diff --git a/.github/dependabot.yml b/.github/dependabot.yml index d42179e..1dc05b4 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -9,6 +9,10 @@ updates: directory: "/" schedule: interval: "monthly" + groups: + pip-dependencies: + patterns: + - "*" # Raise pull requests for version updates # to pip against the `develop` branch target-branch: "develop" @@ -17,6 +21,10 @@ updates: schedule: # Check for updates to GitHub Actions every week interval: "monthly" + groups: + gha-dependencies: + patterns: + - "*" # Raise pull requests for version updates # to pip against the `develop` branch target-branch: "develop" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 295e3dc..fb45b97 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,7 +3,7 @@ default_language_version: repos: - repo: https://github.com/asottile/pyupgrade - rev: v3.15.2 + rev: v3.16.0 hooks: - id: pyupgrade args: [ "--py39-plus" ] @@ -24,7 +24,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.4.6' + rev: 'v0.5.1' hooks: - id: ruff args: [ "--fix" ] @@ -36,7 +36,7 @@ repos: - id: black-jupyter - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.10.0 + rev: v1.10.1 hooks: - id: mypy diff --git a/CHANGELOG.md b/CHANGELOG.md index bc4cf3d..9877d64 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,178 +1,201 @@ # Changelog All notable changes to this project will be documented in this file. -The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), +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). -## [1.9.0] -### Added -- [Issue #210](https://github.com/nasa/ncompare/issues/210): Add gif of usage to readme +## [unreleased] + ### Changed -- [Issue #184](https://github.com/nasa/ncompare/issues/184): Change license to Apache License 2.0. and include copyright header text -- [Issue #200](https://github.com/nasa/ncompare/issues/200): Change dependabot frequency to monthly -### Deprecated + +- Group dependabot updates into fewer PRs ([#233](https://github.com/nasa/ncompare/issues/233)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Change xarray `Dataset.dims` reference to `Dataset.sizes` due to FutureWarning ([#246](https://github.com/nasa/ncompare/issues/246))([**@nannau**](https://github.com/nannau)) + +### Added + +- Add Journal of Open Source Software (JOSS) info to README and CITATION docs ([#229](https://github.com/nasa/ncompare/issues/229)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Make available via conda and add `conda`/`mamba` installation instructions to README.md ([#42](https://github.com/nasa/ncompare/issues/42)) ([**@jhkennedy**](https://github.com/jhkennedy), [**@danielfromearth**](https://github.com/danielfromearth)) + ### Removed + +- Remove upper bounds from dependencies ([#231](https://github.com/nasa/ncompare/issues/231)) ([**@jhkennedy**](https://github.com/jhkennedy), [**@danielfromearth**](https://github.com/danielfromearth)) + ### Fixed -- [Issue #208](https://github.com/nasa/ncompare/issues/208): Fix missing group error -- [Pull #190](https://github.com/nasa/ncompare/pull/190): Fix codecov upload token error -- [Pull #199](https://github.com/nasa/ncompare/pull/199): Resolve linting error -### Security -## [1.8.0] - 2024-03-12 -### Added +- Fix help text for second NetCDF file passed on command line ([#230](https://github.com/nasa/ncompare/pull/230)) ([**@berquist**](https://github.com/berquist)) + + +## [1.9.0] - 2024-05-29 + ### Changed -- update dependencies -- update citation -- [pull/168](https://github.com/nasa/ncompare/pull/168): updated syntax for new linting checks -### Deprecated -### Removed + +- Change license to Apache License 2.0. and include copyright header text ([#184](https://github.com/nasa/ncompare/issues/184)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Change dependabot frequency to monthly ([#200](https://github.com/nasa/ncompare/issues/200)) ([**@danielfromearth**](https://github.com/danielfromearth)) + +### Added + +- Add gif of usage to readme ([#210](https://github.com/nasa/ncompare/issues/210)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ### Fixed -### Security +- Fix missing group error ([#208](https://github.com/nasa/ncompare/issues/208)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Fix codecov upload token error ([#190](https://github.com/nasa/ncompare/pull/190)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Resolve linting error ([#199](https://github.com/nasa/ncompare/pull/199)) ([**@danielfromearth**](https://github.com/danielfromearth)) + + +## [1.8.0] - 2024-03-12 + +### Changed + +- Update dependencies ([#169](https://github.com/nasa/ncompare/pull/169)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Update citation ([`2178b97`](https://github.com/nasa/ncompare/pull/169/commits/2178b970fa32fa820c03d9c8c82b0ef8d8249150)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Update syntax for new linting checks ([#168](https://github.com/nasa/ncompare/pull/168)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ## [1.7.3] - 2024-02-06 -### Added + ### Changed -- add Zenodo badge to readme -### Deprecated -### Removed -### Fixed -### Security + +- Add Zenodo badge to readme ([#149](https://github.com/nasa/ncompare/pull/149)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ## [1.7.2] - 2024-02-06 -### Added + ### Changed -- add pyOpenSci badge to readme -### Deprecated -### Removed -### Fixed -### Security + +- Add pyOpenSci badge to readme ([#148](https://github.com/nasa/ncompare/pull/148)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ## [1.7.1] - 2024-02-06 -### Added + ### Changed -- update dependencies -- update citation -### Deprecated -### Removed -### Fixed -### Security + +- Update dependencies ([#147](https://github.com/nasa/ncompare/pull/147)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Update citation ([#147](https://github.com/nasa/ncompare/pull/147)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ## [1.7.0] - 2024-02-06 -### Added + ### Changed -- [pull/136](https://github.com/nasa/ncompare/pull/136): Replace data in example notebook with those requiring no credentials -### Deprecated -### Removed + +- Replace data in example notebook with those requiring no credentials ([#136](https://github.com/nasa/ncompare/pull/136)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ### Fixed -- [pull/135](https://github.com/nasa/ncompare/pull/135): Fix links in readme -### Security + +- Fix links in readme ([#135](https://github.com/nasa/ncompare/pull/135)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ## [1.6.2] - 2024-01-16 -### Added + ### Changed -- updated PyPI classifiers in pyproject.toml -### Deprecated -### Removed -### Fixed -### Security + +- Update PyPI classifiers in pyproject.toml ([#130](https://github.com/nasa/ncompare/pull/130)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ## [1.6.1] - 2024-01-16 -### Added + ### Changed -### Deprecated + +- Bump jinja2 from 3.1.2 to 3.1.3 ([#125](https://github.com/nasa/ncompare/pull/125)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ### Removed -- removed unused placeholder file and .images folder -### Fixed -### Security -- [pull-request/125](https://github.com/nasa/ncompare/pull/125): Bump jinja2 from 3.1.2 to 3.1.3 + +- Remove unused placeholder file and .images folder ([#128](https://github.com/nasa/ncompare/pull/128)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ## [1.6.0] - 2024-01-16 -### Added -- [pull-request/79](https://github.com/nasa/ncompare/pull/79): Add option to only display variables and attributes that are different -- [pull-request/100](https://github.com/nasa/ncompare/pull/100): Add version to cli -- [pull-request/105](https://github.com/nasa/ncompare/pull/105): Add testing of ncompare with Python version 3.12 -- [issue/118](https://github.com/nasa/ncompare/issues/118): Add citation file + ### Changed -- [pull-request/99](https://github.com/nasa/ncompare/pull/99): Improve readme in a few ways (e.g., license, badges) -- [pull-request/106](https://github.com/nasa/ncompare/pull/106): Use ReadTheDocs instead of GitHub Pages for documentation -- [pull-request/113](https://github.com/nasa/ncompare/pull/113): Add codecov step to tests workflow -- [issue/88](https://github.com/nasa/ncompare/issues/88): Improve test coverage, especially for ncompare/core.py and ncompare/printing.py -- [issue/92](https://github.com/nasa/ncompare/issues/92): Ensure examples utilize publicly accessible data -- [pull-request/121](https://github.com/nasa/ncompare/pull/121): Disable text wrapping to properly show ncompare output in notebook example -- Tweaked wording regarding docstrings in the contributing guide -### Deprecated + +- Improve readme in a few ways (e.g., license, badges) ([#99](https://github.com/nasa/ncompare/pull/99)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Use ReadTheDocs instead of GitHub Pages for documentation ([#106](https://github.com/nasa/ncompare/pull/106)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Add codecov step to tests workflow ([#113](https://github.com/nasa/ncompare/pull/113)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Improve test coverage, especially for ncompare/core.py and ncompare/printing.py ([#88](https://github.com/nasa/ncompare/issues/88)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Ensure examples utilize publicly accessible data ([#92](https://github.com/nasa/ncompare/issues/92)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Disable text wrapping to properly show ncompare output in notebook example ([#121](https://github.com/nasa/ncompare/pull/121)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Tweak wording regarding docstrings in the contributing guide ([`9c20671`](https://github.com/nasa/ncompare/pull/124/commits/9c2067147036947e47daafaf6b31a08821a1417b)) ([**@danielfromearth**](https://github.com/danielfromearth)) + +### Added + +- Add option to only display variables and attributes that are different ([#79](https://github.com/nasa/ncompare/pull/79)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Add version to cli ([#100](https://github.com/nasa/ncompare/pull/100)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Add testing of ncompare with Python version 3.12 ([#105](https://github.com/nasa/ncompare/pull/105)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Add citation file ([#118](https://github.com/nasa/ncompare/issues/118)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ### Removed -- Fixed bug related to extra argument from command line + +- Fix bug related to extra argument from command line ([#124](https://github.com/nasa/ncompare/pull/124)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ### Fixed -- Updated out-dated example snippet in README -### Security + +- Update out-dated example snippet in README ([`eaddcad`](https://github.com/nasa/ncompare/pull/124/commits/eaddcad999ac52a06fdd95b7a8874bad4785111d)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ## [1.5.0] - 2023-10-25 + ### Added -- [pull-request/63](https://github.com/nasa/ncompare/pull/59): Add a tutorial example notebook. -- Added a simple GitHub Pages that links to an quarto-produced version of the tutorial notebook. -### Changed -### Deprecated -### Removed -### Fixed -### Security + +- Add a tutorial example notebook ([#63](https://github.com/nasa/ncompare/pull/63)) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Add a simple GitHub Pages that links to an quarto-produced version of the tutorial notebook. ([#64](https://github.com/nasa/ncompare/pull/64)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ## [1.4.0] - 2023-10-23 + ### Added -- [pull-request/59](https://github.com/nasa/ncompare/pull/59): Add the ability to modify the width of each column in the comparison table. -### Changed -### Deprecated -### Removed + +- Add the ability to modify the width of each column in the comparison table ([#59](https://github.com/nasa/ncompare/pull/59)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ### Fixed -- [pull-request/60](https://github.com/nasa/ncompare/pull/60): Removes an extra line of printed filepaths. -### Security + +- Remove an extra line of printed filepaths ([#60](https://github.com/nasa/ncompare/pull/60)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ## [1.3.0] - 2023-10-20 -### Added -### Changed -### Deprecated -### Removed + ### Fixed -- [pull-request/55](https://github.com/nasa/ncompare/pull/55): Fix variable value matching -### Security + +- Fix variable value matching ([#55](https://github.com/nasa/ncompare/pull/55)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ## [1.2.0] - 2023-10-11 -### Added -- [pull-request/44](https://github.com/nasa/ncompare/pull/44): Added issue templates and markdown guides for CONTRIBUTING and the CODE_OF_CONDUCT + ### Changed -- [pull-request/47](https://github.com/nasa/ncompare/pull/47): Added coverage and move test running to separate workflow yml -### Deprecated -### Removed -### Fixed -### Security -## [1.1.0] - 2023-09-26 +- Add coverage and move test running to separate workflow yml ([#47](https://github.com/nasa/ncompare/pull/47)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ### Added -- [commit/4b98808](https://github.com/nasa/ncompare/commit/4b98808cf3d8424da25a226687d304ce7d46738e): Set up dependabot for automated version updates + +- Add issue templates and markdown guides for CONTRIBUTING and the CODE_OF_CONDUCT ([#44](https://github.com/nasa/ncompare/pull/44)) ([**@danielfromearth**](https://github.com/danielfromearth)) + + +## [1.1.0] - 2023-09-26 + ### Changed -- [pull-request/28](https://github.com/nasa/ncompare/pull/28): Updated CI/CD versions, and updated README.md -### Deprecated -### Removed -### Fixed -### Security -## [1.0.2] - 2023-09-20 +- Update CI/CD versions, and updated README.md ([#28](https://github.com/nasa/ncompare/pull/28)) ([**@danielfromearth**](https://github.com/danielfromearth)) + ### Added -- Add automated publishing (via poetry) to TestPyPI and PyPI in Actions workflow [issue/19](https://github.com/nasa/ncompare/issues/19) + +- Set up dependabot for automated version updates ([`4b98808`](https://github.com/nasa/ncompare/commit/4b98808cf3d8424da25a226687d304ce7d46738e)) ([**@danielfromearth**](https://github.com/danielfromearth)) + + +## [1.0.2] - 2023-09-20 + ### Changed -- Use ruff and black for linting and formatting [issue/23](https://github.com/nasa/ncompare/issues/23) -### Deprecated -### Removed -### Fixed -### Security -## [1.0.1] - 2023-09-06 +- Use ruff and black for linting and formatting [#23](https://github.com/nasa/ncompare/issues/23) ([**@danielfromearth**](https://github.com/danielfromearth)) + ### Added + +- Add automated publishing (via poetry) to TestPyPI and PyPI in Actions workflow [#19](https://github.com/nasa/ncompare/issues/19) ([**@danielfromearth**](https://github.com/danielfromearth)) + + +## [1.0.1] - 2023-09-06 + ### Changed -- Improve test suite [#12](https://github.com/nasa/ncompare/issues/12): -- Enable `ncompare` to work with greater group depths [#13](https://github.com/nasa/ncompare/issues/13): -### Deprecated -### Removed + +- Improve test suite [#12](https://github.com/nasa/ncompare/issues/12) ([**@danielfromearth**](https://github.com/danielfromearth)) +- Enable `ncompare` to work with greater group depths [#13](https://github.com/nasa/ncompare/issues/13) ([**@danielfromearth**](https://github.com/danielfromearth)) + ### Fixed -- Fix author attribute for poetry [#5](https://github.com/nasa/ncompare/issues/5) -### Security + +- Fix author attribute for poetry [#5](https://github.com/nasa/ncompare/issues/5) ([**@danielfromearth**](https://github.com/danielfromearth)) diff --git a/CITATION.cff b/CITATION.cff index 9f457f7..81a0553 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,11 +1,35 @@ -cff-version: 1.2.0 - -message: | - Please cite this software using these metadata. - Authors are listed in alphabetical order. - -title: "ncompare" -abstract: "Compare the structure of two NetCDF files at the command line." +cff-version: "1.2.0" +authors: +- family-names: Kaufman + given-names: Daniel E. + orcid: "https://orcid.org/0000-0002-1487-7298" +- family-names: Baskin + given-names: Walter E. + orcid: "https://orcid.org/0000-0002-2241-3266" +doi: 10.5281/zenodo.11448464 +message: If you use this software, please cite our article in the + Journal of Open Source