Merge pull request #200 from astrofrog/update-infrastructure

Update infrastructure and fix compatibility with Numpy 2.0

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: ".github/workflows"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.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:
+        - "*"

.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
+        - 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 }}

.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@d632683dd7b4114ad314bca15554477dd762a938  # v4.2.0
+        with:
+          ref: main
+
+      - name: Update Changelog
+        uses: stefanzweifel/changelog-updater-action@61ce794778aa787ea8d204d9fe2928543cb2fe40  # v1.11.0
+        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

CHANGES → CHANGES.md

@@ -1,30 +1,20 @@
-0.3.0 (unreleased)
-------------------
+## 0.2.0 (2016-09-29)
 
-- Updated package infrastructure. [#186]
+- Make sure that calling structure_at with an array, list, or tuple all behave the same. [#98]
 
-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 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]
+- 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]
+- Make sure that periodic boundaries (e.g. longitude) are properly supported. [#121]
 
 - Added progress bar for catalog computation. [#127]
 
@@ -36,7 +26,6 @@
 
 - Give HDUs names in FITS output. [#144]
 
-0.1.0 (2013-11-09)
-------------------
+## 0.1.0 (2013-11-09)
 
 Initial release

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)

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)

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

pyproject.toml

@@ -1,7 +1,98 @@
 [build-system]
+build-backend = "setuptools.build_meta"
 
-requires = ["setuptools",
-            "setuptools_scm",
-            "wheel"]
+requires = [
+  "setuptools>=61.2",
+  "setuptools-scm",
+]
 
-build-backend = 'setuptools.build_meta'
+[project]
+name = "astrodendro"
+description = "Python package for computation of astronomical dendrograms"
+readme.content-type = "text/markdown"
+readme.file = "README.md"
+license.text = "MIT"
+authors = [
+  { name = "Thomas Robitaille", email = "[email protected]" },
+  { name = "Chris Beaumont" },
+  { name = "Adam Ginsburg" },
+  { name = "Braden MacDonald" },
+  { name = "and Erik Rosolowsky" },
+]
+requires-python = ">=3.8"
+classifiers = [
+  "Programming Language :: Python :: 3"
+]
+dynamic = [
+  "version",
+]
+dependencies = [
+  "astropy>=5",
+  "h5py>=3",
+  "matplotlib>=3.3",
+  "numpy>=1.20",
+]
+
+[project.optional-dependencies]
+docs = [
+  "aplpy",
+  "numpydoc",
+  "sphinx<7",
+  "sphinx-astropy",
+]
+test = [
+  "pytest",
+  "pytest-cov",
+]
+
+[project.urls]
+homepage = "https://www.dendrograms.org/"
+documentation = "https://dendrograms.readthedocs.io/en/stable/"
+repository = "https://github.com/dendrograms/astrodendro"
+
+[tool.setuptools]
+zip-safe = false
+license-files = [
+  "LICENSE",
+]
+include-package-data = false
+
+[tool.setuptools.packages.find]
+namespaces = false
+
+[tool.setuptools.package-data]
+"astrodendro.tests" = [
+  "*.npz",
+  "benchmark_data/*.fits",
+]
+"astrodendro.io.tests" = [
+  "data/*",
+]
+
+[tool.setuptools_scm]
+write_to = "astrodendro/version.py"
+
+[tool.coverage.run]
+omit = [
+  "astrodendro/conftest.py",
+  "astrodendro/tests/*",
+  "astrodendro/*/tests/*",
+  "astrodendro/extern/*",
+  "astrodendro/version*",
+  "*/astrodendro/conftest.py",
+  "*/astrodendro/tests/*",
+  "*/astrodendro/*/tests/*",
+  "*/astrodendro/extern/*",
+  "*/astrodendro/version*",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+  "pragma: no cover",
+  "except ImportError",
+  "raise AssertionError",
+  "raise NotImplementedError",
+  "def main\\(.*\\):",
+  "pragma: py{ignore_python_version}",
+  "def _ipython_key_completions_",
+]

tox.ini

@@ -29,6 +29,7 @@ deps =
     oldestdeps: h5py==3.0.*
     oldestdeps: matplotlib==3.3.*
     oldestdeps: numpy==1.20.*
+    oldestdeps: pillow==8.0.*
 
 extras =
     test