Release 1.5.4, Merge pull request #791 from sentinel-hub/develop

zigaLuksic · web-flow · commit c7a39ed60183 · 2024-05-13T10:43:16.000+02:00
Release 1.5.4
diff --git a/.github/workflows/ci_action.yml b/.github/workflows/ci_action.yml
@@ -105,13 +105,13 @@ jobs:
         if: ${{ !matrix.full_test_suite }}
         run: pytest -m "not sh_integration and not geopedia"
 
-      - name: Upload code coverage
-        if: ${{ matrix.full_test_suite && github.event_name == 'push' }}
-        uses: codecov/codecov-action@v2
-        with:
-          files: coverage.xml
-          fail_ci_if_error: true
-          verbose: false
+      # - name: Upload code coverage
+      #   if: ${{ matrix.full_test_suite && github.event_name == 'push' }}
+      #   uses: codecov/codecov-action@v2
+      #   with:
+      #     files: coverage.xml
+      #     fail_ci_if_error: true
+      #     verbose: false
 
   mirror-and-integration-test-on-gitlab:
     if: github.event_name == 'push'
@@ -121,11 +121,11 @@ jobs:
       - name: Mirror + trigger CI
         uses: SvanBoxel/gitlab-mirror-and-ci-action@master
         with:
-          args: "https://git.sinergise.com/eo/code/eo-learn/"
+          args: "https://hello.planet.com/code/eo/code/eo-learn"
         env:
           FOLLOW_TAGS: "true"
-          GITLAB_HOSTNAME: "git.sinergise.com"
+          GITLAB_HOSTNAME: "hello.planet.com/code"
           GITLAB_USERNAME: "github-action"
           GITLAB_PASSWORD: ${{ secrets.GITLAB_PASSWORD }}
-          GITLAB_PROJECT_ID: "164"
+          GITLAB_PROJECT_ID: "9715"
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/ci_trigger.yml b/.github/workflows/ci_trigger.yml
@@ -16,4 +16,4 @@ jobs:
             -F ref=main \
             -F variables[CUSTOM_RUN_TAG]=auto \
             -F variables[LAYER_NAME]=dotai-eo \
-            https://git.sinergise.com/api/v4/projects/1031/trigger/pipeline
+            https://hello.planet.com/code/api/v4/projects/9723/trigger/pipeline
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,4 +1,7 @@
-image: python:3.9
+default:
+  image: python:3.9
+  tags:
+    - sinergise-lju
 
 stages:
   - test
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: end-of-file-fixer
       - id: requirements-txt-fixer
@@ -13,18 +13,18 @@ repos:
       - id: debug-statements
 
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.4.2
     hooks:
       - id: black
         language_version: python3
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.1.11"
+    rev: "v0.4.4"
     hooks:
       - id: ruff
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.1
+    rev: 1.8.5
     hooks:
       - id: nbqa-black
       - id: nbqa-ruff
diff --git a/.zenodo.json b/.zenodo.json
@@ -209,6 +209,9 @@
         },
         {
             "id": "101059548"
+        },
+        {
+            "id": "101086461"
         }
     ]
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,8 @@
+## [Version 1.5.4] - 2024-05-13
+
+- Minor fixes for documentation
+
+
 ## [Version 1.5.3] - 2024-01-10
 
 - Fix `numpy<2` in anticipation of numpy 2.0 release.
diff --git a/README.md b/README.md
@@ -202,4 +202,4 @@ See [LICENSE](https://github.com/sentinel-hub/eo-learn/blob/master/LICENSE).
 
 ## Acknowledgements
 
-This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreements No. 776115, No. 101004112 and No. 101059548.
+This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreements No. 776115, No. 101004112, No. 101059548 and No. 101086461.
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -10,6 +10,6 @@ dependencies:
       - sphinx_rtd_theme==1.3.0
       - nbsphinx
       - jupyter
-      - sphinx_mdinclude
+      - sphinx_mdinclude==0.5.4
 
       - ./../.[FULL]
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -265,7 +265,7 @@ def get_subclasses(cls):
 module = "eolearn"
 
 APIDOC_OPTIONS = ["--module-first", "--separate", "--no-toc", "--templatedir", os.path.join(current_dir, "_templates")]
-APIDOC_EXCLUDE = ["graph.py", "eodata_io.py", "eodata_merge.py"]
+APIDOC_EXCLUDE = ["graph.py", "eodata_io.py"]
 
 shutil.rmtree(reference_dir, ignore_errors=True)
 shutil.copytree(custom_reference_dir, reference_dir)
diff --git a/eolearn/__init__.py b/eolearn/__init__.py
@@ -1,6 +1,6 @@
 """Main module of the `eolearn` package."""
 
