Merge branch 'main'

tonywong94 · Dec 29, 2024 · 1dee9ce · 1dee9ce
2 parents 92b7b09 + 50adabb
commit 1dee9ce
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: ".github/workflows"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"
diff --git a/.github/release.yml b/.github/release.yml
@@ -0,0 +1,17 @@
+changelog:
+  exclude:
+    authors:
+      - pre-commit-ci
+  categories:
+    - title: Bug Fixes
+      labels:
+        - bug
+    - title: New Features
+      labels:
+        - enhancement
+    - title: Documentation
+      labels:
+        - Documentation
+    - title: Other Changes
+      labels:
+        - "*"
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -5,15 +5,26 @@ on:
   pull_request:
 
 jobs:
+
   test:
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
     with:
       envs: |
         - linux: codestyle
-          pytest: false
         - linux: py38-test-oldestdeps
         - macos: py39-test
         - windows: py39-test
         - linux: py310-test
-        - linux: py311-test-devdeps
+        - macos: py311-test-viewer
+        - windows: py312-test
+        - linux: py313-test-devdeps
       coverage: 'codecov'
+
+  publish:
+    needs: test
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v1
+    with:
+      test_extras: test
+      test_command: pytest --pyargs astrodendro
+    secrets:
+      pypi_token: ${{ secrets.pypi_token }}
diff --git a/.github/workflows/update-changelog.yaml b/.github/workflows/update-changelog.yaml
@@ -0,0 +1,33 @@
+# This workflow takes the GitHub release notes an updates the changelog on the
+# main branch with the body of the release notes, thereby keeping a log in
+# the git repo of the changes.
+
+name: "Update Changelog"
+
+on:
+  release:
+    types: [released]
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
+        with:
+          ref: main
+
+      - name: Update Changelog
+        uses: stefanzweifel/changelog-updater-action@a938690fad7edf25368f37e43a1ed1b34303eb36  # v1.12.0
+        with:
+          release-notes: ${{ github.event.release.body }}
+          latest-version: ${{ github.event.release.name }}
+          path-to-changelog: CHANGES.md
+
+      - name: Commit updated CHANGELOG
+        uses: stefanzweifel/git-auto-commit-action@8621497c8c39c72f3e2a999a26b4ca1b5058a842  # v5.0.1
+        with:
+          branch: main
+          commit_message: Update CHANGELOG
+          file_pattern: CHANGES.md
diff --git a/CHANGES b/CHANGES
diff --git a/CHANGES.md b/CHANGES.md
@@ -0,0 +1,77 @@
+## v0.3.1 - 2024-11-15
+
+<!-- Release notes generated using configuration in .github/release.yml at main -->
+### What's Changed
+
+#### Bug Fixes
+
+* Fix compatibility of interactive viewer with recent versions of Matplotlib by @astrofrog in https://github.com/dendrograms/astrodendro/pull/202
+
+#### Other Changes
+
+* Bump actions/checkout from 4.2.0 to 4.2.2 in /.github/workflows in the actions group by @dependabot in https://github.com/dendrograms/astrodendro/pull/201
+
+### New Contributors
+
+* @dependabot made their first contribution in https://github.com/dendrograms/astrodendro/pull/201
+
+**Full Changelog**: https://github.com/dendrograms/astrodendro/compare/v0.3.0...v0.3.1
+
+## v0.3.0 - 2024-11-15
+
+<!-- Release notes generated using configuration in .github/release.yml at main -->
+### What's Changed
+
+* update "Iterable" import for Python versions > 3.9 by @nbrunett in https://github.com/dendrograms/astrodendro/pull/184
+* Fix viewer in Python 3 by @indebetouw in https://github.com/dendrograms/astrodendro/pull/181
+* Remove np.int by @keflavich in https://github.com/dendrograms/astrodendro/pull/179
+* h5py removed .value after v3 by @indebetouw in https://github.com/dendrograms/astrodendro/pull/182
+* Update package infrastructure by @astrofrog in https://github.com/dendrograms/astrodendro/pull/186
+* Update plot.py to pass subtree to get_lines by @tonywong94 in https://github.com/dendrograms/astrodendro/pull/168
+* Fix for changes between astropy 5.2.2 and 5.3.1 by @ajrigby in https://github.com/dendrograms/astrodendro/pull/192
+* Fix tests/continuous integration by @astrofrog in https://github.com/dendrograms/astrodendro/pull/193
+* WCSAxes import fix by @Parkerwise in https://github.com/dendrograms/astrodendro/pull/198
+* Update infrastructure and fix compatibility with Numpy 2.0 by @astrofrog in https://github.com/dendrograms/astrodendro/pull/200
+
+### New Contributors
+
+* @nbrunett made their first contribution in https://github.com/dendrograms/astrodendro/pull/184
+* @indebetouw made their first contribution in https://github.com/dendrograms/astrodendro/pull/181
+* @tonywong94 made their first contribution in https://github.com/dendrograms/astrodendro/pull/168
+* @ajrigby made their first contribution in https://github.com/dendrograms/astrodendro/pull/192
+* @Parkerwise made their first contribution in https://github.com/dendrograms/astrodendro/pull/198
+
+**Full Changelog**: https://github.com/dendrograms/astrodendro/compare/v0.2.0...v0.3.0
+
+## 0.2.0 (2016-09-29)
+
+- Make sure that calling structure_at with an array, list, or tuple all behave the same. [#98]
+
+- Added support for linked scatter plots and multiple selections. [#104, #105, #109, #136]
+
+- Added support for custom functions to define what a 'neighbor' is. [#108]
+
+- Fixed a bug that caused the interactive viewer when showing a dendrogram loaded from a file. [#106, #110]
+
+- Added a 'prune' method to prune dendrograms after computing them. [#111]
+
+- Added support for brightness temperatures in Kelvin. [#112]
+
+- Cache/memoize catalog statistics. [#115]
+
+- Make sure that periodic boundaries (e.g. longitude) are properly supported. [#121]
+
+- Added progress bar for catalog computation. [#127]
+
+- Better support for image WCS. [#126, #137]
+
+- Improve the performance of dendrogram loading. [#131]
+
+- Include dendrogram parameters in HDF5 files. [#142, #145]
+
+- Give HDUs names in FITS output. [#144]
+
+
+## 0.1.0 (2013-11-09)
+
+Initial release
diff --git a/astrodendro/analysis.py b/astrodendro/analysis.py
@@ -639,7 +639,7 @@ def _make_catalog(structures, fields, metadata, statistic, verbose=False):
             for index_array, shape in zip(indices, shape_tuple):
                 # catch simple cases where a structure wraps around the image boundary
                 i2 = np.where(index_array < shape/2, index_array+shape, index_array)
-                if i2.ptp() < index_array.ptp():  # more compact with wrapping. Use this
+                if np.ptp(i2) < np.ptp(index_array):  # more compact with wrapping. Use this
                     index_array[:] = i2
 
