diff --git a/.gitignore b/.gitignore index c72102cb..384ca35d 100644 --- a/.gitignore +++ b/.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/* + diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 00000000..eabb0a2f --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,2 @@ +recursive-include server/app/web/templates * +recursive-include server/app/web/static * \ No newline at end of file diff --git a/server/app/rest_api/rest.py b/server/app/rest_api/rest.py index bc15c44d..a953d7ff 100644 --- a/server/app/rest_api/rest.py +++ b/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 = { "metadata": [], "cellcount": 0, @@ -199,8 +199,8 @@ class CellsAPI(Resource): "ranges": {}, } # get query params - filter = parse_filter(request.args, data.schema) - filtered_data = data.filter_cells(filter) + cells_filter = parse_filter(request.args, data.schema) + 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) @@ -251,7 +251,7 @@ class ExpressionAPI(Resource): } }) def get(self): - from app import data + from .. import data expression_data = data.expression() return make_payload(expression_data) @@ -309,7 +309,7 @@ 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", []) @@ -415,7 +415,7 @@ 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", []) diff --git a/server/requirements.txt b/server/requirements.txt index cdd76273..93131d27 100644 --- a/server/requirements.txt +++ b/server/requirements.txt @@ -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 \ No newline at end of file diff --git a/setup.py b/setup.py new file mode 100644 index 00000000..993abc62 --- /dev/null +++ b/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", + ), +)