move common code into server, update tests and makefile (#2425)

* move common code into server, update tests and makefile

remove backend directory, refactor

update smoke tests

.bumpversion.cfg

@@ -2,13 +2,13 @@
 current_version = 0.18.0
 commit = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
-serialize = 
+serialize =
 	{major}.{minor}.{patch}-{prerel}.{prerelversion}
 	{major}.{minor}.{patch}
 
 [bumpversion:part:prerel]
 optional_value = release
-values = 
+values =
 	rc
 	release
 
@@ -20,6 +20,6 @@ replace = version="{new_version}"
 search = "version": "{current_version}"
 replace = "version": "{new_version}"
 
-[bumpversion:file:backend/server/__init__.py]
+[bumpversion:file:server/__init__.py]
 search = __version__ = "{current_version}"
 replace = __version__ = "{new_version}"

.dockerignore

@@ -2,4 +2,4 @@ bin
 client
 dist
 docs
-backend
+server

.github/workflows/compatibility_tests.yml

@@ -41,8 +41,8 @@ jobs:
       run: |
         # 1. only install the dev requirements on top of what is in the cellxgene pip package
         sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev
-        sed -i 's/-r requirements.txt//' backend/server/requirements-dev.txt
-        pip install -r backend/server/requirements-dev.txt
+        sed -i 's/-r requirements.txt//' server/requirements-dev.txt
+        pip install -r server/requirements-dev.txt
         # 2. install cellxgene
         make pydist install-dist
         # 3. install anndata
@@ -71,8 +71,8 @@ jobs:
           cd cellxgene
           # 1. only install the dev requirements on top of what is in the cellxgene pip package
           make dev-env-client
-          sed -i 's/-r requirements.txt//' backend/server/requirements-dev.txt
-          pip install -r backend/server/requirements-dev.txt
+          sed -i 's/-r requirements.txt//' server/requirements-dev.txt
+          pip install -r server/requirements-dev.txt
           # 2. install cellxgene
           pip install --upgrade cellxgene
           # 3. install anndata
@@ -99,7 +99,7 @@ jobs:
       - name: Install dependencies
         run: |
           cd cellxgene
-          sed -i -E 's/^anndata[>=]=[0-9]+.[0-9]+.[0-9]+$/anndata/g' backend/server/requirements.txt
+          sed -i -E 's/^anndata[>=]=[0-9]+.[0-9]+.[0-9]+$/anndata/g' server/requirements.txt
           make pydist install-dist dev-env
           pip install git+https://github.com/theislab/anndata
       - name: Tests

.github/workflows/push_tests.yml

@@ -69,7 +69,7 @@ jobs:
       - name: Unit tests
         run: |
           make unit-test-server unit-test-client
-          bash <(curl -s https://codecov.io/bash) -y .codecov.yml -k backend/server -cF backend,python,unitTest
+          bash <(curl -s https://codecov.io/bash) -y .codecov.yml -k server -cF server,python,unitTest
           cd client && ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,unitTest
 
   smoke-tests:

.gitignore

@@ -19,9 +19,9 @@ venv*/
 cellxgene/
 
 # client build
-backend/server/common/web/static/*
-backend/server/common/web/templates/
-backend/server/common/web/csp-hashes.json
+server/common/web/static/*
+server/common/web/templates/
+server/common/web/csp-hashes.json
 
 # eb build
 artifact.dir

MANIFEST.in

@@ -1,7 +1,7 @@
-recursive-include backend/server/common/web/templates *
-recursive-include backend/server/common/web/static *
+recursive-include server/common/web/templates *
+recursive-include server/common/web/static *
 
-include backend/server/requirements.txt
-include backend/server/requirements-prepare.txt
-include backend/server/converters/schema/hgnc_complete_set.txt.gz
-include backend/server/converters/schema/schema_definitions/*
+include server/requirements.txt
+include server/requirements-prepare.txt
+include server/converters/schema/hgnc_complete_set.txt.gz
+include server/converters/schema/schema_definitions/*

