From ca58a9cd9f2c988adaf752fb789b6044b224019c Mon Sep 17 00:00:00 2001 From: Ross Barnowski Date: Thu, 4 Jun 2026 00:12:25 -0700 Subject: [PATCH 1/2] LIC: Revert licence text to exactly match OSI Apache 2 --- LICENSE | 407 ++++++++++++++++++++++++++++---------------------------- 1 file changed, 202 insertions(+), 205 deletions(-) diff --git a/LICENSE b/LICENSE index 37daa47..003b1b6 100644 --- a/LICENSE +++ b/LICENSE @@ -1,205 +1,202 @@ -Modified Apache License -Version 2.0, January 2004 - -TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - -1. Definitions. - -"License" shall mean the terms and conditions for use, reproduction, -and distribution as defined by Sections 1 through 9 of this document. - -"Licensor" shall mean the copyright owner or entity authorized by -the copyright owner that is granting the License. - -"Legal Entity" shall mean the union of the acting entity and all -other entities that control, are controlled by, or are under common -control with that entity. For the purposes of this definition, -"control" means (i) the power, direct or indirect, to cause the -direction or management of such entity, whether by contract or -otherwise, or (ii) ownership of fifty percent (50%) or more of the -outstanding shares, or (iii) beneficial ownership of such entity. - -"You" (or "Your") shall mean an individual or Legal Entity -exercising permissions granted by this License. - -"Source" form shall mean the preferred form for making modifications, -including but not limited to software source code, documentation -source, and configuration files. - -"Object" form shall mean any form resulting from mechanical -transformation or translation of a Source form, including but -not limited to compiled object code, generated documentation, -and conversions to other media types. - -"Work" shall mean the work of authorship, whether in Source or -Object form, made available under the License, as indicated by a -copyright notice that is included in or attached to the work -(an example is provided in the Appendix below). - -"Derivative Works" shall mean any work, whether in Source or Object -form, that is based on (or derived from) the Work and for which the -editorial revisions, annotations, elaborations, or other modifications -represent, as a whole, an original work of authorship. For the purposes -of this License, Derivative Works shall not include works that remain -separable from, or merely link (or bind by name) to the interfaces of, -the Work and Derivative Works thereof. - -"Contribution" shall mean any work of authorship, including -the original version of the Work and any modifications or additions -to that Work or Derivative Works thereof, that is intentionally -submitted to Licensor for inclusion in the Work by the copyright owner -or by an individual or Legal Entity authorized to submit on behalf of -the copyright owner. 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Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright 2026 Van Valen Lab, Caltech + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. From 7651165a953ed9cdfd30621a60b00613b1bc4c1d Mon Sep 17 00:00:00 2001 From: Ross Barnowski Date: Thu, 4 Jun 2026 00:17:03 -0700 Subject: [PATCH 2/2] Rm per-file notices. --- deepcell_tracking/__init__.py | 26 -------------------------- deepcell_tracking/isbi_utils.py | 25 ------------------------- deepcell_tracking/isbi_utils_test.py | 25 ------------------------- deepcell_tracking/metrics.py | 25 ------------------------- deepcell_tracking/metrics_test.py | 25 ------------------------- deepcell_tracking/test_utils.py | 25 ------------------------- deepcell_tracking/tracking.py | 25 ------------------------- deepcell_tracking/tracking_test.py | 25 ------------------------- deepcell_tracking/trk_io.py | 25 ------------------------- deepcell_tracking/trk_io_test.py | 25 ------------------------- deepcell_tracking/utils.py | 25 ------------------------- deepcell_tracking/utils_test.py | 25 ------------------------- setup.py | 25 ------------------------- 13 files changed, 326 deletions(-) diff --git a/deepcell_tracking/__init__.py b/deepcell_tracking/__init__.py index e8eaed2..8e7a52c 100644 --- a/deepcell_tracking/__init__.py +++ b/deepcell_tracking/__init__.py @@ -1,29 +1,3 @@ -# Copyright 2016-2022 