opened.
+ file_opener = netCDF4.Dataset if self.file_types == "netcdf" else h5py.File
+
+ # Open and go through files.
+ with (
+ file_opener(self.file1.path, mode="r") as ds_a,
+ file_opener(self.file2.path, mode="r") as ds_b,
+ ):
+ self.open_file1 = ds_a
+ self.open_file2 = ds_b
+
+ # Start with the Root Group, printing all the variables from it.
+ group_counter = 0
+ self._print_group_details_side_by_side(
+ ds_a,
+ "/",
+ ds_b,
+ "/",
+ group_counter,
+ )
+ group_counter += 1
+
+ for group_pair in self._dataset_pair_iterator(
+ "",
+ ds_a,
+ get_subgroups(ds_a, self.file_types),
+ "",
+ ds_b,
+ get_subgroups(ds_b, self.file_types),
+ ):
+ if group_pair.group_a_name == "":
+ self.num_group_diffs["right"] += 1
+ elif group_pair.group_b_name == "":
+ self.num_group_diffs["left"] += 1
+ else:
+ self.num_group_diffs["shared"] += 1
+
+ self._print_group_details_side_by_side(
+ group_pair.group_a,
+ group_pair.group_a_name,
+ group_pair.group_b,
+ group_pair.group_b_name,
+ group_counter,
+ )
+ group_counter += 1
+
+ def _print_group_details_side_by_side(
+ self,
+ group_a: Union[netCDF4.Dataset, netCDF4.Group, h5py.Group],
+ group_a_name: str,
+ group_b: Union[netCDF4.Dataset, netCDF4.Group, h5py.Group],
+ group_b_name: str,
+ group_counter: int,
+ ) -> None:
+ """Align and display group details side by side."""
+ self.out.side_by_side(
+ " ", " ", " ", dash_line=False, highlight_diff=False, force_display_even_if_same=True
+ )
+ self.out.side_by_side(
+ f"GROUP #{group_counter:02}",
+ group_a_name.strip(),
+ group_b_name.strip(),
+ dash_line=True,
+ highlight_diff=False,
+ force_display_even_if_same=True,
+ )
+
+ # Count the number of variables in this group as long as this group exists.
+ vars_a_sorted: Union[list, str] = ""
+ vars_b_sorted: Union[list, str] = ""
+ if group_a:
+ vars_a_sorted = get_variables(group_a, self.file_types)
+ if group_b:
+ vars_b_sorted = get_variables(group_b, self.file_types)
+ self.out.side_by_side(
+ "num variables in group:",
+ len(vars_a_sorted),
+ len(vars_b_sorted),
+ highlight_diff=True,
+ force_display_even_if_same=True,
+ )
+ self.out.side_by_side("-", "-", "-", dash_line=True, force_display_even_if_same=True)
+
+ # Count differences between the lists of variables in this group.
+ left, right, shared = count_diffs(vars_a_sorted, vars_b_sorted)
+ self.num_var_diffs["left"] += left
+ self.num_var_diffs["right"] += right
+ self.num_var_diffs["shared"] += shared
+
+ # Go through each variable in the current group.
+ for variable_pair in common_elements(vars_a_sorted, vars_b_sorted):
+ # Get and print the properties of each variable
+ self._print_var_properties_side_by_side(
+ self._create_var_properties(
+ group_a, variable_pair[1], original_dataset=self.open_file1
+ ),
+ self._create_var_properties(
+ group_b, variable_pair[2], original_dataset=self.open_file1
+ ),
+ )
+
+ def _print_var_properties_side_by_side(
+ self,
+ v_a: VarProperties,
+ v_b: VarProperties,
+ ) -> None:
+ """Align and display variable properties side by side."""
+ # Gather all variable property pairs first, before printing,
+ # so we can decide whether to highlight the variable header.
+ pairs_to_check_and_show = [
+ (v_a.dtype, v_b.dtype),
+ (v_a.dimensions, v_b.dimensions),
+ (v_a.shape, v_b.shape),
+ ]
+ if self.show_chunks:
+ pairs_to_check_and_show.append((v_a.chunking, v_b.chunking))
+ if self.show_attributes:
+ for attr_a_key, attr_a, attr_b_key, attr_b in get_and_check_variable_attributes(
+ v_a, v_b
+ ):
+ # Check whether attr_a_key is empty,
+ # because it might be if the variable doesn't exist in File A.
+ pairs_to_check_and_show.append((attr_a, attr_b))
+ # Scale Factor
+ scale_factor_pair = get_and_check_variable_scale_factor(v_a, v_b)
+ if scale_factor_pair:
+ pairs_to_check_and_show.append((scale_factor_pair[0], scale_factor_pair[1]))
+
+ there_is_a_difference = False
+ for pair in pairs_to_check_and_show:
+ if pair[0] != pair[1]:
+ there_is_a_difference = True
+ break
+
+ # If all attributes are the same, and keep-only-diffs is set -> DON'T print
+ # If all attributes are the same, and keep-only-diffs is NOT set -> print
+ # If some attributes are different -> print no matter else
+ if there_is_a_difference or (not self.out.keep_only_diffs):
+ self.out.side_by_side(
+ "-----VARIABLE-----:",
+ v_a.varname[:47],
+ v_b.varname[:47],
+ highlight_diff=False,
+ force_display_even_if_same=True,
+ )
+
+ # Go through each attribute, show differences, and add differences to running tally.
+ def _var_attribute_side_by_side(attribute_name, attribute_a, attribute_b):
+ diff_condition: SummaryDifferenceKeys = self.out.side_by_side(
+ f"{attribute_name}:", attribute_a, attribute_b, highlight_diff=True
+ )
+ self.num_attribute_diffs[diff_condition] += 1
+ if diff_condition in ("left", "right", "both"):
+ self.num_attribute_diffs["difference_types"].add(attribute_name)
+
+ _var_attribute_side_by_side("dtype", v_a.dtype, v_b.dtype)
+ _var_attribute_side_by_side("dimensions", v_a.dimensions, v_b.dimensions)
+ _var_attribute_side_by_side("shape", v_a.shape, v_b.shape)
+ # Chunking
+ if self.show_chunks:
+ _var_attribute_side_by_side("chunksize", v_a.chunking, v_b.chunking)
+ # Scale Factor
+ scale_factor_pair = get_and_check_variable_scale_factor(v_a, v_b)
+ if scale_factor_pair:
+ _var_attribute_side_by_side("scale_factor", scale_factor_pair[0], scale_factor_pair[1])
+ # Other attributes
+ if self.show_attributes:
+ for attr_a_key, attr_a, attr_b_key, attr_b in get_and_check_variable_attributes(
+ v_a, v_b
+ ):
+ # Check whether attr_a_key is empty,
+ # because it might be if the variable doesn't exist in File A.
+ attribute_key = attr_a_key if attr_a_key else attr_b_key
+ _var_attribute_side_by_side(attribute_key, attr_a, attr_b)
+
+ def _print_root_dimensions(self):
+ # Show the dimensions of each file and evaluate differences.
+ self.out.print(Fore.LIGHTBLUE_EX + "\nRoot-level Dimensions:", add_to_history=True)
+ list_a = get_root_dims(self.file1)
+ list_b = get_root_dims(self.file2)
+ _, _, _ = self.out.lists_diff(list_a, list_b)
+
+ def _print_root_groups(self):
+ # Show the groups in each NetCDF file and evaluate differences.