-__version__ = "1.5.3"
+__version__ = "1.5.4"
 
 import importlib.util
 import warnings
diff --git a/eolearn/core/eoexecution.py b/eolearn/core/eoexecution.py
@@ -131,7 +131,7 @@ def __init__(
 
     @staticmethod
     def _parse_and_validate_execution_kwargs(
-        execution_kwargs: Iterable[dict[EONode, dict[str, object]]]
+        execution_kwargs: Iterable[dict[EONode, dict[str, object]]],
     ) -> list[dict[EONode, dict[str, object]]]:
         """Parses and validates execution arguments provided by user and raises an error if something is wrong."""
         for input_kwargs in execution_kwargs:
diff --git a/eolearn/features/extra/interpolation.py b/eolearn/features/extra/interpolation.py
@@ -273,10 +273,12 @@ def interpolate_data(self, data: np.ndarray, times: np.ndarray, resampled_times:
 
         # array defining index correspondence between reference times and resampled times
         min_time, max_time = np.min(resampled_times), np.max(resampled_times)
-        ori2res = np.array([
-            np.abs(resampled_times - orig_time).argmin() if min_time <= orig_time <= max_time else None
-            for orig_time in times
-        ])
+        ori2res = np.array(
+            [
+                np.abs(resampled_times - orig_time).argmin() if min_time <= orig_time <= max_time else None
+                for orig_time in times
+            ]
+        )
 
         # find NaNs that start or end a time-series
         row_nans, col_nans = np.where(self._get_start_end_nans(data))
diff --git a/eolearn/io/sentinelhub_process.py b/eolearn/io/sentinelhub_process.py
@@ -1,4 +1,4 @@
-""" Input tasks that collect data from `Sentinel-Hub Process API
+"""Input tasks that collect data from `Sentinel-Hub Process API
 <https://docs.sentinel-hub.com/api/latest/api/process/>`__
 
 Copyright (c) 2017- Sinergise and contributors
diff --git a/eolearn/visualization/eoexecutor.py b/eolearn/visualization/eoexecutor.py
@@ -163,15 +163,17 @@ def _get_node_descriptions(self) -> list[dict[str, Any]]:
                     f" usually {np.mean(durations):.4g} ± {np.std(durations):.4g} seconds"
                 )
 
-            descriptions.append({
-                "name": f"{node_name} ({node.uid})",
-                "uid": node.uid,
-                "args": {
-                    key: value.replace("<", "&lt;").replace(">", "&gt;")  # type: ignore[attr-defined]
-                    for key, value in node.task.private_task_config.init_args.items()
-                },
-                "duration_report": duration_report,
-            })
+            descriptions.append(
+                {
+                    "name": f"{node_name} ({node.uid})",
+                    "uid": node.uid,
+                    "args": {
+                        key: value.replace("<", "&lt;").replace(">", "&gt;")  # type: ignore[attr-defined]
+                        for key, value in node.task.private_task_config.init_args.items()
+                    },
+                    "duration_report": duration_report,
+                }
+            )
         return descriptions
 
     def _render_execution_tracebacks(self, formatter: pygments.formatter.Formatter) -> list:
diff --git a/examples/core/CoreOverview.ipynb b/examples/core/CoreOverview.ipynb
@@ -801,11 +801,13 @@
     }
    ],
    "source": [
-    "results = workflow.execute({\n",
-    "    load_node: {\"eopatch_folder\": \"TestEOPatch\"},\n",
-    "    add_feature_node: {\"data\": np.zeros((68, 3), dtype=np.uint8)},\n",
-    "    save_node: {\"eopatch_folder\": \"WorkflowEOPatch\"},\n",
-    "})\n",
+    "results = workflow.execute(\n",
+    "    {\n",
+    "        load_node: {\"eopatch_folder\": \"TestEOPatch\"},\n",
+    "        add_feature_node: {\"data\": np.zeros((68, 3), dtype=np.uint8)},\n",
+    "        save_node: {\"eopatch_folder\": \"WorkflowEOPatch\"},\n",
+    "    }\n",
+    ")\n",
     "\n",
     "results"
    ]
diff --git a/examples/io/SentinelHubIO.ipynb b/examples/io/SentinelHubIO.ipynb
@@ -374,10 +374,12 @@
     "workflow_nodes = linearly_connect_tasks(input_task, add_indices, add_l2a_and_scl, add_dem, save, output_task)\n",
     "workflow = EOWorkflow(workflow_nodes)\n",
     "\n",
-    "result = workflow.execute({\n",
-    "    workflow_nodes[0]: {\"bbox\": roi_bbox, \"time_interval\": time_interval},\n",
-    "    workflow_nodes[-2]: {\"eopatch_folder\": \"eopatch\"},\n",
-    "})"
+    "result = workflow.execute(\n",
+    "    {\n",
+    "        workflow_nodes[0]: {\"bbox\": roi_bbox, \"time_interval\": time_interval},\n",
+    "        workflow_nodes[-2]: {\"eopatch_folder\": \"eopatch\"},\n",
+    "    }\n",
+    ")"
    ]
   },
   {
diff --git a/examples/land-cover-map/SI_LULC_pipeline.ipynb b/examples/land-cover-map/SI_LULC_pipeline.ipynb
@@ -744,10 +744,12 @@
     "save_node = workflow_nodes[-1]\n",
     "execution_args = []\n",
     "for idx, bbox in enumerate(bbox_list[patch_ids]):\n",
-    "    execution_args.append({\n",
-    "        input_node: {\"bbox\": bbox, \"time_interval\": time_interval},\n",
-    "        save_node: {\"eopatch_folder\": f\"eopatch_{idx}\"},\n",
-    "    })\n",
+    "    execution_args.append(\n",
+    "        {\n",
+    "            input_node: {\"bbox\": bbox, \"time_interval\": time_interval},\n",
+    "            save_node: {\"eopatch_folder\": f\"eopatch_{idx}\"},\n",
+    "        }\n",
+    "    )\n",
     "\n",
     "# Execute the workflow\n",
     "executor = EOExecutor(workflow, execution_args, save_logs=True)\n",
@@ -1329,11 +1331,13 @@
     "\n",
     "execution_args = []\n",
     "for idx in range(len(patch_ids)):\n",
-    "    execution_args.append({\n",
-    "        workflow_nodes[0]: {\"eopatch_folder\": f\"eopatch_{idx}\"},  # load\n",
-    "        workflow_nodes[-2]: {\"seed\": 42},  # sampling\n",
-    "        workflow_nodes[-1]: {\"eopatch_folder\": f\"eopatch_{idx}\"},  # save\n",
-    "    })\n",
+    "    execution_args.append(\n",
+    "        {\n",
+    "            workflow_nodes[0]: {\"eopatch_folder\": f\"eopatch_{idx}\"},  # load\n",
+    "            workflow_nodes[-2]: {\"seed\": 42},  # sampling\n",
+    "            workflow_nodes[-1]: {\"eopatch_folder\": f\"eopatch_{idx}\"},  # save\n",
+    "        }\n",
+    "    )\n",
     "\n",
     "executor = EOExecutor(workflow, execution_args, save_logs=True)\n",
     "executor.run(workers=5)\n",
@@ -2002,11 +2006,13 @@
     "# Create a list of execution arguments for each patch\n",
     "execution_args = []\n",
     "for i in range(len(patch_ids)):\n",
-    "    execution_args.append({\n",
-    "        workflow_nodes[0]: {\"eopatch_folder\": f\"eopatch_{i}\"},\n",
-    "        workflow_nodes[2]: {\"filename\": f\"{tiff_location}/prediction_eopatch_{i}.tiff\"},\n",
-    "        workflow_nodes[3]: {\"eopatch_folder\": f\"eopatch_{i}\"},\n",
-    "    })\n",
+    "    execution_args.append(\n",
+    "        {\n",
+    "            workflow_nodes[0]: {\"eopatch_folder\": f\"eopatch_{i}\"},\n",
+    "            workflow_nodes[2]: {\"filename\": f\"{tiff_location}/prediction_eopatch_{i}.tiff\"},\n",
+    "            workflow_nodes[3]: {\"eopatch_folder\": f\"eopatch_{i}\"},\n",
+    "        }\n",
+    "    )\n",
     "\n",
     "# Run the executor\n",
     "executor = EOExecutor(workflow, execution_args)\n",
diff --git a/examples/water-monitor/WaterMonitorWorkflow.ipynb b/examples/water-monitor/WaterMonitorWorkflow.ipynb
@@ -430,9 +430,11 @@
     "# The download task requires additional arguments at execution. These are linked to the node the task is in.\n",
     "download_node = workflow_nodes[0]\n",
     "\n",
-    "result = workflow.execute({\n",
-    "    download_node: {\"bbox\": dam_bbox, \"time_interval\": time_interval},\n",
-    "})"
+    "result = workflow.execute(\n",
+    "    {\n",
+    "        download_node: {\"bbox\": dam_bbox, \"time_interval\": time_interval},\n",
+    "    }\n",
+    ")"
    ]
   },
   {
diff --git a/pyproject.toml b/pyproject.toml
@@ -72,19 +72,18 @@ docs = [
     "jupyter",
     "nbsphinx",
     "sphinx==7.1.2",
-    "sphinx_mdinclude",
+    "sphinx_mdinclude==0.5.4",  #0.6 didn't work last time
     "sphinx_rtd_theme==1.3.0",
 ]
 dev = [
     "build",
     "eo-learn[FULL]",
     "hypothesis",
-    "moto",
+    "moto[s3]>=5.0.0",
     "mypy>=0.990",
     "pylint>=2.14.0",
     "pytest>=7.0.0",
     "pytest-cov",
-    "pytest-lazy-fixture",
     "pytest-mock",
     "twine",
     "types-python-dateutil",
diff --git a/tests/core/conftest.py b/tests/core/conftest.py
@@ -10,12 +10,8 @@
 from __future__ import annotations
 