Makefile

@@ -2,7 +2,7 @@ include common.mk
 
 BUILDDIR := build
 CLIENTBUILD := $(BUILDDIR)/client
-SERVERBUILD := $(BUILDDIR)/backend/server
+SERVERBUILD := $(BUILDDIR)/server
 CLEANFILES :=  $(BUILDDIR)/ client/build build dist cellxgene.egg-info
 
 PART ?= patch
@@ -22,7 +22,7 @@ clean-client:
 
 .PHONY: clean-server
 clean-server:
-	cd backend/server && $(MAKE) clean
+	cd server && $(MAKE) clean
 
 
 # BUILDING PACKAGE
@@ -33,33 +33,26 @@ build-client:
 
 .PHONY: build
 build: clean build-client
-	git ls-files backend/server/ | grep -v 'backend/server/test/' | cpio -pdm $(BUILDDIR)
+	git ls-files server/ | cpio -pdm $(BUILDDIR)
 	cp -r client/build/  $(CLIENTBUILD)
 	$(call copy_client_assets,$(CLIENTBUILD),$(SERVERBUILD))
-	cp backend/__init__.py $(BUILDDIR)
-	cp backend/__init__.py $(BUILDDIR)/backend
-	cp -r backend/common $(BUILDDIR)/backend/common
 	cp MANIFEST.in README.md setup.cfg setup.py $(BUILDDIR)
 
 # If you are actively developing in the server folder use this, dirties the source tree
 .PHONY: build-for-server-dev
-build-for-server-dev: clean-server build-client
-	$(call copy_client_assets,client/build,backend/server)
+build-for-server-dev: clean-server build-client copy-client-assets
 
 .PHONY: copy-client-assets
 copy-client-assets:
-	$(call copy_client_assets,client/build,backend/server)
+	$(call copy_client_assets,client/build,server)
 
-.PHONY: copy-client-assets-czi-hosted
-copy-client-assets-czi-hosted:
-	$(call copy_client_assets,client/build)
 
 # TESTING
 .PHONY: test
 test: unit-test smoke-test
 
 .PHONY: unit-test
-unit-test: unit-test-server unit-test-client unit-test-common
+unit-test: unit-test-server unit-test-client
 
 .PHONY: test-server
 test-server: unit-test-server smoke-test
@@ -70,11 +63,13 @@ unit-test-client:
 
 .PHONY: unit-test-server
 unit-test-server:
-	cd backend/server && $(MAKE) unit-test
-
-.PHONY: unit-test-common
-unit-test-common:
-	cd backend/common && $(MAKE) unit-test
+	PYTHONWARNINGS=ignore:ResourceWarning coverage run \
+		--source=server \
+		--omit=.coverage,venv \
+		-m unittest discover \
+		--start-directory test/unit \
+		--verbose; test_result=$$?; \
+	exit $$test_result \
 
 .PHONY: smoke-test
 smoke-test:
@@ -103,7 +98,7 @@ lint: lint-server lint-client
 
 .PHONY: lint-server
 lint-server: fmt-py
-	flake8 backend/server --per-file-ignores='backend/test/fixtures/dataset_config_outline.py:F821 backend/test/fixtures/server_config_outline.py:F821 backend/server/test/performance/scale_test_annotations.py:E501'
+	flake8 server --per-file-ignores='test/fixtures/dataset_config_outline.py:F821 test/fixtures/server_config_outline.py:F821 test/performance/scale_test_annotations.py:E501'
 
 .PHONY: lint-client
 lint-client:
@@ -163,7 +158,7 @@ dev-env-client:
 
 .PHONY: dev-env-server
 dev-env-server:
-	pip install -r backend/server/requirements-dev.txt
+	pip install -r server/requirements-dev.txt
 
