Merge branch 'main' into add_testpypi_to_test

glotzerlab · Feb 19, 2025 · 86d07bd · 86d07bd
2 parents 8fa82ad + f3cdb67
commit 86d07bd
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -35,3 +35,16 @@ repos:
           - python
           - pyi
           - jupyter
+    - repo: https://github.com/glotzerlab/fix-license-header
+      rev: v0.4.1
+      hooks:
+        - id: fix-license-header
+          name: Fix License Headers (Python)
+          exclude: ^docs/|^tests/
+          types_or: [python]
+          args:
+            - --license-file=LICENSE
+            - --start=0
+            - --num=1
+            - --add=This file is from the dupin project, released under the BSD 3-Clause License.
+            - --keep-before=#!
diff --git a/conftest.py b/conftest.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Provide fixture and other testing helpers."""
 
 import freud

diff --git a/docs/environment.yml b/docs/environment.yml
@@ -3,17 +3,17 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python
-  - pip
-  - bottleneck
-  - freud
-  - kneed
-  - numpy
-  - ruptures
-  - scikit-learn
-  - pandas
-  - sphinx
-  - furo
-  - nbsphinx
-  - jupyter_sphinx
-  - pandoc
+  - python==3.13.2
+  - pip==25.0.1
+  - bottleneck==1.4.2
+  - freud==3.2.0
+  - kneed==0.8.5
+  - numpy==2.2.3
+  - ruptures==1.0.6
+  - scikit-learn==1.6.1
+  - pandas==2.2.3
+  - sphinx==8.1.3
+  - furo==2024.8.6
+  - nbsphinx==0.9.6
+  - jupyter_sphinx==0.5.3
+  - pandoc==3.6.3
diff --git a/dupin/__init__.py b/dupin/__init__.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Top-level package for event-detection."""
 
 __author__ = """Brandon Butler"""

diff --git a/dupin/data/__init__.py b/dupin/data/__init__.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Classes and functions for generating and recording system descriptors.
 
 Data Model

diff --git a/dupin/data/aggregate.py b/dupin/data/aggregate.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Helper module for generating/storing features across an entire trajectory.
 
 This class provides the `SignalAggregator` class which takes a pipeline and

diff --git a/dupin/data/base.py b/dupin/data/base.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Base classes for the data module."""
 
 import typing

diff --git a/dupin/data/freud.py b/dupin/data/freud.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Interface from `freud` to dupin.
 
 freud is a Python package for analyzing molecular trajectory data.

diff --git a/dupin/data/logging.py b/dupin/data/logging.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Functions and classes for allowing logging extra data from pipelines.
 
 Logging serves as the only directly supported means of introspecting into the

diff --git a/dupin/data/map.py b/dupin/data/map.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """`dupin.data.base.DataMap` subclasses to transform distributional data.
 
 Mapping in dupin is the idea of taking one distribution and transforming it

diff --git a/dupin/data/reduce.py b/dupin/data/reduce.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Classes for transforming array quantities into scalar features.
 
 Reduction in ``dupin`` takes an array and _reduces_ it to a set number of scalar

diff --git a/dupin/data/spatial.py b/dupin/data/spatial.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Spatial averaging DataMap classes."""
 
 import numpy as np

diff --git a/dupin/detect/__init__.py b/dupin/detect/__init__.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Methods for event detection in molecular simulations.
 
 dupin provides classes and functions to help in the event detection process but

diff --git a/dupin/detect/costs.py b/dupin/detect/costs.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Implements cost functions for use in event detection."""
 
 from abc import ABC, abstractmethod

diff --git a/dupin/detect/detect.py b/dupin/detect/detect.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Implements offline methods for detecting events in molecular simulations."""
 
 import logging

diff --git a/dupin/errors.py b/dupin/errors.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Base error classes or associated classes."""
 
 

diff --git a/dupin/postprocessing.py b/dupin/postprocessing.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """General functions for analyzing change points once detected.
 
 This module is designed to primarly work with logger data and the original

diff --git a/dupin/preprocessing/__init__.py b/dupin/preprocessing/__init__.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Perform various kinds of preprocessing on generated signals.
 
 This module provides resources for the transformation step of the event

diff --git a/dupin/preprocessing/filter.py b/dupin/preprocessing/filter.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Feature selection schemes.
 
 This provides feature selection schemes distinct from packages like

diff --git a/dupin/preprocessing/signal.py b/dupin/preprocessing/signal.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Functions for smoothing a signal.
 
 `scipy.signal` provides many additional methods for signal processing that can

diff --git a/dupin/preprocessing/supervised.py b/dupin/preprocessing/supervised.py
@@ -1,3 +1,6 @@
+# Copyright (c) 2023-2025 The Regents of the University of Michigan.
+# This file is from the dupin project, released under the BSD 3-Clause License.
+
 """Classes for use in utilizing supervised learning for event detection."""
 
 from collections.abc import Sequence