+ self.out.print(Fore.LIGHTBLUE_EX + "\nRoot-level Groups:", add_to_history=True)
+ list_a = get_root_groups(self.file1)
+ list_b = get_root_groups(self.file2)
+ _, _, _ = self.out.lists_diff(list_a, list_b)
+
+ def _print_summary(self):
+ """Print summary counts of similarities and differences."""
+ self.out.side_by_side("-", "-", "-", dash_line=True, force_display_even_if_same=True)
+ self.out.side_by_side("SUMMARY", "-", "-", dash_line=True, force_display_even_if_same=True)
+
+ self.__print_summary_count_comparison_side_by_side("variable", self.num_var_diffs)
+ self.__print_summary_count_comparison_side_by_side("group", self.num_group_diffs)
+ self.__print_summary_count_comparison_side_by_side("attribute", self.num_attribute_diffs)
+
+ if self.num_attribute_diffs["difference_types"]:
+ self.out.print(
+ Fore.LIGHTBLUE_EX + "\nDifferences were found in these attributes:",
+ add_to_history=True,
+ )
+ self.out.print(
+ Fore.LIGHTBLUE_EX + f"\n{sorted(self.num_attribute_diffs['difference_types'])}",
+ add_to_history=True,
+ )
+
+ def __print_summary_count_comparison_side_by_side(
+ self,
+ item_type: str,
+ diff_dictionary: SummaryDifferencesDict,
+ ) -> None:
+ # Tally up instances where there were non-empty entries on both left and right sides.
+ diff_dictionary["left"] += diff_dictionary["both"]
+ diff_dictionary["right"] += diff_dictionary["both"]
+
+ self.out.side_by_side(
+ f"Total # of shared {item_type}s:",
+ str(diff_dictionary["shared"]),
+ str(diff_dictionary["shared"]),
+ force_display_even_if_same=True,
+ )
+
+ self.out.side_by_side(
+ f"Total # of non-shared {item_type}s:",
+ str(diff_dictionary["left"]),
+ str(diff_dictionary["right"]),
+ force_display_even_if_same=True,
+ )
+
+ def _dataset_pair_iterator(
+ self,
+ node_a_name: str,
+ node_a: Union[netCDF4.Dataset, netCDF4.Group, h5py.Dataset, h5py.Group],
+ node_a_subgroups: list,
+ node_b_name: str,
+ node_b: Union[netCDF4.Dataset, netCDF4.Group, h5py.Dataset, h5py.Group],
+ node_b_subgroups: list,
+ ) -> Iterator[GroupPair]:
+ """Yield names and groups, as pairs, from two netCDF or HDF hierarchies.
+
+ Parameters
+ ----------
+ node_a_name
+ name of the first group or dataset
+ node_a
+ the first group or dataset
+ node_b_name
+ name of the second group or dataset
+ node_b
+ the second group or dataset
+
+ Yields
+ ------
+ tuple
+ group A name : str
+ group A object : netCDF4.Group or None
+ group B name : str
+ group B object : netCDF4.Group or None
+ """
+ # get a sorted list of subgroups from both node_a and node_b
+ for _, group_a_name, group_b_name in common_elements(
+ node_a_subgroups if node_a is not None else "",
+ node_b_subgroups if node_b is not None else "",
+ ):
+ yield GroupPair(
+ group_a_name=node_a_name + "/" + group_a_name if group_a_name else "",
+ group_a=(
+ node_a[group_a_name]
+ if (group_a_name and (group_a_name in node_a_subgroups))
+ else None
+ ),
+ group_b_name=node_b_name + "/" + group_b_name if group_b_name else "",
+ group_b=(
+ node_b[group_b_name]
+ if (group_b_name and (group_b_name in node_b_subgroups))
+ else None
+ ),
+ )
+
+ for _, subgroup_a_name, subgroup_b_name in common_elements(
+ node_a_subgroups if node_a is not None else "",
+ node_b_subgroups if node_b is not None else "",
+ ):
+ subnode_a_name = node_a_name + "/" + subgroup_a_name if subgroup_a_name else ""
+ subnode_a = (
+ node_a[subgroup_a_name]
+ if (subgroup_a_name and (subgroup_a_name in node_a_subgroups))
+ else None
+ )
+ subnode_a_subgroups = get_subgroups(subnode_a, file_type=self.file_types)
+
+ subnode_b_name = node_a_name + "/" + subgroup_b_name if subgroup_b_name else ""
+ subnode_b = (
+ node_b[subgroup_b_name]
+ if (subgroup_b_name and (subgroup_b_name in node_b_subgroups))
+ else None
+ )
+ subnode_b_subgroups = get_subgroups(subnode_b, file_type=self.file_types)
+
+ yield from self._dataset_pair_iterator(
+ subnode_a_name,
+ subnode_a,
+ subnode_a_subgroups,
+ subnode_b_name,
+ subnode_b,
+ subnode_b_subgroups,
+ )
+
+ def _create_var_properties(
+ self, group: Union[netCDF4.Dataset, netCDF4.Group], varname: str, original_dataset
+ ) -> VarProperties:
+ """Get the properties of a variable.
+
+ Parameters
+ ----------
+ group
+ a dataset or group of variables
+ varname
+ the name of the variable
+
+ Returns
+ -------
+ VarProperties
+ """
+ if varname:
+ if self.file_types == "netcdf":
+ the_variable = group.variables[varname]
+ elif self.file_types == "hdf5":
+ the_variable = group[varname]
+
+ v_dtype = str(the_variable.dtype)
+
+ if self.file_types == "netcdf":
+ v_dimensions = str(the_variable.dimensions)
+ elif self.file_types == "hdf5":
+ v_dimensions = str([dim.label for dim in the_variable.dims])
+
+ v_shape = str(the_variable.shape).strip()
+
+ if self.file_types == "netcdf":
+ v_chunking = str(the_variable.chunking()).strip()
+ elif self.file_types == "hdf5":
+ v_chunking = str(the_variable.chunks)
+
+ def __name_from_h5_ref(ref):
+ return original_dataset[ref].name
+
+ v_attributes = {}
+ if self.file_types == "netcdf":
+ for name in the_variable.ncattrs():
+ try:
+ retrieved_value = the_variable.getncattr(name)
+ except KeyError as key_err:
+ # Added this check because of "unsupported datatype" error that prevented
+ # fully running comparisons on S5P_OFFL_L1B_IR_UVN collections.
+ retrieved_value = f"netCDF error: {str(key_err)}"
+
+ v_attributes[name] = retrieved_value
+ elif self.file_types == "hdf5":
+ for name in the_variable.attrs.keys():
+ attribute_value = the_variable.attrs[name]
+ if isinstance(attribute_value, np.ndarray):
+ if attribute_value.dtype == h5py.ref_dtype:
+ retrieved_value = __name_from_h5_ref(attribute_value[0][0])
+ else:
+ try:
+ retrieved_value = str(
+ [__name_from_h5_ref(a[0]) for a in attribute_value]
+ )
+ except IndexError:
+ retrieved_value = str(attribute_value)
+
+ else:
+ retrieved_value = str(attribute_value)
+
+ v_attributes[name] = retrieved_value
+ else:
+ the_variable = None
+ v_dtype = ""
+ v_dimensions = ""
+ v_shape = ""
+ v_chunking = ""
+ v_attributes = None
+
+ return VarProperties(
+ varname, the_variable, v_dtype, v_dimensions, v_shape, v_chunking, v_attributes
+ )
diff --git a/ncompare/console.py b/ncompare/console.py
index 8aad37a..764099a 100755
--- a/ncompare/console.py
+++ b/ncompare/console.py
@@ -47,10 +47,10 @@ def _cli(args: Optional[Sequence[str]]) -> argparse.Namespace:
if None, then argparse will use `sys.argv[1:]`
"""
parser = argparse.ArgumentParser(
- description="Compare the variables contained within two different NetCDF datasets"
+ description="Compare the variables contained within two different netCDF datasets"
)
- parser.add_argument("nc_a", help="First NetCDF file")
- parser.add_argument("nc_b", help="Second NetCDF file")
+ parser.add_argument("path_a", help="First (netCDF or HDF) file")
+ parser.add_argument("path_b", help="Second (netCDF or HDF) file")
parser.add_argument(
"--only-diffs",
action="store_true",
diff --git a/ncompare/core.py b/ncompare/core.py
index 9d6ca0b..c404188 100644
--- a/ncompare/core.py
+++ b/ncompare/core.py
@@ -27,44 +27,23 @@
# pylint: disable=no-member
# pylint: disable=fixme
-"""Compare the structure of two NetCDF files."""