 # Increments the release candidate version (i.e. 0.16.2-rc.1 -> 0.16.2-rc.2)
 .PHONY: bump-release-candidate

backend/common/Makefile

@@ -1,11 +0,0 @@
-
-.PHONY: unit-test
-unit-test:
-	PYTHONWARNINGS=ignore:ResourceWarning coverage run \
-		--source=fbs,utils \
-		--omit=.coverage,data_common/fbs/NetEncoding,venv \
-		-m unittest discover \
-		--start-directory ../test/test_common/unit \
-		--top-level-directory ../../ \
-		--verbose; test_result=$$?; \
-	exit $$test_result \

backend/server/Makefile

@@ -1,22 +0,0 @@
-include ../../common.mk
-
-.PHONY: clean
-clean:
-	rm -f common/web/templates/index.html
-	rm -rf common/web/static
-	rm -f common/web/csp-hashes.json
-
-.PHONY: unit-test
-unit-test:
-	PYTHONWARNINGS=ignore:ResourceWarning coverage run \
-		--source=app,cli,common,compute,converters,data_anndata,data_common \
-		--omit=.coverage,venv \
-		-m unittest discover \
-		--start-directory ../test/test_server/unit \
-		--top-level-directory ../../ \
-		--verbose; test_result=$$?; \
-	exit $$test_result \
-
-.PHONY: test-annotations-performance
-test-annotations-performance:
-	python ../test/test_server/performance/performance_test_annotations_backend.py

backend/test/test_common/unit/__init__.py

@@ -1 +0,0 @@
-

client/Makefile

@@ -1,7 +1,7 @@
 include ../common.mk
 
-ANNOTATIONS := $(if $(ANNOTATIONS),$(ANNOTATIONS),../backend/test/fixtures/pbmc3k-annotations.csv)
-GENE_SETS := $(if $(GENE_SETS),$(GENE_SETS),../backend/test/fixtures/pbmc3k-genesets.csv)
+ANNOTATIONS := $(if $(ANNOTATIONS),$(ANNOTATIONS),../test/fixtures/pbmc3k-annotations.csv)
+GENE_SETS := $(if $(GENE_SETS),$(GENE_SETS),../test/fixtures/pbmc3k-genesets.csv)
 ANNOTATIONS_FILENAME := $(shell basename $(ANNOTATIONS))
 GENE_SETS_FILENAME := $(shell basename $(GENE_SETS))
 

pyproject.toml

@@ -17,7 +17,7 @@ exclude = '''
     | buck-out
     | build
     | dist
-    | backend/server/data_common/fbs/NetEncoding
+    | server/common/fbs/NetEncoding
   )/
 
 )

requirements.txt

@@ -1 +1 @@
--r ./backend/server/requirements.txt
+-r ./server/requirements.txt

server/Makefile

@@ -0,0 +1,12 @@
+include ../common.mk
+
+.PHONY: clean
+clean:
+	rm -f common/web/templates/index.html
+	rm -rf common/web/static
+	rm -f common/web/csp-hashes.json
+
+
+.PHONY: test-annotations-performance
+test-annotations-performance:
+	python ../test/performance/performance_test_annotations.py

server/__init__.py

@@ -1,12 +1,12 @@
 import logging
 import sys
-from backend.common.utils.utils import import_plugins
+from server.common.utils.utils import import_plugins
 
 __version__ = "0.18.0"
 display_version = "cellxgene v" + __version__
 
 try:
-    import_plugins("backend.server.plugins")
+    import_plugins("server.plugins")
 except Exception as e:
     # Make sure to exit in this case, as the server may not be configured as expected.
     logging.critical(f"Error in import_plugins: {str(e)}")

server/__main__.py

@@ -5,7 +5,8 @@ if __package__ is None:
 
     PKG_PATH = Path(__file__).parent
     sys.path.insert(0, str(PKG_PATH.parent))
-    import backend.server # noqa F401
+    import server  # noqa F401
+
     __package__ = PKG_PATH.name
 
