Merge pull request #8 from pbashyal-nmdp/clean_up_grim_directory

Clean up grim directory, make packages of subdirectory

Author: pbashyal-nmdp

.github/workflows/python-tests.yml

@@ -28,6 +28,3 @@ jobs:
     - name: Test with pytest
       run: |
         pytest
-    - name: Run BDD Tests
-      run: |
-        behave

grim/algorithm/match.py

@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+
+#
+#    grim Graph Imputation
+#    Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
+#
+#    This library is free software; you can redistribute it and/or modify it
+#    under the terms of the GNU Lesser General Public License as published
+#    by the Free Software Foundation; either version 3 of the License, or (at
+#    your option) any later version.
+#
+#    This library 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 Lesser General Public
+#    License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public License
+#    along with this library;  if not, write to the Free Software Foundation,
+#    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+#
+#    > http://www.fsf.org/licensing/licenses/lgpl.html
+#    > http://www.opensource.org/licenses/lgpl-license.php
+#
+
+
+"""Top-level package for py-grim."""
+
+__organization__ = "NMDP/CIBMTR Bioinformatics"

grim/conf/__init__.py

@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+
+#
+#    grim Graph Imputation
+#    Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
+#
+#    This library is free software; you can redistribute it and/or modify it
+#    under the terms of the GNU Lesser General Public License as published
+#    by the Free Software Foundation; either version 3 of the License, or (at
+#    your option) any later version.
+#
+#    This library 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 Lesser General Public
+#    License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public License
+#    along with this library;  if not, write to the Free Software Foundation,
+#    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+#
+#    > http://www.fsf.org/licensing/licenses/lgpl.html
+#    > http://www.opensource.org/licenses/lgpl-license.php
+#
+
+
+"""Top-level package for py-grim."""
+
+__organization__ = "NMDP/CIBMTR Bioinformatics"

grim/imputation/__init__.py

@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+
+#
+#    grim Graph Imputation
+#    Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
+#
+#    This library is free software; you can redistribute it and/or modify it
+#    under the terms of the GNU Lesser General Public License as published
+#    by the Free Software Foundation; either version 3 of the License, or (at
+#    your option) any later version.
+#
+#    This library 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 Lesser General Public
+#    License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public License
+#    along with this library;  if not, write to the Free Software Foundation,
+#    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+#
+#    > http://www.fsf.org/licensing/licenses/lgpl.html
+#    > http://www.opensource.org/licenses/lgpl-license.php
+#
+
+
+"""Top-level package for py-grim."""
+
+__organization__ = "NMDP/CIBMTR Bioinformatics"

grim/imputation/graph_generation/__init__.py

@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+
+#
+#    grim Graph Imputation
+#    Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
+#
+#    This library is free software; you can redistribute it and/or modify it
+#    under the terms of the GNU Lesser General Public License as published
+#    by the Free Software Foundation; either version 3 of the License, or (at
+#    your option) any later version.
+#
+#    This library 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 Lesser General Public
+#    License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public License
+#    along with this library;  if not, write to the Free Software Foundation,
+#    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+#
+#    > http://www.fsf.org/licensing/licenses/lgpl.html
+#    > http://www.opensource.org/licenses/lgpl-license.php
+#
+
+
+"""Top-level package for py-grim."""
+
+__organization__ = "NMDP/CIBMTR Bioinformatics"

grim/model/allele.py

@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+
+#
+#    grim Graph Imputation
+#    Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
+#
+#    This library is free software; you can redistribute it and/or modify it
+#    under the terms of the GNU Lesser General Public License as published
+#    by the Free Software Foundation; either version 3 of the License, or (at
+#    your option) any later version.
+#
+#    This library 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 Lesser General Public
+#    License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public License
+#    along with this library;  if not, write to the Free Software Foundation,
+#    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+#
+#    > http://www.fsf.org/licensing/licenses/lgpl.html
+#    > http://www.opensource.org/licenses/lgpl-license.php
+#
+
+
+"""Top-level package for py-grim."""
+
+__organization__ = "NMDP/CIBMTR Bioinformatics"

grim/model/slug.py

@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+
+#
+#    grim Graph Imputation
+#    Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
+#
+#    This library is free software; you can redistribute it and/or modify it
+#    under the terms of the GNU Lesser General Public License as published
+#    by the Free Software Foundation; either version 3 of the License, or (at
+#    your option) any later version.
+#
+#    This library 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 Lesser General Public
+#    License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public License
+#    along with this library;  if not, write to the Free Software Foundation,
+#    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+#
+#    > http://www.fsf.org/licensing/licenses/lgpl.html
+#    > http://www.opensource.org/licenses/lgpl-license.php
+#
+
+
+"""Top-level package for py-grim."""
+
+__organization__ = "NMDP/CIBMTR Bioinformatics"