+"""Compare the structure of two netCDF or HDF files."""
-import warnings
-from collections import namedtuple
-from collections.abc import Iterable, Iterator
from pathlib import Path
-from typing import Optional, TypedDict, Union
+from typing import Optional, Union
-import netCDF4
-import xarray as xr
-from colorama import Fore
-
-from ncompare.printing import Outputter, SummaryDifferenceKeys
-from ncompare.sequence_operations import common_elements, count_diffs
-from ncompare.utils import ensure_valid_path_exists, ensure_valid_path_with_suffix
-
-VarProperties = namedtuple(
- "VarProperties", "varname, variable, dtype, dimensions, shape, chunking, attributes"
-)
-
-GroupPair = namedtuple(
- "GroupPair",
- "group_a_name group_a group_b_name group_b",
- defaults=("", None, "", None),
+from ncompare.Comparison import Comparison
+from ncompare.path_and_string_operations import (
+ ensure_valid_path_exists,
+ ensure_valid_path_with_suffix,
+ validate_file_type,
)
-
-
-class SummaryDifferencesDict(TypedDict):
- shared: int
- left: int
- right: int
- both: int
- difference_types: set
+from ncompare.printing import Outputter
def compare(
- nc_a: Union[str, Path],
- nc_b: Union[str, Path],
+ path_a: Union[str, Path],
+ path_b: Union[str, Path],
only_diffs: bool = False,
no_color: bool = False,
show_chunks: bool = False,
@@ -74,14 +53,14 @@ def compare(
file_xlsx: Union[str, Path] = "",
column_widths: Optional[tuple[Union[int, str], Union[int, str], Union[int, str]]] = None,
) -> int:
- """Compare the variables contained within two different netCDF datasets.
+ """Compare the variables contained within two netCDF or HDF files.
Parameters
----------
- nc_a
- filepath to the first netCDF
- nc_b
- filepath to the second netCDF
+ path_a
+ filepath to the first netCDF or HDF
+ path_b
+ filepath to the second netCDF or HDF
only_diffs
Whether to show only the variables/attributes that are different between the two files
no_color
@@ -105,8 +84,8 @@ def compare(
total number of differences found (across variables, groups, and attributes)
"""
# Check the validity of paths.
- nc_a = ensure_valid_path_exists(nc_a)
- nc_b = ensure_valid_path_exists(nc_b)
+ path_a = ensure_valid_path_exists(path_a)
+ path_b = ensure_valid_path_exists(path_b)
if file_text:
file_text = ensure_valid_path_with_suffix(file_text, ".txt")
if file_csv:
@@ -114,6 +93,14 @@ def compare(
if file_xlsx:
file_xlsx = ensure_valid_path_with_suffix(file_xlsx, ".xlsx")
+ # Check the validity of file types
+ file_a = validate_file_type(path_a)
+ file_b = validate_file_type(path_b)
+ if file_a.type != file_b.type:
+ # I'm not sure if there is a use-case where we'd want to compare a netCDF with an HDF file?
+ # This assumption of files being the same type, affects the rest of the comparison logic.
+ raise TypeError("Both files must be of the same type (either both netCDF or both HDF).")
+
# The Outputter object is initialized to handle stdout and optional writing to a text file.
with Outputter(
keep_print_history=True,
@@ -122,528 +109,21 @@ def compare(
text_file=file_text,
column_widths=column_widths,
) as out:
- out.print(f"File A: {nc_a}")
- out.print(f"File B: {nc_b}")
+ out.print(f"File A: {file_a.path}")
+ out.print(f"File B: {file_b.path}")
# Start the comparison process.
- total_diff_count = run_through_comparisons(
- out,
- nc_a,
- nc_b,
- show_chunks=show_chunks,
- show_attributes=show_attributes,
+ comparison = Comparison(
+ file_a, file_b, out, show_chunks=show_chunks, show_attributes=show_attributes
)
+ total_diff_count = comparison.run_through_comparisons()
# Write to CSV and Excel files.
if file_csv:
- out.write_history_to_csv(filename=file_csv)
+ comparison.out.write_history_to_csv(filename=file_csv)
if file_xlsx:
- out.write_history_to_excel(filename=file_xlsx)
+ comparison.out.write_history_to_excel(filename=file_xlsx)
- out.print("\nDone.", colors=False)
+ comparison.out.print("\nDone.", colors=False)
return total_diff_count
-
-
-def run_through_comparisons(
- out: Outputter,
- nc_a: Union[str, Path],
- nc_b: Union[str, Path],
- show_chunks: bool,
- show_attributes: bool,
-) -> int:
- """Execute a series of comparisons between two netCDF files.
-
- Parameters
- ----------
- out
- instance of Outputter
- nc_a
- path to the first netCDF file
- nc_b
- path to the second netCDF file
- show_chunks
- whether to include data chunk sizes in the displayed comparison of variables
- show_attributes
- whether to include variable attributes in the displayed comparison of variables
-
- Returns
- -------
- int
- total number of differences found (across variables, groups, and attributes)
- """
- # Show the dimensions of each file and evaluate differences.
- out.print(Fore.LIGHTBLUE_EX + "\nRoot-level Dimensions:", add_to_history=True)
- list_a = _get_dims(nc_a)
- list_b = _get_dims(nc_b)
- _, _, _ = out.lists_diff(list_a, list_b)
-
- # Show the groups in each NetCDF file and evaluate differences.
- out.print(Fore.LIGHTBLUE_EX + "\nRoot-level Groups:", add_to_history=True)
- list_a = _get_groups(nc_a)
- list_b = _get_groups(nc_b)
- _, _, _ = out.lists_diff(list_a, list_b)
-
- out.print(Fore.LIGHTBLUE_EX + "\nAll variables:", add_to_history=True)
- total_diff_count = compare_two_nc_files(
- out, nc_a, nc_b, show_chunks=show_chunks, show_attributes=show_attributes
- )
-
- return total_diff_count
-
-
-def walk_common_groups_tree(
- top_a_name: str,
- top_a: Union[netCDF4.Dataset, netCDF4.Group],
- top_b_name: str,
- top_b: Union[netCDF4.Dataset, netCDF4.Group],
-) -> Iterator[GroupPair]:
- """Yield names and groups from a netCDF4's group tree.
