Merge pull request #71 from DocOtak/rcaneill_add_citation2

add citation, update readthedoc config, add 3.12 in CI

Author: rcaneill

.github/workflows/ci.yml

@@ -10,29 +10,19 @@ on:
     branches: [ master ]
 
 jobs:
-  style:
-    name: Code linting checks
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: psf/black@stable
-        with:
-          options: "--check --verbose"
-          version: "22.3.0"
-
   build:
     name: build (${{ matrix.os }}, ${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install / build
@@ -41,34 +31,51 @@ jobs:
         pip install .
         
   test:
-    name: test (${{ matrix.os }}, ${{ matrix.python-version }}, ${{ matrix.pint }} Pint)
-    runs-on: ${{ matrix.os }}
+    name: test (ubuntu-latest, ${{ matrix.python-version }}, ${{ matrix.pint }} Pint, packages version ${{ matrix.version }})
+    runs-on: "ubuntu-latest"
+    env:
+      poetry_version: 1.3.2
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-        poetry-version: [1.3.2]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         pint: ["with", "without"]
+        version: ["lock"]
+        include:
+          - python-version: "3.9"
+            version: "minimal"
+            pint: "with"
+          - python-version: "3.12"
+            version: "maximal"
+            pint: "with"
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install poetry
-      run: pipx install poetry==${{ matrix.poetry-version }}
+      run: pipx install poetry==${{ env.poetry_version }}
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'poetry'
     - name: Install udunits
       run: sudo apt-get install -y libudunits2-dev
+    - name: update lock file
+      if: matrix.version == 'maximal'
+      run: poetry update
     - name: Install dependencies
       run: |
-        poetry install
+        poetry install --with dev
         poetry run pip install cf_units==3.0.1
     - if: matrix.pint == 'with'
       name: Install pint and pint-xarray
       run: |
         poetry install -E pint
+    - name: use minimal versions for lock file
+      if: matrix.version == 'minimal'
+      run: |
+        pipx install pdm==2.15.2
+        poetry run pdm lock --strategy direct_minimal_versions -v -G :all
+        poetry run pdm install -v -G :all
     - name: Test with pytest
       run: |
         poetry run pytest gsw_xarray/tests

.github/workflows/publish.yml

@@ -8,8 +8,8 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Build and publish to pypi
         uses: JRubics/[email protected]
         with:
-            pypi_token: ${{ secrets.PYPI_TOKEN }}
+            pypi_token: ${{ secrets.PYPI_TOKEN }}

.github/workflows/ruff.yml

@@ -0,0 +1,26 @@
+name: format and lint
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+    
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      # Update output format to enable automatic inline annotations.
+      - name: Run Ruff
+        run: ruff check --output-format=github .
+      - name: Run Ruff format
+        run: ruff format --check .

.gitignore

@@ -1,3 +1,6 @@
+# ruff
+.ruff_cache
+
 # These files are generated on doc build and shoudl not be kept in VC
 docs/_attr_table.rst
 docs/ARGO_example.nc
@@ -65,16 +68,6 @@ cover/
 *.mo
 *.pot
 
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
 # Scrapy stuff:
 .scrapy
 
@@ -92,18 +85,6 @@ target/
 profile_default/
 ipython_config.py
 
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
 # poetry
 #   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
 #   This is especially recommended for binary packages to ensure reproducibility, and is more

.pre-commit-config.yaml

@@ -1,8 +1,13 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.5
     hooks:
-      - id: black
-        language_version: python3
+      - id: ruff
+        name: lint with ruff
+      - id: ruff
+        name: sort imports with ruff
+        args: [--select, I, --fix]
+      - id: ruff-format
+        name: format with ruff

.readthedocs.yaml

@@ -13,11 +13,9 @@ build:
       # Install poetry
       # https://python-poetry.org/docs/#installing-manually
       - pip install poetry
-      # Tell poetry to not use a virtual environment
-      - poetry config virtualenvs.create false
     post_install:
       # Install dependencies with 'docs' extra
-      - poetry install -E docs
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
 
 sphinx:
    configuration: docs/conf.py

CHANGELOG.rst

@@ -1,6 +1,10 @@
 Changelog
 =========
 
+v0.4.0 - not released
+---------------------
+This release adds an accessor for xarray. Support for python 3.8 is dropped and 3.12 is added.
+
 v0.3.0 - 2022-08-09
 -------------------
 This release focused on supporting Pint quantities.

