Prepare release 0.9.0

.github/workflows/main.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
     - uses: actions/checkout@v2
     - name: Install packages
@@ -27,9 +27,9 @@ jobs:
         if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi
         # pip install the package, command-line unit tests work 
         pip install --no-deps -e .
-#    - name: Lint with flake8
-#      run: flake8 daops tests
-#      if: matrix.python-version == 3.8
+    - name: Lint with flake8
+      run: make lint
+      if: matrix.python-version == 3.8
 #    - name: Check formatting with black
 #      run: black --check --target-version py38 daops tests
 #      if: matrix.python-version == 3.8

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.4.0
     hooks:
       - id: trailing-whitespace
         exclude: 'setup.cfg'
@@ -12,21 +12,21 @@ repos:
       - id: check-yaml
       - id: debug-statements
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.11.0
     hooks:
       - id: black
         args: ["--target-version", "py37"]
   - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+    rev: 6.1.0
     hooks:
       - id: flake8
         args: ['--config=setup.cfg']
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.0.1
+    rev: v3.9.0
     hooks:
       - id: reorder-python-imports
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.32.0
+    rev: v3.15.0
     hooks:
       - id: pyupgrade
   - repo: meta

.readthedocs.yml

@@ -9,26 +9,22 @@ version: 2
 sphinx:
   configuration: docs/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
 # Optionally build your docs in additional formats such as PDF and ePub
-formats: all
+# formats:
+#    - pdf
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-22.9"
+
+conda:
+  environment: environment.yml
 
 # Optionally set the version of Python and requirements required to build your docs
-#python:
-#  version: 3.6
 python:
-  version: 3.7
   install:
     - method: pip
       path: .
       extra_requirements:
         - docs
-
-#conda:
-#  environment: docs/environment.yml
-
-build:
-  image: stable

CONTRIBUTING.rst

@@ -121,12 +121,14 @@ Logging
 ``daops`` uses the `loguru <https://loguru.readthedocs.io/en/stable/index.html>`_ library as its primary logging engine. In order to integrate this kind of logging in processes, we can use their logger:
 
 .. code-block:: python
+
     from loguru import logger
     logger.warning("This a warning message!")
 
 The mechanism for enabling log reporting in scripts/notebooks using ``loguru`` is as follows:
 
 .. code-block:: python
+
     import sys
     from loguru import logger
 
@@ -139,6 +141,7 @@ The mechanism for enabling log reporting in scripts/notebooks using ``loguru`` i
 For convenience, a preset logger configuration can be enabled via `daops.enable_logging()`.
 
 .. code-block:: python
+
     from daops import enable_logging
 
     enable_logging()

HISTORY.rst

@@ -1,6 +1,21 @@
 Version History
 ===============
 
+v0.9.0 (2023-11-17)
+-------------------
+
+Breaking Changes
+^^^^^^^^^^^^^^^^
+* ``clisops``>=0.10.0 required.
+
+Other Changes
+^^^^^^^^^^^^^
+* Updated requirements.
+* Updated pre-commit.
+* Support tests on Python 3.10 and 3.11.
+* Enabled linting test.
+
+
 v0.8.1 (2022-05-12)
 -------------------
 
@@ -56,7 +71,7 @@ New Features
 * ``intake_catalog_url`` has been added to ``etc/roocs.ini``
 
 v0.5.0 (2021-02-26)
-------------------
+-------------------
 
 New Features
 ^^^^^^^^^^^^
@@ -68,7 +83,7 @@ Other Changes
 
 
 v0.4.0 (2021-02-23)
-------------------
+-------------------
 
 Breaking Changes
 ^^^^^^^^^^^^^^^^
@@ -91,7 +106,7 @@ Other Changes
 
 
 v0.3.0 (2020-11-19)
-------------------
+-------------------
 
 Updating doc strings and documentation.
 
@@ -127,12 +142,12 @@ Other Changes
 * Functions that take the ``data_ref`` parameter have been changed to use ``dset`` parameter instead.
 
 v0.2.0 (2020-06-22)
-------------------
+-------------------
 
 * Updated to use clisops v0.2.0 (#17)
 * Added xarray aggregation tests (#16)
 
 v0.1.0 (2020-04-27)
-------------------
+-------------------
 
 * First release with clisops v0.1.0.

daops/__init__.py

@@ -6,7 +6,7 @@
 __contact__ = "[email protected]"
 __copyright__ = "Copyright 2018 United Kingdom Research and Innovation"
 __license__ = "BSD"
-__version__ = "0.8.1"
+__version__ = "0.9.0"
 
 from loguru import logger
 

daops/cli.py

@@ -1,7 +1,7 @@
 """Console script for daops."""
 
 __author__ = """Alan Iwi"""
-__contact__ = '[email protected]'
+__contact__ = "[email protected]"
 __copyright__ = "Copyright 2023 United Kingdom Research and Innovation"
 __license__ = "BSD - see LICENSE file in top-level package directory"
 
@@ -14,47 +14,83 @@
 from daops.ops.subset import subset
 from roocs_utils.utils.file_utils import FileMapper
 
-def parse_args():
 
+def parse_args():
     parser = argparse.ArgumentParser()
     sub_parsers = parser.add_subparsers()
     sub_parsers.required = True
 
