License under GPLv3+

README.md

@@ -105,9 +105,9 @@ The plot shows alignment regions as annotations: green annotations (genetic part
 
 Ediacara uses the [semantic versioning](https://semver.org) scheme.
 
-## Copyright
+## License = GPLv3+
 
-Copyright 2021 Edinburgh Genome Foundry
+Copyright 2021 Edinburgh Genome Foundry, University of Edinburgh
 
 Ediacara was written at the [Edinburgh Genome Foundry](https://edinburgh-genome-foundry.github.io/)
-by [Peter Vegh](https://github.com/veghp).
+by [Peter Vegh](https://github.com/veghp), and is released under the GPLv3 license.

ediacara/Assembly.py

@@ -1,3 +1,13 @@
+# Copyright 2021 Edinburgh Genome Foundry, University of Edinburgh
+#
+# This file is part of Ediacara.
+#
+# Ediacara is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Ediacara 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with Ediacara. If not, see <https://www.gnu.org/licenses/>.
+
 import os
 
 import pandas as pd
@@ -100,8 +110,10 @@ def __init__(
             plan_df = pd.read_csv(assembly_plan, skiprows=1, header=None)  # skip header
             self.assembly_plan = plan_df[plan_df[0] == self.reference.id]
             if len(self.assembly_plan) == 0:
-                raise ValueError("Error! Assembly plan doesn't contain the reference! "
-                        "(Have you ensured that the plan contains a header line?)")
+                raise ValueError(
+                    "Error! Assembly plan doesn't contain the reference! "
+                    "(Have you ensured that the plan contains a header line?)"
+                )
             if len(self.assembly_plan) > 1:
                 raise ValueError(
                     "Error! More than one assembly plan entry matches the reference!"

ediacara/Comparator.py

@@ -1,3 +1,13 @@
+# Copyright 2021 Edinburgh Genome Foundry, University of Edinburgh
+#
+# This file is part of Ediacara.
+#
+# Ediacara is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Ediacara 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with Ediacara. If not, see <https://www.gnu.org/licenses/>.
+
 import itertools
 import re
 import statistics

ediacara/reports.py

@@ -1,3 +1,13 @@
+# Copyright 2021 Edinburgh Genome Foundry, University of Edinburgh
+#
+# This file is part of Ediacara.
+#
+# Ediacara is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Ediacara 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with Ediacara. If not, see <https://www.gnu.org/licenses/>.
+
 from datetime import datetime
 import os
 

setup.py

@@ -11,7 +11,8 @@
     description="EGF's alignment reporter",
     long_description=open("pypi-readme.rst").read(),
     long_description_content_type="text/x-rst",
-    keywords="biology",
+    license="GPLv3+",
+    keywords="biology, sequencing",
     packages=find_packages(exclude="docs"),
     include_package_data=True,
     install_requires=[

tests/test_Comparator.py

@@ -1,3 +1,13 @@
+# Copyright 2021 Edinburgh Genome Foundry, University of Edinburgh
+#
+# This file is part of Ediacara.
+#
+# Ediacara is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Ediacara 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with Ediacara. If not, see <https://www.gnu.org/licenses/>.
+
 import os
 
 from Bio import SeqIO

tests/test_reports.py

@@ -1,3 +1,13 @@
+# Copyright 2021 Edinburgh Genome Foundry, University of Edinburgh
+#
+# This file is part of Ediacara.
+#
+# Ediacara is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Ediacara 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with Ediacara. If not, see <https://www.gnu.org/licenses/>.
+
 import os
 import pandas as pd