-
- Parameters
- ----------
- top_a_name
- name of the first group or dataset
- top_a
- the first group or dataset
- top_b_name
- name of the second group or dataset
- top_b
- the second group or dataset
-
- Yields
- ------
- tuple
- group A name : str
- group A object : netCDF4.Group or None
- group B name : str
- group B object : netCDF4.Group or None
- """
- for _, group_a_name, group_b_name in common_elements(
- top_a.groups if top_a is not None else "",
- top_b.groups if top_b is not None else "",
- ):
- yield GroupPair(
- group_a_name=top_a_name + "/" + group_a_name if group_a_name else "",
- group_a=(
- top_a[group_a_name] if (group_a_name and (group_a_name in top_a.groups)) else None
- ),
- group_b_name=top_b_name + "/" + group_b_name if group_b_name else "",
- group_b=(
- top_b[group_b_name] if (group_b_name and (group_b_name in top_b.groups)) else None
- ),
- )
-
- for _, subgroup_a_name, subgroup_b_name in common_elements(
- top_a.groups if top_a is not None else "",
- top_b.groups if top_b is not None else "",
- ):
- yield from walk_common_groups_tree(
- top_a_name + "/" + subgroup_a_name if subgroup_a_name else "",
- (
- top_a[subgroup_a_name]
- if (subgroup_a_name and (subgroup_a_name in top_a.groups))
- else None
- ),
- top_a_name + "/" + subgroup_b_name if subgroup_b_name else "",
- (
- top_b[subgroup_b_name]
- if (subgroup_b_name and (subgroup_b_name in top_b.groups))
- else None
- ),
- )
-
-
-def compare_two_nc_files(
- out: Outputter,
- nc_one: Union[str, Path],
- nc_two: Union[str, Path],
- show_chunks: bool = False,
- show_attributes: bool = False,
-) -> int:
- """Go through all groups and all variables, and show them side by side,
- highlighting whether they align and where they don't.
-
- Parameters
- ----------
- out
- instance of Outputter
- nc_one
- path to the first dataset
- nc_two
- path to the second dataset
- show_chunks
- whether to include chunks alongside variables
- show_attributes
- whether to include variable attributes
-
- Returns
- -------
- int
- total number of differences found (across variables, groups, and attributes)
- """
- out.side_by_side(" ", "File A", "File B", force_display_even_if_same=True)
- num_group_diffs: SummaryDifferencesDict = {
- "shared": 0,
- "left": 0,
- "right": 0,
- "both": 0,
- "difference_types": set(),
- }
- num_var_diffs: SummaryDifferencesDict = {
- "shared": 0,
- "left": 0,
- "right": 0,
- "both": 0,
- "difference_types": set(),
- }
- num_attribute_diffs: SummaryDifferencesDict = {
- "shared": 0,
- "left": 0,
- "right": 0,
- "both": 0,
- "difference_types": set(),
- }
- with netCDF4.Dataset(nc_one) as nc_a, netCDF4.Dataset(nc_two) as nc_b:
- out.side_by_side(
- "All Variables", " ", " ", dash_line=False, force_display_even_if_same=True
- )
- out.side_by_side("-", "-", "-", dash_line=True, force_display_even_if_same=True)
-
- group_counter = 0
- _print_group_details_side_by_side(
- out,
- nc_a,
- "/",
- nc_b,
- "/",
- group_counter,
- num_var_diffs,
- num_attribute_diffs,
- show_attributes,
- show_chunks,
- )
- group_counter += 1
-
- for group_pair in walk_common_groups_tree("", nc_a, "", nc_b):
- if group_pair.group_a_name == "":
- num_group_diffs["right"] += 1
- elif group_pair.group_b_name == "":
- num_group_diffs["left"] += 1
- else:
- num_group_diffs["shared"] += 1
-
- _print_group_details_side_by_side(
- out,
- group_pair.group_a,
- group_pair.group_a_name,
- group_pair.group_b,
- group_pair.group_b_name,
- group_counter,
- num_var_diffs,
- num_attribute_diffs,
- show_attributes,
- show_chunks,
- )
- group_counter += 1
-
- out.side_by_side("-", "-", "-", dash_line=True, force_display_even_if_same=True)
- out.side_by_side("SUMMARY", "-", "-", dash_line=True, force_display_even_if_same=True)
-
- _print_summary_count_comparison_side_by_side(out, "variable", num_var_diffs)
- _print_summary_count_comparison_side_by_side(out, "group", num_group_diffs)
- _print_summary_count_comparison_side_by_side(out, "attribute", num_attribute_diffs)
- if num_attribute_diffs["difference_types"]:
- out.print(
- Fore.LIGHTBLUE_EX + "\nDifferences were found in these attributes:", add_to_history=True
- )
- out.print(
- Fore.LIGHTBLUE_EX + f"\n{sorted(num_attribute_diffs['difference_types'])}",
- add_to_history=True,
- )
-
- # Return the total number of differences; thus, zero means no differences were found.
- total_diff_count = sum(
- [x["left"] + x["right"] for x in [num_var_diffs, num_group_diffs, num_attribute_diffs]]
- )
-
- return total_diff_count
-
-
-def _print_summary_count_comparison_side_by_side(
- out: Outputter,
- item_type: str,
- diff_dictionary: SummaryDifferencesDict,
-) -> None:
- # Tally up instances where there were non-empty entries on both left and right sides.
- diff_dictionary["left"] += diff_dictionary["both"]
- diff_dictionary["right"] += diff_dictionary["both"]
-
- out.side_by_side(
- f"Total # of shared {item_type}s:",
- str(diff_dictionary["shared"]),
- str(diff_dictionary["shared"]),
- force_display_even_if_same=True,
- )
-
- out.side_by_side(
- f"Total # of non-shared {item_type}s:",
- str(diff_dictionary["left"]),
- str(diff_dictionary["right"]),
- force_display_even_if_same=True,
- )
-
-
-def _print_group_details_side_by_side(
- out: Outputter,
- group_a: Union[netCDF4.Dataset, netCDF4.Group],
- group_a_name: str,
- group_b: Union[netCDF4.Dataset, netCDF4.Group],
- group_b_name: str,
- group_counter: int,
- num_var_diffs: SummaryDifferencesDict,
- num_attribute_diffs: SummaryDifferencesDict,
- show_attributes: bool,
- show_chunks: bool,
-) -> None:
- """Align and display group details side by side."""
- out.side_by_side(
- " ", " ", " ", dash_line=False, highlight_diff=False, force_display_even_if_same=True
- )
- out.side_by_side(
- f"GROUP #{group_counter:02}",
- group_a_name.strip(),
- group_b_name.strip(),
- dash_line=True,
- highlight_diff=False,
- force_display_even_if_same=True,
- )
-
- # Count the number of variables in this group as long as this group exists.
- vars_a_sorted: Union[list, str] = ""
- vars_b_sorted: Union[list, str] = ""
- if group_a:
- vars_a_sorted = sorted(group_a.variables)
- if group_b:
- vars_b_sorted = sorted(group_b.variables)
- out.side_by_side(
- "num variables in group:",
- len(vars_a_sorted),
- len(vars_b_sorted),
- highlight_diff=True,
- force_display_even_if_same=True,
- )
- out.side_by_side("-", "-", "-", dash_line=True, force_display_even_if_same=True)
-
- # Count differences between the lists of variables in this group.
- left, right, shared = count_diffs(vars_a_sorted, vars_b_sorted)
- num_var_diffs["left"] += left
- num_var_diffs["right"] += right
- num_var_diffs["shared"] += shared
-
- # Go through each variable in the current group.
