Clean up grim directory, make packages of subdirectory

.github/workflows/python-tests.yml

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

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/validation/__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/validation/simulation/__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/validation/simulation/data/__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"

requirements-deploy.txt

@@ -1,2 +0,0 @@
-connexion[swagger-ui]==2.13.0
-gunicorn==20.1.0

requirements-dev.txt

@@ -1,6 +1,5 @@
-allure-behave==2.9.45
-flake8==4.0.1
+flake8==5.0.4
 bump2version==1.0.1
-coverage==6.3.2
+coverage==6.4.4
 wheel==0.37.1
-pre-commit==2.18.1
+pre-commit==2.20.0

requirements-tests.txt

@@ -1,3 +1,2 @@
 pytest==7.1.2
-behave==1.2.6
 PyHamcrest==2.0.3

setup.py

@@ -62,7 +62,15 @@
     long_description_content_type="text/markdown",
     include_package_data=True,
     keywords="grim",
-    packages=find_packages(include=["grim"]),
+    packages=find_packages(
+        include=[
+            "grim",
+            "grim.imputation",
+            "grim.imputegl",
+            "grim.imputation.graph_generation",
+            "grim.validation",
+        ]
+    ),
     test_suite="tests",
     tests_require=test_requirements,
     url="https://github.com/nmdp-bioinformatics/py-grim",