Reorganize into proper Python package

Author: buske

.travis.yml

@@ -5,11 +5,12 @@ python:
   - "2.7"
   - "3.3"
   - "3.4"
+  - "3.5"
 install:
-  - pip install -r requirements.txt
-  - python main.py quickstart
+  - pip install -e .
+  - mme-server quickstart
 script:
-  - coverage run -m unittest
+  - coverage run --source=mme_server setup.py test
 services:
   - elasticsearch
 before_script:

MANIFEST.in

@@ -0,0 +1,5 @@
+# Include static package files
+include LICENSE.txt
+include README.md
+include MANIFEST.in
+recursive-include mme_server/schemas *.json

README.md

@@ -7,54 +7,54 @@ This code is intended to be illustrative and is **not** guaranteed to perform we
 
 
 ## Dependencies
-- Python 2.7 or 3.X
+- Python 2.7 or 3.3+
 - ElasticSearch
 
 
 ## Quickstart
 
 1. Clone the repository:
 
-    ```bash
+    ```sh
     git clone https://github.com/MatchmakerExchange/reference-server.git
     cd reference-server
     ```
 
-1. Install the Python package dependencies (it's recommended that you use a [Python virtual environment](#install-es)):
+1. Install the Python package dependencies (it's recommended that you do this inside a [Python virtual environment](#install-venv)):
 
-    ```bash
-    pip install -r requirements.txt
+    ```sh
+    pip install -e .
     ```
 
 1. Start up your elasticsearch server in another shell (see the [ElasticSearch instructions](#install-es) for more information).
 
-    ```bash
+    ```sh
     ./path/to/elasticsearch
     ```
 
 1. Download and index vocabularies and sample data:
 
-    ```bash
-    python server.py quickstart
+    ```sh
+    mme-server quickstart
     ```
 
 1. Run tests:
 
-    ```bash
-    python test.py
+    ```sh
+    mme-server test
     ```
 
 1. Start up MME reference server:
 
-    ```bash
-    python server.py run
+    ```sh
+    mme-server start
     ```
 
     By default, the server listens globally (`--host 0.0.0.0`) on port 8000 (`--port 8000`).
 
 1. Try it out:
 
-    ```bash
+    ```sh
     curl -XPOST -H 'Content-Type: application/vnd.ga4gh.matchmaker.v1.0+json' \
          -H 'Accept: application/vnd.ga4gh.matchmaker.v1.0+json' \
          -d '{"patient":{
@@ -73,32 +73,32 @@ It's recommended that you run the server within a Python virtual environment so
 
 To set up your Python virtual environment:
 
-```bash
+```sh
 # Set up virtual environment within a folder '.virtualenv' (add `-p python3` to force python 3)
 virtualenv .virtualenv
 
 # Install dependencies
-pip install -r requirements.txt
+pip install -e .
 ```
 
 You can then activate this environment within a particular shell with:
 
-```bash
+```sh
 source .virtualenv/bin/activate
 ```
 
 ### <a name="install-es"></a> ElasticSearch
 
 First, download elasticsearch:
 
-```bash
+```sh
 wget https://download.elasticsearch.org/elasticsearch/release/org/elasticsearch/distribution/tar/elasticsearch/2.1.1/elasticsearch-2.1.1.tar.gz
 tar -xzf elasticsearch-2.1.1.tar.gz
 ```
 
 Then, start up a local elasticsearch cluster to serve as our database (`-Des.path.data=data` puts the elasticsearch indices in a subdirectory called `data`):
 
-```bash
+```sh
 ./elasticsearch-2.1.1/bin/elasticsearch -Des.path.data=data
 ```
 
@@ -109,22 +109,22 @@ Then, start up a local elasticsearch cluster to serve as our database (`-Des.pat
 Custom patient data can be indexed by the server in two ways (if a patient 'id' matches an existing patient, the existing patient is updated):
 
 1. Batch index from the command line:
-    ```bash
-    python server.py index patients --filename patients.json
+    ```sh
+    mme-server index patients --filename patients.json
     ```
 
 1. Batch index from the Python interface:
 
-    ```python
-    >>> from models import DatastoreConnection
+    ```py
+    >>> from mme_server.models import DatastoreConnection
     >>> db = DatastoreConnection()
     >>> db.patients.index('/path/to/patients.json')
     ```
 
 1. Single patient index the Python interface:
 
-    ```python
-    >>> from models import Patient, DatastoreConnection
+    ```py
+    >>> from mme_server.models import Patient, DatastoreConnection
     >>> db = DatastoreConnection()
     >>> patient = Patient.from_api({...})
     >>> db.patients.index_patient(patient)

mme_server/__init__.py

@@ -0,0 +1 @@
+from .cli import main

mme_server/__main__.py

@@ -0,0 +1,3 @@
+from .cli import main
+
+main()

main.py mme_server/cli.pymain.py renamed to mme_server/cli.py

@@ -6,11 +6,11 @@
 import sys
 import os
 import logging
+import unittest
 
-from compat import urlretrieve
-
-from models import get_backend
-from server import app
+from .compat import urlretrieve
+from .models import get_backend
+from .server import app
 
 
 DEFAULT_HOST = '0.0.0.0'
@@ -73,6 +73,11 @@ def fetch_resource(filename, url):
         logger.info('Saved file to: {}'.format(filename))
 
 
+def run_tests():
+    suite = unittest.TestLoader().discover('.'.join([__package__, 'tests']))
+    unittest.TextTestRunner().run(suite)
+
+
 def parse_args(args):
     from argparse import ArgumentParser
 
@@ -102,7 +107,7 @@ def parse_args(args):
                            help="Download data from the following url")
     subparser.set_defaults(function=index_file)
 
-    subparser = subparsers.add_parser('run', description="Start running a simple Matchmaker Exchange API server")
+    subparser = subparsers.add_parser('start', description="Start running a simple Matchmaker Exchange API server")
     subparser.add_argument("-p", "--port", default=DEFAULT_PORT,
                            dest="port", type=int, metavar="PORT",
                            help="The port the server will listen on (default: %(default)s)")
@@ -111,6 +116,9 @@ def parse_args(args):
                            help="The host the server will listen to (0.0.0.0 to listen globally; 127.0.0.1 to listen locally; default: %(default)s)")
     subparser.set_defaults(function=app.run)
 
+    subparser = subparsers.add_parser('test', description="Run tests")
+    subparser.set_defaults(function=run_tests)
+
     args = parser.parse_args(args)
     if not hasattr(args, 'function'):
         parser.error('a subcommand must be specified')

compat.py mme_server/compat.pycompat.py renamed to mme_server/compat.py

@@ -14,7 +14,8 @@
 import codecs
 
 from elasticsearch import Elasticsearch
-from parsers import OBOParser, GeneParser
+
+from .parsers import OBOParser, GeneParser
 
 
 logger = logging.getLogger(__name__)
@@ -56,7 +57,7 @@ def __init__(self, index='patients', backend=None):
 
     def index(self, filename):
         """Populate the database with patient data from the given file"""
-        from models import Patient
+        from .models import Patient
 
         with codecs.open(filename, encoding='utf-8') as ifp:
             data = json.load(ifp)

datastore.py mme_server/datastore.pydatastore.py renamed to mme_server/datastore.py

@@ -8,7 +8,8 @@
 from copy import deepcopy
 
 import flask
-from datastore import DatastoreConnection
+
+from .datastore import DatastoreConnection
 
 
 class Feature: