Release version 1.5.0, Merge pull request #751 from sentinel-hub/develop

Release version 1.5.0

Author: zigaLuksic

.github/workflows/ci_action.yml

@@ -51,26 +51,14 @@ jobs:
           # caching the entire environment is faster when cache exists but slower for cache creation
 
       - name: Install packages
-        run: |
-          pip install -r requirements-dev.txt --upgrade --upgrade-strategy eager
-          python install_all.py
-          pip install -r ml_tools/requirements-tdigest.txt
+        run: pip install .[DEV] --upgrade --upgrade-strategy eager
 
       - name: Run pylint
-        run: make pylint
+        run: pylint eolearn
 
       - name: Run mypy
         if: success() || failure()
-        run: |
-          mypy \
-            core/eolearn/core \
-            coregistration/eolearn/coregistration \
-            geometry/eolearn/geometry \
-            features/eolearn/features \
-            io/eolearn/io \
-            mask/eolearn/mask \
-            ml_tools/eolearn/ml_tools \
-            visualization/eolearn/visualization
+        run: mypy eolearn
 
   test-on-github:
     runs-on: ubuntu-latest
@@ -95,24 +83,26 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-          # cache: pip # uncomment when all requirements are in `pyproject.toml`
+          cache: pip
 
       - name: Install packages
-        run: |
-          pip install -r requirements-dev.txt --upgrade --upgrade-strategy eager
-          python install_all.py -e
+        run: pip install -e .[DEV] --upgrade --upgrade-strategy eager
 
       - name: Run full tests and code coverage
         if: ${{ matrix.full_test_suite }}
         run: |
           sentinelhub.config \
             --sh_client_id "${{ secrets.SH_CLIENT_ID }}" \
             --sh_client_secret "${{ secrets.SH_CLIENT_SECRET }}"
-          pytest --cov --cov-report=term --cov-report=xml
+          if [ ${{ github.event_name }} == 'push' ]; then
+            pytest -m "not geopedia" --cov=eolearn --cov-report=term --cov-report=xml
+          else
+            pytest -m "not geopedia"
+          fi
 
       - name: Run reduced tests
         if: ${{ !matrix.full_test_suite }}
-        run: pytest -m "not sh_integration"
+        run: pytest -m "not sh_integration and not geopedia"
 
       - name: Upload code coverage
         if: ${{ matrix.full_test_suite && github.event_name == 'push' }}

.gitlab-ci.yml

@@ -10,7 +10,6 @@ run_sh_integration_tests:
     - apt-get update
     - apt-get install -y build-essential libgdal-dev graphviz proj-bin gcc libproj-dev libspatialindex-dev
   script:
-    - pip install -r requirements-dev.txt --upgrade
-    - python install_all.py
+    - pip install .[DEV]
     - sentinelhub.config --sh_client_id "$SH_CLIENT_ID" --sh_client_secret "$SH_CLIENT_SECRET" > /dev/null # Gitlab can't mask SH_CLIENT_SECRET in logs
     - pytest -m sh_integration

.pre-commit-config.yaml

@@ -13,13 +13,13 @@ repos:
       - id: debug-statements
 
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
       - id: black
         language_version: python3
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.269"
+    rev: "v0.0.282"
     hooks:
       - id: ruff
 