Software. +preferred-citation: + authors: + - family-names: Kaufman + given-names: Daniel E. + orcid: "https://orcid.org/0000-0002-1487-7298" + - family-names: Baskin + given-names: Walter E. + orcid: "https://orcid.org/0000-0002-2241-3266" + date-published: 2024-06-06 + doi: 10.21105/joss.06490 + issn: 2475-9066 + issue: 98 + journal: Journal of Open Source Software + publisher: + name: Open Journals + start: 6490 + title: "ncompare: A Python package for comparing netCDF structures" + type: article + url: "https://joss.theoj.org/papers/10.21105/joss.06490" + volume: 9 +title: "ncompare: A Python package for comparing netCDF structures" contact: - name: "The NASA ncompare issues page" @@ -14,18 +38,5 @@ keywords: - "netcdf" - "data comparison" - "hierarchical data" - url: "https://ncompare.readthedocs.io" repository-code: "https://github.com/nasa/ncompare" - -version: 1.9.0 -date-released: 2024-05-29 - -authors: -- family-names: "Baskin" - given-names: "Walter" - orcid: "https://orcid.org/0000-0002-2241-3266" -- family-names: "Kaufman" - given-names: "Daniel E" - orcid: "https://orcid.org/0000-0002-1487-7298" - website: "https://github.com/danielfromearth" diff --git a/README.md b/README.md index 5cd2628..5633037 100644 --- a/README.md +++ b/README.md @@ -31,6 +31,9 @@ _____ pyOpenSci + + DOI badge + Compare the structure of two NetCDF files at the command line. `ncompare` generates a view of the matching and non-matching groups and variables between two NetCDF datasets. @@ -38,11 +41,25 @@ Compare the structure of two NetCDF files at the command line. ## Installing -Install the latest version of the package from the Python Package Index (PyPI): -```console -pip install ncompare +The latest release of `ncompare` can be installed with `mamba`, `conda` or `pip`. + +#### Using `mamba` + +```bash +mamba install -c conda-forge ncompare ``` +#### Using `conda` + +```bash +conda install -c conda-forge ncompare +``` + +#### Using `pip` + +```bash +pip install ncompare +``` ## Usage diff --git a/ncompare/console.py b/ncompare/console.py index dd99d62..91f85a2 100755 --- a/ncompare/console.py +++ b/ncompare/console.py @@ -29,13 +29,15 @@ import importlib.metadata import sys import traceback +from collections.abc import Sequence +from typing import Optional from ncompare.core import compare __version__ = importlib.metadata.version('ncompare') -def _cli(args) -> argparse.Namespace: +def _cli(args: Optional[Sequence[str]]) -> argparse.Namespace: """Parse input arguments from the command line. Parameters @@ -47,7 +49,7 @@ def _cli(args) -> argparse.Namespace: 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="First NetCDF file") + parser.add_argument("nc_b", help="Second NetCDF file") parser.add_argument("-v", "--comparison_var_name", help="Comparison variable name") parser.add_argument("-g", "--comparison_var_group", help="Comparison variable group") parser.add_argument( @@ -97,7 +99,7 @@ def _cli(args) -> argparse.Namespace: return parser.parse_args(args) -def main(): # pragma: no cover +def main() -> None: # pragma: no cover """Run from the command line.""" args = _cli(None) diff --git a/ncompare/core.py b/ncompare/core.py index 113efa9..8b8d040 100644 --- a/ncompare/core.py +++ b/ncompare/core.py @@ -636,7 +636,7 @@ def _get_groups(nc_filepath: Union[str, Path]) -> list: def _get_dims(nc_filepath: Union[str, Path]) -> list: def __get_dim_list(decode_times=True): with xr.open_dataset(nc_filepath, decode_times=decode_times) as dataset: - return list(dataset.dims.items()) + return list(dataset.sizes.items()) try: dims_list = __get_dim_list() diff --git a/ncompare/utils.py b/ncompare/utils.py index 160120d..0c03149 100644 --- a/ncompare/utils.py +++ b/ncompare/utils.py @@ -29,36 +29,16 @@ def ensure_valid_path_exists(should_be_path: Union[str, Path]) -> Path: - """Convert input to a pathlib.Path and check that the resulting filepath exists.""" - fails_to_exist_msg = "Expected file does not exist: " - wrong_type_msg = "Unexpected type for something that should be convertable to a Path: " - - if isinstance(should_be_path, str): - # Convert to a Path object - path_obj = Path(should_be_path) - if path_obj.exists(): - return path_obj - raise FileNotFoundError(fails_to_exist_msg + str(should_be_path)) - - if isinstance(should_be_path, Path): - if should_be_path.exists(): - return should_be_path - raise FileNotFoundError(fails_to_exist_msg + str(should_be_path)) - - raise TypeError(wrong_type_msg + str(type(should_be_path))) + """Coerce input to a pathlib.Path and check that the resulting filepath exists.""" + path_obj = _coerce_str_or_path_to_path(should_be_path) + if path_obj.exists(): + return path_obj + raise FileNotFoundError("Expected file does not exist: " + str(should_be_path)) def ensure_valid_path_with_suffix(should_be_path: Union[str, Path], suffix: str) -> Path: """Coerce input to a pathlib.Path with given suffix.""" - wrong_type_msg = "Unexpected type for something that should be convertable to a Path: " - - if isinstance(should_be_path, str): - path_obj = Path(should_be_path) - elif isinstance(should_be_path, Path): - path_obj = should_be_path - else: - raise TypeError(wrong_type_msg + str(type(should_be_path))) - + path_obj = _coerce_str_or_path_to_path(should_be_path) return path_obj.with_suffix(suffix) @@ -72,3 +52,13 @@ def coerce_to_str(some_object: Union[str, int, tuple]): return str(some_object) raise TypeError(f"Unable to coerce value to str. Unexpected type <{type(some_object)}>.") + + +def _coerce_str_or_path_to_path(should_be_path: Union[Path, str]) -> Path: + wrong_type_msg = "Unexpected type for something that should be convertable to a Path: " + if isinstance(should_be_path, str): + return Path(should_be_path) + elif isinstance(should_be_path, Path): + return should_be_path + else: + raise TypeError(wrong_type_msg + str(type(should_be_path))) diff --git a/poetry.lock b/poetry.lock index 0cbbd8f..47d1654 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "appnope" @@ -50,13 +50,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p [[package]] name = "babel" -version = "2.14.0" +version = "2.15.0" description = "Internationalization utilities" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"}, - {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"}, + {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, + {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"}, ] [package.extras] @@ -149,13 +149,13 @@ css = ["tinycss2 (>=1.1.0,<1.3)"] [[package]] name = "certifi" -version = "2024.2.2" +version = "2024.7.4" description = "Python package for providing 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"jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" -python-versions = ">=3.9,<3.13" -content-hash = "a6ab01232dbd3f7b2dae8fde33e2fafb049242478e1e16b0978e2b2a6f9ecdf0" +python-versions = "^3.9" +content-hash = "1e1a19b9fbc028f75cd997bdbdd72ca0f86f1b010c0dee34a76960a81e63a433" diff --git a/pyproject.toml b/pyproject.toml index aceeecf..6a45321 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "ncompare" -version = "1.9.0" +version = "1.10.0rc1" description = "Compare the structure of two NetCDF files at the command line" authors = ["Daniel Kaufman "] readme = "README.md" @@ -23,25 +23,25 @@ classifiers = [ ncompare = "ncompare.console:main" [tool.poetry.dependencies] -python = ">=3.9,<3.13" -numpy = "^1.26.0" -netCDF4 = "^1.6.4" -xarray = ">=2023.9,<2025.0" -colorama = "^0.4.6" -openpyxl = "^3.1.2" +python = "^3.9" +numpy = ">=1.26.0" +netCDF4 = ">=1.6.4" +xarray = ">=2023.9" +colorama = ">=0.4.6" +openpyxl = ">=3.1.2" [tool.poetry.group.dev.dependencies] pytest = ">=7.4.2,<9.0.0" -ruff = ">=0.0.291,<0.4.6" +ruff = ">=0.5.0,<0.5.1" black = ">=23.9.1,<25.0.0" -mypy = "^1.5.1" +mypy = ">=1.5.1" pytest-cov = ">=4.1,<6.0" -mkdocs = "^1.5.3" -markdown-callouts = "^0.4.0" -markdown-include = "^0.8.1" +mkdocs = ">=1.5.3" +markdown-callouts = ">=0.4.0" +markdown-include = ">=0.8.1" mkdocstrings = ">=0.24.1,<0.26.0" -mkdocs-jupyter = "^0.24.6" -mkdocs-material = "^9.5.12" +mkdocs-jupyter = ">=0.24.6" +mkdocs-material = ">=9.5.12" [build-system] requires = ["poetry-core>=1.0.0"] diff --git a/tests/conftest.py