marEx 3.0.2__tar.gz → 3.1__tar.gz

{marex-3.0.2 → marex-3.1}/.github/workflows/release.yml

@@ -27,7 +27,7 @@ jobs:
     - name: Validate and parse version
       id: version
       run: |
-        if [[ "${GITHUB_REF}" =~ ^refs/tags/v([0-9]+\.[0-9]+\.[0-9]+.*)$ ]]; then
+        if [[ "${GITHUB_REF}" =~ ^refs/tags/v([0-9]+\.[0-9]+(\.[0-9]+)?.*)$ ]]; then
           VERSION="${BASH_REMATCH[1]}"
           echo "version=${VERSION}" >> $GITHUB_OUTPUT
 

marex-3.1/CITATION.cff

@@ -0,0 +1,52 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+title: "MarEx: Marine Extremes Detection and Tracking"
+abstract: "Efficient & scalable Marine Extremes detection, identification, & tracking for Exascale Climate Data. A high-performance Python framework for identifying and tracking extreme oceanographic events (such as Marine Heatwaves or Acidity Extremes) in massive climate datasets."
+authors:
+  - family-names: "Wienkers"
+    given-names: "Aaron"
+    email: "aaron@wienkers.com"
+    orcid: "https://orcid.org/0000-0002-8464-3139"
+repository-code: "https://github.com/wienkers/marEx"
+url: "https://github.com/wienkers/marEx"
+doi: "10.5281/zenodo.16922881"
+identifiers:
+  - type: doi
+    value: "10.5281/zenodo.16922881"
+    description: "DOI for this software"
+keywords:
+  - "marine heatwaves"
+  - "extreme events"
+  - "oceanography"
+  - "extremes tracking"
+  - "ocean extremes"
+  - "marine extremes"
+  - "climate data"
+  - "distributed computing"
+  - "dask"
+  - "python"
+version: "3.1"
+date-released: "2025-08-22"
+preferred-citation:
+  type: software
+  title: "MarEx: Marine Extremes Detection and Tracking"
+  authors:
+    - family-names: "Wienkers"
+      given-names: "Aaron"
+      email: "aaron@wienkers.com"
+      orcid: "https://orcid.org/0000-0002-8464-3139"
+  doi: "10.5281/zenodo.16922881"
+  url: "https://github.com/wienkers/marEx"
+  version: "3.1"
+  year: 2025
+funding:
+  - agency: "European Commission"
+    program: "Horizon Europe"
+    grant-id: "101081383"
+    title: "EERIE (European Eddy-Rich ESMs) Project"
+  - agency: "Swiss State Secretariat for Education, Research and Innovation (SERI)"
+    grant-id: "22.00366"
+contact:
+  - email: "aaron@wienkers.com"
+    name: "Aaron Wienkers"

{marex-3.0.2/marEx.egg-info → marex-3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: marEx
-Version: 3.0.2
+Version: 3.1
 Summary: Marine Extremes Detection and Tracking
 Author-email: Aaron Wienkers <aaron@wienkers.com>
 Project-URL: Homepage, https://github.com/wienkers/marEx
@@ -86,15 +86,15 @@ Requires-Dist: pytest-xdist; extra == "test"
 Requires-Dist: coverage[toml]>=6.0.0; extra == "test"
 Requires-Dist: psutil; extra == "test"
 
-
-![Logo](media/logo.png)
+![logo](https://github.com/user-attachments/assets/df99a84b-c88f-447d-a362-ac538d9b924b)
 
 [![Continuous Integration](https://github.com/wienkers/marEx/actions/workflows/ci.yml/badge.svg)](https://github.com/wienkers/marEx/actions/workflows/ci.yml)
 [![Tests](https://github.com/wienkers/marEx/workflows/Tests/badge.svg)](https://github.com/wienkers/marEx/actions/workflows/tests.yml)
 [![codecov](https://codecov.io/gh/wienkers/marEx/branch/main/graph/badge.svg)](https://codecov.io/gh/wienkers/marEx)
 [![PyPI version](https://badge.fury.io/py/marEx.svg)](https://badge.fury.io/py/marEx)
 [![Documentation Status](https://readthedocs.org/projects/marex/badge/?version=latest)](https://marex.readthedocs.io/en/latest/)
-[![PyPI Downloads](https://static.pepy.tech/badge/marex)](https://pepy.tech/projects/marex)
+[![PyPI Downloads](https://static.pepy.tech/badge/marex)](https://pepy.tech/projects/marex) \
+[![DOI](https://zenodo.org/badge/945834123.svg)](https://doi.org/10.5281/zenodo.16922881)
 
