Merge pull request #102 from MiraGeoscience/GEOPY-2741

GEOPY-2741: Continue update to Python 3.12

Author: sebhmg

.github/workflows/python_analysis.yml

@@ -33,7 +33,7 @@ jobs:
     with:
       package-manager: 'conda'
       app-name: 'curve_apps'
-      python-version: '3.10'
+      python-version: '3.12'
   call-workflow-pytest:
     name: Pytest
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest.yml@v2
@@ -42,10 +42,10 @@ jobs:
       pull-requests: read
     with:
       package-manager: 'conda'
-      python-versions: '["3.10", "3.11", "3.12"]'
+      python-versions: '["3.12", "3.13"]'
       os: '["ubuntu-latest", "windows-latest"]'
       cache-number: 1
-      codecov-reference-python-version: '3.10'
+      codecov-reference-python-version: '3.12'
       codecov-reference-os: '["windows-latest"]'
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/python_deploy_dev.yml

@@ -20,7 +20,7 @@ jobs:
       contents: write
     with:
       package-name: 'curve-apps'
-      python-version: '3.10'
+      python-version: '3.12'
       source-repo-names: '["public-noremote-conda-dev"]'
       conda-channels: '["conda-forge"]'
       publish-repo-names: '["public-noremote-conda-dev"]'
@@ -37,7 +37,7 @@ jobs:
       package-manager: 'poetry'
       package-name: 'curve-apps'
       version-tag: ${{ github.ref_name }}
-      python-version: '3.10'
+      python-version: '3.12'
       virtual-repo-names: '["public-pypi-dev", "test-pypi"]'
     secrets:
       JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }}

.idea/curve-apps.iml

@@ -35,8 +35,8 @@ repos:
     hooks:
     -   id: mypy
         additional_dependencies: [
-            numpy==1.26.*,
-            pydantic==2.5.*,
+            numpy==2.4.*,
+            pydantic==2.12.*,
             types-toml,
             types-waitress==3.0.*,
             types-PyYAML,

.pre-commit-config.yaml

@@ -91,7 +91,12 @@ def has_intervals(self) -> bool:
     def intervals(self) -> list[float]:
         """Returns arange of requested contour intervals."""
 
-        if self.has_intervals:
+        if (
+            self.interval_min is not None
+            and self.interval_max is not None
+            and self.interval_spacing is not None
+            and self.interval_spacing != 0
+        ):
             intervals = np.arange(
                 self.interval_min,
                 self.interval_max + self.interval_spacing / 2,  # type: ignore

curve_apps/contours/options.py

@@ -14,6 +14,7 @@
 
 import numpy as np
 
+from curve_apps.peak_finder.anomaly import Anomaly
 from curve_apps.peak_finder.anomaly_group import AnomalyGroup
 from curve_apps.peak_finder.line_data import LineData
 from curve_apps.peak_finder.line_position import LinePosition
@@ -282,11 +283,12 @@ def group_n_groups(self, groups: list[AnomalyGroup]) -> list[AnomalyGroup]:
 
         return_groups: list[AnomalyGroup] = []
         all_starts = np.array([group.start for group in groups])
-        sort_inds = np.argsort(all_starts)
-        sorted_groups: list[AnomalyGroup] = list(np.array(groups)[sort_inds])
-
-        max_separation = np.ceil(self.max_separation / self.position.sampling)
-        neighbours_list = self.find_neighbour_groups(sorted_groups, max_separation)
+        sorted_groups: list[AnomalyGroup] = list(
+            np.array(groups)[np.argsort(all_starts)]
+        )
+        neighbours_list = self.find_neighbour_groups(
+            sorted_groups, np.ceil(self.max_separation / self.position.sampling)
+        )
 
         if len(neighbours_list) == 0:
             return return_groups
@@ -304,8 +306,12 @@ def group_n_groups(self, groups: list[AnomalyGroup]) -> list[AnomalyGroup]:
                 if len(indices) < self.n_groups:
                     continue
 
+                anomalies: list[Anomaly] = []
+                for ind in indices:
+                    anomalies += sorted_groups[ind].anomalies.tolist()
+
                 new_group = AnomalyGroup(
-                    np.concatenate([sorted_groups[ind].anomalies for ind in indices]),
+                    anomalies,
                     self.property_group,
                     subgroups={sorted_groups[ind] for ind in indices},
                 )

curve_apps/peak_finder/line_group.py

@@ -117,7 +117,9 @@ def get_contour_list(params: ContourDetectionParameters) -> list[float]:
     """
 
     if (
-        None not in [params.interval_min, params.interval_max, params.interval_spacing]
+        params.interval_min is not None
+        and params.interval_max is not None
+        and params.interval_spacing is not None
         and params.interval_spacing != 0
     ):
         interval_contours = np.arange(

curve_apps/utils.py

@@ -1,8 +1,7 @@
 include_dev: True
 py_versions:
-  - "3.10"
-  - "3.11"
   - "3.12"
+  - "3.13"
 suffix_for_extras:
   "": ["webview"]
   "raw": [""]

deps-lock-config.yaml

@@ -1,3 +1,3 @@
 dependencies:
-  - python=3.10.*
+  - python=3.13.*
   - pip

environments/env-python-3.10.yml environments/env-python-3.13.ymlenvironments/env-python-3.10.yml renamed to environments/env-python-3.13.yml

@@ -1,3 +1,3 @@
 dependencies:
-  - python=3.11.*
+  - python=3.14.*
   - pip