chore: upgrade backend dependencies (#2641)

chore: upgrade backend dependencies (#2641)

server/app/app.py

@@ -48,12 +48,12 @@ def _cache_control(always, **cache_kwargs):
 
 
 def cache_control(**cache_kwargs):
-    """ config driven """
+    """config driven"""
     return _cache_control(False, **cache_kwargs)
 
 
 def cache_control_always(**cache_kwargs):
-    """ always generate headers, regardless of the config """
+    """always generate headers, regardless of the config"""
     return _cache_control(True, **cache_kwargs)
 
 
@@ -228,7 +228,7 @@ def get_api_dataroot_resources(bp_dataroot):
 class Server:
     @staticmethod
     def _before_adding_routes(app, app_config):
-        """ will be called before routes are added, during __init__.  Subclass protocol """
+        """will be called before routes are added, during __init__.  Subclass protocol"""
         pass
 
     def __init__(self, app_config):

server/app/session.py

@@ -6,7 +6,7 @@ CXGUID = "cxguid"
 
 
 def get_user_id(session: SessionMixin) -> str:
-    """ Gets a session-persistent user id. Creates one in the Flask session if non-extant """
+    """Gets a session-persistent user id. Creates one in the Flask session if non-extant"""
     if CXGUID not in session:
         session[CXGUID] = uuid4().hex
         session.permanent = True

server/cli/annotate.py

@@ -26,9 +26,7 @@ def annotate_args(func):
 
 
 @sort_options
-@click.command(
-    options_metavar="<options>"
-)
+@click.command(options_metavar="<options>")
 @click.argument(
     "input_h5ad_file",
     type=click.Path(exists=True, dir_okay=False, readable=True),
@@ -51,8 +49,8 @@ def annotate_args(func):
     "--output-h5ad-file",
     default="",
     help="The output H5AD file that will contain the generated annotation values. If this option is not provided, "
-         "the input file will be overwritten to include the new annotations; in this case you must specify "
-         "--overwrite.",
+    "the input file will be overwritten to include the new annotations; in this case you must specify "
+    "--overwrite.",
     metavar="<filename>",
 )
 @click.option(
@@ -60,7 +58,7 @@ def annotate_args(func):
     default=False,
     is_flag=True,
     help="Allow overwriting of the specified H5AD output file, if it exists. For safety, you must specify this "
-         "flag if the specified output file already exists or if the --output-h5ad-file option is not provided.",
+    "flag if the specified output file already exists or if the --output-h5ad-file option is not provided.",
     show_default=True,
 )
 @click.option(

server/common/annotations/local_file_csv.py

@@ -145,7 +145,7 @@ class AnnotationsLocalFile(Annotations):
     def write_gene_sets(self, gene_sets, tid, data_adaptor):
         self.check_gene_sets_save_enabled()  # raises
 
-        if type(tid) != int or tid < 0:
+        if type(tid) is not int or tid < 0:
             raise ValueError("tid must be a positive integer")
 
         # may raise
@@ -175,7 +175,7 @@ class AnnotationsLocalFile(Annotations):
 
             # update the cache
             self.last_geneset_fname = fname
-            self.last_geneset = gene_sets if type(gene_sets) == dict else {g["geneset_name"]: g for g in gene_sets}
+            self.last_geneset = gene_sets if isinstance(gene_sets, dict) else {g["geneset_name"]: g for g in gene_sets}
 
     def _get_userdata_idhash(self, data_adaptor):
         """

server/common/compute/diffexp_generic.py

@@ -56,7 +56,7 @@ def diffexp_ttest_from_mean_var(meanA, varA, nA, meanB, varB, nB, top_n, diffexp
 
     # degrees of freedom for Welch's t-test
     with np.errstate(divide="ignore", invalid="ignore"):
-        dof = sum_vn ** 2 / (vnA ** 2 / (nA - 1) + vnB ** 2 / (nB - 1))
+        dof = sum_vn**2 / (vnA**2 / (nA - 1) + vnB**2 / (nB - 1))
     dof[np.isnan(dof)] = 1
 
