Code for automatically updating license headers (DeepLabCut#2028)

CONTRIBUTING.md

@@ -65,6 +65,10 @@ Now, please make a [pull request](https://github.com/DeepLabCut/DeepLabCut/pull/
 - Please run black on the code to conform to our Black code style (see more at https://pypi.org/project/black/). 
 - Please assign a reviewer, typically @AlexEMG, @mmathislab, or @jeylau (i/e. the [core-developers](https://github.com/orgs/DeepLabCut/teams/core-developers/members))
 
+**Code headers**
+
+- The code headers can be standardized by running `python tools/update_license_headers.py`
+- Edit `NOTICE.yml` to update the header. 
 
 **DeepLabCut is an open-source tool and has benefited from suggestions and edits by many individuals:**
 

NOTICE.yml

@@ -0,0 +1,118 @@
+# This notice file contains license headers for all code files
+# in the repository (currently all *.py files).
+# 
+# When updating headers, lower entries take precedence over higher
+# entries. For each header, include/exclude statements can be used
+# to define files to apply them to.
+#
+# When adding code from an external repo, make sure to cover the 
+# added code files with the correct license header.
+
+# Main repository license
+- header: |
+    DeepLabCut Toolbox (deeplabcut.org)
+    © A. & M.W. Mathis Labs
+    https://github.com/DeepLabCut/DeepLabCut
+
+    Please see AUTHORS for contributors.
+    https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+
+    Licensed under GNU Lesser General Public License v3.0
+  include:
+    - 'deeplabcut/**/*.py'
+    - 'tests/**/*.py' 
+    - 'examples/**/*.py'
+    - 'docs/**/*.py'
+    - 'conda-environments/**/*.yaml'
+
+# License for files adapted from DeeperCut by Eldar Insafutdinov
+# https://github.com/eldar/pose-tensorflow
+# Applies to most files in deeplabcut.pose_estimation_tensorflow
+- header: |
+    DeepLabCut Toolbox (deeplabcut.org)
+    © A. & M.W. Mathis Labs
+    https://github.com/DeepLabCut/DeepLabCut
+
+    Please see AUTHORS for contributors.
+    https://github.com/DeepLabCut/DeepLabCut/blob/master/AUTHORS
+
+    Adapted from DeeperCut by Eldar Insafutdinov
+    https://github.com/eldar/pose-tensorflow
+
+    Licensed under GNU Lesser General Public License v3.0
+  include:
+    # This filelist was generated by running
+    # find deeplabcut/pose_estimation_tensorflow -iname '*.py' | xargs grep 'Eldar Insafutdinov'
+    # from the repo base directory.
+    - deeplabcut/pose_estimation_tensorflow/config.py
+    - deeplabcut/pose_estimation_tensorflow/datasets/factory.py
+    - deeplabcut/pose_estimation_tensorflow/vis_dataset.py
+    - deeplabcut/pose_estimation_tensorflow/core/train.py
+    - deeplabcut/pose_estimation_tensorflow/core/predict.py
+    - deeplabcut/pose_estimation_tensorflow/core/test.py
+    - deeplabcut/pose_estimation_tensorflow/default_config.py
+    - deeplabcut/pose_estimation_tensorflow/util/visualize.py
+    - deeplabcut/pose_estimation_tensorflow/util/__init__.py
+    - deeplabcut/pose_estimation_tensorflow/util/logging.py
+    - deeplabcut/pose_estimation_tensorflow/nnets/resnet.py
+    - deeplabcut/pose_estimation_tensorflow/__init__.py
+  exclude: []
+
+# Tensorflow licenses
+- header: |
+    Copyright 2019 The TensorFlow Authors. All Rights Reserved.
+    
+    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.
+  include:
+    - deeplabcut/pose_estimation_tensorflow/backbones/*.py
+    - deeplabcut/pose_estimation_tensorflow/nnets/utils.py
+
+- header: |
+    Copyright 2018 The TensorFlow Authors. All Rights Reserved.
+
+    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.
+  include:
+    - deeplabcut/pose_estimation_tensorflow/nnets/conv_blocks.py
+    - deeplabcut/pose_estimation_tensorflow/backbones/mobilenet.py
+    - deeplabcut/pose_estimation_tensorflow/backbones/mobilenet_v2.py
+
+# TIMM license
+- header: |
+    Copyright 2019 Ross Wightman
+
+    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.
+
+    Hacked together by / Copyright 2020 Ross Wightman
+    https://github.com/rwightman/pytorch-image-models/blob/main/timm/scheduler/scheduler_factory.py
+  include:
+    - deeplabcut/pose_tracking_pytorch/solver/scheduler_factory.py

tools/README.md

@@ -0,0 +1,13 @@
+# Developer tools useful for maintaining the repository
+
+## Code headers
+
+The code headers can be standardized by running
+
+``` bash
+python tools/update_license_headers.py
+```
+
+from the repository root.
+
+You can edit the `NOTICE.yml` to update the header.

tools/update_license_headers.py

@@ -0,0 +1,63 @@
+"""Apply copyright headers to all code files in the repository.
+
+This file can be called as a python script without arguments. For
+configuration, see the instructions in NOTICE.yml.
+"""
+
+import tempfile
+import glob
+import yaml
+import fnmatch
+import subprocess
+
+
+def load_config(filename):
+    with open(filename, "r") as fh:
+        config = yaml.safe_load(fh)
+    return config
+
+
+def walk_directory(entry):
+    """Talk the directory"""
+
+    if "header" not in entry:
+        raise ValueError("Current entry does not have a header.")
+    if "include" not in entry:
+        raise ValueError("Current entry does not have an include list.")
+
+    def _list_include():
+        """List all files specified in the include list."""
+        for include_pattern in entry["include"]:
+            for filename in glob.iglob(include_pattern, recursive=True):
+                yield filename
+
+    def _filter_exclude(iterable):
+        """Filter filenames from an iterator by the exclude patterns."""
+        for filename in iterable:
+            for exclude_pattern in entry.get("exclude", []):
+                if fnmatch.fnmatch(filename, exclude_pattern):
+                    break
+            else:
+                yield filename
+
+    files = _filter_exclude(set(_list_include()))
+    return list(files)
+
+
+def main(input_file="NOTICE.yml"):
+    config = load_config(input_file)
+    for entry in config:
+        filelist = list(walk_directory(entry))
+        with tempfile.NamedTemporaryFile(mode="w") as header_file:
+            header_file.write(entry["header"])
+            header_file.flush()
+            header_file.seek(0)
+            command = ["licenseheaders", "-t", str(header_file.name), "-f"] + filelist
+            result = subprocess.run(command, capture_output=True)
+            if result.returncode != 0:
+                print(result.stdout.decode())
+                print(result.stderr.decode())
+
+
+if __name__ == "__main__":
+    main()