From 8ee031f4441a6819147b5fde3ce776802c5a5e53 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Fri, 6 Sep 2024 10:27:49 -0400 Subject: [PATCH 1/7] clean comments --- concatenator/attribute_handling.py | 7 ++-- concatenator/dimension_cleanup.py | 53 +++++++++++++++++------------- tests/unit/test_harmony_adapter.py | 2 +- 3 files changed, 34 insertions(+), 28 deletions(-) diff --git a/concatenator/attribute_handling.py b/concatenator/attribute_handling.py index 3ec3e46..7d730e4 100644 --- a/concatenator/attribute_handling.py +++ b/concatenator/attribute_handling.py @@ -1,8 +1,5 @@ -""" -attribute_handling.py - -Functions for converting "coordinates" in netCDF variable attributes - between paths that reference a group hierarchy and flattened paths. +"""Functions for converting "coordinates" in netCDF variable attributes + between paths that reference a group hierarchy and flattened paths. """ import json diff --git a/concatenator/dimension_cleanup.py b/concatenator/dimension_cleanup.py index a989e27..3c70b17 100644 --- a/concatenator/dimension_cleanup.py +++ b/concatenator/dimension_cleanup.py @@ -1,8 +1,8 @@ -""" -dimension_cleanup.py +"""Functions for renaming duplicated dimension names for netCDF variables. -Functions for renaming duplicated dimension names for netCDF variables, so that xarray can handle the dataset. +So that xarray can handle the dataset. """ + import collections import netCDF4 as nc @@ -29,16 +29,20 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset: dup_vars[var_name] = var # populate dictionary with variables with vars with dup dims for dup_var_name, dup_var in dup_vars.items(): - dim_list = list(dup_var.dimensions) # original dimensions of the variable with duplicated dims + dim_list = list( + dup_var.dimensions + ) # original dimensions of the variable with duplicated dims # Dimension(s) that are duplicated are retrieved. # Note: this is not yet tested for more than one duplicated dimension. dim_dup = [item for item, count in collections.Counter(dim_list).items() if count > 1][0] - dim_dup_length = dup_var.shape[dup_var.dimensions.index(dim_dup)] # length of the duplicated dimension + dim_dup_length = dup_var.shape[ + dup_var.dimensions.index(dim_dup) + ] # length of the duplicated dimension # New dimension and variable names are created. - dim_dup_new = dim_dup + '_1' - var_name_new = dup_var_name + '_1' + dim_dup_new = dim_dup + "_1" + var_name_new = dup_var_name + "_1" dup_new_varnames.append(var_name_new) # The last dimension for the variable is replaced with the new name in a temporary list. @@ -48,9 +52,9 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset: new_dup_var = {} # Attributes for the original variable are retrieved. - attrs_contents = get_attributes_minus_fillvalue_and_renamed_coords(original_var_name=dup_var_name, - new_var_name=dim_dup_new, - original_dataset=nc_dataset) + attrs_contents = get_attributes_minus_fillvalue_and_renamed_coords( + original_var_name=dup_var_name, new_var_name=dim_dup_new, original_dataset=nc_dataset + ) # for attrname in dup_var.ncattrs(): # if attrname != '_FillValue': # contents: str = nc_dataset.variables[dup_var_name].getncattr(attrname) @@ -71,11 +75,15 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset: if dim_dup in nc_dataset.variables.keys(): # New variable object is created for the renamed, previously duplicated dimension. - new_dup_var[dim_dup_new] = nc_dataset.createVariable(dim_dup_new, nc_dataset.variables[dim_dup].dtype, - (dim_dup_new,), fill_value=fill_value) - dim_var_attr_contents = get_attributes_minus_fillvalue_and_renamed_coords(original_var_name=dim_dup, - new_var_name=dim_dup_new, - original_dataset=nc_dataset) + new_dup_var[dim_dup_new] = nc_dataset.createVariable( + dim_dup_new, + nc_dataset.variables[dim_dup].dtype, + (dim_dup_new,), + fill_value=fill_value, + ) + dim_var_attr_contents = get_attributes_minus_fillvalue_and_renamed_coords( + original_var_name=dim_dup, new_var_name=dim_dup_new, original_dataset=nc_dataset + ) for attr_name, contents in dim_var_attr_contents.items(): new_dup_var[dim_dup_new].setncattr(attr_name, contents) @@ -85,8 +93,9 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset: del nc_dataset.variables[dup_var_name] # Replace original *Variable* with new variable with no duplicated dimensions. - new_dup_var[dup_var_name] = nc_dataset.createVariable(dup_var_name, str(dup_var[:].dtype), - tuple(new_dim_list), fill_value=fill_value) + new_dup_var[dup_var_name] = nc_dataset.createVariable( + dup_var_name, str(dup_var[:].dtype), tuple(new_dim_list), fill_value=fill_value + ) for attr_name, contents in attrs_contents.items(): new_dup_var[dup_var_name].setncattr(attr_name, contents) new_dup_var[dup_var_name][:] = dup_var[:] @@ -94,16 +103,16 @@ def remove_duplicate_dims(nc_dataset: nc.Dataset) -> nc.Dataset: return nc_dataset -def get_attributes_minus_fillvalue_and_renamed_coords(original_var_name: str, - new_var_name: str, - original_dataset: nc.Dataset) -> dict: +def get_attributes_minus_fillvalue_and_renamed_coords( + original_var_name: str, new_var_name: str, original_dataset: nc.Dataset +) -> dict: """Variable attributes are retrieved.""" attrs_contents = {} for ncattr in original_dataset.variables[original_var_name].ncattrs(): - if ncattr != '_FillValue': + if ncattr != "_FillValue": contents: str = original_dataset.variables[original_var_name].getncattr(ncattr) - if ncattr == 'coordinates': + if ncattr == "coordinates": contents.replace(original_var_name, new_var_name) attrs_contents[ncattr] = contents diff --git a/tests/unit/test_harmony_adapter.py b/tests/unit/test_harmony_adapter.py index 5526506..73eb183 100644 --- a/tests/unit/test_harmony_adapter.py +++ b/tests/unit/test_harmony_adapter.py @@ -27,7 +27,7 @@ def test_service_invoke(self, temp_output_dir): # test with both paged catalogs and un-paged catalogs for in_catalog_name in ["catalog.json", "catalog0.json"]: - # Copy granule files, because stitchee modifies the Dataset's variable names during flattening. + # Copy granule files, because Dataset's variable names are modified during flattening. # If stitchee is run two times on the same file, it will likely fail the second time. _ = prep_input_files(self.__granules_path, self.__granule_copies_path) From 621829795d82ffc2b7326b2c0e218583e0a8984a Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Fri, 6 Sep 2024 10:52:04 -0400 Subject: [PATCH 2/7] update poetry dependencies, removing dask --- poetry.lock | 1428 +++++++++++++++++++++++++----------------------- pyproject.toml | 6 +- 2 files changed, 756 insertions(+), 678 deletions(-) diff --git a/poetry.lock b/poetry.lock index e5135a1..1820ddf 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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| 25 +++++++++++++--------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/concatenator/dataset_and_group_handling.py b/concatenator/dataset_and_group_handling.py index 8e44a2a..d387137 100644 --- a/concatenator/dataset_and_group_handling.py +++ b/concatenator/dataset_and_group_handling.py @@ -1,12 +1,8 @@ -""" -dataset_and_group_handling.py - -Functions for converting multidimensional data structures - between a group hierarchy and a flat structure -""" +"""Functions to convert data structures between a group hierarchy and a flat structure.""" from __future__ import annotations +import logging import re from logging import Logger @@ -20,6 +16,8 @@ regroup_coordinate_attribute, ) +module_logger = logging.getLogger(__name__) + # Match dimension names such as "__char28" or "__char16". Used for CERES datasets. _string_dimension_name_pattern = re.compile(r"__char[0-9]+") @@ -51,7 +49,7 @@ def walk( var_group_name = f"{group_path}{concatenator.group_delim}{var_name}" new_dataset.variables[var_group_name] = var - # Flatten the paths of