- for variable_pair in common_elements(vars_a_sorted, vars_b_sorted):
- # Get and print the properties of each variable
- _print_var_properties_side_by_side(
- out,
- _var_properties(group_a, variable_pair[1]),
- _var_properties(group_b, variable_pair[2]),
- num_attribute_diffs,
- show_chunks=show_chunks,
- show_attributes=show_attributes,
- )
-
-
-def _print_var_properties_side_by_side(
- out: Outputter,
- v_a: VarProperties,
- v_b: VarProperties,
- num_attribute_diffs: SummaryDifferencesDict,
- show_chunks: bool = False,
- show_attributes: bool = False,
-) -> None:
- """Align and display variable properties side by side."""
- # Gather all variable property pairs first, before printing,
- # so we can decide whether to highlight the variable header.
- pairs_to_check_and_show = [
- (v_a.dtype, v_b.dtype),
- (v_a.dimensions, v_b.dimensions),
- (v_a.shape, v_b.shape),
- ]
- if show_chunks:
- pairs_to_check_and_show.append((v_a.chunking, v_b.chunking))
- if show_attributes:
- for attr_a_key, attr_a, attr_b_key, attr_b in _get_and_check_variable_attributes(v_a, v_b):
- # Check whether attr_a_key is empty,
- # because it might be if the variable doesn't exist in File A.
- pairs_to_check_and_show.append((attr_a, attr_b))
- # Scale Factor
- scale_factor_pair = _get_and_check_variable_scale_factor(v_a, v_b)
- if scale_factor_pair:
- pairs_to_check_and_show.append((scale_factor_pair[0], scale_factor_pair[1]))
-
- there_is_a_difference = False
- for pair in pairs_to_check_and_show:
- if pair[0] != pair[1]:
- there_is_a_difference = True
- break
-
- # If all attributes are the same, and keep-only-diffs is set -> DON'T print
- # If all attributes are the same, and keep-only-diffs is NOT set -> print
- # If some attributes are different -> print no matter else
- if there_is_a_difference or (not out.keep_only_diffs):
- out.side_by_side(
- "-----VARIABLE-----:",
- v_a.varname[:47],
- v_b.varname[:47],
- highlight_diff=False,
- force_display_even_if_same=True,
- )
-
- # Go through each attribute, show differences, and add differences to running tally.
- def _var_attribute_side_by_side(attribute_name, attribute_a, attribute_b):
- diff_condition: SummaryDifferenceKeys = out.side_by_side(
- f"{attribute_name}:", attribute_a, attribute_b, highlight_diff=True
- )
- num_attribute_diffs[diff_condition] += 1
- if diff_condition in ("left", "right", "both"):
- num_attribute_diffs["difference_types"].add(attribute_name)
-
- _var_attribute_side_by_side("dtype", v_a.dtype, v_b.dtype)
- _var_attribute_side_by_side("dimensions", v_a.dimensions, v_b.dimensions)
- _var_attribute_side_by_side("shape", v_a.shape, v_b.shape)
- # Chunking
- if show_chunks:
- _var_attribute_side_by_side("chunksize", v_a.chunking, v_b.chunking)
- # Scale Factor
- scale_factor_pair = _get_and_check_variable_scale_factor(v_a, v_b)
- if scale_factor_pair:
- _var_attribute_side_by_side("scale_factor", scale_factor_pair[0], scale_factor_pair[1])
- # Other attributes
- if show_attributes:
- for attr_a_key, attr_a, attr_b_key, attr_b in _get_and_check_variable_attributes(v_a, v_b):
- # Check whether attr_a_key is empty,
- # because it might be if the variable doesn't exist in File A.
- attribute_key = attr_a_key if attr_a_key else attr_b_key
- _var_attribute_side_by_side(attribute_key, attr_a, attr_b)
-
-
-def _get_and_check_variable_scale_factor(
- v_a: VarProperties, v_b: VarProperties
-) -> Union[None, tuple[str, str]]:
- """Get a string representation of the scale factor for two variables."""
- if getattr(v_a.variable, "scale_factor", None):
- sf_a = v_a.variable.scale_factor
- else:
- sf_a = " "
- if getattr(v_b.variable, "scale_factor", None):
- sf_b = v_b.variable.scale_factor
- else:
- sf_b = " "
- if (sf_a != " ") or (sf_b != " "):
- return str(sf_a), str(sf_b)
- else:
- return None
-
-
-def _get_and_check_variable_attributes(
- v_a: VarProperties, v_b: VarProperties
-) -> Iterator[tuple[str, str, str, str]]:
- """Go through and yield each attribute pair for two variables."""
- # Get the name of attributes if they exist
- attrs_a_names = []
- if v_a.attributes:
- attrs_a_names = v_a.attributes.keys()
- attrs_b_names = []
- if v_b.attributes:
- attrs_b_names = v_b.attributes.keys()
- # Iterate and print each attribute
- for _, attr_a_key, attr_b_key in common_elements(attrs_a_names, attrs_b_names):
- attr_a = _get_attribute_value_as_str(v_a, attr_a_key)
- attr_b = _get_attribute_value_as_str(v_b, attr_b_key)
- yield attr_a_key, attr_a, attr_b_key, attr_b
-
-
-def _var_properties(group: Union[netCDF4.Dataset, netCDF4.Group], varname: str) -> VarProperties:
- """Get the properties of a variable.
-
- Parameters
- ----------
- group
- a dataset or group of variables
- varname
- the name of the variable
-
- Returns
- -------
- VarProperties
- """
- if varname:
- the_variable = group.variables[varname]
- v_dtype = str(the_variable.dtype)
- v_dimensions = str(the_variable.dimensions)
- v_shape = str(the_variable.shape).strip()
- v_chunking = str(the_variable.chunking()).strip()
-
- v_attributes = {}
- for name in the_variable.ncattrs():
- try:
- v_attributes[name] = the_variable.getncattr(name)
- except KeyError as key_err:
- # Added this check because of "unsupported datatype" error that prevented
- # fully running comparisons on S5P_OFFL_L1B_IR_UVN collections.
- v_attributes[name] = f"netCDF error: {str(key_err)}"
- else:
- the_variable = None
- v_dtype = ""
- v_dimensions = ""
- v_shape = ""
- v_chunking = ""
- v_attributes = None
-
- return VarProperties(
- varname, the_variable, v_dtype, v_dimensions, v_shape, v_chunking, v_attributes
- )
-
-
-def _get_attribute_value_as_str(varprops: VarProperties, attribute_key: str) -> str:
- """Get a string representation of the attribute value."""
- if attribute_key and (attribute_key in varprops.attributes):
- attr = varprops.attributes[attribute_key]
- if isinstance(attr, Iterable) and not isinstance(attr, (str, float)):
- # TODO: by truncating a list (or other iterable) here,
- # we are preventing any subsequent difference checker from detecting
- # differences past the 5th element in the iterable.
- # So, we need to figure out a way to still check for other differences past the 5th element.
- return "[" + ", ".join([str(x) for x in attr[:5]]) + ", ..." + "]" # type:ignore[index]
-
- return str(attr)
-
- return ""
-
-
-def _get_groups(nc_filepath: Union[str, Path]) -> list:
- """Get a list of groups from a netCDF."""
- with netCDF4.Dataset(nc_filepath) as dataset:
- groups_list = list(dataset.groups.keys())
- return groups_list
-
-
-def _get_dims(nc_filepath: Union[str, Path]) -> list:
- """Get a list of dimensions from a netCDF."""
