Modernize library and coding conventions

.github/workflows/main.yml

@@ -1,15 +1,18 @@
 name: build
 
-on: [ push, pull_request ]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
 
 jobs:
   build:
-
     name: Conda Build with Python${{ matrix.python-version }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     defaults:
       run:
         shell: bash -l {0}
@@ -24,18 +27,12 @@ jobs:
       with:
         cache-downloads: true
         cache-environment: true
-        environment-file: environment.yml
+        environment-file: environment-docs.yml
         create-args: >-
-          conda
           python=${{ matrix.python-version }}
-    - name: Conda and Mamba versions
-      run: |
-        conda --version
-        echo "micromamba: $(micromamba --version)"
     - name: Install dependencies
       run: |
-        python -m pip install --no-user --editable "."
-        if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi
+        python -m pip install --no-user --editable ".[dev]"
     - name: Lint with flake8
       run: make lint
       if: matrix.python-version == 3.9

.gitignore

@@ -101,3 +101,6 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# JetBrains
+.idea

.pre-commit-config.yaml

@@ -3,32 +3,49 @@ default_language_version:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
-        exclude: 'setup.cfg'
       - id: end-of-file-fixer
-        exclude: 'setup.cfg'
       - id: check-yaml
       - id: debug-statements
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.19.0
+    hooks:
+      - id: pyupgrade
+        args: [ '--py39-plus' ]
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 24.10.0
     hooks:
       - id: black
-        args: ["--target-version", "py37"]
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.0
     hooks:
-      - id: flake8
-        args: ['--config=setup.cfg']
-  - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.9.0
+      - id: ruff
+        args: [ '--fix', '--show-fixes' ]
+        exclude: 'tests|docs'
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
     hooks:
-      - id: reorder-python-imports
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+#      - id: python-check-blanket-noqa
+#      - id: python-check-blanket-type-ignore
+      - id: python-no-eval
+      - id: python-no-log-warn
+      - id: python-use-type-annotations
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+      - id: text-unicode-replacement-char
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.3.9
     hooks:
-      - id: pyupgrade
+      - id: blackdoc
+        additional_dependencies: [ 'black==24.10.0' ]
+      - id: blackdoc-autoupdate-black
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.29.4
+    hooks:
+      - id: check-github-workflows
+      - id: check-readthedocs
   - repo: meta
     hooks:
       - id: check-hooks-apply
@@ -42,5 +59,5 @@ ci:
   autoupdate_branch: ''
   autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
   autoupdate_schedule: weekly
-  skip: []
+  skip: [ ]
   submodules: false

.readthedocs.yml

@@ -19,7 +19,7 @@ build:
     python: "mambaforge-22.9"
 
 conda:
-  environment: environment.yml
+  environment: environment-docs.yml
 
 # Optionally set the version of Python and requirements required to build your docs
 python:

CONTRIBUTING.rst

@@ -123,6 +123,7 @@ Logging
 .. 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:

Dockerfile

@@ -1,7 +1,7 @@
 ##=================================================================================
 ##
 ##    EXAMPLE USAGE
-##    
+##
 ##    $ docker build -t daops .
 ##    $ mkdir ~/container-outputs
 ##    $ docker run -it \
@@ -48,7 +48,7 @@ RUN apt-get update                                                          && \
 ARG mconda=Miniconda3-py311_23.10.0-1-Linux-x86_64.sh
 RUN wget https://repo.anaconda.com/miniconda/$mconda    && \
     bash ./$mconda -b -p $MINICONDA_PREFIX              && \
-    apt-get clean autoremove --yes                      && \ 
+    apt-get clean autoremove --yes                      && \
     rm -fr $MINICONDA_PREFIX/pkgs
 
 #    wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba --strip-components=1  && \
@@ -115,5 +115,3 @@ RUN rm -fr /var/lib/{apt,dpkg,cache,log}
 #RUN ROOCS_CONFIG=$config_file $MINICONDA_PREFIX/envs/daops/bin/daops subset --area 0,-10,120,40 \
 #  --time 2085-01-16/2120-12-16 --levels / --time-components year:2090,2091,2092 \
 #  --output-dir /tmp --file-namer simple cmip5.output1.MOHC.HadGEM2-ES.rcp85.mon.atmos.Amon.r1i1p1.latest.tas
-
-

Makefile

@@ -77,11 +77,10 @@ servedocs: docs ## compile the docs watching for changes
 	watchmedo shell-command -p '*.md' -c '$(MAKE) -C docs html' -R -D .
 
 release: dist ## package and upload a release
-	twine upload dist/*
+	python -m flit publish
 
 dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
+	python -m flit build
 	ls -l dist
 
 install: clean ## install the package to the active Python's site-packages

README.rst

@@ -1,24 +1,21 @@
-
 daops - data-aware operations
 =============================
 
-
 .. image:: https://img.shields.io/pypi/v/daops.svg
-   :target: https://pypi.python.org/pypi/daops
-   :alt: Pypi
-
-
+    :target: https://pypi.python.org/pypi/daops
+    :alt: PyPI
 