-    parser_subset = sub_parsers.add_parser('subset', help='subset data')
-    parser_subset.add_argument('--area', '-a', type=str, 
-                               help=('area in format w,s,e,n. Hint: if w is negative, include an "=" sign '
-                                     'e.g. --area=-10,...'))
-    parser_subset.add_argument('--time', '-t', type=str, metavar='time_window',
-                               help='time window e.g. 1999-01-01T00:00:00/2100-12-30T00:00:00')
-    parser_subset.add_argument('--time-components', '-c', type=str, 
-                               help="time components e.g. month:dec,jan,feb or 'year:1970,1980|month:01,02,03'")
-    parser_subset.add_argument('--levels', '-l', type=str,
-                               help=('comma-separated list of levels (e.g. 500,1000,2000) '
-                                     'or slash-separated range (e.g. 50/2000 for 50 to 2000)'))
-    parser_subset.add_argument('--output-format', '-f', type=str, metavar='format',
-                               choices=('netcdf', 'nc', 'zarr'), default='netcdf')
-    parser_subset.add_argument('--file-namer', '-F', type=str, 
-                               choices=('simple', 'standard'), default='standard')
-    parser_subset.add_argument('--output-dir', '-d', type=str, metavar='output_directory', required=True)
-    parser_subset.add_argument('collection', type=str, nargs='+', default=list)
+    parser_subset = sub_parsers.add_parser("subset", help="subset data")
+    parser_subset.add_argument(
+        "--area",
+        "-a",
+        type=str,
+        help=(
+            'area in format w,s,e,n. Hint: if w is negative, include an "=" sign '
+            "e.g. --area=-10,..."
+        ),
+    )
+    parser_subset.add_argument(
+        "--time",
+        "-t",
+        type=str,
+        metavar="time_window",
+        help="time window e.g. 1999-01-01T00:00:00/2100-12-30T00:00:00",
+    )
+    parser_subset.add_argument(
+        "--time-components",
+        "-c",
+        type=str,
+        help="time components e.g. month:dec,jan,feb or 'year:1970,1980|month:01,02,03'",
+    )
+    parser_subset.add_argument(
+        "--levels",
+        "-l",
+        type=str,
+        help=(
+            "comma-separated list of levels (e.g. 500,1000,2000) "
+            "or slash-separated range (e.g. 50/2000 for 50 to 2000)"
+        ),
+    )
+    parser_subset.add_argument(
+        "--output-format",
+        "-f",
+        type=str,
+        metavar="format",
+        choices=("netcdf", "nc", "zarr"),
+        default="netcdf",
+    )
+    parser_subset.add_argument(
+        "--file-namer",
+        "-F",
+        type=str,
+        choices=("simple", "standard"),
+        default="standard",
+    )
+    parser_subset.add_argument(
+        "--output-dir", "-d", type=str, metavar="output_directory", required=True
+    )
+    parser_subset.add_argument("collection", type=str, nargs="+", default=list)
 
     return parser.parse_args()
 
 
 def get_params(args):
-
-    collection = args.collection if len(args.collection) == 1 else FileMapper(args.collection)
-
-    return {'collection': collection,
-            'time': args.time,
-            'time_components': args.time_components,
-            'area': args.area,
-            'level': args.levels,
-            'output_type': args.output_format,
-            'output_dir': args.output_dir,
-            'file_namer': args.file_namer,
-            'apply_fixes': False            
-            }
+    collection = (
+        args.collection if len(args.collection) == 1 else FileMapper(args.collection)
+    )
+
+    return {
+        "collection": collection,
+        "time": args.time,
+        "time_components": args.time_components,
+        "area": args.area,
+        "level": args.levels,
+        "output_type": args.output_format,
+        "output_dir": args.output_dir,
+        "file_namer": args.file_namer,
+        "apply_fixes": False,
+    }
 
 
 def check_env():
@@ -64,14 +100,16 @@ def check_env():
     so exit might not always be graceful in these cases).
     Call this after get_params() so that 'help' still works even if this is not set.
     """
-    config_env_var = 'ROOCS_CONFIG'
+    config_env_var = "ROOCS_CONFIG"
     c = configparser.ConfigParser()
     try:
         ret = c.read(os.environ[config_env_var])
     except (KeyError, configparser.Error):
         ret = None
     if not ret:
-        print(f'Environment variable {config_env_var} must contain the path name of a config file in ini format')
+        print(
+            f"Environment variable {config_env_var} must contain the path name of a config file in ini format"
+        )
         sys.exit(1)
 
 

docs/conf.py

@@ -74,7 +74,7 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.8.1"
+version = "0.9.0"
 # The full version, including alpha/beta/rc tags.
 release = version
 
@@ -83,7 +83,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs/index.rst

@@ -9,7 +9,6 @@ Welcome to daops's documentation!
    installation
    usage
    api
-   notebooks/index
    contributing
    authors
    history

environment.yml

@@ -9,7 +9,7 @@ dependencies:
   - xarray>=0.15
   - dask
   - netcdf4
-  - clisops>=0.9.1
+  - clisops>=0.10.0
   - elasticsearch>=7.9.1
   - roocs-utils>=0.6.2
   # logging

requirements.txt

@@ -4,8 +4,7 @@ dask[complete]
 cftime
 netcdf4
 elasticsearch>=8.0.1
-clisops>=0.9.1
-## clisops @ git+https://github.com/roocs/clisops.git@master#egg=clisops
+clisops>=0.10.0
 roocs-utils>=0.6.2
 # logging
 loguru>=0.5.3

requirements_dev.txt

@@ -3,7 +3,7 @@ bumpversion
 wheel
 watchdog
 flake8
-tox
+tox>=4.0
 coverage
 Sphinx
 sphinx-rtd-theme
@@ -14,6 +14,6 @@ twine
 pytest>=6.0
 pytest-loguru
 pytest-runner
-pre-commit>=2.9.0
-black>=22.3.0
-GitPython==3.1.37
+pre-commit>=3.0.0
+black>=23.7.0
+GitPython>=3.1.37