CITATION.cff

@@ -0,0 +1,25 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: gsw-xarray
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Romain
+    family-names: Caneill
+    email: [email protected]
+    orcid: 'https://orcid.org/0000-0001-6649-4275'
+  - given-names: Andrew
+    family-names: Barna
+    orcid: 'https://orcid.org/0000-0002-5203-8954'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.8297618
+repository-code: 'https://github.com/DocOtak/gsw-xarray'
+abstract: >-
+  Wrapper for gsw that will add CF attributes to
+  xarray.DataArray outputs
+license: BSD-3-Clause

README.rst

@@ -9,10 +9,13 @@
    :alt: pypi package
 .. |conda forge| image:: https://img.shields.io/conda/vn/conda-forge/gsw-xarray
    :target: https://anaconda.org/conda-forge/gsw-xarray
+.. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8297618.svg
+   :target: https://doi.org/10.5281/zenodo.8297618
+   :alt: zenodo DOI
 
 gsw-xarray: Wrapper for gsw that adds CF attributes
 ===================================================
-|CI Status| |Documentation Status| |pypi| |conda forge|
+|CI Status| |Documentation Status| |pypi| |conda forge| |zenodo|
 
 gsw-xarray is a wrapper for `gsw python <https://github.com/TEOS-10/GSW-python>`_
 that will add CF attributes to xarray.DataArray outputs.
@@ -229,11 +232,22 @@ Conda
 
 Inside a conda environment:  ``conda install -c conda-forge gsw-xarray``.
 
-Pipenv
-......
 
-Inside a pipenv environment: ``pipenv install gsw-xarray``.
+Citation
+--------
 
+If you use gsw-xarray, please cite the reference paper for the upstream gsw library:  McDougall, T.J. and P.M. Barker, 2011: Getting started with TEOS-10 and the Gibbs Seawater (GSW) Oceanographic Toolbox, 28pp., SCOR/IAPSO WG127, ISBN 978-0-646-55621-5
+
+.. code:: bibtex
+    @book{mcdougall2011getting,
+      author = {McDougall, T. J. and Barker, P. M.},
+      title = {Getting started with TEOS-10 and the Gibbs Seawater (GSW) Oceanographic Toolbox},
+      year = {2011},
+      pages = {28},
+      publisher = {SCOR/IAPSO WG127},
+      isbn = {978-0-646-55621-5}
+    }
+You can also cite gsw-xarray by using the zenodo DOI |zenodo|.
 
 Contributor guide
 -----------------
@@ -257,7 +271,7 @@ Then go to your local clone of gsw-xarray and launch installation:
 .. code:: bash
 
    cd /path/to/your/gsw-xarray
-   poetry install
+   poetry install --with dev
 
 You can then activate the environment by launching a shell
 within the virtual environment:
@@ -272,6 +286,9 @@ You can check that the tests pass locally:
 
    pytest gsw_xarray/tests
 
+You can install `pre-commit <https://pre-commit.com/#install>`_ to run the linting
+automatically at each commit.
+   
 Release (for maintainers only)
 ..............................
 

docs/gen_attr_table.py

@@ -1,11 +1,11 @@
-from sphinx.util import progress_message
-
 from inspect import signature
 
+from sphinx.util import progress_message
+
 import gsw_xarray
-from gsw_xarray._names import _names
-from gsw_xarray._attributes import _func_attrs
 from gsw_xarray._arguments import input_properties
+from gsw_xarray._attributes import _func_attrs
+from gsw_xarray._names import _names
 
 input_units = {i: input_properties[i]["units"] for i in input_properties}
 
@@ -33,7 +33,7 @@ def _add_attrs(list_table, attrs, label):
                     props["standard_name"] = "sea_ice_temperature"
                 else:
                     props["standard_name"] = "sea_water_temperature"
-            if arg == "p" and not "ice" in name:
+            if arg == "p" and "ice" not in name:
                 props["standard_name"] = "sea_water_pressure"
             for prop in props:
                 list_table += f"  * {prop}: ``{props.get(prop)}``\n"

gsw_xarray/__init__.py

@@ -1,12 +1,18 @@
 __version__ = "0.3.0"
 
-from importlib import import_module
-
 import gsw
+
+import gsw_xarray._accessor  # noqa: F401
+
 from ._core import _wrapped_funcs
-from ._util import submodule_all_compat, get_attribute, _compat
-import gsw_xarray._accessor
-from ._options import set_options, get_options, set_non_cf_name, set_cf_name_preference
+from ._options import (  # noqa: F401
+    get_options,
+    set_cf_name_preference,
+    set_non_cf_name,
+    set_options,
+)
+from ._util import _compat, get_attribute
+from ._util_module import submodule_all_compat
 
 gsw_xarray_specific_functions = [
     "set_options",
@@ -15,10 +21,10 @@
     "set_cf_name_preference",
 ]
 
-_compat_modules = {name: import_module(f".{name}", "gsw_xarray") for name in _compat}
 
 __all__ = submodule_all_compat("gsw") + list(_compat)
 
+
 # See PEP 562
 def __getattr__(name):
     return get_attribute(name)