Merge pull request #302 from openvax/rc6-license-docstring-cleanup

[codex] Normalize Python license headers for rc6

Author: iskandr

README.md

@@ -20,10 +20,10 @@ Have a bugfix or other contribution? We would love your help. See our [contribut
 ## 2.3.0 release candidate
 
 > [!IMPORTANT]
-> 2.3.0 is currently a release candidate (`2.3.0rc5`), not yet a final release.
+> 2.3.0 is currently a release candidate (`2.3.0rc6`), not yet a final release.
 > It keeps the same public API and pre-trained models as 2.2.x. Install it with
 > `pip install --pre mhcflurry`, or pin the version with
-> `pip install mhcflurry==2.3.0rc5`. A plain `pip install --upgrade mhcflurry`
+> `pip install mhcflurry==2.3.0rc6`. A plain `pip install --upgrade mhcflurry`
 > stays on the latest stable release (2.2.x) until 2.3.0 is final, since pip
 > skips pre-releases.
 

docs/conf.py

@@ -1,5 +1,17 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
+# 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.
+
 #
 # MHCflurry documentation build configuration file, created by
 # sphinx-quickstart on Sun Dec 10 20:25:16 2017.

downloads-generation/allele_sequences/filter_sequences.py

@@ -1,3 +1,15 @@
+# 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.
+
 """
 Filter and combine class I sequence fastas.
 """

downloads-generation/allele_sequences/make_allele_sequences.py

@@ -1,3 +1,15 @@
+# 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.
+
 """
 Generate allele sequences for pan-class I models.
 

downloads-generation/allele_sequences/select_alleles_to_disambiguate.py

@@ -1,3 +1,15 @@
+# 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.
+
 """
 Select alleles to disambiguate
 

downloads-generation/analysis_predictor_info/generate_artifacts.py

@@ -1,3 +1,15 @@
+# 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.
+
 """
 Generate images for MHC binding motifs.
 

downloads-generation/analysis_predictor_info/generate_model_selection_with_decoys.py

@@ -1,3 +1,15 @@
+# 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 affinity predictor model selection data, add decoys so that AUCs can be
 calculated per-allele.

downloads-generation/analysis_predictor_info/predict_on_model_selection_data.py

@@ -1,3 +1,15 @@
+# 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.
+
 """
 Evaluate affinity predictor on its held-out model selection data, using only
 the individual models that were not trained on each particular data point.

downloads-generation/data_curated/curate.py

@@ -1,3 +1,15 @@
+# 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.
+
 """
 Filter and combine various peptide/MHC datasets to derive a composite training set,
 optionally including eluted peptides identified by mass-spec.

downloads-generation/data_curated/curate_ms_by_pmid.py

@@ -1,3 +1,15 @@
+# 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.
+
 """
 Filter and combine various peptide/MHC datasets to derive a composite training set,
 optionally including eluted peptides identified by mass-spec.