 Marine Extremes Python Package
 ==============================

{marex-3.0.2 → marex-3.1}/README.md

@@ -1,12 +1,12 @@
-
-![Logo](media/logo.png)
+![logo](https://github.com/user-attachments/assets/df99a84b-c88f-447d-a362-ac538d9b924b)
 
 [![Continuous Integration](https://github.com/wienkers/marEx/actions/workflows/ci.yml/badge.svg)](https://github.com/wienkers/marEx/actions/workflows/ci.yml)
 [![Tests](https://github.com/wienkers/marEx/workflows/Tests/badge.svg)](https://github.com/wienkers/marEx/actions/workflows/tests.yml)
 [![codecov](https://codecov.io/gh/wienkers/marEx/branch/main/graph/badge.svg)](https://codecov.io/gh/wienkers/marEx)
 [![PyPI version](https://badge.fury.io/py/marEx.svg)](https://badge.fury.io/py/marEx)
 [![Documentation Status](https://readthedocs.org/projects/marex/badge/?version=latest)](https://marex.readthedocs.io/en/latest/)
-[![PyPI Downloads](https://static.pepy.tech/badge/marex)](https://pepy.tech/projects/marex)
+[![PyPI Downloads](https://static.pepy.tech/badge/marex)](https://pepy.tech/projects/marex) \
+[![DOI](https://zenodo.org/badge/945834123.svg)](https://doi.org/10.5281/zenodo.16922881)
 
 Marine Extremes Python Package
 ==============================

{marex-3.0.2 → marex-3.1/marEx.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: marEx
-Version: 3.0.2
+Version: 3.1
 Summary: Marine Extremes Detection and Tracking
 Author-email: Aaron Wienkers <aaron@wienkers.com>
 Project-URL: Homepage, https://github.com/wienkers/marEx
@@ -86,15 +86,15 @@ Requires-Dist: pytest-xdist; extra == "test"
 Requires-Dist: coverage[toml]>=6.0.0; extra == "test"
 Requires-Dist: psutil; extra == "test"
 
-
-![Logo](media/logo.png)
+![logo](https://github.com/user-attachments/assets/df99a84b-c88f-447d-a362-ac538d9b924b)
 
 [![Continuous Integration](https://github.com/wienkers/marEx/actions/workflows/ci.yml/badge.svg)](https://github.com/wienkers/marEx/actions/workflows/ci.yml)
 [![Tests](https://github.com/wienkers/marEx/workflows/Tests/badge.svg)](https://github.com/wienkers/marEx/actions/workflows/tests.yml)
 [![codecov](https://codecov.io/gh/wienkers/marEx/branch/main/graph/badge.svg)](https://codecov.io/gh/wienkers/marEx)
 [![PyPI version](https://badge.fury.io/py/marEx.svg)](https://badge.fury.io/py/marEx)
 [![Documentation Status](https://readthedocs.org/projects/marex/badge/?version=latest)](https://marex.readthedocs.io/en/latest/)
-[![PyPI Downloads](https://static.pepy.tech/badge/marex)](https://pepy.tech/projects/marex)
+[![PyPI Downloads](https://static.pepy.tech/badge/marex)](https://pepy.tech/projects/marex) \
+[![DOI](https://zenodo.org/badge/945834123.svg)](https://doi.org/10.5281/zenodo.16922881)
 
