Update with develop

.github/workflows/build_package.yml

@@ -13,9 +13,9 @@ jobs:
         python-version: [ '3.8', '3.9', '3.10' ]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

.github/workflows/formatting.yml

@@ -7,9 +7,9 @@ jobs:
       matrix:
         python-version: [ '3.10' ]
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }} for Black
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install Black
@@ -25,6 +25,7 @@ jobs:
           git config --global user.email "[email protected]"
           git config --global author.email "[email protected]"
           git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY
+          git fetch origin
           git checkout $GITHUB_HEAD_REF
           git pull
           git commit -am "Apply Black formatting to Python code."

.github/workflows/markdown-altimetry.yml

@@ -8,14 +8,14 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout site
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive # Fetch Hugo themes and all extra projects
           fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod
           path: site
 
       - name: Checkout coast
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: British-Oceanographic-Data-Centre/COAsT
           ref: develop

.github/workflows/markdown-general.yml

@@ -8,20 +8,20 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout site
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive # Fetch Hugo themes and all extra projects
           fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod
           path: site
 
       - name: Checkout coast
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: British-Oceanographic-Data-Centre/COAsT
           ref: develop
           path: external
 
-      - name: Prepare environement
+      - name: Prepare environment
         uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: coast
@@ -38,5 +38,11 @@ jobs:
           mkdir -p ./example_scripts/notebook_tutorials/markdown/general
           ls ./example_scripts/notebook_tutorials
           pip install .
+          sudo apt-get update
+          sudo apt-get install -y libgeos-dev
+          pip install cartopy==0.21.0
+          pip install zarr
+          pip install xarray[complete]
+          pip install aiohttp requests
           mv config ./example_scripts/notebook_tutorials/runnable_notebooks/general/config
           bash notebook_to_md.sh general

.github/workflows/markdown-gridded.yml

@@ -8,14 +8,14 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout site
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive # Fetch Hugo themes and all extra projects
           fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod
           path: site
 
       - name: Checkout coast
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: British-Oceanographic-Data-Centre/COAsT
           ref: develop

.github/workflows/markdown-profile.yml

@@ -8,14 +8,14 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout site
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive # Fetch Hugo themes and all extra projects
           fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod
           path: site
 
       - name: Checkout coast
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: British-Oceanographic-Data-Centre/COAsT
           ref: develop

.github/workflows/markdown-tidegauge.yml

@@ -8,14 +8,14 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout site
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive # Fetch Hugo themes and all extra projects
           fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod
           path: site
 
       - name: Checkout coast
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: British-Oceanographic-Data-Centre/COAsT
           ref: develop

.github/workflows/publish_package.yml

@@ -10,12 +10,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ 3.8 ]
+        python-version: [ '3.10' ]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

.github/workflows/pylint_checking.yml

@@ -9,7 +9,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }} for Pylint
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install Pylint
@@ -31,16 +31,14 @@ jobs:
             git config --global user.email "[email protected]"
             git config --global author.email "[email protected]"
             git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY
-            git status
-            git checkout -b $GITHUB_HEAD_REF
-            git pull --rebase origin $GITHUB_HEAD_REF
-            git status
+            git fetch origin
+            git checkout $GITHUB_HEAD_REF
+            git pull
             echo "NEW_SCORE is greater than THESHOLD_SCORE"
             echo "Updating THESHOLD_SCORE"
             echo "$NEW_SCORE" > .pylint-score
-            git status
             git commit -am "Update pylint THESHOLD score"
-            git push --set-upstream origin $GITHUB_HEAD_REF
+            git push
           elif [ "$(echo "$NEW_SCORE == $THESHOLD_SCORE" | bc -l)" -eq 1 ] ; then
             echo "NEW_SCORE is equal to THESHOLD_SCORE"
           else

.github/workflows/unit_test_contents.yml

@@ -10,15 +10,21 @@ jobs:
         python-version: [ '3.10' ]
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }} for running python script.
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Generate contents.
         run: |
-          pip install .
+          pip install . 
           mkdir -p example_files
+          sudo apt-get update
+          sudo apt-get install -y libgeos-dev
+          pip install cartopy==0.21.0
+          pip install zarr
+          pip install xarray[complete]
+          pip install aiohttp requests
           python unit_testing/generate_unit_test_contents.py
       - name: Commit changes
         run: |
@@ -27,6 +33,7 @@ jobs:
           git config --global user.email "[email protected]"
           git config --global author.email "[email protected]"
           git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY
+          git fetch origin
           git checkout $GITHUB_HEAD_REF
           git pull
           git diff-index --quiet $GITHUB_HEAD_REF || git commit -am "Commit generated unit test contents."

.github/workflows/verify_package.yml

@@ -11,9 +11,9 @@ jobs:
         python-version: [ '3.8', '3.9', '3.10' ]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -31,4 +31,8 @@ jobs:
         run: |
           pip install dask[complete]
           pip install -r requirements.txt
+          sudo apt-get update
+          sudo apt-get install -y libgeos-dev
+          pip install cartopy==0.21.0
+          pip install zarr
           pytest tests

.gitignore

@@ -36,4 +36,4 @@ docstring2md.log
 example_scripts/notebook_tutorials/markdown/*
 
 markdown/
-.python-version
+.python-version

.pylint-score

@@ -1 +1 @@
-5.73
+5.99

CITATION.cff

@@ -29,6 +29,9 @@ authors:
  - family-names: "Cazaly"
    given-names: "Matthew"
    orcid: "https://orcid.org/0000-0002-0679-4054"
+ - family-names: "Ferreira"
+   given-names: "Tobias"
+   orcid: "https://orcid.org/0000-0002-0888-9751"
  - family-names: "Hearn"
    given-names: "Malcolm"
  - family-names: "Jennings"
@@ -43,6 +46,6 @@ authors:
  - family-names: "de Mora"
    given-names: "Lee"
    orcid: "https://orcid.org/0000-0002-5080-3149"
-title: "British-Oceanographic-Data-Centre/COAsT: v3.2.1"
-version: v3.2.1
-date-released: 2023-04-04
+title: "British-Oceanographic-Data-Centre/COAsT: v3.3.0"
+version: v3.3.0
+date-released: 2023-12-11

README.md

@@ -1,7 +1,7 @@
 [![PyPI version](https://badge.fury.io/py/coast.svg)](https://badge.fury.io/py/coast)
 [![Conda COAsT version](https://img.shields.io/conda/v/bodc/coast.svg)](https://anaconda.org/bodc/coast)
 [![Anaconda-Server Badge](https://anaconda.org/bodc/coast/badges/latest_release_relative_date.svg)](https://anaconda.org/bodc/coast)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7799863.svg)](https://zenodo.org/record/7799863)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4041413.svg)](https://zenodo.org/record/4041413)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 ```
 __________________________________________________________________________________________
@@ -22,7 +22,7 @@ ________________________________________________________________________________
 COAsT is Diagnostic and Assessment toolbox for kilometric scale regional models.
 It's aim is to deliver a flexible, community-ready framework for assessing kilometric scale ocean models. The focus, initially, is be on delivering novel diagnostics for processes that are emergent at the kilometric scale and with NEMO model output. The framework leans heavily on xarray.
 
-Documentation can be found [here](https://british-oceanographic-data-centre.github.io/COAsT/docs/).
+Documentation can be found [here](https://british-oceanographic-data-centre.github.io/COAsT/).
 
 ![PyPI version](https://badge.fury.io/py/COAsT.svg)
 ![Anaconda version](https://anaconda.org/bodc/coast/badges/version.svg)

coast/__init__.py

@@ -24,7 +24,7 @@
 from .diagnostics.tidegauge_analysis import TidegaugeAnalysis
 from .data.config_parser import ConfigParser
 from ._utils.xesmf_convert import xesmf_convert
-from ._utils.process_data import Process_data
+from ._utils.process_data import Process_data, ProcessData
 from .data.opendap import OpendapInfo
 from .data.copernicus import Copernicus, Product
 from ._utils.experiments_file_handling import experiments

coast/_utils/logging_util.py

@@ -2,14 +2,30 @@
 import logging
 import sys
 import io
+import functools
 import warnings
 import inspect
 import traceback
 
-
+warnings.simplefilter("always", DeprecationWarning)
+warnings.formatwarning = (
+    lambda message, category, filename, lineno, line=None: f"{filename}:{lineno}: {category.__name__}: {message}\n"
+)
 DEFAULT_FORMAT = "%(asctime)s %(levelname)s %(message)s"
 
 
+def deprecated(message=""):
+    def decorator(func):
+        @functools.wraps(func)
+        def new_func(*args, **kwargs):
+            warnings.warn(f"{func.__name__} is deprecated: {message}", DeprecationWarning)
+            return func(*args, **kwargs)
+
+        return new_func
+
+    return decorator
+
+
 def get_logger(name: str = None, level: int = logging.CRITICAL):
     logger = logging.getLogger(name=name)
     logger.setLevel(level)