Merge pull request #26 from yfukai/change_license_BSD

Change license to The 3-Clause BSD License

.cookiecutter.json

@@ -5,7 +5,7 @@
   "email": "[email protected]",
   "friendly_name": "LapTrack",
   "github_user": "yfukai",
-  "license": "GPL-3.0-only",
+  "license": "BSD-3-Clause",
   "package_name": "laptrack",
   "project_name": "laptrack",
   "version": "0.0.0"

CONTRIBUTING.rst

@@ -2,7 +2,7 @@ Contributor Guide
 =================
 
 Thank you for your interest in improving this project.
-This project is open-source under the `GNU General Public License version 3`_ and
+This project is open-source under the `The 3-Clause BSD License`_ and
 welcomes contributions in the form of bug reports, feature requests, and pull requests.
 
 Here is a list of important resources for contributors:
@@ -12,7 +12,7 @@ Here is a list of important resources for contributors:
 - `Issue Tracker`_
 - `Code of Conduct`_
 
-.. _GNU General Public License version 3: https://opensource.org/licenses/GPL-3.0
+.. _The 3-Clause BSD License: https://opensource.org/licenses/BSD-3-Clause
 .. _Source Code: https://github.com/yfukai/laptrack
 .. _Documentation: https://laptrack.readthedocs.io/
 .. _Issue Tracker: https://github.com/yfukai/laptrack/issues
@@ -43,7 +43,7 @@ Request features on the `Issue Tracker`_.
 How to set up your development environment
 ------------------------------------------
 
-You need Python 3.6+ and the following tools:
+You need Python 3.8+ and the following tools:
 
 - Poetry_
 - Nox_

README.rst

@@ -17,7 +17,7 @@ LapTrack
    :target: https://pypi.org/project/laptrack
    :alt: Python Version
 .. |License| image:: https://img.shields.io/pypi/l/laptrack
-   :target: https://opensource.org/licenses/GPL-3.0
+   :target: https://opensource.org/licenses/BSD-3-Clause
    :alt: License
 .. |Read the Docs| image:: https://img.shields.io/readthedocs/laptrack/latest.svg?label=Read%20the%20Docs
    :target: https://laptrack.readthedocs.io/
@@ -66,7 +66,7 @@ To learn more, see the `Contributor Guide`_.
 License
 -------
 
-Distributed under the terms of the `GNU General Public License version 3`_,
+Distributed under the terms of the `The 3-Clause BSD License`_,
 *LapTrack* is free and open source software.
 
 
@@ -94,7 +94,7 @@ Credits
 
 .. _@cjolowicz: https://github.com/cjolowicz
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _GNU General Public License version 3: https://opensource.org/licenses/GPL-3.0
+.. _The 3-Clause BSD License: https://opensource.org/licenses/BSD-3-Clause
 .. _PyPI: https://pypi.org/
 .. _Hypermodern Python Cookiecutter: https://github.com/cjolowicz/cookiecutter-hypermodern-python
 .. _file an issue: https://github.com/yfukai/laptrack/issues

pyproject.toml

@@ -1,9 +1,9 @@
 [tool.poetry]
 name = "laptrack"
-version = "0.1.1"
+version = "0.1.2"
 description = "LapTrack"
 authors = ["Yohsuke Fukai <[email protected]>"]
-license = "GPL-3.0-only"
+license = "BSD-3-Clause"
 readme = "README.rst"
 homepage = "https://github.com/yfukai/laptrack"
 repository = "https://github.com/yfukai/laptrack"
@@ -16,7 +16,7 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
-    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "License :: OSI Approved :: BSD License",
 ]
 
 [tool.poetry.urls]

src/laptrack/_cost_matrix.py

@@ -95,8 +95,6 @@ def build_segment_cost_matrix(
     cost_matrix : Optional[FloatArray]
         the cost matrix for frame linking, None if not appropriate
     """
-    # https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/costmatrix/JaqamanSegmentCostMatrixCreator.java # noqa:
-    # https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/SparseLAPSegmentTracker.java#L148 # noqa:
     M = gap_closing_dist_matrix.shape[0]
     assert gap_closing_dist_matrix.shape[1] == M
     assert splitting_dist_matrix.shape[0] == M
@@ -116,8 +114,17 @@ def build_segment_cost_matrix(
     if len(all_data) == 0:
         return None
 
-    # https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/costmatrix/DefaultCostMatrixCreator.java#L186 # noqa :
-    # https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java # noqa :
+    # Note:
+    # Though the way of assigning track_start_cost, track_end_cost, no_splitting_cost, no_merging_cost # noqa :
+    # and min_val is similar to that of TrackMate (link1, link2), GPL3 of TrackMate does not apply. (See link3 for license discussion.) # noqa :
+    #   link1 https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/costmatrix/DefaultCostMatrixCreator.java#L186 # noqa :
+    #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/costmatrix/JaqamanSegmentCostMatrixCreator.java # noqa:
+    #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/SparseLAPSegmentTracker.java#L148 # noqa:
+    #   link2 (default parameters for alternative_cost_percentile, alternative_cost_factor) # noqa :
+    #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java # noqa :
+    #   link3 https://forum.image.sc/t/linear-assignment-problem-based-tracking-package-in-python/57793 # noqa :
+    #         https://web.archive.org/web/20210921134401/https://forum.image.sc/t/linear-assignment-problem-based-tracking-package-in-python/57793 # noqa :
+
     if (
         track_start_cost is None
         or track_end_cost is None

src/laptrack/_tracking.py

@@ -185,14 +185,14 @@ def laptrack(
             def to_gap_closing_candidates(row):
                 target_coord = row["last_frame_coords"]
                 frame_diff = np.abs(segments_df["first_frame"] - row["last_frame"])
-                # https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/costmatrix/JaqamanSegmentCostMatrixCreator.java#L242 # noqa :
                 indices = (1 <= frame_diff) & (
                     frame_diff <= gap_closing_max_frame_count
                 )
                 df = segments_df[indices]
                 # note: can use KDTree if metric is distance,
                 # but might not be appropriate for general metrics
                 # https://stackoverflow.com/questions/35459306/find-points-within-cutoff-distance-of-other-points-with-scipy # noqa
+                # TrackMate also uses this (trivial) implementation.
                 if len(df) > 0:
                     target_dist_matrix = cdist(
                         [target_coord],