 Marine Extremes Python Package
 ==============================

{marex-3.0.2 → marex-3.1}/tests/test_unstructured_tracking.py

@@ -346,11 +346,11 @@ class TestUnstructuredTracking:
         assert_reasonable_bounds(
             tracked_ds.attrs["preprocessed_area_fraction"],
             2.2,
-            tolerance_relative=0.3,
+            tolerance_relative=0.2,
         )
-        assert_count_in_reasonable_range(tracked_ds.attrs["N_objects_prefiltered"], 15, tolerance=10)
-        assert_count_in_reasonable_range(tracked_ds.attrs["N_objects_filtered"], 8, tolerance=5)
-        assert_count_in_reasonable_range(tracked_ds.attrs["N_events_final"], 3, tolerance=3)
+        assert_count_in_reasonable_range(tracked_ds.attrs["N_objects_prefiltered"], 15, tolerance=5)
+        assert_count_in_reasonable_range(tracked_ds.attrs["N_objects_filtered"], 8, tolerance=2)
+        assert_count_in_reasonable_range(tracked_ds.attrs["N_events_final"], 3, tolerance=1)
 
     @pytest.mark.slow
     def test_unstructured_different_filtering_parameters(self, dask_client_unstructured):
@@ -439,13 +439,13 @@ class TestUnstructuredTracking:
         # Assert tracking statistics are within reasonable bounds for low filter case
         assert_reasonable_bounds(
             tracked_low_filter.attrs["preprocessed_area_fraction"],
-            2.2,
-            tolerance_relative=0.4,
+            1.4,
+            tolerance_relative=0.2,
         )
         # Expected ranges for full dataset (732 timesteps × 1000 cells)
-        assert_count_in_reasonable_range(tracked_low_filter.attrs["N_objects_prefiltered"], 15, tolerance=10)
-        assert_count_in_reasonable_range(tracked_low_filter.attrs["N_objects_filtered"], 15, tolerance=10)
-        assert_count_in_reasonable_range(tracked_low_filter.attrs["N_events_final"], 3, tolerance=3)
+        assert_count_in_reasonable_range(tracked_low_filter.attrs["N_objects_prefiltered"], 15, tolerance=5)
+        assert_count_in_reasonable_range(tracked_low_filter.attrs["N_objects_filtered"], 15, tolerance=2)
+        assert_count_in_reasonable_range(tracked_low_filter.attrs["N_events_final"], 3, tolerance=1)
 
     @pytest.mark.slow
     def test_unstructured_temporal_gap_filling(self, dask_client_unstructured):
@@ -539,12 +539,12 @@ class TestUnstructuredTracking:
         assert_reasonable_bounds(
             tracked_no_gaps.attrs["preprocessed_area_fraction"],
             2.2,
-            tolerance_relative=0.4,
+            tolerance_relative=0.2,
         )
         # Expected ranges for full dataset (732 timesteps × 1000 cells)
-        assert_count_in_reasonable_range(tracked_no_gaps.attrs["N_objects_prefiltered"], 15, tolerance=10)
-        assert_count_in_reasonable_range(tracked_no_gaps.attrs["N_objects_filtered"], 10, tolerance=5)
-        assert_count_in_reasonable_range(tracked_no_gaps.attrs["N_events_final"], 5, tolerance=5)
+        assert_count_in_reasonable_range(tracked_no_gaps.attrs["N_objects_prefiltered"], 15, tolerance=5)
+        assert_count_in_reasonable_range(tracked_no_gaps.attrs["N_objects_filtered"], 7, tolerance=2)
+        assert_count_in_reasonable_range(tracked_no_gaps.attrs["N_events_final"], 2, tolerance=1)
 
     @pytest.mark.slow
     def test_unstructured_grid_requirements(self, dask_client_unstructured):
@@ -715,28 +715,23 @@ class TestUnstructuredTracking:
             cell_areas=renamed_data.cell_areas,
         )
 
-        # Attempt to run tracking with custom dimensions (may fail due to internal dimension handling issues)
-        try:
-            tracked_ds_no_merge = tracker_no_merge.run()
+        tracked_ds_no_merge = tracker_no_merge.run()
 
-            # If successful, verify output structure for no merge case
-            assert isinstance(tracked_ds_no_merge, xr.Dataset)
-            assert "ID_field" in tracked_ds_no_merge.data_vars
+        # If successful, verify output structure for no merge case
+        assert isinstance(tracked_ds_no_merge, xr.Dataset)
+        assert "ID_field" in tracked_ds_no_merge.data_vars
 
-            # Verify custom dimensions are preserved
-            assert "t" in tracked_ds_no_merge.ID_field.dims
-            assert "cell" in tracked_ds_no_merge.ID_field.dims
+        # Verify custom dimensions are preserved
+        assert "t" in tracked_ds_no_merge.ID_field.dims
+        assert "cell" in tracked_ds_no_merge.ID_field.dims
 
