Merge branch 'release_0.3' into release_0.3_test

.github/workflows/build-push-docker_pr.yml

@@ -13,7 +13,7 @@ jobs:
       run: echo "TAG=$(date +'%Y.%m.%d.%H.%M')" >> $GITHUB_ENV
     - uses: actions/setup-python@v1
       with:
-        python-version: 3.9
+        python-version: 3.11
     - name: Install WHEEL tool
       run: pip install wheel
     - name: Build WHEEL file

.github/workflows/build-push-docker_release.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: "3.9"
+        python-version: 3.11
     - name: Install WHEEL tool
       run: pip install wheel
     - name: Build WHEEL file
@@ -32,4 +32,4 @@ jobs:
         file: ./Dockerfile
         push: true
         tags: | 
-          ${{ vars.GEOKUBE_REGISTRY }}/geokube:${{ env.TAG }}
+          ${{ vars.GEOKUBE_REGISTRY }}/geokube:${{ env.RELEASE_TAG }}

.github/workflows/pypi_publish.yml

@@ -7,10 +7,10 @@ on:
 
 jobs:
   build-and-publish:
-    name: Build Kit4DL and publish to PyPI
+    name: Build geokube package and publish to PyPI
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.11"]
         os: [ubuntu-latest]
     runs-on: ${{ matrix.os }}
     environment: release

.github/workflows/testpypi_publish.yml

@@ -10,11 +10,8 @@ jobs:
     name: Build geokube and publish to TestPyPI
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.11"]
         os: [ubuntu-latest]
-#    environment:
-#        name: testpypi
-#        url: https://test.pypi.org/p/geokube
     permissions:
         id-token: write
     runs-on: ${{ matrix.os }}

.github/workflows/main.yml → .github/workflows/unit_tests.yml

@@ -29,7 +29,7 @@ jobs:
         run: conda activate gk       
 
       - run: |
-          conda install -c conda-forge --yes --freeze-installed xesmf cartopy psycopg2 'bokeh>=2.4.2,<3' pandas=1.4.3 netCDF4 scipy xarray=2022.6.0
+          conda install -c conda-forge --yes --freeze-installed xesmf
           
       - run: |
           conda run pip install geopandas       

Dockerfile

@@ -7,6 +7,6 @@ RUN conda clean -afy \
     && find /opt/conda/ -follow -type f -name '*.pyc' -delete \
     && find /opt/conda/ -follow -type f -name '*.js.map' -delete \
     && find /opt/conda/lib/python*/site-packages/bokeh/server/static -follow -type f -name '*.js' ! -name '*.min.js' -delete
-COPY dist/geokube-0.2a0-py3-none-any.whl /
-RUN pip install /geokube-0.2a0-py3-none-any.whl
-RUN rm /geokube-0.2a0-py3-none-any.whl
+COPY dist/geokube-0.3.0a0-py3-none-any.whl /
+RUN pip install /geokube-0.3.0a0-py3-none-any.whl
+RUN rm /geokube-0.3.0a0-py3-none-any.whl

README.md

@@ -2,7 +2,7 @@
 
 ## Description
 
-geokube is a Python package for analysis of Earth Science Data.
+geokube is a Python package based on xarray for GeoScience Data Analysis.
 
 ## Authors
 
@@ -14,42 +14,24 @@ geokube is a Python package for analysis of Earth Science Data.
 
 ## Installation 
 
-#### Requirements
-You need to install xesmf and cartopy to use geokube. This can be done during the creation of conda virtual environment, as shown below
+You can use pip to install `geokube`.
 
-Add or append conda-forge channel
-```bash
-conda config --add channels conda-forge
-```
-or
 ```bash
-conda config --append channels conda-forge
+pip install geokube
 ```
 
-#### Conda Environment
-Create virtual environment with installing xesmf and cartopy package
-```bash
-conda create -n geokube python=3.9 xesmf=0.6.2 cartopy -y
-```
-Activate virtual environment
-```bash
-conda activate geokube
-```
-Install geokube framework
-```bash
-python setup.py install
-```
+#### Requirements
+You need to install `xesmf` if you want to use `geokube` regridding. This can be done during the creation of conda virtual environment, as shown below
 