CHANGELOG.md

@@ -1,4 +1,32 @@
-## [Version 1.4.2] - 2023-3-14
+## [Version 1.5.0] - 2023-09-06
+
+The release focuses on making `eo-learn` much simpler to install, reducing the number of dependencies, and improving validation of soundness of `EOPatch` data.
+
+- `eo-learn` is now distributed as a single package. Installation of `eo-learn-mask` and similar is no longer necessary and users are warned when such installations are detected.
+- Changes to `timestamps` and `bbox` attributes of `EOPatch` objects:
+    - `FeatureType.TIMESTAMPS` and `FeatureType.BBOX` have been deprecated, data should be accessed via attributes. Feature parsers no longer return these values (for instance when calling `EOPatch.get_features`).
+    - EOPatches without temporal information now have a timestamp value of `None`, whereas a timestamp value `[]` signifies that the EOPatch has a temporal dimension of 0.
+    - Introduced a `get_timestamps` method that will fail if `timestamps` are `None`. This can be used in cases where timestamps are assumed to be present (to avoid issues with type-checking and ill formed inputs).
+    - Loading, saving, and copying of EOPatches will take `timestamps` into account either when processing the full eopatch (i.e. `features=...`) or if the selection contains a temporal feature. The behavior can be controlled via the `load_timestamps`/`save_timestamps`/`copy_timestamps` parameter.
+- Saving and loading of `FeatureType.META_INFO` now processes each feature as a separate file, allowing better filtering and preventing accidental overwriting.
+- The default backend for `SpatialResizeTask` has been switched to `cv2` to reduce the number of dependencies.
+- `eolearn.geometry.morphology` tasks now use `cv2` instead of `scikit-image` to reduce the number of dependencies. The task interfaces have been slightly adjusted.
+- Improved reports:
+  - Exception grouping is now done by exception origin instead of exception message, resulting in shorter reports.
+  - Added execution time statistics per node
+- `CloudMaskTask` has been restricted to mono-temporal predictions using the `s2cloudless` package. For the multi-temporal one check [here](https://github.com/sentinel-hub/eo-learn-examples/blob/main/extra-tasks/cloud_mask/cloud_mask.py).
+- Certain tasks (for instance `SaveTask` and `LoadTask`) no longer pass arguments to the super-class via **kwargs in order to improve documentation and type-checking.
+- `SaveTask` and `LoadTask` now raise `OSError` exceptions instead of `IOError`.
+- Project-specific and outdated EOTasks were moved to extras or to the example repository [eo-learn-examples/extra-tasks](https://github.com/sentinel-hub/eo-learn-examples/tree/main/extra-tasks).
+- The submodule `eolearn.features.bands_extraction` has been renamed to `eolearn.features.ndi`.
+- The submodule `eolearn.ml_tools.extra.plotting` has been moved to `eolearn.visualization.utils`.
+- Compression of EOPatch files has been hardcoded. The parameter `compression_level` has been deprecated and has no effect.
+- Introduced experimental `zarr` support for loading/saving temporal slices of temporal features. The API might be changed in future releases.
+- Limited `rasterio` to 1.3.7 due to an issue with importing rasters from AWS S3
+- Updated examples, simplified tests, various improvements.
+
+
+## [Version 1.4.2] - 2023-03-14
 
 - Introduced support for Python 3.11.
 - Removed support for Python 3.7.
@@ -13,7 +41,7 @@
 - Various refactoring efforts and dependency improvements.
 - Various improvements to tests and code.
 
-## [Version 1.4.1] - 2023-3-14
+## [Version 1.4.1] - 2023-03-14
 
 - The codebase is now fully annotated and type annotations are mandatory for all new code.
 - In the future `EOPatch` objects will **require** a valid `bbox`. For now the users are warned when no such value is provided.
@@ -27,7 +55,7 @@
 - Various other minor improvements and deprecations.
 
 
-## [Version 1.4.0] - 2023-1-20
+## [Version 1.4.0] - 2023-01-20
 
 - (**codebreaking**) Complete overhaul of `eolearn.coregistration`. See documentation for details.
 - (**codebreaking**) Removed non-working HVPlot backend for `eolearn.visualization`.

CONTRIBUTING.md

@@ -22,7 +22,7 @@ For any question, feel free to contact us at [eoresearch@sinergise.com](eoresear
 
 We strive to provide high-quality working code, but bugs happen nevertheless.
 
-When reporting a bug, please check [here][open-bug-list] whether the bug was already reported. If not, open an issue with the **bug** label and report the following information:
+When reporting a bug, please check [the issue tracker][open-bug-list] whether the bug was already reported. If not, open an issue with the **bug** label and report the following information:
 
 * Issue description
 * How to reproduce the issue
@@ -36,7 +36,7 @@ This information helps us to reproduce, pinpoint, and fix the reported issue. If
 
 ## Feature Requests
 
-Existing feature requests can be found [here][existing-feature-requests].
+Existing feature requests can be found [in the issues][existing-feature-requests].
 
 A new feature request can be created by opening a new issue with the **enhancement** label, and describing how the feature would benefit the **eo-learn** community. Providing an example use-case would help assessing the scope of the feature request.
 

MANIFEST.in

@@ -1,187 +1,21 @@
 # Makefile for creating a new release of the package and uploading it to PyPI
 
 PYTHON = python3
-PACKAGES = core coregistration features geometry io mask ml_tools visualization
-PYLINT = pylint
 
 .PHONY: $(PACKAGES:test)
-.SILENT: pylint pylint-fast
 
 help:
-	@echo "Use 'make upload-<package>' to upload the package to PyPi"
-	@echo "Use 'make pylint' to run pylint on the code of all subpackages"
+	@echo "Use 'make test-upload' to upload the package to testPyPi"
+	@echo "Use 'make upload' to upload the package to PyPi"
 
-mypy:
-	mypy \
-	core/eolearn/core \
-	coregistration/eolearn/coregistration \
-	geometry/eolearn/geometry \
-	features/eolearn/features \
-	io/eolearn/io \
-	mask/eolearn/mask \
-	ml_tools/eolearn/ml_tools \
-	visualization/eolearn/visualization
 