-            # Verify attributes are set
-            assert "N_events_final" in tracked_ds_no_merge.attrs
-            assert "allow_merging" in tracked_ds_no_merge.attrs
-            assert tracked_ds_no_merge.attrs["allow_merging"] == 0
+        # Verify attributes are set
+        assert "N_events_final" in tracked_ds_no_merge.attrs
+        assert "allow_merging" in tracked_ds_no_merge.attrs
+        assert tracked_ds_no_merge.attrs["allow_merging"] == 0
 
-            # Verify ID_field is int
-            assert np.issubdtype(tracked_ds_no_merge.ID_field.dtype, np.integer), "ID_field should be integer type"
-        except (marEx.exceptions.TrackingError, KeyError):
-            # This is expected if custom dimension handling has issues or insufficient data
-            pass
+        # Verify ID_field is int
+        assert np.issubdtype(tracked_ds_no_merge.ID_field.dtype, np.integer), "ID_field should be integer type"
 
         # Verify tracker was created successfully with custom dimension and coordinate names (no merging)
         assert tracker_no_merge is not None
@@ -763,35 +758,30 @@ class TestUnstructuredTracking:
             cell_areas=renamed_data.cell_areas,
         )
 
-        # Attempt to run tracking with custom dimensions and merging (may fail due to internal dimension handling issues)
-        try:
-            tracked_ds_with_merge = tracker_with_merge.run()
-
-            # If successful, verify output structure for merge case
-            assert isinstance(tracked_ds_with_merge, xr.Dataset)
-            assert "ID_field" in tracked_ds_with_merge.data_vars
-            assert "global_ID" in tracked_ds_with_merge.data_vars
-            assert "area" in tracked_ds_with_merge.data_vars
-            assert "centroid" in tracked_ds_with_merge.data_vars
-            assert "presence" in tracked_ds_with_merge.data_vars
-            assert "time_start" in tracked_ds_with_merge.data_vars
-            assert "time_end" in tracked_ds_with_merge.data_vars
-            assert "merge_ledger" in tracked_ds_with_merge.data_vars
-
-            # Verify custom dimensions are preserved
-            assert "t" in tracked_ds_with_merge.ID_field.dims
-            assert "cell" in tracked_ds_with_merge.ID_field.dims
-
-            # Verify advanced tracking attributes
-            assert tracked_ds_with_merge.attrs["allow_merging"] == 1
-            assert tracked_ds_with_merge.attrs["T_fill"] == 2
-            assert "total_merges" in tracked_ds_with_merge.attrs
-
-            # Verify ID_field is int
-            assert np.issubdtype(tracked_ds_with_merge.ID_field.dtype, np.integer), "ID_field should be integer type"
-        except (marEx.exceptions.TrackingError, KeyError):
-            # This is expected if custom dimension handling has issues or insufficient data
-            pass
+        tracked_ds_with_merge = tracker_with_merge.run()
+
+        # If successful, verify output structure for merge case
+        assert isinstance(tracked_ds_with_merge, xr.Dataset)
+        assert "ID_field" in tracked_ds_with_merge.data_vars
+        assert "global_ID" in tracked_ds_with_merge.data_vars
+        assert "area" in tracked_ds_with_merge.data_vars
+        assert "centroid" in tracked_ds_with_merge.data_vars
+        assert "presence" in tracked_ds_with_merge.data_vars
+        assert "time_start" in tracked_ds_with_merge.data_vars
+        assert "time_end" in tracked_ds_with_merge.data_vars
+        assert "merge_ledger" in tracked_ds_with_merge.data_vars
+
+        # Verify custom dimensions are preserved
+        assert "t" in tracked_ds_with_merge.ID_field.dims
+        assert "cell" in tracked_ds_with_merge.ID_field.dims
+
+        # Verify advanced tracking attributes
+        assert tracked_ds_with_merge.attrs["allow_merging"] == 1
+        assert tracked_ds_with_merge.attrs["T_fill"] == 2
+        assert "total_merges" in tracked_ds_with_merge.attrs
+
+        # Verify ID_field is int
+        assert np.issubdtype(tracked_ds_with_merge.ID_field.dtype, np.integer), "ID_field should be integer type"
 
