Simplify Licensing

LICENSE

@@ -1,3 +1,7 @@
+Copyright 2022 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
+Shaurya Chanana, Izaak Miller, Jason C. Kwan
+
+
                     GNU AFFERO GENERAL PUBLIC LICENSE
                        Version 3, 19 November 2007
 

autometa/binning/recursive_dbscan.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 
 Cluster contigs recursively searching for bins with highest completeness and purity.
 """

autometa/binning/summary.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 
 Script to summarize Autometa binning results
 """

autometa/common/coverage.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 
 Calculates coverage of contigs
 """

autometa/common/exceptions.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 
 File containing customized AutometaErrors for more specific exception handling
 """

autometa/common/external/bedtools.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 Script containing wrapper functions for bedtools.
 """
 
@@ -124,7 +107,9 @@ def parse(bed, out=None, force=False):
     if out and (not os.path.exists(out) or (os.path.exists(out) and force)):
         dff.to_csv(out, sep="\t", index=True, header=True)
         logger.debug(f"{out} written")
-    msg = f"{os.path.basename(out)} shape: {dff.shape}" if out else f"shape: {dff.shape}"
+    msg = (
+        f"{os.path.basename(out)} shape: {dff.shape}" if out else f"shape: {dff.shape}"
+    )
     logger.debug(msg)
     return dff[["coverage"]]
 

autometa/common/external/bowtie.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 Script containing wrapper functions for bowtie2.
 """
 

autometa/common/external/diamond.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 Class and functions related to running diamond on metagenome sequences
 """
 

autometa/common/external/hmmscan.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 Functions related to running hmmer on metagenome sequences
 """
 

autometa/common/external/prodigal.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 
 Functions to retrieve orfs from provided assembly using prodigal
 """

autometa/common/kmers.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 
 Count, normalize and embed k-mers given nucleotide sequences
 """

autometa/common/markers.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 
 Autometa Marker class consisting of various methods to annotate sequences with
 marker sets depending on sequence set taxonomy

autometa/common/metagenome.py

@@ -1,25 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 
 Script containing Metagenome class for general handling of metagenome assembly
 """
@@ -398,7 +381,9 @@ def main():
             out=args.output_fasta, cutoff=args.cutoff, force=args.force
         )
     except FileExistsError as err:
-        logger.debug(f"FileAlreadyExists: {args.output_fasta} Skipping length-filter...")
+        logger.debug(
+            f"FileAlreadyExists: {args.output_fasta} Skipping length-filter..."
+        )
         filtered_mg = Metagenome(assembly=args.output_fasta)
     if args.output_stats:
         stats_df = filtered_mg.describe()

autometa/common/utilities.py

@@ -1,24 +1,7 @@
 #!/usr/bin/env python
 """
-COPYRIGHT
-Copyright 2021 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
-Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
-This file is part of Autometa.
-
-Autometa is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Autometa is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with Autometa. If not, see <http://www.gnu.org/licenses/>.
-COPYRIGHT
+# License: GNU Affero General Public License v3 or later
+# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
 
 File containing common utilities functions to be used by Autometa scripts.
 """