variables referenced in the coordinates attribute + # Flatten the paths of variables referenced in the 'coordinates' attribute flatten_coordinate_attribute_paths(new_dataset, var, var_group_name) if (len(var.dimensions) == 1) and _string_dimension_name_pattern.fullmatch( @@ -99,6 +97,7 @@ def flatten_grouped_dataset( ---------- nc_dataset : nc.Dataset netCDF4 Dataset that contains groups + ensure_all_dims_are_coords Returns ------- @@ -124,7 +123,7 @@ def flatten_grouped_dataset( # Copy variables to root group with new name nc_dataset.variables[new_var_name] = var - # Flatten the paths of variables referenced in the coordinates attribute. + # Flatten the paths of variables referenced in the 'coordinates' attribute. flatten_coordinate_attribute_paths(nc_dataset, var, new_var_name) del nc_dataset.variables[var_name] # Delete old variable @@ -173,6 +172,7 @@ def regroup_flattened_dataset( List of xarray datasets to be combined output_file : str Name of the output file to write the resulting NetCDF file to. + history_to_append : str """ with nc.Dataset(output_file, mode="w", format="NETCDF4") as base_dataset: # Copy global attributes @@ -325,7 +325,9 @@ def _get_dimension_size(dataset: nc.Dataset, dim_name: str) -> int: return dim_size -def validate_workable_files(files: list[str], logger: Logger) -> tuple[list[str], int]: +def validate_workable_files( + files: list[str], logger: Logger | None = module_logger +) -> tuple[list[str], int]: """Remove files from a list that are not open-able as netCDF or that are empty.""" workable_files = [] for file in files: @@ -335,7 +337,10 @@ def validate_workable_files(files: list[str], logger: Logger) -> tuple[list[str] if is_empty is False: workable_files.append(file) except OSError: - logger.debug("Error opening <%s> as a netCDF dataset. Skipping.", file) + if logger: + logger.debug("Error opening <%s> as a netCDF dataset. Skipping.", file) + else: + print("Error opening <%s> as a netCDF dataset. Skipping.") # addressing GitHub issue 153: propagate the first empty file if all input files are empty if (len(workable_files)) == 0 and (len(files) > 0): From ae72131f1f7dbbe1e0753fce8504598d1001b43a Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Fri, 6 Sep 2024 10:59:47 -0400 Subject: [PATCH 4/7] remove dask for real this time --- poetry.lock | 159 +------------------------------------------------ pyproject.toml | 1 - 2 files changed, 1 insertion(+), 159 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1820ddf..cb529d5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -433,17 +433,6 @@ files = [ [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} -[[package]] -name = "cloudpickle" -version = "3.0.0" -description = "Pickler class to extend the standard pickle.Pickler functionality" -optional = false -python-versions = ">=3.8" -files = [ - {file = "cloudpickle-3.0.0-py3-none-any.whl", hash = "sha256:246ee7d0c295602a036e86369c77fecda4ab17b506496730f2f576d9016fd9c7"}, - {file = "cloudpickle-3.0.0.tar.gz", hash = "sha256:996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882"}, -] - [[package]] name = "colorama" version = "0.4.6" @@ -572,35 +561,6 @@ files = [ [package.dependencies] requests = "*" -[[package]] -name = "dask" -version = "2024.8.2" -description = "Parallel PyData with Task Scheduling" -optional = false -python-versions = ">=3.10" -files = [ - {file = "dask-2024.8.2-py3-none-any.whl", hash = "sha256:484c317ee870140dbeccc759a91fd98821bba98d71a43eda7856fc9e859b03a1"}, - {file = "dask-2024.8.2.tar.gz", hash = "sha256:1d05e09166ac7927a54401e998aa1599e86aac666edbdaeb3096bf4b957029e0"}, -] - -[package.dependencies] -click = ">=8.1" -cloudpickle = ">=3.0.0" -fsspec = ">=2021.09.0" -importlib-metadata = {version = ">=4.13.0", markers = "python_version < \"3.12\""} -packaging = ">=20.0" -partd = ">=1.4.0" -pyyaml = ">=5.3.1" -toolz = ">=0.10.0" - -[package.extras] -array = ["numpy (>=1.24)"] -complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=14.0.1)"] -dataframe = ["dask-expr (>=1.1,<1.2)", "dask[array]", "pandas (>=2.0)"] -diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"] -distributed = ["distributed (==2024.8.2)"] -test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"] - [[package]] name = "debugpy" version = "1.8.5" @@ -710,45 +670,6 @@ files = [ [package.extras] devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] -[[package]] -name = "fsspec" -version = "2024.9.0" -description = "File-system specification" -optional = false -python-versions = ">=3.8" -files = [ - {file = "fsspec-2024.9.0-py3-none-any.whl", hash = "sha256:a0947d552d8a6efa72cc2c730b12c41d043509156966cca4fb157b0f2a0c574b"}, - {file = "fsspec-2024.9.0.tar.gz", hash = "sha256:4b0afb90c2f21832df142f292649035d80b421f60a9e1c027802e5a0da2b04e8"}, -] - -[package.extras] -abfs = ["adlfs"] -adl = ["adlfs"] -arrow = ["pyarrow (>=1)"] -dask = ["dask", "distributed"] -dev = ["pre-commit", "ruff"] -doc = ["numpydoc", "sphinx", "sphinx-design", "sphinx-rtd-theme", "yarl"] -dropbox = ["dropbox", "dropboxdrivefs", "requests"] -full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs", "smbprotocol", "tqdm"] -fuse = ["fusepy"] -gcs = ["gcsfs"] -git = ["pygit2"] -github = ["requests"] -gs = ["gcsfs"] -gui = ["panel"] -hdfs = ["pyarrow (>=1)"] -http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)"] -libarchive = ["libarchive-c"] -oci = ["ocifs"] -s3 = ["s3fs"] -sftp = ["paramiko"] -smb = ["smbprotocol"] -ssh = ["paramiko"] -test = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "numpy", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "requests"] -test-downstream = ["aiobotocore (>=2.5.4,<3.0.0)", "dask-expr", "dask[dataframe,test]", "moto[server] (>4,<5)", "pytest-timeout", "xarray"] -test-full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "cloudpickle", "dask", "distributed", "dropbox", "dropboxdrivefs", "fastparquet", "fusepy", "gcsfs", "jinja2", "kerchunk", "libarchive-c", "lz4", "notebook", "numpy", "ocifs", "pandas", "panel", "paramiko", "pyarrow", "pyarrow (>=1)", "pyftpdlib", "pygit2", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "python-snappy", "requests", "smbprotocol", "tqdm", "urllib3", "zarr", "zstandard"] -tqdm = ["tqdm"] - [[package]] name = "ghp-import" version = "2.1.0" @@ -820,25 +741,6 @@ files = [ {file = "idna-3.8.tar.gz", hash = "sha256:d838c2c0ed6fced7693d5e8ab8e734d5f8fda53a039c0164afb0b82e771e3603"}, ] -[[package]] -name = "importlib-metadata" -version = "8.4.0" -description = "Read metadata from Python packages" -optional = false -python-versions = ">=3.8" -files = [ - {file = "importlib_metadata-8.4.0-py3-none-any.whl", hash = "sha256:66f342cc6ac9818fc6ff340576acd24d65ba0b3efabb2b4ac08b598965a4a2f1"}, - {file = "importlib_metadata-8.4.0.tar.gz", hash = "sha256:9a547d3bc3608b025f93d403fdd1aae741c24fbb8314df4b155675742ce303c5"}, -] - -[package.dependencies] -zipp = ">=0.5" - -[package.extras] -doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -perf = ["ipython"] -test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"] - [[package]] name = "iniconfig" version = "2.0.0" @@ -1085,17 +987,6 @@ test-functional = ["pytest", "pytest-randomly", "pytest-xdist"] test-integration = ["ipykernel", "jupyter-server (!=2.11)", "nbconvert", "pytest", "pytest-randomly", "pytest-xdist"] test-ui = ["calysto-bash"] -[[package]] -name = "locket" -version = "1.0.0" -description = "File-based locks for Python on Linux and Windows" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -files = [ - {file = "locket-1.0.0-py2.py3-none-any.whl", hash = "sha256:b6c819a722f7b6bd955b80781788e4a66a55628b858d347536b7e81325a3a5e3"}, - {file = "locket-1.0.0.tar.gz", hash = "sha256:5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632"}, -] - [[package]] name = "markdown" version = "3.7" @@ -1826,24 +1717,6 @@ files = [ qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"] testing = ["docopt", "pytest"] -[[package]] -name = "partd" -version = "1.4.2" -description = "Appendable key-value storage" -optional = false -python-versions = ">=3.9" -files = [ - {file = "partd-1.4.2-py3-none-any.whl", hash = "sha256:978e4ac767ec4ba5b86c6eaa52e5a2a3bc748a2ca839e8cc798f1cc6ce6efb0f"}, - {file = "partd-1.4.2.tar.gz", hash = "sha256:d022c33afbdc8405c226621b015e8067888173d85f7f5ecebb3cafed9a20f02c"}, -] - -[package.dependencies] -locket = "*" -toolz = "*" - -[package.extras] -complete = ["blosc", "numpy (>=1.20.0)", "pandas (>=1.3)", "pyzmq"] - [[package]] name = "pathspec" version = "0.12.1" @@ -2838,17 +2711,6 @@ files = [ {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"}, ] -[[package]] -name = "toolz" -version = "0.12.1" -description = "List processing tools and functional utilities" -optional = false -python-versions = ">=3.7" -files = [ - {file = "toolz-0.12.1-py3-none-any.whl", hash = "sha256:d22731364c07d72eea0a0ad45bafb2c2937ab6fd38a3507bf55eae8744aa7d85"}, - {file = "toolz-0.12.1.tar.gz", hash = "sha256:ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d"}, -] - [[package]] name = "tornado" version = "6.4.1" @@ -3010,26 +2872,7 @@ io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zar parallel = ["dask[complete]"] viz = ["matplotlib", "nc-time-axis", "seaborn"] -[[package]] -name = "zipp" -version = "3.20.1" -description = "Backport of pathlib-compatible object wrapper for zip files" -optional = false -python-versions = ">=3.8" -files = [ - {file = "zipp-3.20.1-py3-none-any.whl", hash = "sha256:9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064"}, - {file = "zipp-3.20.1.tar.gz", hash = "sha256:c22b14cc4763c5a5b04134207736c107db42e9d3ef2d9779d465f5f1bcba572b"}, -] - -[package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] -cover = ["pytest-cov"] -doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -enabler = ["pytest-enabler (>=2.2)"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] -type = ["pytest-mypy"] - [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "debaccb09772787c9363353c837d9dd705bfe7646acdd4f536b8eb6bb11c757f" +content-hash = "b556bf8d913b02f1f9975431bf088acacd2c1171d608e9f8142415948e564263" diff --git a/pyproject.toml b/pyproject.toml index a34abf3..9a9bb3f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,6 @@ stitchee = 'concatenator.run_stitchee:main' python = "^3.10" netcdf4 = ">=1.6.5" xarray = ">=2024.3.0" -dask = ">=2024.4.1" pystac = ">=0.5.3" [tool.poetry.group.dev.dependencies] From 44ee5d3e00779bd8bf46f2e0ccb6ab1647fd7e08 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Fri, 6 Sep 2024 11:04:23 -0400 Subject: [PATCH 5/7] add 'importlib-resources' to dependencies --- poetry.lock | 21 ++++++++++++++++++++- pyproject.toml | 1 + 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index cb529d5..56895f9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -741,6 +741,25 @@ files = [ {file = "idna-3.8.tar.gz", hash = "sha256:d838c2c0ed6fced7693d5e8ab8e734d5f8fda53a039c0164afb0b82e771e3603"}, ] +[[package]] +name = "importlib-resources" +version = "6.4.4" +description = "Read resources from Python packages" +optional = false +python-versions = ">=3.8" +files = [ + {file = "importlib_resources-6.4.4-py3-none-any.whl", hash = "sha256:dda242603d1c9cd836c3368b1174ed74cb4049ecd209e7a1a0104620c18c5c11"}, + {file = "importlib_resources-6.4.4.tar.gz", hash = "sha256:20600c8b7361938dc0bb2d5ec0297802e575df486f5a544fa414da65e13721f7"}, +] + +[package.extras] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["jaraco.test (>=5.4)", "pytest (>=6,!=8.1.