 # Main thing

server/app/app.py

@@ -13,12 +13,12 @@ from flask import (
 )
 from flask_restful import Api, Resource
 
-import backend.server.common.rest as common_rest
-from backend.common.errors import DatasetAccessError, RequestException
-from backend.server.common.health import health_check
-from backend.common.utils.utils import StrictJSONEncoder
+import server.common.rest as common_rest
+from server.common.errors import DatasetAccessError, RequestException
+from server.common.health import health_check
+from server.common.utils.utils import StrictJSONEncoder
 
-webbp = Blueprint("webapp", "backend.server.common.web", template_folder="templates")
+webbp = Blueprint("webapp", "server.common.web", template_folder="templates")
 
 ONE_WEEK = 7 * 24 * 60 * 60
 

server/cli/cli.py

@@ -20,7 +20,10 @@ from .. import __version__
     help="Show the software version and exit.",
 )
 @click.option(
-    "--upgrade-check/--no-upgrade-check", default=True, show_default=True, help="Check for release upgrades on start.",
+    "--upgrade-check/--no-upgrade-check",
+    default=True,
+    show_default=True,
+    help="Check for release upgrades on start.",
 )
 def cli(upgrade_check):
     if upgrade_check:

server/cli/launch.py

@@ -8,11 +8,11 @@ import click
 from flask_compress import Compress
 from flask_cors import CORS
 
-from backend.server.default_config import default_config
-from backend.server.app.app import Server
-from backend.server.common.config.app_config import AppConfig
-from backend.common.errors import DatasetAccessError, ConfigurationError
-from backend.common.utils.utils import sort_options
+from server.default_config import default_config
+from server.app.app import Server
+from server.common.config.app_config import AppConfig
+from server.common.errors import DatasetAccessError, ConfigurationError
+from server.common.utils.utils import sort_options
 
 DEFAULT_CONFIG = AppConfig()
 

server/cli/prepare.py

@@ -5,7 +5,7 @@ import pandas as pd
 from numpy import ndarray, unique
 from scipy.sparse.csc import csc_matrix
 
-from backend.common.utils.utils import sort_options
+from server.common.utils.utils import sort_options
 
 
 @sort_options
@@ -24,7 +24,11 @@ from backend.common.utils.utils import sort_options
     show_default=True,
 )
 @click.option(
-    "--recipe", "-r", default="none", type=click.Choice(["none", "seurat", "zheng17"]), show_default=True,
+    "--recipe",
+    "-r",
+    default="none",
+    type=click.Choice(["none", "seurat", "zheng17"]),
+    show_default=True,
 )
 @click.option("--output", "-o", default="", help="Save a new file to filename.", metavar="<filename>")
 @click.option("--plotting", "-p", default=False, is_flag=True, help="Generate plots.", show_default=True)

server/common/annotations/annotations.py

@@ -1,8 +1,8 @@
 from abc import ABCMeta, abstractmethod
 
-from backend.common.errors import DisabledFeatureError
-from backend.common.utils.type_conversion_utils import get_schema_type_hint_of_array
-from backend.common.genesets import write_gene_sets_tidycsv
+from server.common.errors import DisabledFeatureError
+from server.common.utils.type_conversion_utils import get_schema_type_hint_of_array
+from server.common.genesets import write_gene_sets_tidycsv
 
 
 class Annotations(metaclass=ABCMeta):

server/common/annotations/local_file_csv.py

@@ -8,12 +8,12 @@ from hashlib import blake2b
 import pandas as pd
 from flask import session
 