-
- def __get_dim_list(decode_times=True):
- with warnings.catch_warnings():
- warnings.simplefilter("ignore")
- with xr.open_dataset(nc_filepath, decode_times=decode_times) as dataset:
- return list(dataset.sizes.items())
-
- try:
- dims_list = __get_dim_list()
- except ValueError as err:
- if "decode_times" in str(err): # then try again without decoding the times
- dims_list = __get_dim_list(decode_times=False)
- else:
- raise err from None # "from None" prevents additional trace (see https://stackoverflow.com/a/18188660)
-
- return dims_list
diff --git a/ncompare/getters.py b/ncompare/getters.py
new file mode 100644
index 0000000..9996759
--- /dev/null
+++ b/ncompare/getters.py
@@ -0,0 +1,124 @@
+import warnings
+from collections.abc import Iterable, Iterator
+from typing import Union
+
+import h5py
+import netCDF4
+import xarray as xr
+
+from ncompare.sequence_operations import common_elements
+from ncompare.utility_types import FileToCompare, VarProperties
+
+
+def get_and_check_variable_scale_factor(
+ v_a: VarProperties, v_b: VarProperties
+) -> Union[None, tuple[str, str]]:
+ """Get a string representation of the scale factor for two variables."""
+ sf_a = getattr(v_a.variable, "scale_factor", " ")
+ sf_b = getattr(v_b.variable, "scale_factor", " ")
+
+ if (sf_a != " ") or (sf_b != " "):
+ return str(sf_a), str(sf_b)
+ else:
+ return None
+
+
+def get_and_check_variable_attributes(
+ v_a: VarProperties, v_b: VarProperties
+) -> Iterator[tuple[str, str, str, str]]:
+ """Go through and yield each attribute pair for two variables."""
+ # Get the name of attributes if they exist
+ attrs_a_names = []
+ if v_a.attributes:
+ attrs_a_names = v_a.attributes.keys()
+ attrs_b_names = []
+ if v_b.attributes:
+ attrs_b_names = v_b.attributes.keys()
+ # Iterate and print each attribute
+ for _, attr_a_key, attr_b_key in common_elements(attrs_a_names, attrs_b_names):
+ attr_a = get_attribute_value_as_str(v_a, attr_a_key)
+ attr_b = get_attribute_value_as_str(v_b, attr_b_key)
+ yield attr_a_key, attr_a, attr_b_key, attr_b
+
+
+def get_attribute_value_as_str(varprops: VarProperties, attribute_key: str) -> str:
+ """Get a string representation of the attribute value."""
+ if attribute_key and (attribute_key in varprops.attributes):
+ attr = varprops.attributes[attribute_key]
+ if isinstance(attr, Iterable) and not isinstance(attr, (str, float)):
+ # TODO: by truncating a list (or other iterable) here,
+ # we are preventing any subsequent difference checker from detecting
+ # differences past the 5th element in the iterable.
+ # So, we need to figure out a way to still check for other differences past the 5th element.
+ return "[" + ", ".join([str(x) for x in attr[:5]]) + ", ..." + "]" # type:ignore[index]
+
+ return str(attr)
+
+ return ""
+
+
+def get_root_groups(file: FileToCompare) -> list:
+ """Get a list of groups from a netCDF."""
+ if file.type == "netcdf":
+ with netCDF4.Dataset(file.path) as dataset:
+ groups_list = list(dataset.groups.keys())
+ elif file.type == "hdf5":
+ with h5py.File(file.path) as dataset:
+ groups_list = list(dataset.keys())
+ return groups_list
+
+
+def get_subgroups(node: Union[netCDF4.Dataset, netCDF4.Group, h5py.Group], file_type: str) -> list:
+ """Get a list of subgroups from a netCDF or HDF5 group.
+
+ Parameters
+ ----------
+ node
+ file_type
+
+ Returns
+ -------
+ list or None
+ subgroups under the node
+ """
+ if node is None:
+ return []
+ elif file_type == "hdf5":
+ return [key for key in node.keys() if isinstance(node[key], h5py.Group)]
+ else: # should be "netcdf"
+ return list(node.groups)
+
+
+def get_variables(node: Union[netCDF4.Dataset, netCDF4.Group, h5py.Group], file_type: str) -> list:
+ """Get a sorted list of variables from a netCDF or HDF5 group."""
+ if file_type == "hdf5":
+ return [key for key in node.keys() if isinstance(node[key], h5py.Dataset)]
+ else: # should be "netcdf"
+ return sorted(node.variables)
+
+
+def get_root_dims(file: FileToCompare) -> list:
+ """Get a list of dimensions from a netCDF or HDF5."""
+
+ def __get_dim_list(decode_times=True):
+ with warnings.catch_warnings():
+ warnings.simplefilter("ignore")
+ if file.type == "netcdf":
+ xarray_engine = "netcdf4"
+ elif file.type == "hdf5":
+ xarray_engine = "h5netcdf"
+
+ with xr.open_dataset(
+ file.path, decode_times=decode_times, engine=xarray_engine
+ ) as dataset:
+ return list(dataset.sizes.items())
+
+ try:
+ dims_list = __get_dim_list()
+ except ValueError as err:
+ if "decode_times" in str(err): # then try again without decoding the times
+ dims_list = __get_dim_list(decode_times=False)
+ else:
+ raise err from None # "from None" prevents additional trace (see https://stackoverflow.com/a/18188660)
+
+ return dims_list
diff --git a/ncompare/utils.py b/ncompare/path_and_string_operations.py
similarity index 78%
rename from ncompare/utils.py
rename to ncompare/path_and_string_operations.py
index 7ad79db..fbc3e05 100644
--- a/ncompare/utils.py
+++ b/ncompare/path_and_string_operations.py
@@ -28,6 +28,8 @@
from pathlib import Path
from typing import Union
+from ncompare.utility_types import FileToCompare, valid_file_type_ids
+
def ensure_valid_path_exists(should_be_path: Union[str, Path]) -> Path:
"""Coerce input to a pathlib.Path and check that the resulting filepath exists."""
@@ -49,3 +51,19 @@ def coerce_to_str(some_object: Union[str, int, tuple]) -> str:
if isinstance(some_object, (str, int, tuple)):
return str(some_object)
raise TypeError(f"Unable to coerce value to str. Unexpected type <{type(some_object)}>.")
+
+
+def validate_file_type(file_path: Path) -> FileToCompare:
+ """Validate a file type and return a FileToCompare instance."""
+ if file_path.suffix.lower() in (".h5", ".hdf5", ".he5"):
+ file_type: valid_file_type_ids = "hdf5"
+ elif file_path.suffix.lower() in (".nc", ".nc4", ".nc3"):
+ file_type = "netcdf"
+ else:
+ raise TypeError(
+ f"{file_path.suffix} is not a valid file type. "
+ f"Expected a netcdf ('.nc', '.nc4', '.nc3') or "
+ f"hdf5 ('.h5', '.hdf5', '.he5)."
+ )
+
+ return FileToCompare(path=file_path, type=file_type)
diff --git a/ncompare/printing.py b/ncompare/printing.py
index 5224b30..b031d87 100644
--- a/ncompare/printing.py
+++ b/ncompare/printing.py
@@ -31,7 +31,7 @@
import warnings
from collections.abc import Iterable, Iterator
from pathlib import Path
-from typing import Literal, Optional, TextIO, Union
+from typing import Optional, TextIO, Union
import colorama
import openpyxl
@@ -40,8 +40,7 @@
from openpyxl.styles import Font
from ncompare.sequence_operations import common_elements, count_diffs
-
-SummaryDifferenceKeys = Literal["shared", "left", "right", "both"]
+from ncompare.utility_types import SummaryDifferenceKeys
# Set up regex remover of ANSI color escape sequences
# From
diff --git a/ncompare/sequence_operations.py b/ncompare/sequence_operations.py
index c673f90..9a9c998 100644
--- a/ncompare/sequence_operations.py
+++ b/ncompare/sequence_operations.py
@@ -28,17 +28,18 @@
from collections.abc import Generator, Iterable
from typing import Union
-from ncompare.utils import coerce_to_str
+from ncompare.path_and_string_operations import coerce_to_str
def common_elements(
sequence_a: Iterable, sequence_b: Iterable
) -> Generator[tuple[int, str, str], None, None]:
- """Loop over combined items of two iterables, and yield aligned item pairs.