*)", "zipp (>=3.17)"] +type = ["pytest-mypy"] + [[package]] name = "iniconfig" version = "2.0.0" @@ -2875,4 +2894,4 @@ viz = ["matplotlib", "nc-time-axis", "seaborn"] [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "b556bf8d913b02f1f9975431bf088acacd2c1171d608e9f8142415948e564263" +content-hash = "e6568f626cd85b171ac5fa92e71478613c09a9aa6bc3fdc660b3cbd166fdd183" diff --git a/pyproject.toml b/pyproject.toml index 9a9bb3f..26d0dec 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,6 +22,7 @@ python = "^3.10" netcdf4 = ">=1.6.5" xarray = ">=2024.3.0" pystac = ">=0.5.3" +importlib-resources = ">=6.4.4" [tool.poetry.group.dev.dependencies] pytest = ">=8.1.1" From 663c6fd9c6a5be8ca1eeb94a0028fd923cfab068 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Fri, 6 Sep 2024 11:06:41 -0400 Subject: [PATCH 6/7] change importlib-resources to importlib-metadata --- poetry.lock | 41 ++++++++++++++++++++++++++++++----------- pyproject.toml | 2 +- 2 files changed, 31 insertions(+), 12 deletions(-) diff --git a/poetry.lock b/poetry.lock index 56895f9..794e4e4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -742,23 +742,23 @@ files = [ ] [[package]] -name = "importlib-resources" -version = "6.4.4" -description = "Read resources from Python packages" +name = "importlib-metadata" +version = "8.4.0" +description = "Read metadata from Python packages" optional = false python-versions = ">=3.8" files = [ - {file = "importlib_resources-6.4.4-py3-none-any.whl", hash = "sha256:dda242603d1c9cd836c3368b1174ed74cb4049ecd209e7a1a0104620c18c5c11"}, - {file = "importlib_resources-6.4.4.tar.gz", hash = "sha256:20600c8b7361938dc0bb2d5ec0297802e575df486f5a544fa414da65e13721f7"}, + {file = "importlib_metadata-8.4.0-py3-none-any.whl", hash = "sha256:66f342cc6ac9818fc6ff340576acd24d65ba0b3efabb2b4ac08b598965a4a2f1"}, + {file = "importlib_metadata-8.4.0.tar.gz", hash = "sha256:9a547d3bc3608b025f93d403fdd1aae741c24fbb8314df4b155675742ce303c5"}, ] +[package.dependencies] +zipp = ">=0.5" + [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] -cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -enabler = ["pytest-enabler (>=2.2)"] -test = ["jaraco.test (>=5.4)", "pytest (>=6,!=8.1.*)", "zipp (>=3.17)"] -type = ["pytest-mypy"] +perf = ["ipython"] +test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"] [[package]] name = "iniconfig" @@ -2891,7 +2891,26 @@ io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zar parallel = ["dask[complete]"] viz = ["matplotlib", "nc-time-axis", "seaborn"] +[[package]] +name = "zipp" +version = "3.20.1" +description = "Backport of pathlib-compatible object wrapper for zip files" +optional = false +python-versions = ">=3.8" +files = [ + {file = "zipp-3.20.1-py3-none-any.whl", hash = "sha256:9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064"}, + {file = "zipp-3.20.1.tar.gz", hash = "sha256:c22b14cc4763c5a5b04134207736c107db42e9d3ef2d9779d465f5f1bcba572b"}, +] + +[package.extras] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] + [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "e6568f626cd85b171ac5fa92e71478613c09a9aa6bc3fdc660b3cbd166fdd183" +content-hash = "79504b81a3a9a7c0655791b6d1d70b9ee8d0aff3805ab274881aca4bc49d29dc" diff --git a/pyproject.toml b/pyproject.toml index 26d0dec..baa108e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,7 +22,7 @@ python = "^3.10" netcdf4 = ">=1.6.5" xarray = ">=2024.3.0" pystac = ">=0.5.3" -importlib-resources = ">=6.4.4" +importlib-metadata = "^8.4.0" [tool.poetry.group.dev.dependencies] pytest = ">=8.1.1" From 2bced18f1b3ceda7f409325cbaeee9003e8233fa Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Fri, 6 Sep 2024 11:25:45 -0400 Subject: [PATCH 7/7] update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9347f32..f14fa46 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - Allow single netCDF file input in addition to single text file listings ([#230](https://github.com/nasa/stitchee/issues/230))([**@danielfromearth**](https://github.com/danielfromearth)) +- Remove the dask dependency ([#235](https://github.com/nasa/stitchee/issues/235))([**@danielfromearth**](https://github.com/danielfromearth)) ## [1.3.0] - 2024-07-11