mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-24 01:58:12 +08:00
server update
This commit is contained in:
Timmy Huang
+11
-6
@@ -294,7 +294,9 @@ def layout_obs_get(request, data_adaptor):
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try:
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return make_response(
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data_adaptor.layout_to_fbs_matrix(fields, data_adaptor.get_spatial()), HTTPStatus.OK, {"Content-Type": "application/octet-stream"}
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data_adaptor.layout_to_fbs_matrix(fields, data_adaptor.get_spatial()),
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HTTPStatus.OK,
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{"Content-Type": "application/octet-stream"},
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)
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except (KeyError, DatasetAccessError) as e:
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return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
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@@ -380,7 +382,7 @@ def summarize_var_helper(request, data_adaptor, key, raw_query):
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HTTPStatus.OK,
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{"Content-Type": "application/octet-stream"},
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)
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except (ValueError) as e:
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except ValueError as e:
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return abort(HTTPStatus.NOT_FOUND, description=str(e))
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except (UnsupportedSummaryMethod, FilterError) as e:
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return abort(HTTPStatus.BAD_REQUEST, description=str(e))
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@@ -399,9 +401,10 @@ def summarize_var_post(request, data_adaptor):
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key = request.args.get("key", default=None)
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return summarize_var_helper(request, data_adaptor, key, request.get_data())
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def spatial_image_get(request, data_adaptor):
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import io
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import matplotlib.pyplot
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import matplotlib.pyplot
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resolution = "hires"
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spatial = data_adaptor.get_spatial()
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@@ -417,7 +420,9 @@ def spatial_image_get(request, data_adaptor):
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return abort_and_log(HTTPStatus.BAD_REQUEST, "spatial information does not contain images")
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if resolution not in spatial[library_id]["images"]:
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return abort_and_log(HTTPStatus.BAD_REQUEST, f"spatial information does not contain requested resolution '{resolution}'")
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return abort_and_log(
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HTTPStatus.BAD_REQUEST, f"spatial information does not contain requested resolution '{resolution}'"
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)
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response_image = io.BytesIO()
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img = spatial[library_id]["images"][resolution]
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@@ -425,7 +430,7 @@ def spatial_image_get(request, data_adaptor):
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response_image.seek(0)
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try:
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return send_file(response_image, attachment_filename=f"{library_id}-{resolution}.png", mimetype="image/png")
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return send_file(response_image, download_name=f"{library_id}-{resolution}.png", mimetype="image/png")
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except (KeyError, DatasetAccessError) as e:
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return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
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except PrepareError:
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@@ -434,4 +439,4 @@ def spatial_image_get(request, data_adaptor):
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f"No spatial image available {request.path}",
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loglevel=logging.ERROR,
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include_exc_info=True,
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)
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)
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+23
-169
@@ -1,171 +1,25 @@
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alembic==1.4.2
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aniso8601==8.0.0
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anndata==0.8.0
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appdirs==1.4.4
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astroid==2.4.2
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attrs==19.3.0
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Authlib==0.14.3
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autopep8==1.5.4
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aws-sam-translator==1.25.0
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aws-xray-sdk==2.6.0
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bitarray==2.7.3
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black==23.12.1
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bleach==3.1.5
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boto==2.49.0
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boto3==1.26.94
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botocore==1.29.165
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Brotli==1.0.7
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bump2version==1.0.0
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bumpversion==0.6.0
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-e git+git@github.com:chanzuckerberg/cellxgene.git@7d61f47a31a661f49cef6c7d2356228d0aeb044c#egg=cellxgene
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certifi==2020.4.5.1
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cffi==1.14.0
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cfn-lint==0.34.0
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chalice==1.12.0
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chardet==3.0.4
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charset-normalizer==3.3.2
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click==8.1.3
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clickclick==1.2.2
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codecov==2.1.3
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connexion==2.7.0
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contourpy==1.1.1
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coverage==7.4.0
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cryptography==2.9.2
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cycler==0.10.0
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decorator==4.4.2
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docker==4.2.2
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docutils==0.15.2
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ecdsa==0.18.0
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enum-compat==0.0.3
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envyaml==1.10.211231
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fastobo==0.7.2
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flake8==7.0.0
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flake8-black==0.2.0
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# NOTE: If you update 'anndata' min version, also update the 'anndata_version'
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# matrix value in .github/workflows/compatibility_tests.yml
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anndata>=0.7.6 # we need to_memory(), added in 0.7.6
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boto3>=1.12.18
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click>=7.1.2
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Flask==2.2.3
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Flask-Caching==1.8.0
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Flask-Compress==1.13
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Flask-Cors==3.0.10
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Flask-RESTful==0.3.9
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flask-server-timing==0.1.2
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flask-talisman==1.0.0
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flatbuffers==1.12
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flatten-dict==0.4.2
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fonttools==4.47.2
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fsspec==0.7.4
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furl==2.1.0
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future==0.18.2