-from backend.server import __version__ as cellxgene_version
-from backend.server.app.session import get_user_id
-from backend.server.common.annotations.annotations import Annotations
-from backend.common.genesets import read_gene_sets_tidycsv
-from backend.common.errors import AnnotationsError, ObsoleteRequest
-from backend.common.utils.data_locator import DataLocator
+from server import __version__ as cellxgene_version
+from server.app.session import get_user_id
+from server.common.annotations.annotations import Annotations
+from server.common.genesets import read_gene_sets_tidycsv
+from server.common.errors import AnnotationsError, ObsoleteRequest
+from server.common.utils.data_locator import DataLocator
 
 
 class AnnotationsLocalFile(Annotations):

server/common/colors.py

@@ -1,6 +1,6 @@
 import re
 
-from backend.common.errors import ColorFormatException
+from server.common.errors import ColorFormatException
 
 HEX_COLOR_FORMAT = re.compile("^#[a-fA-F0-9]{6,6}$")
 

server/common/compute/diffexp_generic.py

@@ -1,6 +1,6 @@
 import numpy as np
 from scipy import sparse, stats
-from backend.common.constants import XApproximateDistribution
+from server.common.constants import XApproximateDistribution
 
 
 def diffexp_ttest(adaptor, maskA, maskB, top_n=8, diffexp_lfc_cutoff=0.01):
@@ -27,7 +27,8 @@ def diffexp_ttest(adaptor, maskA, maskB, top_n=8, diffexp_lfc_cutoff=0.01):
     :param top_n: number of variables to return stats for
     :param diffexp_lfc_cutoff: minimum
     absolute value returning [ varindex, logfoldchange, pval, pval_adj ] for top N genes
-    :return:  for top N genes, {"positive": for top N genes, [ varindex, foldchange, pval, pval_adj ], "negative": for top N genes, [ varindex, foldchange, pval, pval_adj ]}
+    :return:  for top N genes, {"positive": for top N genes, [ varindex, foldchange, pval, pval_adj ],
+    "negative": for top N genes, [ varindex, foldchange, pval, pval_adj ]}
     """
 
     X_approximate_distribution = adaptor.get_X_approximate_distribution()

server/common/compute/estimate_distribution.py

@@ -3,7 +3,7 @@ import numba
 import concurrent.futures
 import numpy as np
 from scipy import sparse
-from backend.common.constants import XApproximateDistribution
+from server.common.constants import XApproximateDistribution
 
 
 @numba.njit(error_model="numpy", nogil=True)

server/common/config/app_config.py

@@ -1,11 +1,11 @@
 import yaml
 from flatten_dict import unflatten
 
-from backend.server.default_config import get_default_config
-from backend.server.common.config.dataset_config import DatasetConfig
-from backend.server.common.config.server_config import ServerConfig
-from backend.server.common.config.external_config import ExternalConfig
-from backend.common.errors import ConfigurationError
+from server.default_config import get_default_config
+from server.common.config.dataset_config import DatasetConfig
+from server.common.config.server_config import ServerConfig
+from server.common.config.external_config import ExternalConfig
+from server.common.errors import ConfigurationError
 
 
 class AppConfig(object):

server/common/config/base_config.py

@@ -1,7 +1,7 @@
 import copy
 
 from flatten_dict import flatten
-from backend.common.errors import ConfigurationError
+from server.common.errors import ConfigurationError
 
 
 class BaseConfig(object):

server/common/config/client_config.py

@@ -1,4 +1,4 @@
-from backend.server import display_version as cellxgene_display_version
+from server import display_version as cellxgene_display_version
 
 
 def get_client_config(app_config, data_adaptor):

server/common/config/dataset_config.py

@@ -1,10 +1,10 @@
 import os
 from os.path import splitext, isdir
 
-from backend.server.common.annotations.local_file_csv import AnnotationsLocalFile
-from backend.server.common.config.base_config import BaseConfig
-from backend.common.errors import ConfigurationError, AnnotationsError
-from backend.server.data_common.matrix_loader import MatrixDataLoader
+from server.common.annotations.local_file_csv import AnnotationsLocalFile
+from server.common.config.base_config import BaseConfig
+from server.common.errors import ConfigurationError, AnnotationsError
+from server.data_common.matrix_loader import MatrixDataLoader
 
