From d0875077082c6062cfac0515497462977ffc6667 Mon Sep 17 00:00:00 2001 From: stitchee bot Date: Wed, 10 Jul 2024 13:40:40 +0000 Subject: [PATCH 01/13] /version 1.4.0a0 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 08e922a..018a62f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "stitchee" -version = "1.3.0a24" +version = "1.4.0a0" description = "NetCDF4 Along-existing-dimension Concatenation Service" authors = ["Daniel Kaufman "] readme = "README.md" From 02465eefc51862806b6b4da1994f56bc75007c41 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 15 Jul 2024 13:03:26 +0000 Subject: [PATCH 02/13] Bump the pip-dependencies group with 4 updates Bumps the pip-dependencies group with 4 updates: [dask](https://github.com/dask/dask), [ruff](https://github.com/astral-sh/ruff), [mkdocs-jupyter](https://github.com/danielfrg/mkdocs-jupyter) and [mkdocs-material](https://github.com/squidfunk/mkdocs-material). Updates `dask` from 2024.6.2 to 2024.7.0 - [Release notes](https://github.com/dask/dask/releases) - [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md) - [Commits](https://github.com/dask/dask/compare/2024.6.2...2024.7.0) Updates `ruff` from 0.5.0 to 0.5.2 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.5.0...0.5.2) Updates `mkdocs-jupyter` from 0.24.7 to 0.24.8 - [Changelog](https://github.com/danielfrg/mkdocs-jupyter/blob/main/CHANGELOG.md) - [Commits](https://github.com/danielfrg/mkdocs-jupyter/compare/0.24.7...0.24.8) Updates `mkdocs-material` from 9.5.28 to 9.5.29 - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](https://github.com/squidfunk/mkdocs-material/compare/9.5.28...9.5.29) --- updated-dependencies: - dependency-name: dask dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip-dependencies - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-patch dependency-group: pip-dependencies - dependency-name: mkdocs-jupyter dependency-type: direct:development update-type: version-update:semver-patch dependency-group: pip-dependencies - dependency-name: mkdocs-material dependency-type: direct:development update-type: version-update:semver-patch dependency-group: pip-dependencies ... 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+0000 Subject: [PATCH 03/13] /version 1.4.0a1 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 018a62f..27921e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "stitchee" -version = "1.4.0a0" +version = "1.4.0a1" description = "NetCDF4 Along-existing-dimension Concatenation Service" authors = ["Daniel Kaufman "] readme = "README.md" From 614fc1a8e5340c614352c457a277d685ed9b5c5b Mon Sep 17 00:00:00 2001 From: stitchee bot Date: Wed, 17 Jul 2024 16:53:30 +0000 Subject: [PATCH 04/13] /version 1.4.0a2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 27921e6..f72cb69 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "stitchee" -version = "1.4.0a1" +version = "1.4.0a2" description = "NetCDF4 Along-existing-dimension Concatenation Service" authors = ["Daniel Kaufman "] readme = "README.md" From d08bcc0b65636eff6868a3c67ef77e818a22e37d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 1 Aug 2024 22:41:49 +0000 Subject: [PATCH 05/13] Bump the pip-dependencies group with 7 updates Bumps the pip-dependencies group with 7 updates: | Package | From | To | | --- | --- | --- | | [xarray](https://github.com/pydata/xarray) | `2024.6.0` | `2024.7.0` | | [dask](https://github.com/dask/dask) | `2024.7.0` | `2024.7.1` | | [pytest](https://github.com/pytest-dev/pytest) | `8.2.2` | `8.3.2` | | [mypy](https://github.com/python/mypy) | `1.10.1` | `1.11.1` | | [ruff](https://github.com/astral-sh/ruff) | `0.5.2` | `0.5.5` | | [mkdocstrings](https://github.com/mkdocstrings/mkdocstrings) | `0.25.1` | `0.25.2` | | [mkdocs-material](https://github.com/squidfunk/mkdocs-material) | `9.5.29` | `9.5.30` | Updates `xarray` from 2024.6.0 to 2024.7.0 - [Release notes](https://github.com/pydata/xarray/releases) - [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md) - [Commits](https://github.com/pydata/xarray/compare/v2024.06.0...v2024.07.0) Updates `dask` from 2024.7.0 to 2024.7.1 - [Release notes](https://github.com/dask/dask/releases) - [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md) - [Commits](https://github.com/dask/dask/compare/2024.7.0...2024.7.1) Updates `pytest` from 8.2.2 to 8.3.2 - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/8.2.2...8.3.2) Updates `mypy` from 1.10.1 to 1.11.1 - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](https://github.com/python/mypy/compare/v1.10.1...v1.11.1) Updates `ruff` from 0.5.2 to 0.5.5 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.5.2...0.5.5) Updates `mkdocstrings` from 0.25.1 to 0.25.2 - [Release notes](https://github.com/mkdocstrings/mkdocstrings/releases) - [Changelog](https://github.com/mkdocstrings/mkdocstrings/blob/main/CHANGELOG.md) - [Commits](https://github.com/mkdocstrings/mkdocstrings/compare/0.25.1...0.25.2) Updates `mkdocs-material` from 9.5.29 to 9.5.30 - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](https://github.com/squidfunk/mkdocs-material/compare/9.5.29...9.5.30) --- updated-dependencies: - dependency-name: xarray dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip-dependencies - dependency-name: dask dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip-dependencies - dependency-name: pytest dependency-type: direct:development 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b/CHANGELOG.md @@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file. The format is based on [Common Changelog](https://common-changelog.org/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## Unreleased + +### 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)) + + ## [1.3.0] - 2024-07-11 ### Changed From 3d69bcabf62751dafddf799694b3d45310152d1e Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Thu, 8 Aug 2024 11:11:45 -0400 Subject: [PATCH 08/13] expand allowable single file input from just text files to also a netCDF file --- concatenator/file_ops.py | 17 +++++++++++++++-- tests/unit/test_run_stitchee.py | 19 +++++++++++++++++++ 2 files changed, 34 insertions(+), 2 deletions(-) diff --git a/concatenator/file_ops.py b/concatenator/file_ops.py index 84dbeab..70e1094 100644 --- a/concatenator/file_ops.py +++ b/concatenator/file_ops.py @@ -8,6 +8,8 @@ logger = logging.getLogger(__name__) +netcdf_extensions = [".nc", ".nc4", ".netcdf"] + def add_label_to_path(x: str, label="_flat_intermediate") -> str: """Constructs new filepath with label at end.""" @@ -55,7 +57,15 @@ def validate_output_path(filepath: str, overwrite: bool = False) -> str: def validate_input_path(path_or_paths: list[str]) -> list[str]: - """Checks whether input is a valid directory, list of files, or a text file containing paths.""" + """Checks whether input is a list of files, a directory, or a text file containing paths. + + If the input is... + - a list of filepaths, then use those filepaths. + - a valid directory, then get the paths for all the files in the directory. + - a single file: + - that is a valid text file, then get the names of the files from each row in the text file. + - that is a valid netCDF file, then use that one filepath + """ print(f"parsed_input === {path_or_paths}") if len(path_or_paths) > 1: input_files = path_or_paths @@ -64,7 +74,10 @@ def validate_input_path(path_or_paths: list[str]) -> list[str]: if directory_or_path.is_dir(): input_files = _get_list_of_filepaths_from_dir(directory_or_path) elif directory_or_path.is_file(): - input_files = _get_list_of_filepaths_from_file(directory_or_path) + if directory_or_path.suffix in netcdf_extensions: + input_files = [str(directory_or_path)] + else: + input_files = _get_list_of_filepaths_from_file(directory_or_path) else: raise TypeError( "If one path is provided for 'data_dir_or_file_or_filepaths', " diff --git a/tests/unit/test_run_stitchee.py b/tests/unit/test_run_stitchee.py index 11e58d1..643c8d5 100644 --- a/tests/unit/test_run_stitchee.py +++ b/tests/unit/test_run_stitchee.py @@ -70,3 +70,22 @@ def test_run_stitchee_cli_with_one_directorypath(self, temp_output_dir): with patch.object(sys, "argv", test_args): concatenator.run_stitchee.main() + + def test_run_stitchee_cli_with_one_netCDFpath(self, temp_output_dir): + test_args = [ + concatenator.run_stitchee.__file__, + path_str( + self.__granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4" + ), + "--copy_input_files", + "--verbose", + "-o", + path_str(temp_output_dir, "test_run_stitchee_output.nc"), + "--concat_method", + "xarray-concat", + "--concat_dim", + "mirror_step", + ] + + with patch.object(sys, "argv", test_args): + concatenator.run_stitchee.main() From c0efe9e9b5bee70ea0dd3370e55481944b40eed2 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Thu, 8 Aug 2024 12:08:17 -0400 Subject: [PATCH 09/13] add unit test for case of text input with list of file paths --- tests/conftest.py | 28 +++++++++++++++++++++ tests/unit/test_run_stitchee.py | 44 +++++++++++++++++++-------------- 2 files changed, 53 insertions(+), 19 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index b917654..457b43a 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -8,6 +8,11 @@ import numpy as np import pytest +test_path = Path(__file__).parents[0].resolve() +data_path = test_path.joinpath("data") +harmony_path = data_path.joinpath("harmony") +granules_path = harmony_path.joinpath("granules") + class DataDirs(typing.NamedTuple): test_path: Path @@ -160,3 +165,26 @@ def ds_3dims_3vars_4coords_1group_part3(temp_toy_data_dir): f.close() return filepath + + +@pytest.fixture(scope="function") +def text_file_with_three_paths(temp_toy_data_dir) -> Path: + filepath = temp_toy_data_dir / "text_file_with_paths.txt" + + paths = [ + path_str(granules_path, x) + for x in [ + "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4", + "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4", + "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4", + ] + ] + + contents = f"""{paths[0]} +{paths[1]} +{paths[2]} +""" + with open(filepath, "w") as f: + f.write(contents) + + return filepath diff --git a/tests/unit/test_run_stitchee.py b/tests/unit/test_run_stitchee.py index 643c8d5..96c2006 100644 --- a/tests/unit/test_run_stitchee.py +++ b/tests/unit/test_run_stitchee.py @@ -1,5 +1,4 @@ import sys -from pathlib import Path from unittest.mock import patch import pytest @@ -7,7 +6,7 @@ import concatenator from concatenator.run_stitchee import parse_args -from ..conftest import path_str +from ..conftest import granules_path, path_str def test_parser(): @@ -24,23 +23,13 @@ def test_parser(): @pytest.mark.usefixtures("pass_options") class TestBatching: - __test_path = Path(__file__).parents[1].resolve() - __data_path = __test_path.joinpath("data") - __harmony_path = __data_path.joinpath("harmony") - __granules_path = __harmony_path.joinpath("granules") def test_run_stitchee_cli_with_three_filepaths(self, temp_output_dir): test_args = [ concatenator.run_stitchee.__file__, - path_str( - self.__granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4" - ), - path_str( - self.__granules_path, "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4" - ), - path_str( - self.__granules_path, "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4" - ), + path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4"), + path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4"), + path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4"), "--copy_input_files", "--verbose", "-o", @@ -57,7 +46,7 @@ def test_run_stitchee_cli_with_three_filepaths(self, temp_output_dir): def test_run_stitchee_cli_with_one_directorypath(self, temp_output_dir): test_args = [ concatenator.run_stitchee.__file__, - str(self.__granules_path), + str(granules_path), "--copy_input_files", "--verbose", "-o", @@ -74,9 +63,26 @@ def test_run_stitchee_cli_with_one_directorypath(self, temp_output_dir): def test_run_stitchee_cli_with_one_netCDFpath(self, temp_output_dir): test_args = [ concatenator.run_stitchee.__file__, - path_str( - self.__granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4" - ), + path_str(granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4"), + "--copy_input_files", + "--verbose", + "-o", + path_str(temp_output_dir, "test_run_stitchee_output.nc"), + "--concat_method", + "xarray-concat", + "--concat_dim", + "mirror_step", + ] + + with patch.object(sys, "argv", test_args): + concatenator.run_stitchee.main() + + def test_run_stitchee_cli_with_one_path_to_text_listing_of_three_files( + self, temp_output_dir, text_file_with_three_paths + ): + test_args = [ + concatenator.run_stitchee.__file__, + str(text_file_with_three_paths), "--copy_input_files", "--verbose", "-o", From e7ced6f50b06853491fb30a889c8872dcb71038c Mon Sep 17 00:00:00 2001 From: stitchee bot Date: Tue, 13 Aug 2024 13:58:14 +0000 Subject: [PATCH 10/13] /version 1.4.0a4 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index da03cd5..e14c97b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "stitchee" -version = "1.4.0a3" +version = "1.4.0a4" description = "NetCDF4 Along-existing-dimension Concatenation Service" authors = ["Daniel Kaufman "] readme = "README.md" From 7ddba704bc7927568aaaf9cb2998b2933b289c78 Mon Sep 17 00:00:00 2001 From: stitchee bot Date: Mon, 19 Aug 2024 14:14:03 +0000 Subject: [PATCH 11/13] /version 1.4.0rc1 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index e14c97b..19e68d6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "stitchee" -version = "1.4.0a4" +version = "1.4.0rc1" description = "NetCDF4 Along-existing-dimension Concatenation Service" authors = ["Daniel Kaufman "] readme = "README.md" From 0a02b4f2cd39c679f4f189a2b9f7c4243e29289a Mon Sep 17 00:00:00 2001 From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com> Date: Mon, 19 Aug 2024 12:19:09 -0400 Subject: [PATCH 12/13] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9347f32..a050735 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file. The format is based on [Common Changelog](https://common-changelog.org/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## Unreleased +## [1.4.0] - 2024-08-19 ### 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)) From f71f2418f39a80c0a99492adfebfb539f22faa58 Mon Sep 17 00:00:00 2001 From: stitchee bot Date: Mon, 19 Aug 2024 16:21:19 +0000 Subject: [PATCH 13/13] /version 1.4.0rc2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 19e68d6..1ecbce4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "stitchee" -version = "1.4.0rc1" +version = "1.4.0rc2" description = "NetCDF4 Along-existing-dimension Concatenation Service" authors = ["Daniel Kaufman "] readme = "README.md"