 import os
-from typing import Callable
 
-import boto3
 import pytest
-from fs_s3fs import S3FS
-from moto import mock_s3
 
 from eolearn.core import EOPatch
 
@@ -28,26 +24,3 @@ def test_eopatch_path_fixture() -> str:
 @pytest.fixture(name="test_eopatch")
 def test_eopatch_fixture(test_eopatch_path) -> EOPatch:
     return EOPatch.load(test_eopatch_path)
-
-
-@pytest.fixture(name="create_mocked_s3fs", scope="session")
-def s3_mocking_fixture() -> Callable[[str], S3FS]:
-    """Provides a function for mocking S3 buckets"""
-
-    @mock_s3
-    def create_mocked_s3fs(bucket_name: str = "mocked-test-bucket") -> S3FS:
-        """Creates a new empty mocked s3 bucket. If one such bucket already exists it deletes it first."""
-        s3resource = boto3.resource("s3", region_name="eu-central-1")
-
-        bucket = s3resource.Bucket(bucket_name)
-
-        if bucket.creation_date:  # If bucket already exists
-            for key in bucket.objects.all():
-                key.delete()
-            bucket.delete()
-
-        s3resource.create_bucket(Bucket=bucket_name, CreateBucketConfiguration={"LocationConstraint": "eu-central-1"})
-
-        return S3FS(bucket_name=bucket_name)
-
-    return create_mocked_s3fs
diff --git a/tests/core/test_core_tasks.py b/tests/core/test_core_tasks.py
@@ -54,13 +54,15 @@
 
 @pytest.fixture(name="patch")
 def patch_fixture() -> EOPatch:
-    patch = generate_eopatch({
-        FeatureType.DATA: ["bands", "CLP"],
-        FeatureType.MASK: ["CLM"],
-        FeatureType.MASK_TIMELESS: ["mask", "LULC", "RANDOM_UINT8"],
-        FeatureType.SCALAR: ["values", "CLOUD_COVERAGE"],
-        FeatureType.META_INFO: ["something"],
-    })
+    patch = generate_eopatch(
+        {
+            FeatureType.DATA: ["bands", "CLP"],
+            FeatureType.MASK: ["CLM"],
+            FeatureType.MASK_TIMELESS: ["mask", "LULC", "RANDOM_UINT8"],
+            FeatureType.SCALAR: ["values", "CLOUD_COVERAGE"],
+            FeatureType.META_INFO: ["something"],
+        }
+    )
     patch.data["CLP_S2C"] = np.zeros_like(patch.data["CLP"])
     return patch
 
diff --git a/tests/core/test_eodata.py b/tests/core/test_eodata.py
diff --git a/tests/core/test_eodata_io.py b/tests/core/test_eodata_io.py
diff --git a/tests/core/test_utils/test_fs.py b/tests/core/test_utils/test_fs.py
diff --git a/tests/core/test_utils/test_parsing.py b/tests/core/test_utils/test_parsing.py

Original file line number	Diff line number	Diff line change
`@@ -209,6 +209,9 @@`
`209`	`209`	`},`
`210`	`210`	`{`
`211`	`211`	`"id": "101059548"`
	`212`	`+ },`
	`213`	`+ {`
	`214`	`+ "id": "101086461"`
`212`	`215`	`}`
`213`	`216`	`]`
`214`	`217`	`}`
Original file line number	Diff line number	Diff line change
`@@ -202,4 +202,4 @@ See [LICENSE](https://github.com/sentinel-hub/eo-learn/blob/master/LICENSE).`
`202`	`202`
`203`	`203`	`## Acknowledgements`
`204`	`204`
`205`		`-This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreements No. 776115, No. 101004112 and No. 101059548.`
	`205`	`+This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreements No. 776115, No. 101004112, No. 101059548 and No. 101086461.`