 
 class DatasetConfig(BaseConfig):

server/common/config/external_config.py

@@ -1,8 +1,8 @@
 import os
 
-from backend.server.common.config.base_config import BaseConfig
-from backend.common.errors import ConfigurationError
-from backend.common.utils.type_conversion_utils import convert_string_to_value
+from server.common.config.base_config import BaseConfig
+from server.common.errors import ConfigurationError
+from server.common.utils.type_conversion_utils import convert_string_to_value
 
 
 class ExternalConfig(BaseConfig):

server/common/config/server_config.py

@@ -4,12 +4,12 @@ import warnings
 from os.path import basename
 from urllib.parse import urlparse
 
-from backend.server.common.config.base_config import BaseConfig
-from backend.server.common.config import DEFAULT_SERVER_PORT, BIG_FILE_SIZE_THRESHOLD
-from backend.common.utils.data_locator import discover_s3_region_name
-from backend.common.errors import ConfigurationError, DatasetAccessError
-from backend.common.utils.utils import is_port_available, find_available_port, custom_format_warning
-from backend.server.data_common.matrix_loader import MatrixDataLoader
+from server.common.config.base_config import BaseConfig
+from server.common.config import DEFAULT_SERVER_PORT, BIG_FILE_SIZE_THRESHOLD
+from server.common.utils.data_locator import discover_s3_region_name
+from server.common.errors import ConfigurationError, DatasetAccessError
+from server.common.utils.utils import is_port_available, find_available_port, custom_format_warning
+from server.data_common.matrix_loader import MatrixDataLoader
 
 
 class ServerConfig(BaseConfig):

server/common/corpora.py

@@ -8,8 +8,8 @@ https://github.com/chanzuckerberg/corpora-data-portal/blob/main/backend/schema/c
 import collections
 import json
 
-from backend.server.cli.upgrade import validate_version_str
-from backend.server.common.utils.corpora_constants import CorporaConstants
+from server.cli.upgrade import validate_version_str
+from server.common.utils.corpora_constants import CorporaConstants
 
 
 def corpora_get_versions_from_anndata(adata):

server/common/fbs/matrix.py

@@ -5,16 +5,16 @@ import pandas as pd
 from flatbuffers import Builder
 from scipy import sparse
 
-from backend.common.utils.type_conversion_utils import get_encoding_dtype_of_array
+from server.common.utils.type_conversion_utils import get_encoding_dtype_of_array
 
-import backend.common.fbs.NetEncoding.Column as Column
-import backend.common.fbs.NetEncoding.Float32Array as Float32Array
-import backend.common.fbs.NetEncoding.Float64Array as Float64Array
-import backend.common.fbs.NetEncoding.Int32Array as Int32Array
-import backend.common.fbs.NetEncoding.JSONEncodedArray as JSONEncodedArray
-import backend.common.fbs.NetEncoding.Matrix as Matrix
-import backend.common.fbs.NetEncoding.TypedArray as TypedArray
-import backend.common.fbs.NetEncoding.Uint32Array as Uint32Array
+import server.common.fbs.NetEncoding.Column as Column
+import server.common.fbs.NetEncoding.Float32Array as Float32Array
+import server.common.fbs.NetEncoding.Float64Array as Float64Array
+import server.common.fbs.NetEncoding.Int32Array as Int32Array
+import server.common.fbs.NetEncoding.JSONEncodedArray as JSONEncodedArray
+import server.common.fbs.NetEncoding.Matrix as Matrix
+import server.common.fbs.NetEncoding.TypedArray as TypedArray
+import server.common.fbs.NetEncoding.Uint32Array as Uint32Array
 
