Prepare for release

.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

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.

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)

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

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:

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))

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

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:

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"
    ]

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",
+    ")"
    ]
   },
   {

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",

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",
+    ")"
    ]
   },
   {

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
 

tests/core/test_eodata.py

@@ -31,12 +31,14 @@
 
 @pytest.fixture(name="mini_eopatch")
 def mini_eopatch_fixture() -> EOPatch:
-    return generate_eopatch({
-        FeatureType.DATA: ["A", "B"],
-        FeatureType.MASK: ["C", "D"],
-        FeatureType.MASK_TIMELESS: ["E"],
-        FeatureType.META_INFO: ["beep"],
-    })
+    return generate_eopatch(
+        {
+            FeatureType.DATA: ["A", "B"],
+            FeatureType.MASK: ["C", "D"],
+            FeatureType.MASK_TIMELESS: ["E"],
+            FeatureType.META_INFO: ["beep"],
+        }
+    )
 
 
 def test_numpy_feature_types() -> None:
@@ -382,12 +384,14 @@ def test_get_spatial_dimension(feature: Feature, expected_dim: tuple[int, int],
     ("patch", "expected_features"),
     [
         (
-            generate_eopatch({
-                FeatureType.DATA: ["A", "B"],
-                FeatureType.MASK: ["C", "D"],
-                FeatureType.MASK_TIMELESS: ["E"],
-                FeatureType.META_INFO: ["beep"],
-            }),
+            generate_eopatch(
+                {
+                    FeatureType.DATA: ["A", "B"],
+                    FeatureType.MASK: ["C", "D"],
+                    FeatureType.MASK_TIMELESS: ["E"],
+                    FeatureType.META_INFO: ["beep"],
+                }
+            ),
             [
                 (FeatureType.DATA, "A"),
                 (FeatureType.DATA, "B"),

tests/core/test_eodata_io.py

@@ -86,13 +86,15 @@ def _silence_warnings_fixture():
 
 @pytest.fixture(name="eopatch")
 def eopatch_fixture():
-    eopatch = generate_eopatch({
-        FeatureType.DATA: ["data"],
-        FeatureType.MASK_TIMELESS: ["mask", "mask2"],
-        FeatureType.SCALAR: ["my scalar with spaces"],
-        FeatureType.SCALAR_TIMELESS: ["my timeless scalar with spaces"],
-        FeatureType.META_INFO: ["something", "something-else"],
-    })
+    eopatch = generate_eopatch(
+        {
+            FeatureType.DATA: ["data"],
+            FeatureType.MASK_TIMELESS: ["mask", "mask2"],
+            FeatureType.SCALAR: ["my scalar with spaces"],
+            FeatureType.SCALAR_TIMELESS: ["my timeless scalar with spaces"],
+            FeatureType.META_INFO: ["something", "something-else"],
+        }
+    )
     eopatch.vector["my-df"] = GeoDataFrame(
         {
             "values": [1, 2],

tests/core/test_utils/test_parsing.py

@@ -152,12 +152,14 @@ def test_allowed_feature_types_iterable(test_input: FeaturesSpecification, allow
 
 @pytest.fixture(name="eopatch", scope="module")
 def eopatch_fixture():
-    return generate_eopatch({
-        FeatureType.DATA: ["data", "CLP"],
-        FeatureType.MASK: ["data", "IS_VALID"],
-        FeatureType.MASK_TIMELESS: ["LULC"],
-        FeatureType.META_INFO: ["something"],
-    })
+    return generate_eopatch(
+        {
+            FeatureType.DATA: ["data", "CLP"],
+            FeatureType.MASK: ["data", "IS_VALID"],
+            FeatureType.MASK_TIMELESS: ["LULC"],
+            FeatureType.META_INFO: ["something"],
+        }
+    )
 
 
 @pytest.mark.parametrize(