Get template ready for py-grim

Author: pbashyal-nmdp

CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/nmdp-bioinformatics/my_project_template/issues.
+Report bugs at https://github.com/nmdp-bioinformatics/py-grim/issues.
 
 If you are reporting a bug, please include:
 
@@ -38,14 +38,14 @@ and "help wanted" is open to whoever wants to implement it.
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-My Project Template could always use more documentation, whether as part of the
-official My Project Template docs, in docstrings, or even on the web in blog posts,
+py-grim could always use more documentation, whether as part of the
+official py-grim docs, in docstrings, or even on the web in blog posts,
 articles, and such.
 
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/nmdp-bioinformatics/my_project_template/issues.
+The best way to send feedback is to file an issue at https://github.com/nmdp-bioinformatics/py-grim/issues.
 
 If you are proposing a feature:
 
@@ -57,16 +57,16 @@ If you are proposing a feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up `my_project_template` for local development.
+Ready to contribute? Here's how to set up `py-grim` for local development.
 
-1. Fork the `my_project_template` repo on GitHub.
+1. Fork the `py-grim` repo on GitHub.
 2. Clone your fork locally::
 
-    $ git clone [email protected]:your_name_here/my_project_template.git
+    $ git clone [email protected]:your_name_here/py-grim.git
 
 3. Install your local copy into a virtual environment. This is how you set up your fork for local development::
 
-    $ cd my_project_template/
+    $ cd py-grim/
     $ make venv
     $ source venv/bin/activate
     $ make install
@@ -109,7 +109,7 @@ Tips
 
 To run a subset of tests::
 
-$ pytest tests.test_my_project_template
+$ pytest tests.test_grim
 
 
 Deploying

Dockerfile

@@ -14,6 +14,6 @@ RUN pip install --no-cache-dir -r requirements-deploy.txt
 COPY app.py /app/
 COPY api.py /app/
 COPY api-spec.yaml /app/
-COPY my_project_template /app/my_project_template
+COPY grim /app/grim
 
 CMD ["gunicorn"  , "--bind", "0.0.0.0:8080", "--worker-tmp-dir", "/dev/shm", "app:app"]

HEADER.txt

@@ -1,5 +1,5 @@
 #
-#    my_project_template My Project Template.
+#    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

Makefile

@@ -1,5 +1,5 @@
 PROJECT_NAME := $(shell basename `pwd`)
-PACKAGE_NAME := my_project_template
+PACKAGE_NAME := py-grim
 
 .PHONY: clean clean-test clean-pyc clean-build docs help test test-all
 .DEFAULT_GOAL := help
@@ -71,7 +71,7 @@ test: clean-test ## run all(BDD and unit) tests
 	behave
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source my_project_template -m pytest
+	coverage run --source py-grim -m pytest
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html

README.md

@@ -58,18 +58,18 @@ How to use the template:
     |   |-- HLA_alleles.py
     |   `-- SLUG_match.py
     `-- unit
-        `-- test_my_project_template.py
+        `-- test_grim.py
     ```
-8. Package Module files go in the `my_project_template` directory.
+8. Package Module files go in the `grim` directory.
     ```
-    my_project_template
+    grim
     |-- __init__.py
     |-- algorithm
     |   `-- match.py
     |-- model
     |   |-- allele.py
     |   `-- slug.py
-    `-- my_project_template.py
+    `-- grim.py
     ```
 9. Run all tests with `make test` or different tests with `make behave` or `make pytest`. `make behave` will generate report files and open the browser to the report.
 10. Use `python app.py` to run the Flask service app in debug mode. Service will be available at http://localhost:8080/

api.py

@@ -1,7 +1,7 @@
 from flask import request
 
-from my_project_template.model.allele import InvalidAllele
-from my_project_template.my_project_template import match
+from grim.model.allele import InvalidAllele
+from grim.grim import match
 
 
 def slug_match_controller():

my_project_template/__init__.py renamed to grim/__init__.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 #
-#    my_project_template My Project Template.
+#    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
@@ -10,7 +10,7 @@
 #    your option) any later version.
 #
 #    This library is distributed in the hope that it will be useful, but WITHOUT
-#    ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
+#    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.
 #
@@ -23,7 +23,7 @@
 #
 
 
-"""Top-level package for My Project Template."""
+"""Top-level package for py-grim."""
 
 __organization__ = "NMDP/CIBMTR Bioinformatics"
 __version__ = "0.0.1"

my_project_template/algorithm/match.py renamed to grim/algorithm/match.py

@@ -1,4 +1,4 @@
-from my_project_template.model.slug import SLUG
+from grim.model.slug import SLUG
 
 
 # SLUG match

my_project_template/my_project_template.py renamed to grim/grim.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 #
-#    my_project_template My Project Template.
+#    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

my_project_template/model/allele.py renamed to grim/model/allele.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 #
-#    my_project_template My Project Template.
+#    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
@@ -10,7 +10,7 @@
 #    your option) any later version.
 #
 #    This library is distributed in the hope that it will be useful, but WITHOUT
-#    ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
+#    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.
 #