 
 # Serialization helper

server/common/genesets.py

@@ -75,7 +75,7 @@ def read_gene_sets_tidycsv(gs_locator, context=None):
                 # if this is the first non-comment row, assume it is a header and validate
                 # column names.  OK if the user has extra columns after our initial set.
                 if not haveReadHeader:
-                    if row[0:len(GENESETS_TIDYCSV_HEADER)] != GENESETS_TIDYCSV_HEADER:
+                    if row[0 : len(GENESETS_TIDYCSV_HEADER)] != GENESETS_TIDYCSV_HEADER:
                         raise AnnotationsError("Gene set CSV file missing the required column header.")
                     haveReadHeader = True
                     continue

server/common/health.py

@@ -1,8 +1,8 @@
 from http import HTTPStatus
 from flask import make_response, jsonify
 
-from backend.server import __version__ as cellxgene_version
-from backend.common.utils.data_locator import DataLocator
+from server import __version__ as cellxgene_version
+from server.common.utils.data_locator import DataLocator
 
 
 def _is_accessible(path, config):

server/common/rest.py

@@ -8,9 +8,9 @@ import json
 from flask import make_response, jsonify, current_app, abort
 from werkzeug.urls import url_unquote
 
-from backend.server.common.config.client_config import get_client_config
-from backend.common.constants import Axis, DiffExpMode, JSON_NaN_to_num_warning_msg
-from backend.common.errors import (
+from server.common.config.client_config import get_client_config
+from server.common.constants import Axis, DiffExpMode, JSON_NaN_to_num_warning_msg
+from server.common.errors import (
     FilterError,
     JSONEncodingValueError,
     PrepareError,
@@ -22,8 +22,8 @@ from backend.common.errors import (
     ObsoleteRequest,
     UnsupportedSummaryMethod,
 )
-from backend.common.genesets import summarizeQueryHash
-from backend.common.fbs.matrix import decode_matrix_fbs
+from server.common.genesets import summarizeQueryHash
+from server.common.fbs.matrix import decode_matrix_fbs
 
 
 def abort_and_log(code, logmsg, loglevel=logging.DEBUG, include_exc_info=False):

server/common/utils/utils.py

@@ -10,7 +10,7 @@ from urllib.parse import urlsplit, urljoin
 import numpy as np
 from flask import json
 
-from backend.common.errors import ConfigurationError
+from server.common.errors import ConfigurationError
 
 
 def find_available_port(host, port=5005):

server/data_anndata/anndata_adaptor.py

@@ -6,15 +6,15 @@ from packaging import version
 from pandas.core.dtypes.dtypes import CategoricalDtype
 from scipy import sparse
 
-import backend.common.compute.diffexp_generic as diffexp_generic
-import backend.common.compute.estimate_distribution as estimate_distribution
-from backend.common.colors import convert_anndata_category_colors_to_cxg_category_colors
-from backend.common.constants import Axis, MAX_LAYOUTS, XApproximateDistribution
-from backend.server.common.corpora import corpora_get_props_from_anndata
-from backend.common.errors import PrepareError, DatasetAccessError
-from backend.common.utils.type_conversion_utils import get_schema_type_hint_of_array
-from backend.server.data_common.data_adaptor import DataAdaptor
-from backend.common.fbs.matrix import encode_matrix_fbs
+import server.common.compute.diffexp_generic as diffexp_generic
+import server.common.compute.estimate_distribution as estimate_distribution
+from server.common.colors import convert_anndata_category_colors_to_cxg_category_colors
+from server.common.constants import Axis, MAX_LAYOUTS, XApproximateDistribution
+from server.common.corpora import corpora_get_props_from_anndata
+from server.common.errors import PrepareError, DatasetAccessError
+from server.common.utils.type_conversion_utils import get_schema_type_hint_of_array
+from server.data_common.data_adaptor import DataAdaptor
+from server.common.fbs.matrix import encode_matrix_fbs
 
 anndata_version = version.parse(str(anndata.__version__)).release
 

server/data_common/data_adaptor.py

@@ -5,12 +5,12 @@ import pandas as pd
 from scipy import sparse
 from server_timing import Timing as ServerTiming
 
-from backend.server.common.config.app_config import AppConfig
-from backend.common.constants import Axis, XApproximateDistribution
-from backend.common.errors import FilterError, JSONEncodingValueError, ExceedsLimitError, UnsupportedSummaryMethod
-from backend.common.utils.utils import jsonify_strict
-from backend.common.fbs.matrix import encode_matrix_fbs
-from backend.common.genesets import validate_gene_sets
+from server.common.config.app_config import AppConfig
+from server.common.constants import Axis, XApproximateDistribution
+from server.common.errors import FilterError, JSONEncodingValueError, ExceedsLimitError, UnsupportedSummaryMethod
+from server.common.utils.utils import jsonify_strict
+from server.common.fbs.matrix import encode_matrix_fbs
+from server.common.genesets import validate_gene_sets
 
 
 class DataAdaptor(metaclass=ABCMeta):

server/data_common/matrix_loader.py

@@ -1,7 +1,7 @@
 from enum import Enum
 
-from backend.common.utils.data_locator import DataLocator
-from backend.common.errors import DatasetAccessError
+from server.common.utils.data_locator import DataLocator
+from server.common.errors import DatasetAccessError
 from http import HTTPStatus
 
 
@@ -30,7 +30,7 @@ class MatrixDataLoader(object):
             raise DatasetAccessError("Dataset does not have an allowed type.")
 
         if self.matrix_data_type == MatrixDataType.H5AD:
-            from backend.server.data_anndata.anndata_adaptor import AnndataAdaptor
+            from server.data_anndata.anndata_adaptor import AnndataAdaptor
 
             self.matrix_type = AnndataAdaptor
 

setup.cfg

@@ -1,4 +1,4 @@
 [flake8]
 max-line-length = 120
 ignore = E203, W503
-exclude = backend/common/fbs/NetEncoding/,.git,__pycache__,venv,old,build,dist
+exclude = server/common/fbs/NetEncoding/,.git,__pycache__,venv,old,build,dist

setup.py

@@ -3,10 +3,10 @@ from setuptools import setup, find_packages
 with open("README.md", "rb") as fh:
     long_description = fh.read().decode()
 
-with open("backend/server/requirements.txt") as fh:
+with open("server/requirements.txt") as fh:
     requirements = fh.read().splitlines()
 
-with open("backend/server/requirements-prepare.txt") as fh:
+with open("server/requirements-prepare.txt") as fh:
     requirements_prepare = fh.read().splitlines()
 
 setup(
@@ -39,6 +39,6 @@ setup(
         "Programming Language :: Python :: 3 :: Only",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
-    entry_points={"console_scripts": ["cellxgene = backend.server.cli.cli:cli"]},
+    entry_points={"console_scripts": ["cellxgene = server.cli.cli:cli"]},
     extras_require=dict(prepare=requirements_prepare),
 )

test/__init__.py

@@ -3,7 +3,7 @@ import string
 from os import popen
 
 PROJECT_ROOT = popen("git rev-parse --show-toplevel").read().strip()
-FIXTURES_ROOT = PROJECT_ROOT + "/backend/test/fixtures"
+FIXTURES_ROOT = PROJECT_ROOT + "/test/fixtures"
 H5AD_FIXTURE = FIXTURES_ROOT + "/pbmc3k-CSC-gz.h5ad"
 
 

test/decode_fbs.py

@@ -5,8 +5,8 @@ This code will need to be updated if fbs/matrix.fbs changes. For more informatio
 server/data_common/fbs/
 """
 
-import backend.common.fbs.NetEncoding.Matrix as Matrix
-from backend.common.fbs.matrix import deserialize_typed_array
+import server.common.fbs.NetEncoding.Matrix as Matrix
+from server.common.fbs.matrix import deserialize_typed_array
 
 
 def decode_matrix_FBS(buf):