-#### Conda Package
-Create virtual environment with installing conda-build package
+Create virtual environment with `xesmf`
 ```bash
-conda create -n geokube python=3.9 conda-build -y
+conda create -n geokube python=3.11 xesmf -y
 ```
 Activate virtual environment
 ```bash
 conda activate geokube
 ```
-Execute the script
+Install geokube framework
 ```bash
-./conda/build_and_install.sh
+pip install geokube
 ```

docs/about.md

@@ -0,0 +1,10 @@
+# About
+
+## Authors
+Following authors contributed to the `geokube` framework.
+
+| Authors             |
+|--------------------|
+| Marco Mancini    <a href="https://orcid.org/0000-0002-9150-943X"><img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>  |
+| Mirko Stojiljković <a href="https://orcid.org/0000-0003-2256-1645"><img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a> |
+| Jakub Walczak   <a href="https://orcid.org/0000-0002-5632-9484"><img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>   |

docs/axis.md

@@ -0,0 +1 @@
+::: geokube.core.axis

docs/coord_system.md

@@ -0,0 +1 @@
+::: geokube.core.coord_system

docs/crs.md

@@ -0,0 +1 @@
+::: geokube.core.crs

docs/domain.md

@@ -0,0 +1 @@
+::: geokube.core.domain

docs/feature.md

@@ -0,0 +1 @@
+::: geokube.core.feature

docs/field.md

@@ -0,0 +1 @@
+::: geokube.core.field

docs/index.md

@@ -0,0 +1,5 @@
+# Welcome to geokube
+
+**geokube** is an open source Python package for geoscience data analysis that provides the user with a simple application programming interface (API) for performing geospatial operations (e.g., extracting a bounding box or regridding) and temporal operations (e.g., resampling) on different types of scientific feature types like grids, profiles and points, using on `xarray` data structures like `xarray.Dataset` and custom `xarray.Dataset.indexes` and xarray ecosystem frameworks such as `xesmf` and `cf-xarray`.
+
+Furthermore, based on xarray IO engines, geokube provides built-in drivers for reading geoscientific datasets produced by Earth Observations (e.g. satellite data) and Earth Systems Models (e.g., weather, climate and oceanographic models)

mkdocs.yml

@@ -0,0 +1,48 @@
+site_name: geokube
+site_description: geokube - a Python package based on xarray for Geoscience Data Analysis and Visualization
+theme:
+  name: material
+  palette:
+  - media: '(prefers-color-scheme: light)'
+    scheme: default
+    primary: blue grey
+    accent: amber
+  features:
+  - search.suggest
+  - search.highlight
+  - content.tooltips
+  - content.code.annotate
+  - content.code.copy
+  - content.code.select
+  icon:
+    repo: fontawesome/brands/github-alt
+  logo: img/favicon.svg
+  favicon: img/favicon.svg
+  language: en
+repo_name: CMCC-Foundation/geokube
+repo_url: https://github.com/CMCC-Foundation/geokube
+edit_uri: ''
+use_directory_urls: false
+
+plugins:
+- mkdocstrings:
+    enabled: !ENV [ENABLE_MKDOCSTRINGS, true]
+    default_handler: python
+    handlers:
+      python:
+        options:
+          docstring_style: numpy
+
+nav:
+- geokube: index.md
+- API:
+  - axis.md
+  - crs.md
+  - coord_system.md
+  - feature.md
+  - domain.md
+  - field.md
+# - Drivers:
+#  - open_collection.md
+- about.md
+

pyproject.toml

@@ -16,14 +16,14 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "geokube"
-version = "0.3a0"
+version = "0.3.0a0"
 authors = [
     {name = "geokube Contributors", email = "[email protected]"}
 ]
 maintainers = [
     {name = "geokube Contributors", email = "[email protected]"}
 ]
-description = "Python package for Earth Science Data Analysis"
+description = "a Python package based on xarray for GeoScience Data Analysis"
 keywords = ["Earth science", "data analysis"]
 license = {file = "LICENSE"}
 readme = "README.md"
@@ -35,7 +35,7 @@ classifiers = [
     "Natural Language :: English",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Topic :: Scientific/Engineering :: Earth Science",
+    "Topic :: Scientific/Engineering",
 ]
 requires-python = ">=3.11"
 dependencies = [
@@ -49,26 +49,14 @@ dependencies = [
     "pyproj>=3.4",
     "shapely>=2.0",
     "xarray>=2023.6.0",
-    "pyarrow>=12.0.1"
 ]
-# dynamic = ["version", "description", "optional-dependencies"]
 
 [project.urls]
 Homepage = "https://github.com/geokube/geokube"
-# Documentation = "https://readthedocs.org"
-Repository = "https://github.com/opengeokube/geokube.git"
+Documentation = "https://geokube.github.io"
+Repository = "https://github.com/CMCC-Foundation/geokube.git"
 # Changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
 
 [project.optional-dependencies]
 geo_science = ["gsw>=3.6", "shapely>=2.0"]
 regridding = ["xesmf"]
-#sentinel_data = ["rasterio>=1.3.8.post2", "rioxarray>=0.15"]
-
-# [project.scripts]
-# spam-cli = "spam:main_cli"
-
-# [project.gui-scripts]
-# spam-gui = "spam:main_gui"
-
-# [project.entry-points."spam.magical"]
-# tomatoes = "spam:main_tomatoes"

tests/core/test_domain.py

@@ -270,17 +270,16 @@ def test_bounding_box_grids(grid, bbox_all, bbox_partial, bbox_noone):
 def test_nearest_horizontal_grid(grid):
     grid_ = grid.nearest_horizontal(latitude=41, longitude=-11)
 