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get-version==2.1
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gevent==23.9.1
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greenlet==3.0.3
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gunicorn==20.0.4
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h5py==3.10.0
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idna==2.8
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importlib-metadata==7.0.1
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importlib-resources==6.1.1
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inflection==0.5.0
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isort==4.3.21
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itsdangerous==2.1.2
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Jinja2==3.1.3
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jmespath==0.10.0
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joblib==0.16.0
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jsondiff==1.1.2
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jsonpatch==1.26
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jsonpickle==1.4.1
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jsonpointer==2.0
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jsonschema==3.2.0
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junit-xml==1.9
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keyring==21.2.1
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kiwisolver==1.2.0
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lazy-object-proxy==1.4.3
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legacy-api-wrap==1.2
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llvmlite==0.39.1
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Mako==1.1.3
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MarkupSafe==2.1.4
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matplotlib==3.7.4
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mccabe==0.7.0
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mock==4.0.2
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more-itertools==8.3.0
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moto==1.3.14
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mypy==1.8.0
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mypy-extensions==0.4.3
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natsort==7.0.1
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networkx==2.4
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numba==0.56.4
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numexpr==2.7.1
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numpy==1.23.5
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openapi-spec-validator==0.2.8
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orderedmultidict==1.0.1
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Owlready2==0.24
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packaging==20.4
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pandas==1.5.3
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parameterized==0.7.4
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pathlib2==2.3.5
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pathspec==0.12.1
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patsy==0.5.1
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Pillow==7.2.0
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pkginfo==1.5.0.1
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platformdirs==4.1.0
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pluggy==0.13.1
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psycopg2-binary==2.8.5
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py==1.8.1
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pyasn1==0.4.8
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pycodestyle==2.11.1
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pycparser==2.20
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pydantic==1.10.6
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pyflakes==3.2.0
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Pygments==2.6.1
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pylint==2.5.3
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PyMySQL==0.9.3
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pyparsing==2.4.7
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pyrsistent==0.16.0
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pytest==5.4.2
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pytest-subtests==0.11.0
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python-dateutil==2.8.1
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python-editor==1.0.4
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python-jose==3.3.0
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python-json-logger==2.0.7
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pytz==2020.1
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PyYAML==6.0.1
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readme-renderer==26.0
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regex==2020.5.14
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requests==2.28.2
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requests-toolbelt==0.9.1
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responses==0.10.15
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rsa==4.9
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s3fs==0.4.2
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s3transfer==0.6.2
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scanpy==1.4.6
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scikit-learn==0.23.2
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scipy==1.10.1
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seaborn==0.10.1
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setuptools-scm==4.1.2
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sinfo==0.3.1
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six==1.15.0
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SQLAlchemy==1.3.19
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sshpubkeys==3.1.0
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statsmodels==0.12.0rc0
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stdlib-list==0.7.0
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swagger-ui-bundle==0.0.6
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tables==3.6.1
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threadpoolctl==2.1.0
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tiledb==0.21.4
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toml==0.10.1
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tomli==2.0.1
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tqdm==4.46.0
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twine==3.1.1
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typed-ast==1.4.1
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types-PyYAML==6.0.12.12
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types-requests==2.31.0.20240106
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types-setuptools==69.0.0.20240115
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typing-extensions==3.7.4.3
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umap-learn==0.4.6
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urllib3==1.25.9
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wcwidth==0.2.2
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webencodings==0.5.1
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websocket-client==0.57.0
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Flask-Compress>=1.4.0
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Flask-Cors>=3.0.9 # CVE-2020-25032
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Flask-RESTful>=0.3.6
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flask-server-timing>=0.1.2
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flask-talisman>=0.7.0
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flatbuffers>=1.11.0,<2.0.0 # cellxgene is not compatible with 2.0.0. Requires migration
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flatten-dict>=0.2.0
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fsspec>=0.4.4,<0.8.0
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gunicorn>=20.0.4
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h5py>=3.0.0
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matplotlib>=3.5.0
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numba>=0.51.2
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numpy>=1.17.5
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packaging>=20.0
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pandas>=1.0,!=1.1 # pandas 1.1 breaks tests, https://github.com/pandas-dev/pandas/issues/35446
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PyYAML>=5.4 # CVE-2020-14343
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scipy>=1.4
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requests>=2.22.0
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Werkzeug==2.2.3
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wrapt==1.12.1
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xmltodict==0.12.0
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zipp==3.1.0
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zope.event==5.0
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zope.interface==6.1
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