Initial packaging working

pip install works if client files are built and moved manually

.gitignore

@@ -44,3 +44,8 @@ server/app/web/static/css/
 server/app/web/static/img/
 server/app/web/static/js/
 server/app/web/templates/index\.html
+
+
+*.egg-info
+dist/*
+

MANIFEST.in

@@ -0,0 +1,2 @@
+recursive-include server/app/web/templates *
+recursive-include server/app/web/static *

server/app/__init__.py

@@ -13,7 +13,6 @@ Compress(app)
 CORS(app)
 
 # Config
-CONFIG_FILE = os.environ.get("CXG_CONFIG_FILE", default="scanpy-test.cfg")
 CXG_DIR = os.environ.get("CXG_DIRECTORY", default="/Users/charlotteweaver/Documents/Git/cxg-v2/data/")
 SECRET_KEY = os.environ.get("CXG_SECRET_KEY", default="SparkleAndShine")
 ENGINE = os.environ.get("CXG_ENGINE", default="scanpy")
@@ -24,8 +23,6 @@ CXG_API_BASE = os.environ.get("CXG_API_BASE2", default="http://0.0.0.0:5005/api/
 if not CONFIG_FILE:
     raise ValueError("No config file set for Flask application")
 
-# TODO check what is actually being configured here
-app.config.from_pyfile(os.path.join(CXG_DIR, "config", CONFIG_FILE), silent=True)
 app.config.update(
     SECRET_KEY=SECRET_KEY,
     CXG_API_BASE=CXG_API_BASE,

server/app/rest_api/rest.py

@@ -88,7 +88,7 @@ class InitializeAPI(Resource):
         }
     })
     def get(self):
-        from app import data, REACTIVE_LIMIT
+        from .. import data, REACTIVE_LIMIT
         return make_payload({
             "schema": data.schema,
             "cellcount": data.cell_count,
@@ -191,7 +191,7 @@ class CellsAPI(Resource):
         }
     })
     def get(self):
-        from app import data
+        from .. import data
         payload = {
             "cellids": [],
             "metadata": [],
@@ -200,8 +200,8 @@ class CellsAPI(Resource):
             "ranges": {},
         }
         # get query params
-        filter = parse_filter(request.args, data.schema)
+        cells_filter = parse_filter(request.args, data.schema)
-        filtered_data = data.filter_cells(filter)
+        filtered_data = data.filter_cells(cells_filter)
         payload["metadata"] = data.metadata(filtered_data)
         payload["ranges"] = data.metadata_ranges(filtered_data)
         payload["graph"] = data.create_graph(filtered_data)
@@ -253,7 +253,7 @@ class ExpressionAPI(Resource):
         }
     })
     def get(self):
-        from app import data
+        from .. import data
         expression_data = data.expression()
         return make_payload(expression_data)
 
@@ -311,7 +311,7 @@ class ExpressionAPI(Resource):
         }
     })
     def post(self):
-        from app import data
+        from .. import data
         args = request.get_json()
         cell_list = args.get("celllist", [])
         gene_list = args.get("genelist", [])
@@ -417,7 +417,7 @@ class DifferentialExpressionAPI(Resource):
         }
     })
     def post(self):
-        from app import data
+        from .. import data
         args = request.get_json()
         cell_list_1 = args.get("celllist1", [])
         cell_list_2 = args.get("celllist2", [])

server/requirements.txt

@@ -1,11 +1,11 @@
 aniso8601==3.0.2
-anndata==0.6.4
+anndata==0.6.1
 certifi==2018.4.16
 chardet==3.0.4
 click==6.7
 cycler==0.10.0
 decorator==4.3.0
-Flask==1.0.2
+Flask==0.12.4
 Flask-Compress==1.4.0
 Flask-Cors==3.0.6
 Flask-RESTful==0.3.6
@@ -38,4 +38,4 @@ six==1.11.0
 statsmodels==0.9.0
 tables==3.4.4
 urllib3==1.23
-Werkzeug==0.14.1
+Werkzeug==0.14.1

setup.py

@@ -0,0 +1,27 @@
+from setuptools import setup, find_packages
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+with open('server/requirements.txt') as fh:
+    requirements = fh.read().splitlines()
+
+setup(
+    name='cellxgene',
+    version='0.0.1',
+    packages=find_packages(),
+    url='https://github.com/chanzuckerberg/cellxgene',
+    license='MIT',
+    author='Colin Megill, Charlotte Weaver',
+    author_email='cweaver@chanzuckerberg.com',
+    description='Web application for exploration of large scale scRNA-seq datasets',
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    install_requires=requirements,
+    include_package_data=True,
+    zip_safe=False,
+    classifiers=(
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+    ),
+)