-def test_nearest_vertical_points(grid):
+def test_nearest_vertical_grid(grid):
     grid_ = grid.nearest_vertical(10.7)
 
     grid_ = grid.nearest_vertical(-100.0)
 
-def test_time_range_profiles(grid):
+def test_time_range_grid(grid):
     pass
 
-def test_latest_points(grid):
+def test_latest_grid(grid):
     pass
 
-def test_to_netcdf_points(grid):
-#    grid.to_netcdf('data/test_grid.nc')
-    pass
+def test_to_netcdf_grid(grid):
+    grid.to_netcdf('test_grid.nc')

tests/core/test_field.py

@@ -24,6 +24,6 @@ def test_create_profiles(f_profiles_no_ancillary):
 # Field Grid Test
 #
 
-#def test_create_grid(f_grid_no_ancillary):
-#    assert f_grid_no_ancillary.dim_axes == (axis.vertical, axis.latitude, axis.longitude)
+def test_create_grid(f_grid_no_ancillary):
+    assert f_grid_no_ancillary.dim_axes == (axis.time, axis.vertical, axis.latitude, axis.longitude)
 

tests/fixtures/features.py

@@ -44,7 +44,7 @@ def geodetic_cs():
 @pytest.fixture
 def points1(geodetic_cs):
     pts = Points(
-        coords = [('2001-01-01', 10.5, 42.2, -12.2), ('2001-01-02', 11.2, 56.2, 10.2)],
+        coords = [('2001-01-01', 10.5, 42.2, -12.2), ('2001-01-05', 11.2, 56.2, 10.2)],
         coord_system = geodetic_cs
     )
     return pts
@@ -56,7 +56,7 @@ def points2(geodetic_cs):
             axis.latitude: [42.2, 56.2],
             axis.longitude: [-12.2, 10.2],
             axis.vertical: [10.5, 11.2],
-            axis.time: ['2001-01-01', '2001-01-02']
+            axis.time: ['2001-01-01', '2001-01-05']
         },
         coord_system = geodetic_cs
     )
@@ -69,7 +69,7 @@ def profiles(geodetic_cs):
             axis.latitude: [42.2, 56.2],
             axis.longitude: [-12.2, 10.2],
             axis.vertical: [[10.5, 11.2, 12.3], [10.7, 11.5, 12.5, 13.5]],
-            axis.time: ['2001-01-01', '2001-01-02']
+            axis.time: ['2001-01-01', '2001-01-05']
         },
         coord_system = geodetic_cs
     )
@@ -82,7 +82,7 @@ def grid(geodetic_cs):
             axis.latitude: [42.2, 56.2],
             axis.longitude: [-12.2, 10.2],
             axis.vertical: [10.5, 11.2, 12.3],
-            axis.time: ['2001-01-01', '2001-01-02']
+            axis.time: ['2001-01-01', '2001-01-05']
         },
         coord_system = geodetic_cs
     )
@@ -96,7 +96,7 @@ def grid(geodetic_cs):
 @pytest.fixture
 def f_points_no_ancillary(points1):
     return PointsField(
-        data = [22.5, 27.5] * units['degree_C'],
+        data = [22.5, 27.5] * units('degree_C'),
         domain = points1,
         name = 'field_points',
         properties = {'test_property': 'this is a field test property'},
@@ -105,12 +105,12 @@ def f_points_no_ancillary(points1):
 @pytest.fixture
 def f_points(points1):
     return PointsField(
-        data = [22.5, 27.5] * units['degree_C'],
+        data = [22.5, 27.5] * units('degree_C'),
         domain = points1,
         name = 'field_points',
         properties = {'test_property': 'this is a field test property'},
         ancillary = {
-            'anc_1': [0, 1] * units['']
+            'anc_1': [0, 1] * units('')
         },
     )
 
@@ -139,7 +139,7 @@ def f_profiles(profiles):
 def f_grid_no_ancillary(grid):
     a = np.arange(24).reshape(2,3,2,2)
     return GridField(
-        data = a * units['degree_C'],
+        data = a * units('degree_C'),
         domain = grid,
         name = 'field_grid',
         properties = {'test_property': 'this is a field test property'},
@@ -149,11 +149,11 @@ def f_grid_no_ancillary(grid):
 def f_grid(grid):
     a = np.arange(24).reshape(2,3,2,2)
     return GridField(
-        data = a * units['degree_C'],
+        data = a * units('degree_C'),
         domain = grid,
         name = 'field_grid',
         properties = {'test_property': 'this is a field test property'},
         ancillary = {
-            'anc_grid_1': a * units['']
+            'anc_grid_1': a * units('')
         },
     )