-pylint:
-	# Runs pylint on all subpackages consecutively and makes sure any error status code gets propagated.
-	export PYLINT_STATUS=0
-	for package in $(PACKAGES) ; do \
-    	$(PYLINT) $$package/eolearn/$$package || export PYLINT_STATUS=$$?; \
-	done;
-	exit $$PYLINT_STATUS
-
-
-pylint-fast:
-	# Runs pylint on all subpackages in parallel. Because of that output verdicts are not in the order of package
-	# names and this process cannot be interrupted.
-	for package in $(PACKAGES) ; do \
-    	$(PYLINT) $$package/eolearn/$$package & \
-	done;
-	wait
-
-.ONESHELL:
-build-core:
-	cd core
-	cp ../LICENSE LICENSE
-	rm -r dist build | true
-	$(PYTHON) setup.py sdist bdist_wheel
-	rm LICENSE
-
-.ONESHELL:
-build-coregistration:
-	cd coregistration
-	cp ../LICENSE LICENSE
-	rm -r dist build | true
-	$(PYTHON) setup.py sdist bdist_wheel
-	rm LICENSE
-
-.ONESHELL:
-build-features:
-	cd features
-	cp ../LICENSE LICENSE
-	rm -r dist build | true
-	$(PYTHON) setup.py sdist bdist_wheel
-	rm LICENSE
-
-.ONESHELL:
-build-geometry:
-	cd geometry
-	cp ../LICENSE LICENSE
-	rm -r dist build | true
-	$(PYTHON) setup.py sdist bdist_wheel
-	rm LICENSE
-
-.ONESHELL:
-build-io:
-	cd io
-	cp ../LICENSE LICENSE
-	rm -r dist build | true
-	$(PYTHON) setup.py sdist bdist_wheel
-	rm LICENSE
-
-.ONESHELL:
-build-mask:
-	cd mask
-	cp ../LICENSE LICENSE
-	rm -r dist build | true
-	$(PYTHON) setup.py sdist bdist_wheel
-	rm LICENSE
-
-.ONESHELL:
-build-ml-tools:
-	cd ml_tools
-	cp ../LICENSE LICENSE
-	rm -r dist build | true
-	$(PYTHON) setup.py sdist bdist_wheel
-	rm LICENSE
-
-.ONESHELL:
-build-visualization:
-	cd visualization
-	cp ../LICENSE LICENSE
-	rm -r dist build | true
-	$(PYTHON) setup.py sdist bdist_wheel
-	rm LICENSE
-
-.ONESHELL:
-build-abstract-package:
-	rm -r dist build | true
-	$(PYTHON) setup.py sdist bdist_wheel
-
-upload-core: build-core
-	twine upload core/dist/*
-
-upload-coregistration: build-coregistration
-	twine upload coregistration/dist/*
-
-upload-features: build-features
-	twine upload features/dist/*
-
-upload-geometry: build-geometry
-	twine upload geometry/dist/*
-
-upload-io: build-io
-	twine upload io/dist/*
-
-upload-mask: build-mask
-	twine upload mask/dist/*
-
-upload-ml-tools: build-ml-tools
-	twine upload ml_tools/dist/*
-
-upload-visualization: build-visualization
-	twine upload visualization/dist/*
-
-upload-abstract-package: build-abstract-package
-	twine upload dist/*
-
-upload-all: \
- 	upload-core \
-	upload-coregistration \
-	upload-features \
-	upload-geometry \
-	upload-io \
-	upload-mask \
-	upload-ml-tools \
-	upload-visualization \
-	upload-abstract-package
+upload:
+	rm -r dist | true
+	python -m build --sdist --wheel
+	twine upload --skip-existing dist/*
 
 # For testing:
-
-test-upload-core: build-core
-	twine upload --repository testpypi core/dist/*
-
-test-upload-coregistration: build-coregistration
-	twine upload --repository testpypi coregistration/dist/*
-
-test-upload-features: build-features
-	twine upload --repository testpypi features/dist/*
-
-test-upload-geometry: build-geometry
-	twine upload --repository testpypi geometry/dist/*
-
-test-upload-io: build-io
-	twine upload --repository testpypi io/dist/*
-
-test-upload-mask: build-mask
-	twine upload --repository testpypi mask/dist/*
-
-test-upload-ml-tools: build-ml-tools
-	twine upload --repository testpypi ml_tools/dist/*
-
-test-upload-visualization: build-visualization
-	twine upload --repository testpypi visualization/dist/*
-
-test-upload-abstract-package: build-abstract-package
-	twine upload --repository testpypi dist/*
-
-test-upload-all: \
- 	test-upload-core \
-	test-upload-coregistration \
-	test-upload-features \
-	test-upload-geometry \
-	test-upload-io \
-	test-upload-mask \
-	test-upload-ml-tools \
-	test-upload-visualization \
-	test-upload-abstract-package
+test-upload:
+	rm -r dist | true
+	python -m build --sdist --wheel
+	twine upload --repository testpypi --skip-existing dist/*