diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b9f295a..c9a55bf 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -1,5 +1,4 @@ # ... -# Copyright 2021 Brooks M. Musangu and Jan Drugowitsch. # license Modified BSD, see LICENSE.txt for details. # ... name: CI Tests and Docs @@ -12,8 +11,12 @@ on: jobs: test: - name: Run Pytest Suite + name: Test Python ${{ matrix.python-version }} runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.10", "3.11", "3.12", "3.13"] steps: - name: Checkout repository @@ -22,7 +25,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: '3.x' + python-version: ${{ matrix.python-version }} - name: Install package and test dependencies run: | @@ -44,7 +47,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: '3.x' + python-version: "3.13" - name: Install Pandoc run: | diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..de48851 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,27 @@ +cff-version: 1.2.0 +message: "If you use this software, please cite it using the metadata below." +type: software +title: "BlockInvGPFA" +abstract: >- + A scikit-learn-compatible implementation of Gaussian-process factor + analysis using block matrix inversion for efficient inference with + variable-length time series. +authors: + - family-names: "Musangu" + given-names: "Brooks M." + email: "brooks_musangu@hms.harvard.edu" + affiliation: "Department of Neurobiology, Harvard Medical School" + orcid: "https://orcid.org/0000-0002-7137-3707" + - family-names: "Drugowitsch" + given-names: "Jan" + email: "jan_drugowitsch@hms.harvard.edu" + affiliation: "Department of Neurobiology, Harvard Medical School" + orcid: "https://orcid.org/0000-0002-7846-0408" +version: "0.1.0" +license: "BSD-3-Clause" +repository-code: "https://github.com/CausalityInMotion/BlockInverseGPFA" +url: "https://blockinversegpfa.readthedocs.io/en/latest/" +keywords: + - "Gaussian Processes" + - "block matrices" + - "latent variable models" diff --git a/LICENSE.txt b/LICENSE.txt index 58faeb4..817d0b3 100755 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,5 +1,5 @@ Code based on Elephant - Electrophysiology Analysis Toolkit: Copyright (c) 2014-2019, Elephant authors and contributors -Modifications and additions: Copyright (c) 2021 Brooks M. Musangu and Jan Drugowitsch +Modifications and additions: Copyright (c) 2021-2026 Brooks M. Musangu and Jan Drugowitsch All rights reserved. diff --git a/README.md b/README.md index b5b285d..65f393e 100644 --- a/README.md +++ b/README.md @@ -82,10 +82,6 @@ Tests are automatically run via [GitHub Actions](https://github.com/CausalityInM Modified BSD License based on Elephant, see [LICENSE.txt](LICENSE.txt) for details. -## Copyright - -:copyright: 2021-2025 Brooks M. Musangu and Jan Drugowitsch - ## Acknowledgments -See [acknowledgments](docs/acknowledgments.rst). \ No newline at end of file +See [acknowledgments](docs/acknowledgments.rst). diff --git a/blockinvgpfa/__init__.py b/blockinvgpfa/__init__.py index 856eeb7..ad7fe91 100644 --- a/blockinvgpfa/__init__.py +++ b/blockinvgpfa/__init__.py @@ -1,6 +1,5 @@ """ -:copyright: Copyright 2021 Brooks M. Musangu and Jan Drugowitsch. -:license: Modified BSD, see LICENSE.txt for details. +:license: Modified BSD, see LICENSE.txt for details. """ from .blockinvgpfa import BlockInvGPFA from .preprocessing import EventTimesToCounts diff --git a/blockinvgpfa/blockinvgpfa.py b/blockinvgpfa/blockinvgpfa.py index cd99d94..95362f2 100644 --- a/blockinvgpfa/blockinvgpfa.py +++ b/blockinvgpfa/blockinvgpfa.py @@ -1,7 +1,5 @@ # ... -# Copyright 2021 Brooks M. Musangu and Jan Drugowitsch. -# Copyright 2014-2020 by the Elephant team. -# Modified BSD, see LICENSE.txt for details. +# Modified BSD, see LICENSE.txt for details. # ... from __future__ import division, print_function, unicode_literals diff --git a/blockinvgpfa/preprocessing.py b/blockinvgpfa/preprocessing.py index e0f7aca..f24bf6e 100644 --- a/blockinvgpfa/preprocessing.py +++ b/blockinvgpfa/preprocessing.py @@ -1,5 +1,4 @@ # ... -# Copyright 2021 Brooks M. Musangu and Jan Drugowitsch. # license Modified BSD, see LICENSE.txt for details. # ... @@ -53,7 +52,7 @@ class EventTimesToCounts(sklearn.base.TransformerMixin): Examples -------- >>> import numpy as np - >>> from gpfa import EventTimesToCounts + >>> from blockinvgpfa import EventTimesToCounts >>> bin_size = 0.1 # [s] >>> t_stop = 0.8 # [s] >>> X = [ diff --git a/docs/conf.py b/docs/conf.py index fb78a23..77c3158 100755 --- a/docs/conf.py +++ b/docs/conf.py @@ -5,7 +5,6 @@ import sys import os -from datetime import date # include root path to allow autodoc to find blockgpfa module sys.path.insert(0, os.path.abspath('../')) @@ -24,9 +23,8 @@ project = 'BlockInvGPFA Documentation' authors = 'Brooks M. Musangu and Jan Drugowitsch' -copyright = "2021-{this_year}, {authors}".format( - this_year=date.today().year, authors=authors) -release = '0.1.0.' +copyright = f"2021, {authors}" +release = '0.1.0' version = '0.1.0' # -- General configuration --------------------------------------------------- diff --git a/pyproject.toml b/pyproject.toml index 2fb27b7..ce70420 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,12 +7,12 @@ name = "blockinversegpfa" version = "0.1.0" description = "A scikit-learn-compatible GPFA implementation using block matrix inversion." authors = [ - {name = "Brooks M. MUSANGU", email = "brooks_musangu@hms.harvard.edu"}, - {name = "Jan DRUGOWITSCH", email = "jan_drugowitsch@hms.harvard.edu"} + {name = "Brooks M. Musangu", email = "brooks_musangu@hms.harvard.edu"}, + {name = "Jan Drugowitsch", email = "jan_drugowitsch@hms.harvard.edu"} ] license = {file = "LICENSE.txt"} readme = "README.md" -requires-python = ">=3.9" +requires-python = ">=3.10,<3.14" dependencies = [ "numpy==2.2.1", "scikit-learn==1.6.0", diff --git a/test/test_blockinvgpfa.py b/test/test_blockinvgpfa.py index 1348a06..b81f606 100644 --- a/test/test_blockinvgpfa.py +++ b/test/test_blockinvgpfa.py @@ -1,5 +1,4 @@ # ... -# Copyright 2021 Brooks M. Musangu and Jan Drugowitsch. # license Modified BSD, see LICENSE.txt for details. # ... """ diff --git a/test/test_preprocessing.py b/test/test_preprocessing.py index 51556e2..9682aff 100644 --- a/test/test_preprocessing.py +++ b/test/test_preprocessing.py @@ -1,5 +1,4 @@ # ... -# Copyright 2021 Brooks M. Musangu and Jan Drugowitsch. # license Modified BSD, see LICENSE.txt for details. # ... """