 .. image:: https://github.com/roocs/daops/workflows/build/badge.svg
     :target: https://github.com/roocs/daops/actions
     :alt: Build Status
 
-
-
 .. image:: https://readthedocs.org/projects/daops/badge/?version=latest
-   :target: https://daops.readthedocs.io/en/latest/?badge=latest
-   :alt: Documentation
+    :target: https://daops.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation
 
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+    :target: https://github.com/python/black
+    :alt: Python Black
 
 The ``daops`` library (pronounced "day-ops") provides a python interface to a
 set of operations suitable for working with climate simulation outputs. It is
@@ -32,7 +29,6 @@ The data will be loaded and *fixed* using the `xarray <http://xarray.pydata.org/
 library before the any actual operations are sent to its sister library
 `clisops <https://github.com/roocs/clisops>`_.
 
-
 * Free software: BSD
 * Documentation: https://daops.readthedocs.io
 
@@ -41,7 +37,6 @@ Features
 
 The package has the following features:
 
-
 * Ability to run *data-reduction* operations on large climate data sets.
 * Knowledge of irregularities/anomalies in some climate data sets.
 * Ability to apply *fixes* to those data sets before operating on them.
@@ -52,11 +47,5 @@ Credits
 
 This package was created with ``Cookiecutter`` and the ``cedadev/cookiecutter-pypackage`` project template.
 
-
 * Cookiecutter: https://github.com/audreyr/cookiecutter
 * cookiecutter-pypackage: https://github.com/cedadev/cookiecutter-pypackage
-
-
-.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
-   :target: https://github.com/python/black
-   :alt: Python Black

app-package.cwl

@@ -54,15 +54,15 @@ $graph:
             collection: collection
             file_namer: file_namer
             output_dir: output_dir
-        out: 
+        out:
           - results
 
   - class: CommandLineTool
     id: clt
     requirements:
       InlineJavascriptRequirement: {}
       EnvVarRequirement:
-        envDef:  
+        envDef:
            ROOCS_CONFIG: /root/roocs.ini
 #          PATH: /srv/conda/envs/env_crop/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 #      ResourceRequirement:

cli.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Console script for daops."""
 
 __author__ = """Elle Smith"""

docs/conf.py

@@ -19,8 +19,6 @@
 import os
 import sys
 
-import sphinx_rtd_theme
-
 sys.path.insert(0, os.path.abspath(".."))
 
 # -- General configuration ---------------------------------------------

eg-cli-params.yml

@@ -3,4 +3,3 @@ time: "2085-01-16/2188-12-16"
 file_namer: "simple"
 output_dir: "."
 collection: "cmip5.output1.MOHC.HadGEM2-ES.rcp85.mon.atmos.Amon.r1i1p1.latest.tas"
-

docs/environment.yml → environment-docs.yml

@@ -1,21 +1,21 @@
-# conda env create -f environment.yml
+# conda env create -f environment-docs.yml
 name: daops-docs
 channels:
   - conda-forge
   - defaults
 dependencies:
-  - sphinx
-  - nbsphinx
+  - clisops>=0.6.1
+  - dask
+  - elasticsearch>=7.9.1
   - ipython
+  - nbsphinx
+  - netcdf4
+  - numpy>=1.16
   - pandoc
   - pip
-  - numpy>=1.16
-  - xarray>=0.15
-  - dask
-  - netcdf4
-  - clisops>=0.6.1
-  - elasticsearch>=7.9.1
   - roocs-utils>=0.2.1
+  - sphinx
+  - xarray>=0.15
 # - pip:
 #     - roocs-utils @ git+https://github.com/roocs/roocs-utils.git@master#egg=roocs-utils
 #     - clisops @ git+https://github.com/roocs/clisops.git@master#egg=clisops

environment.yml

@@ -1,19 +1,20 @@
-# conda env create -f environment.yml
+# conda env create -f environment-docs.yml
 name: daops
 channels:
   - conda-forge
   - defaults
 dependencies:
   - pip
-  - numpy >=1.16
-  - xarray >=0.21,<2023.3.0 # https://github.com/pydata/xarray/issues/7794
+  - cftime
+  - clisops >=0.14.0
   - dask
+  - elasticsearch>=8.0.1
   - netcdf4
-  - clisops >=0.12.1
+  - numpy >=1.23.0
   - roocs-grids >=0.1.2
+  - roocs-utils >=0.6.4
+  - xarray >=0.21,<2023.3.0 # https://github.com/pydata/xarray/issues/7794
   - xesmf >=0.8.2
-  - elasticsearch>=7.9.1
-  - roocs-utils>=0.6.2
   # logging
   - loguru >=0.5.3
   # catalog

notebooks/subset.ipynb

@@ -6,10 +6,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from daops.ops.subset import subset\n",
-    "\n",
     "# remove previosuly created example file\n",
     "import os\n",
+    "\n",
+    "from daops.ops.subset import subset\n",
+    "\n",
     "if os.path.exists(\"./output_001.nc\"):\n",
     "    os.remove(\"./output_001.nc\")"
    ]