+ """Yield all items from two iterables, sorted and as aligned pairs.
Note
----
- When there isn't a matching item, an empty string is used instead.
+ When there isn't a matching item for one of the iterables,
+ an empty string is used instead.
Yields
------
diff --git a/ncompare/utility_types.py b/ncompare/utility_types.py
new file mode 100644
index 0000000..7ac94b0
--- /dev/null
+++ b/ncompare/utility_types.py
@@ -0,0 +1,44 @@
+from collections import namedtuple
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Literal, TypedDict, Union
+
+valid_file_type_ids = Literal["netcdf", "hdf5"]
+
+
+@dataclass
+class FileToCompare:
+ """Represents an input file to compare against, and its file type."""
+
+ path: Union[Path, str]
+ type: valid_file_type_ids = "netcdf"
+
+ def __post_init__(self):
+ # We'll validate the inputs here.
+ if not isinstance(self.path, (str, Path)):
+ raise TypeError(f"'path' must be a str or Path, was {type(self.path)}")
+ if self.type not in ("netcdf", "hdf5"):
+ raise ValueError("'type' must be either 'netcdf' or 'hdf5'")
+
+
+class SummaryDifferencesDict(TypedDict):
+ """Represents the number and type of differences between two files."""
+
+ shared: int
+ left: int
+ right: int
+ both: int
+ difference_types: set
+
+
+SummaryDifferenceKeys = Literal["shared", "left", "right", "both"]
+
+VarProperties = namedtuple(
+ "VarProperties", "varname, variable, dtype, dimensions, shape, chunking, attributes"
+)
+
+GroupPair = namedtuple(
+ "GroupPair",
+ "group_a_name group_a group_b_name group_b",
+ defaults=("", None, "", None),
+)
diff --git a/poetry.lock b/poetry.lock
index bac9f2d..371e7d8 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand.
[[package]]
name = "appnope"
@@ -13,37 +13,34 @@ files = [
[[package]]
name = "asttokens"
-version = "2.4.1"
+version = "3.0.0"
description = "Annotate AST trees with source code positions"
optional = false
-python-versions = "*"
+python-versions = ">=3.8"
files = [
- {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
- {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
+ {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"},
+ {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"},
]
-[package.dependencies]
-six = ">=1.12.0"
-
[package.extras]
-astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
-test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
+astroid = ["astroid (>=2,<4)"]
+test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"]
[[package]]
name = "attrs"
-version = "24.2.0"
+version = "24.3.0"
description = "Classes Without Boilerplate"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
- {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
+ {file = "attrs-24.3.0-py3-none-any.whl", hash = "sha256:ac96cd038792094f438ad1f6ff80837353805ac950cd2aa0e0625ef19850c308"},
+ {file = "attrs-24.3.0.tar.gz", hash = "sha256:8f5c07333d543103541ba7be0e2ce16eeee8130cb0b3f9238ab904ce1e85baff"},
]
[package.extras]
benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
@@ -95,6 +92,7 @@ files = [
]
[package.dependencies]
+tinycss2 = {version = ">=1.1.0,<1.5", optional = true, markers = "extra == \"css\""}
webencodings = "*"
[package.extras]
@@ -102,13 +100,13 @@ css = ["tinycss2 (>=1.1.0,<1.5)"]
[[package]]
name = "certifi"
-version = "2024.8.30"
+version = "2024.12.14"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
python-versions = ">=3.6"
files = [
- {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
- {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
+ {file = "certifi-2024.12.14-py3-none-any.whl", hash = "sha256:1275f7a45be9464efc1173084eaa30f866fe2e47d389406136d332ed4967ec56"},
+ {file = "certifi-2024.12.14.tar.gz", hash = "sha256:b650d30f370c2b724812bee08008be0c4163b163ddaec3f2546c1caf65f191db"},
]
[[package]]
@@ -243,127 +241,114 @@ numpy = [
[[package]]
name = "charset-normalizer"
-version = "3.4.0"
+version = "3.4.1"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
optional = false
-python-versions = ">=3.7.0"
+python-versions = ">=3.7"
files = [
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+
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name = "idna"
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@@ -740,13 +781,13 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
[[package]]
name = "jinja2"
-version = "3.1.4"
+version = "3.1.5"
description = "A very fast and expressive template engine."
optional = false
python-versions = ">=3.7"
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@@ -846,13 +887,13 @@ files = [
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name = "jupytext"
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description = "Jupyter notebooks as Markdown documents, Julia, Python or R scripts"
optional = false
python-versions = ">=3.8"
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tomli = {version = "*", markers = "python_version < \"3.11\""}
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test-ui = ["calysto-bash"]
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+version = "3.1.0"
description = "A sane and fast Markdown parser with useful plugins and renderers"
optional = false
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version = "1.6.1"
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+version = "0.10.2"
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defusedxml = "*"
importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
jinja2 = ">=3.0"
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pygments = ">=2.4.1"
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traitlets = ">=5.1"
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[[package]]
name = "rpds-py"
-version = "0.21.0"
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description = "Python bindings to Rust's persistent data structures (rpds)"
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python-versions = ">=3.9"
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[[package]]
@@ -2372,13 +2428,13 @@ files = [
[[package]]
name = "six"
-version = "1.16.0"
+version = "1.17.0"
description = "Python 2 and 3 compatibility utilities"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
files = [
- {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
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]
[[package]]
@@ -2431,13 +2487,43 @@ test = ["pytest", "ruff"]
[[package]]
name = "tomli"
-version = "2.1.0"
+version = "2.2.1"
description = "A lil' TOML parser"
optional = false
python-versions = ">=3.8"
files = [
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- {file = "tomli-2.1.0.tar.gz", hash = "sha256:3f646cae2aec94e17d04973e4249548320197cfabdf130015d023de4b74d8ab8"},
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+ {file = "tomli-2.2.1-cp313-cp313-win_amd64.whl", hash = "sha256:a38aa0308e754b0e3c67e344754dff64999ff9b513e691d0e786265c93583c69"},
+ {file = "tomli-2.2.1-py3-none-any.whl", hash = "sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc"},
+ {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"},
]
[[package]]
@@ -2499,13 +2585,13 @@ files = [
[[package]]
name = "urllib3"
-version = "2.2.3"
+version = "2.3.0"
description = "HTTP library with thread-safe connection pooling, file post, and more."
optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
files = [
- {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"},
- {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"},
+ {file = "urllib3-2.3.0-py3-none-any.whl", hash = "sha256:1cee9ad369867bfdbbb48b7dd50374c0967a0bb7710050facf0dd6911440e3df"},
+ {file = "urllib3-2.3.0.tar.gz", hash = "sha256:f8c5449b3cf0861679ce7e0503c7b44b5ec981bec0d1d3795a07f1ba96f0204d"},
]
[package.extras]
@@ -2624,4 +2710,4 @@ type = ["pytest-mypy"]
[metadata]
lock-version = "2.0"
python-versions = "^3.9"
-content-hash = "563eafd03cf4755d613d36ed8fb0feb6cfd15a2fd893aa240a171899c1c74a28"
+content-hash = "a193dfef3cbd636299b9675ba69077c9b2b760d960550d72ca16dfab3993aa0d"
diff --git a/pyproject.toml b/pyproject.toml
index c1665e7..78ce3cd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,6 +29,8 @@ netCDF4 = ">=1.6.4"
xarray = ">=2023.9"
colorama = ">=0.4.6"
openpyxl = ">=3.1.2"
+h5py = "^3.12.1"
+h5netcdf = "^1.4.1"
[tool.poetry.group.dev.dependencies]
pytest = ">=7.4.2,<9.0.0"
diff --git a/tests/conftest.py b/tests/conftest.py
index 6a11927..4a763a4 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -147,6 +147,8 @@ def ds_3dims_3vars_4coords_1group(temp_data_dir):
#
grp1.createVariable("step", "f4", ("step",), fill_value=False)
grp1["step"][:] = [-0.9, -1.8, -2.7]
+ grp1["step"].scale_factor = 0.5
+ grp1["step"].add_offset = 5
#
grp1.createVariable("w", "u1", ("x", "step"), fill_value=False)
diff --git a/tests/data/icesat-2-ATL06/ATL06_20230816161508_08782002_006_02.h5 b/tests/data/icesat-2-ATL06/ATL06_20230816161508_08782002_006_02.h5
new file mode 100644
index 0000000..469647e
--- /dev/null
+++ b/tests/data/icesat-2-ATL06/ATL06_20230816161508_08782002_006_02.h5
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:64184f7b614bc12a0107d4521f56ad566e958f4f657a3bda50a8cae0acb39e59
+size 3494063
diff --git a/tests/data/icesat-2-ATL06/ATL06_20230816234629_08822013_006_01.h5 b/tests/data/icesat-2-ATL06/ATL06_20230816234629_08822013_006_01.h5
new file mode 100644
index 0000000..41032ed
--- /dev/null
+++ b/tests/data/icesat-2-ATL06/ATL06_20230816234629_08822013_006_01.h5
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d0ae713f6f3d686600eafd66b36ea020ffb926198849db23a067414bd14c4280
+size 1577886
diff --git a/tests/test_cli.py b/tests/test_cli.py
index d314ae8..9c81308 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -41,8 +41,8 @@ def test_console_help():
def test_arg_parser():
parsed = _cli(["first_netcdf.nc", "second_netcdf.nc"])
- assert getattr(parsed, "nc_a") == "first_netcdf.nc"
- assert getattr(parsed, "nc_b") == "second_netcdf.nc"
+ assert getattr(parsed, "path_a") == "first_netcdf.nc"
+ assert getattr(parsed, "path_b") == "second_netcdf.nc"
assert getattr(parsed, "show_attributes") is False
assert getattr(parsed, "show_chunks") is False
assert getattr(parsed, "only_diffs") is False
diff --git a/tests/test_core.py b/tests/test_core.py
index b8595d2..ca8e30c 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -31,12 +31,11 @@
from contextlib import nullcontext as does_not_raise
-import netCDF4 as nc
+import pytest
-from ncompare.core import (
- _var_properties,
- compare,
-)
+from ncompare.core import compare
+
+from . import data_for_tests_dir
def compare_ab(a, b):
@@ -75,11 +74,24 @@ def test_zero_for_comparison_with_no_differences(ds_3dims_3vars_4coords_1subgrou
assert compare(ds_3dims_3vars_4coords_1subgroup, ds_3dims_3vars_4coords_1subgroup) == 0
-def test_var_properties(ds_3dims_3vars_4coords_1group):
- with nc.Dataset(ds_3dims_3vars_4coords_1group) as ds:
- result = _var_properties(ds.groups["Group1"], varname="step")
- assert result.varname == "step"
- assert result.dtype == "float32"
- assert result.shape == "(3,)"
- assert result.chunking == "contiguous"
- assert result.attributes == {}
+def test_icesat(temp_data_dir):
+ # Compare the `ncompare` output when testing ICESat
+ out_path = temp_data_dir / "output_file_icesat-2-atl06.txt"
+
+ num_differences = compare(
+ data_for_tests_dir / "icesat-2-ATL06" / "ATL06_20230816161508_08782002_006_02.h5",
+ data_for_tests_dir / "icesat-2-ATL06" / "ATL06_20230816234629_08822013_006_01.h5",
+ show_chunks=True,
+ show_attributes=True,
+ file_text=str(out_path),
+ )
+
+ assert num_differences == 5280
+
+
+def test_error_on_different_file_types(temp_data_dir):
+ file1 = data_for_tests_dir / "icesat-2-ATL06" / "ATL06_20230816161508_08782002_006_02.h5"
+ file2 = data_for_tests_dir / "test_a.nc"
+
+ with pytest.raises(TypeError):
+ compare(file1, file2)
diff --git a/tests/test_getters.py b/tests/test_getters.py
new file mode 100644
index 0000000..0c2e1ae
--- /dev/null
+++ b/tests/test_getters.py
@@ -0,0 +1,16 @@
+# def test_var_properties(ds_3dims_3vars_4coords_1group):
+# with nc.Dataset(ds_3dims_3vars_4coords_1group) as ds:
+# result = get_var_properties(ds.groups["Group1"], varname="step", file_type="netcdf")
+# assert result.varname == "step"
+# assert result.dtype == "float32"
+# assert result.shape == "(3,)"
+# assert result.chunking == "contiguous"
+# assert result.attributes == {"add_offset": 5, "scale_factor": 0.5}
+#
+#
+# def test_get_scale_factor(ds_3dims_3vars_4coords_1group):
+# with nc.Dataset(ds_3dims_3vars_4coords_1group) as ds:
+# step_varProps = get_var_properties(ds.groups["Group1"], varname="step", file_type="netcdf")
+#
+# result = get_and_check_variable_scale_factor(step_varProps, step_varProps)
+# assert result == ("0.5", "0.5")
diff --git a/tests/test_utils.py b/tests/test_path_and_string_operations.py
similarity index 91%
rename from tests/test_utils.py
rename to tests/test_path_and_string_operations.py
index b87f535..4b476e7 100644
--- a/tests/test_utils.py
+++ b/tests/test_path_and_string_operations.py
@@ -27,7 +27,11 @@
import pytest
-from ncompare.utils import coerce_to_str, ensure_valid_path_exists
+from ncompare.path_and_string_operations import (
+ coerce_to_str,
+ ensure_valid_path_exists,
+ validate_file_type,
+)
def test_make_valid_path_with_simple_invalid_str_path():
@@ -50,6 +54,11 @@ def test_make_valid_path_from_Path_in_repo():
assert isinstance(returnval, Path)
+def test_validate_file_type():
+ with pytest.raises(TypeError):
+ validate_file_type(Path(__file__))
+
+
def test_error_from_wrong_path_type():
with pytest.raises(TypeError):
ensure_valid_path_exists((0, 1))
diff --git a/tests/test_utility_types.py b/tests/test_utility_types.py
new file mode 100644
index 0000000..a5fe1d4
--- /dev/null
+++ b/tests/test_utility_types.py
@@ -0,0 +1,13 @@
+from pathlib import Path
+
+import pytest
+
+from ncompare.utility_types import FileToCompare
+
+
+def test_FileToCompare():
+ with pytest.raises(TypeError):
+ assert FileToCompare(path=123, type="netcdf")
+
+ with pytest.raises(ValueError):
+ assert FileToCompare(path=Path(__file__), type="beebop_type")