sentinel-hub · zigaLuksic · Aug 16, 2023 · Jun 27, 2023 · Jun 27, 2023 · Jun 27, 2023
diff --git a/.github/workflows/ci_action.yml b/.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
@@ -95,19 +83,10 @@ 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
-        if: matrix.python-version != '3.9'
-        run: |
-          pip install -r requirements-dev.txt --upgrade --upgrade-strategy eager
-          python install_all.py -e
-
-      - name: Install zarr backend # this will run Zarr backend tests on 3.9
-        if: matrix.python-version == '3.9'
-        run: |
-          pip install -r requirements-dev.txt -r core/requirements-zarr.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 }}

diff --git a/.gitlab-ci.yml b/.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 eolearn[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
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -22,7 +22,7 @@ For any question, feel free to contact us at [[email protected]](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.
 

diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/Makefile b/Makefile
@@ -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/*
diff --git a/README.md b/README.md
@@ -149,7 +149,7 @@ Examples and introductions to the package can be found [here](https://github.com
 
 ## Contributions
 
-The list of all `eo-learn` contributors can be found [here](./CONTRIBUTING.md). If you would like to contribute to `eo-learn`, please check our [contribution guidelines](./CONTRIBUTING.md).
+The list of all `eo-learn` contributors are listed in the [credits file](./CREDITS.md). If you would like to contribute to `eo-learn`, please check our [contribution guidelines](./CONTRIBUTING.md).
 
 ## Blog posts and papers
 

diff --git a/core/MANIFEST.in b/core/MANIFEST.in
diff --git a/core/eolearn/__init__.py b/core/eolearn/__init__.py
diff --git a/coregistration/MANIFEST.in b/coregistration/MANIFEST.in
diff --git a/coregistration/eolearn/__init__.py b/coregistration/eolearn/__init__.py
diff --git a/coregistration/eolearn/coregistration/py.typed b/coregistration/eolearn/coregistration/py.typed
diff --git a/docker/eolearn.dockerfile b/docker/eolearn.dockerfile
@@ -4,12 +4,12 @@ LABEL maintainer="Sinergise EO research team <[email protected]>"
 LABEL description="An official eo-learn docker image with a full eo-learn installation and Jupyter notebook."
 
 RUN apt-get update && apt-get install -y \
-        gcc \
-        libgdal-dev \
-        graphviz \
-        proj-bin \
-        libproj-dev \
-        libspatialindex-dev \
+    gcc \
+    libgdal-dev \
+    graphviz \
+    proj-bin \
+    libproj-dev \
+    libspatialindex-dev \
     && apt-get clean && apt-get autoremove -y && rm -rf /var/lib/apt/lists/*
 
 ENV CPLUS_INCLUDE_PATH=/usr/include/gdal
@@ -20,25 +20,10 @@ RUN pip3 install --no-cache-dir shapely --no-binary :all:
 
 WORKDIR /tmp
 
-COPY core core
-COPY coregistration coregistration
-COPY features features
-COPY geometry geometry
-COPY io io
-COPY mask mask
-COPY ml_tools ml_tools
-COPY visualization visualization
-COPY setup.py README.md requirements-dev.txt ./
+COPY eolearn eolearn
+COPY pyproject.toml README.md LICENSE ./
 
-RUN pip3 install --no-cache-dir \
-    ./core[RAY] \
-    ./coregistration \
-    ./features \
-    ./geometry \
-    ./io[METEOBLUE] \
-    ./mask \
-    ./ml_tools \
-    ./visualization
+RUN pip3 install --no-cache-dir .[FULL]
 
 RUN pip3 install --no-cache-dir \
     . \
@@ -56,4 +41,4 @@ WORKDIR /home/eolearner
 
 EXPOSE 8888
 CMD ["/usr/local/bin/jupyter", "notebook", "--no-browser", "--port=8888", "--ip=0.0.0.0", \
-     "--NotebookApp.token=''", "--allow-root"]
+    "--NotebookApp.token=''", "--allow-root"]
diff --git a/docs/Makefile b/docs/Makefile
@@ -19,4 +19,4 @@ help:
 %: Makefile
 	rm -rf ./build/
 	$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-	rm -r source/examples source/markdowns source/reference source/eotasks.rst
+	# rm -r source/examples source/markdowns source/reference source/eotasks.rst