Merge branch 'feature/xarray_dims_to_sizes' into xarray_dims_to_sizes

.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"

.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
 

CHANGELOG.md

@@ -4,9 +4,19 @@ 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/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [unreleased]
+### Added
+- [Issue #229](https://github.com/nasa/ncompare/issues/229): Added Journal of Open Source Software (JOSS) info to README and CITATION docs.
+- [Issue #42](https://github.com/nasa/ncompare/issues/42): Made available via conda and added `conda`/`mamba` installation instructions to README.md
 ### Changed
+- [Issue #233](https://github.com/nasa/ncompare/issues/233): Group dependabot updates into fewer PRs.
 - [Issue #246](https://github.com/nasa/ncompare/issues/246): Changed xarray Dataset.dims reference to Dataset.sizes due to FutureWarning
+### Deprecated
+### Removed
+- [Issue #231](https://github.com/nasa/ncompare/issues/231): Removed upper bounds from dependencies
+### Fixed
+- [Pull #230](https://github.com/nasa/ncompare/pull/230): Fixed help text for second NetCDF file passed on command line
+### Security
 
 ## [1.9.0]
 ### Added

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"

README.md

@@ -31,18 +31,35 @@ _____
 <a href="https://github.com/pyOpenSci/software-review/issues/146" target="_blank">
     <img src="https://tinyurl.com/y22nb8up?" alt="pyOpenSci">
 </a>
+<a style="border-width:0" href="https://doi.org/10.21105/joss.06490">
+  <img src="https://joss.theoj.org/papers/10.21105/joss.06490/status.svg" alt="DOI badge" >
+</a>
 
 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.
 
 
 ## 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
 

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)
 

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)))