         # Verify tracker was created successfully with custom dimension and coordinate names (with merging)
         assert tracker_with_merge is not None
@@ -851,36 +841,31 @@ class TestUnstructuredTracking:
             cell_areas=renamed_data.cell_areas,
         )
 
-        # Attempt to run both trackers (may fail due to custom dimension handling issues)
-        try:
-            tracked_ds_original = tracker_original.run()
-            tracked_ds_custom = tracker_custom.run()
-
-            # If successful, verify output structure for both
-            assert isinstance(tracked_ds_original, xr.Dataset)
-            assert isinstance(tracked_ds_custom, xr.Dataset)
-            assert "ID_field" in tracked_ds_original.data_vars
-            assert "ID_field" in tracked_ds_custom.data_vars
-
-            # Verify original dimensions
-            assert "time" in tracked_ds_original.ID_field.dims
-            assert "ncells" in tracked_ds_original.ID_field.dims
-
-            # Verify custom dimensions
-            assert "t" in tracked_ds_custom.ID_field.dims
-            assert "cell" in tracked_ds_custom.ID_field.dims
-
-            # Verify both have integer ID fields
-            assert np.issubdtype(tracked_ds_original.ID_field.dtype, np.integer), "Original ID_field should be integer type"
-            assert np.issubdtype(tracked_ds_custom.ID_field.dtype, np.integer), "Custom ID_field should be integer type"
-
-            # Verify both have same number of events (should produce equivalent results)
-            assert (
-                tracked_ds_original.attrs["N_events_final"] == tracked_ds_custom.attrs["N_events_final"]
-            ), "Different event counts between original and custom dimensions"
-        except (marEx.exceptions.TrackingError, KeyError):
-            # This is expected if custom dimension handling has issues or insufficient data
-            pass
+        tracked_ds_original = tracker_original.run()
+        tracked_ds_custom = tracker_custom.run()
+
+        # If successful, verify output structure for both
+        assert isinstance(tracked_ds_original, xr.Dataset)
+        assert isinstance(tracked_ds_custom, xr.Dataset)
+        assert "ID_field" in tracked_ds_original.data_vars
+        assert "ID_field" in tracked_ds_custom.data_vars
+
+        # Verify original dimensions
+        assert "time" in tracked_ds_original.ID_field.dims
+        assert "ncells" in tracked_ds_original.ID_field.dims
+
+        # Verify custom dimensions
+        assert "t" in tracked_ds_custom.ID_field.dims
+        assert "cell" in tracked_ds_custom.ID_field.dims
+
+        # Verify both have integer ID fields
+        assert np.issubdtype(tracked_ds_original.ID_field.dtype, np.integer), "Original ID_field should be integer type"
+        assert np.issubdtype(tracked_ds_custom.ID_field.dtype, np.integer), "Custom ID_field should be integer type"
+
+        # Verify both have same number of events (should produce equivalent results)
+        assert (
+            tracked_ds_original.attrs["N_events_final"] == tracked_ds_custom.attrs["N_events_final"]
+        ), "Different event counts between original and custom dimensions"
 
         # Verify both trackers were created successfully
         assert tracker_original is not None

marex-3.0.2/CITATION.cff

@@ -1,21 +0,0 @@
-cff-version: 1.2.0
-message: "If you use this software, please cite it as below."
-type: software
-title: "MarEx: Marine Extremes Detection and Tracking"
-abstract: "Efficient & scalable Marine Extremes detection, identification, & tracking for Exascale Climate Data. A high-performance Python framework for identifying and tracking extreme oceanographic events (such as Marine Heatwaves or Acidity Extremes) in massive climate datasets."
-authors:
-  - family-names: "Wienkers"
-    given-names: "Aaron"
-    email: "aaron@wienkers.com"
-    orcid: "https://orcid.org/0000-0002-8464-3139"
-repository-code: "https://github.com/wienkers/marEx"
-url: "https://github.com/wienkers/marEx"
-keywords:
-  - "marine heatwaves"
-  - "extreme events"
-  - "oceanography"
-  - "extremes tracking"
-  - "ocean extremes"
-  - "marine extremes"
-version: "3.0.0"
-date-released: "2025-07-28"