         stat = ScalarStatistic(values, indices)

diff --git a/astrodendro/dendrogram.py b/astrodendro/dendrogram.py
@@ -625,6 +625,10 @@ def __init__(self, dendrogram):
         uniq, bins = np.unique(index_map, return_inverse=True)
         packed = dict((u, i) for i, u in enumerate(uniq))
 
+        # starting with numpy 2.0 or later, bins is no longer 1-dimensional,
+        # so we always ravel the array to make it 1-d
+        bins = bins.ravel()
+
         flat_idx = index_map.ravel()
         ri = np.argsort(bins)
         idx_ct = np.bincount(bins)

diff --git a/astrodendro/tests/test_viewer.py b/astrodendro/tests/test_viewer.py
@@ -0,0 +1,41 @@
+import pytest
+import numpy as np
+
+import matplotlib.pyplot as plt
+from ..dendrogram import Dendrogram
+from matplotlib.backend_bases import MouseEvent
+
+
+DATA = np.array([[1, 3, 4, 4, 1, 4],
+                 [1, 2, 3, 2, 1, 3],
+                 [2, 1, 1, 3, 1, 2],
+                 [1, 1, 1, 1, 1, 1],
+                 [2, 3, 2, 1, 1, 2],
+                 [2, 3, 5, 3, 1, 1]])
+
+
+def test_viewer(capsys):
+
+    original_backend = plt.get_backend()
+
+    try:
+        plt.switch_backend('qtagg')
+    except ImportError:
+        pytest.skip("This test requires Qt to be installed")
+
+    d = Dendrogram.compute(DATA)
+    viewer = d.viewer()
+
+    plt.show(block=False)
+
+    cb = viewer.fig.canvas.callbacks
+
+    cb.process('button_press_event', MouseEvent('button_press_event', viewer.fig.canvas, 660, 520, 1))
+    cb.process('button_press_event', MouseEvent('button_press_event', viewer.fig.canvas, 890, 800, 1))
+    cb.process('button_press_event', MouseEvent('button_press_event', viewer.fig.canvas, 700, 700, 1))
+
+    plt.switch_backend(original_backend)
+
+    captured = capsys.readouterr()
+    assert captured.out == ""
+    assert captured.err == ""
diff --git a/astrodendro/viewer.py b/astrodendro/viewer.py
@@ -1,7 +1,6 @@
 # Licensed under an MIT open source license - see LICENSE
 
 from collections import defaultdict
-import warnings
 from functools import reduce
 
 import numpy as np
@@ -87,23 +86,14 @@ def __init__(self, dendrogram):
 
         ax_image_limits = [0.1, 0.1, 0.4, 0.7]
 
-        try:
-            from wcsaxes import WCSAxes
-            __wcaxes_imported = True
-        except ImportError:
-            __wcaxes_imported = False
-            if self.dendrogram.wcs is not None:
-                warnings.warn("`WCSAxes` package required for wcs coordinate display.")
-
-        if self.dendrogram.wcs is not None and __wcaxes_imported:
+        if self.dendrogram.wcs is not None:
 
             if self.array.ndim == 2:
                 slices = ('x', 'y')
             else:
                 slices = ('x', 'y', 1)
 
-            ax_image = WCSAxes(self.fig, ax_image_limits, wcs=self.dendrogram.wcs, slices=slices)
-            self.ax_image = self.fig.add_axes(ax_image)
+            self.ax_image = self.fig.add_axes(ax_image_limits, projection=self.dendrogram.wcs, slices=slices)
 
         else:
             self.ax_image = self.fig.add_axes(ax_image_limits)
@@ -287,7 +277,7 @@ def _update_lines(self, selection_id):
 
         # Remove previously selected collection
         if selection_id in self.selected_lines:
-            self.ax_dendrogram.collections.remove(self.selected_lines[selection_id])
+            self.selected_lines[selection_id].remove()
             del self.selected_lines[selection_id]
 
         if structure is None:
@@ -318,15 +308,13 @@ def _update_lines(self, selection_id):
         self.ax_dendrogram.add_collection(self.selected_lines[selection_id])
 
     def remove_contour(self, selection_id):
-
         if selection_id in self.selected_contour:
-            for collection in self.selected_contour[selection_id].collections:
-                self.ax_image.collections.remove(collection)
+            self.selected_contour[selection_id].remove()
             del self.selected_contour[selection_id]
 
     def remove_all_contours(self):
         """ Remove all selected contours. """
-        for key in self.selected_contour.keys():
+        for key in list(self.selected_contour):
             self.remove_contour(key)
 
     def update_contours(self):