b/tests/conftest.py index 838a2b0..1e33e03 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -74,6 +74,34 @@ def ds_3dims_2vars_4coords(temp_data_dir) -> Path: return filepath +@pytest.fixture(scope="session") +def ds_1dim_1var_1coord(temp_data_dir) -> Path: + ds = Dataset( + data_vars=dict(z1=(["y"], np.array([5, 6]))), + coords=dict( + y=range(2), + ), + ) + filepath = temp_data_dir / "test_1dim_1var_1coord.nc" + ds.to_netcdf(path=filepath) + + return filepath + + +@pytest.fixture(scope="session") +def ds_1dim_1var_allnan_1coord(temp_data_dir) -> Path: + ds = Dataset( + data_vars=dict(z1=(["y"], np.array([np.nan, np.nan]))), + coords=dict( + y=range(2), + ), + ) + filepath = temp_data_dir / "test_1dim_1var_allnan_1coord.nc" + ds.to_netcdf(path=filepath) + + return filepath + + @pytest.fixture(scope="session") def ds_4dims_3vars_5coords(temp_data_dir): ds = Dataset( diff --git a/tests/test_complete_file_output.py b/tests/test_complete_file_output.py index e24cbc8..d989733 100644 --- a/tests/test_complete_file_output.py +++ b/tests/test_complete_file_output.py @@ -94,13 +94,4 @@ def test_full_run_to_xlsx_output(temp_data_dir): difference = df1[df1 != df2] rows_with_differences = [(idx, row) for idx, row in difference.notnull().iterrows() if any(row)] - if len(rows_with_differences) != 0: - print( - f"Test will fail because of differences in <{len(rows_with_differences)}> rows. " - f"Differences identified (Row index ----> row contents):" - ) - for idx, row in rows_with_differences: - diff = difference.loc[idx] - print(f" {idx} ----> {diff}") - assert len(rows_with_differences) == 0 diff --git a/tests/test_core.py b/tests/test_core.py index e4d5890..e106274 100644 --- a/tests/test_core.py +++ b/tests/test_core.py @@ -72,10 +72,14 @@ def test_matching_random_values( ds_3dims_2vars_4coords, ds_4dims_3vars_5coords, ds_3dims_3vars_4coords_1group, + ds_1dim_1var_1coord, + ds_1dim_1var_allnan_1coord, outputter_to_console, ): variable_array_1 = xr.open_dataset(ds_3dims_2vars_4coords).variables['z1'] variable_array_2 = xr.open_dataset(ds_4dims_3vars_5coords).variables['z1'] + variable_array_3 = xr.open_dataset(ds_1dim_1var_1coord).variables['z1'] + variable_array_allnan = xr.open_dataset(ds_1dim_1var_allnan_1coord).variables['z1'] assert ( _match_random_value( @@ -93,6 +97,32 @@ def test_matching_random_values( ) is False ) + assert ( + _match_random_value( + outputter_to_console, + variable_array_3, + variable_array_3, + ) + is True + ) + # NaN to non-NaN is NOT considered a match + assert ( + _match_random_value( + outputter_to_console, + variable_array_3, + variable_array_allnan, + ) + is None + ) + # NaN to NaN is considered a match + assert ( + _match_random_value( + outputter_to_console, + variable_array_allnan, + variable_array_allnan, + ) + is True + ) def test_print_values_runs_with_no_error(ds_3dims_3vars_4coords_1group, outputter_to_console): @@ -137,10 +167,7 @@ def test_comparison_group_no_error_for_duplicate_dataset( if "Variables within specified group :" in line: found_expected = True - if found_expected: - assert True - else: - assert False + assert found_expected def test_comparison_var_no_error_for_duplicate_dataset( @@ -160,10 +187,7 @@ def test_comparison_var_no_error_for_duplicate_dataset( if "Sample values within specified variable :" in line: found_expected = True - if found_expected: - assert True - else: - assert False + assert found_expected def test_get_vars_with_group(ds_3dims_3vars_4coords_1group): diff --git a/tests/test_utils.py b/tests/test_utils.py index 182d9fa..fe800e0 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -50,9 +50,19 @@ def test_make_valid_path_from_Path_in_repo(): assert isinstance(returnval, Path) +def test_error_from_wrong_path_type(): + with pytest.raises(TypeError): + ensure_valid_path_exists((0, 1)) + + def test_coerce_int_to_str(): assert coerce_to_str(5) == "5" def test_coerce_tuple_to_str(): assert coerce_to_str(('step', 123)) == "('step', 123)" + + +def test_error_from_not_able_to_coerce_to_str(): + with pytest.raises(TypeError): + coerce_to_str(list[5, 6, 7])