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== - from __future__ import absolute_import from __future__ import division from __future__ import print_function diff --git a/deepcell_tracking/isbi_utils.py b/deepcell_tracking/isbi_utils.py index f4a00a6..fd8a86c 100644 --- a/deepcell_tracking/isbi_utils.py +++ b/deepcell_tracking/isbi_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Utility functions for the ISBI data format.""" from __future__ import absolute_import diff --git a/deepcell_tracking/isbi_utils_test.py b/deepcell_tracking/isbi_utils_test.py index 5cec280..fa8ffcd 100644 --- a/deepcell_tracking/isbi_utils_test.py +++ b/deepcell_tracking/isbi_utils_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for utility functions for the ISBI data format.""" from __future__ import absolute_import diff --git a/deepcell_tracking/metrics.py b/deepcell_tracking/metrics.py index ca806bf..a64b33d 100644 --- a/deepcell_tracking/metrics.py +++ b/deepcell_tracking/metrics.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Functions for evaluating tracking performance""" from __future__ import absolute_import diff --git a/deepcell_tracking/metrics_test.py b/deepcell_tracking/metrics_test.py index 4823bda..eab1abf 100644 --- a/deepcell_tracking/metrics_test.py +++ b/deepcell_tracking/metrics_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for utility functions for the ISBI data format.""" from __future__ import absolute_import diff --git a/deepcell_tracking/test_utils.py b/deepcell_tracking/test_utils.py index 128b389..155c653 100644 --- a/deepcell_tracking/test_utils.py +++ b/deepcell_tracking/test_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Utilities for testing deepcell-tracking""" from __future__ import absolute_import from __future__ import division diff --git a/deepcell_tracking/tracking.py b/deepcell_tracking/tracking.py index 33690ef..16c0b4b 100644 --- a/deepcell_tracking/tracking.py +++ b/deepcell_tracking/tracking.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """A cell tracking class capable of extending labels across sequential frames.""" from __future__ import absolute_import diff --git a/deepcell_tracking/tracking_test.py b/deepcell_tracking/tracking_test.py index 188d384..4a7cc37 100644 --- a/deepcell_tracking/tracking_test.py +++ b/deepcell_tracking/tracking_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for tracking.py""" from __future__ import absolute_import diff --git a/deepcell_tracking/trk_io.py b/deepcell_tracking/trk_io.py index 4a41652..cced064 100644 --- a/deepcell_tracking/trk_io.py +++ b/deepcell_tracking/trk_io.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 Van Valen Lab at California Institute of Technology -# (Caltech), with support from the Paul Allen Family Foundation, Google, -# & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Functions for reading and writing trk files""" from __future__ import absolute_import diff --git a/deepcell_tracking/trk_io_test.py b/deepcell_tracking/trk_io_test.py index f360b0c..2c8eded 100644 --- a/deepcell_tracking/trk_io_test.py +++ b/deepcell_tracking/trk_io_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for trk_io""" from __future__ import absolute_import from __future__ import division diff --git a/deepcell_tracking/utils.py b/deepcell_tracking/utils.py index a98e386..11fc497 100644 --- a/deepcell_tracking/utils.py +++ b/deepcell_tracking/utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 Van Valen Lab at California Institute of Technology -# (Caltech), with support from the Paul Allen Family Foundation, Google, -# & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Utilities for tracking cells""" from __future__ import absolute_import diff --git a/deepcell_tracking/utils_test.py b/deepcell_tracking/utils_test.py index 603ed71..e939101 100644 --- a/deepcell_tracking/utils_test.py +++ b/deepcell_tracking/utils_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for tracking_utils""" from __future__ import absolute_import from __future__ import division diff --git a/setup.py b/setup.py index a457842..a7650e8 100644 --- a/setup.py +++ b/setup.py @@ -1,28 +1,3 @@ -# Copyright 2016-2022 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tracking/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== import os from codecs import open