Merge pull request #7 from esa-cci/main

Merging ESA-CCI Main into Fork

.github/workflows/publish_pypi.yml

@@ -0,0 +1,35 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish to PyPI
+      run: |
+        pip install twine
+        python -m twine upload --username __token__ --password ${{ secrets.PYPI_API_TOKEN }} dist/*

CHANGES.md

@@ -1,3 +1,25 @@
+## Changes in 1.1
+
+* Support numpy >= 2.0 and pydap >= 3.4
+* Automatically publish packages on pypi at release
+* Improved support of vector data cubes
+* Support HR LC data
+* Added user functions for regions:
+  * `get_land_mask`:  Gets a land mask for a dataset.
+  * `get_regions_mask`: Gets a regions mask for a dataset.
+  * `make_regions_dataset`: Rasterize country and continent polygons into a 
+grid provided by a template dataset.
+  * `mask_dataset_by_land`: Masks out non-land-pixels of a dataset.
+  * `mask_dataset_by_regions`: Masks out pixels of a dataset which are not in 
+one of the specified regions.
+* Added notebooks:
+  * `ESA CCI Toolbox Vector Data Cube Access`: Explaining the handling of 
+vector data cubes
+  * `Using the ESA CCI Toolbox with the xcube Viewer`: Explaining how to access
+the xcube viewer from within a Jupyter Notebook
+* Extended documentation by a section on how to configure an xcube server to 
+serve data from the ESA CCI Toolbox
+
 ## Changes in 1.0.2
 
 * Updated list of dataset states

appveyor.yml

@@ -1,54 +1,68 @@
 version: '{build}'
 
 image:
+  - Ubuntu2204
   - macOS
-  - Ubuntu2004
 
 configuration: Release
 
 platform:
   - x64
 
-environment:
-  # For the unit-tests, disable Numba JIT, otherwise Coverage wont reach the actual Python code
-  NUMBA_DISABLE_JIT: 1
+# Do not build feature branch with open Pull Requests.
+# Note that a feature branch build may still occur on the first push to
+# the branch -- see
+# https://help.appveyor.com/discussions/questions/18437-skip_branch_with_pr-setting-doesnt-work
+skip_branch_with_pr: true
 
 for:
 -
   matrix:
     only:
-      - image: macos
+      - image: macOS
   install:
-    - curl -L https://repo.anaconda.com/miniconda/Miniconda3-py310_23.3.1-0-MacOSX-x86_64.sh > miniconda.sh
-    - bash miniconda.sh -b -p $HOME/miniconda
+    - curl -Ls https://micro.mamba.pm/api/micromamba/osx-64/latest | tar -xvj bin/micromamba
+    - mv bin/micromamba ./micromamba
 -
   matrix:
     only:
-      - image: Ubuntu2004
+      - image: Ubuntu2204
   install:
-    - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
-    - bash miniconda.sh -b -p $HOME/miniconda
+    - curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+    - mv bin/micromamba ./micromamba
 
 build_script:
-  - export PATH="$HOME/miniconda/bin:$PATH"
+  # Diagnostics
+  - echo $PLATFORM
+  - echo $APPVEYOR_BUILD_WORKER_IMAGE
+  - echo $APPVEYOR_BUILD_FOLDER
+  - uname -a
+  - pwd
+  - ls
+
+  # Set up micromamba
+  - ./micromamba shell init -s bash --root-prefix ~/micromamba
+  - source ~/.bashrc
+  - source ~/.profile
   - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  # - conda update -q conda # makes travis build fail
-  # Useful for debugging any issues with conda
-  - conda info -a
-  - conda init bash
-  - export CONDA_BASE=$(conda info --base)
-  - source $CONDA_BASE/etc/profile.d/conda.sh
-
-  # Install mamba as a dramatically faster conda replacement. Specifying a
-  # fixed version makes the installation of mamba itself much faster, and
-  # avoids potential breakage due to changes in mamba behaviour.
-  - conda install -c conda-forge mamba
-
-  - mamba env create
-  - conda activate ect
+  - mkdir -p ~/micromamba/pkgs/
+  - export MAMBA_ROOT_PREFIX=~/micromamba
+  - export MAMBA_EXE=$(pwd)/micromamba
+  - . $MAMBA_ROOT_PREFIX/etc/profile.d/mamba.sh
+
+  # Create environment from build folder environment.yml and install xcube
+  - micromamba create --name ect --file $APPVEYOR_BUILD_FOLDER/environment.yml
+  - micromamba activate ect
+  - cd $APPVEYOR_BUILD_FOLDER
   - pip install --no-deps .
-  - conda list
 
-  # Run the test suite.
-  - pytest -v --cov=esa-climate-toolbox test
+  # Make sure pytest is installed
+  - micromamba install --yes --name ect --channel conda-forge pytest attrs
+
+  # Print some diagnostics (useful for debugging)
+  - git status
+  - micromamba list
+  - python -c "from esa_climate_toolbox import __version__; print(f'ESA CCI Toolbox version {__version__}')"
+
+  # Run the test suite
+  - pytest -v --cov=esa_climate_toolbox

docs/source/about.rst

@@ -104,5 +104,8 @@ In addition to operations provided by the ESA CII Toolbox, the Python packages
 `xarray`_, `pandas`_, and `geopandas`_ provide a rich and powerful low-level
 data processing interface for the datasets opened through the Toolbox.
 
-You can find detailed listings of the provided functionality in
+Also, there are further functions which are not operations but which have been found
+to be useful for working with cci data.
+
+You can find detailed listings of the provided functionalities in
 :doc:`api_reference`.

docs/source/api_reference.rst

@@ -50,6 +50,25 @@ Reading and Writing Data
 .. autofunction:: esa_climate_toolbox.core.write_data
 
 
+Functions
+=========
+
+.. _regions:
+
+Region
+------
+
+.. autofunction:: esa_climate_toolbox.functions.regions.get_land_mask
+
+.. autofunction:: esa_climate_toolbox.functions.regions.get_regions_mask
+
+.. autofunction:: esa_climate_toolbox.functions.regions.make_regions_dataset
+
+.. autofunction:: esa_climate_toolbox.functions.regions.mask_dataset_by_land
+
+.. autofunction:: esa_climate_toolbox.functions.regions.mask_dataset_by_regions
+
+
 Operations
 ==========
 

docs/source/conf.py

@@ -14,7 +14,7 @@
 # -- Project information
 
 project = 'ESA CCI Toolbox'
-copyright = '2023, Brockmann Consult GmbH'
+copyright = '2024, Brockmann Consult GmbH'
 author = 'Brockmann Consult GmbH'
 
 release = __version__

docs/source/index.rst

@@ -96,4 +96,5 @@ For support with the CCI Toolbox, please visit our `Helpdesk`_.
    about
    installation_guide
    quick_start
+   viewer
    api_reference