     # Welch's t-test score calculation

server/common/compute/estimate_distribution.py

@@ -97,7 +97,7 @@ def estimate_approximate_distribution(X) -> XApproximateDistribution:
     if Xdata.size > CHUNKSIZE:
         min_val = max_val = Xdata[0]
         with concurrent.futures.ThreadPoolExecutor() as tp:
-            for (_min, _max) in tp.map(min_max, [Xdata[i : i + CHUNKSIZE] for i in range(0, Xdata.size, CHUNKSIZE)]):
+            for _min, _max in tp.map(min_max, [Xdata[i : i + CHUNKSIZE] for i in range(0, Xdata.size, CHUNKSIZE)]):
                 min_val = min(_min, min_val)
                 max_val = max(_max, max_val)
 

server/common/config/__init__.py

@@ -1,2 +1,2 @@
 DEFAULT_SERVER_PORT = 5005
-BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20  # 100MB
+BIG_FILE_SIZE_THRESHOLD = 100 * 2**20  # 100MB

server/common/config/app_config.py

@@ -19,7 +19,6 @@ class AppConfig(object):
     """
 
     def __init__(self):
-
         # the default configuration (see default_config.py)
         # TODO @madison -- if we always read from the default config (hard coded path) can we set those values as
         #  defaults within the config class?

server/common/config/base_config.py

@@ -50,7 +50,7 @@ class BaseConfig(object):
                     f"Invalid type for attribute: {attrname}, expected types ({tnames}), got {type(val).__name__}"
                 )
         else:
-            if type(val) != vtype:
+            if type(val) is not vtype:
                 raise ConfigurationError(
                     f"Invalid type for attribute: {attrname}, "
                     f"expected type {vtype.__name__}, got {type(val).__name__}"
@@ -70,7 +70,7 @@ class BaseConfig(object):
             if not hasattr(self, key):
                 raise ConfigurationError(f"unknown config parameter {key}.")
             try:
-                if type(value) == tuple:
+                if type(value) is tuple:
                     # convert tuple values to list values
                     value = list(value)
                 setattr(self, key, value)

server/common/config/external_config.py

@@ -29,7 +29,7 @@ class ExternalConfig(BaseConfig):
             if name is None:
                 raise ConfigurationError("environment: 'name' is missing")
             required = envdict.get("required", False)
-            if type(required) != bool:
+            if type(required) is not bool:
                 raise ConfigurationError("environment: 'required' must be a bool")
             path = envdict.get("path")
             if path is None:

server/common/fbs/matrix.py

@@ -19,7 +19,7 @@ import server.common.fbs.NetEncoding.Uint32Array as Uint32Array
 
 # Serialization helper
 def serialize_column(builder, typed_arr):
-    """ Serialize NetEncoding.Column """
+    """Serialize NetEncoding.Column"""
 
     (u_type, u_value) = typed_arr
     Column.ColumnStart(builder)
@@ -30,7 +30,7 @@ def serialize_column(builder, typed_arr):
 
 # Serialization helper
 def serialize_matrix(builder, n_rows, n_cols, columns, col_idx):
-    """ Serialize NetEncoding.Matrix """
+    """Serialize NetEncoding.Matrix"""
 
     Matrix.MatrixStart(builder)
     Matrix.MatrixAddNRows(builder, n_rows)

server/common/genesets.py

@@ -136,7 +136,7 @@ def write_gene_sets_tidycsv(f, genesets):
 
 
 def summarizeQueryHash(raw_query):
-    """ generate a cache key (hash) from the raw query string """
+    """generate a cache key (hash) from the raw query string"""
     return hashlib.sha1(raw_query).hexdigest()
 
 
@@ -187,7 +187,7 @@ def validate_gene_sets(genesets, var_names, context=None):
     # 1. check gene set character set and format
     illegal_name = re.compile(r"^\s|  |[\u0000-\u001F\u007F-\uFFFF]|\s$")
     for name in geneset_names:
-        if type(name) != str or len(name) == 0:
+        if type(name) is not str or len(name) == 0:
             raise KeyError("Gene set names must be non-null string.")
         if illegal_name.search(name):
             messagefn(

server/common/rest.py

@@ -6,7 +6,7 @@ import zlib
 import json
 
 from flask import make_response, jsonify, current_app, abort
-from werkzeug.urls import url_unquote
+from urllib.parse import unquote
 
 from server.common.config.client_config import get_client_config
 from server.common.constants import Axis, DiffExpMode, JSON_NaN_to_num_warning_msg
@@ -64,22 +64,22 @@ def _query_parameter_to_filter(args):
             axis, name = key.split(":")
             if axis not in ("obs", "var"):
                 raise FilterError("unknown filter axis")
-            name = url_unquote(name)
+            name = unquote(name)
             current = filters[axis].setdefault(name, {"name": name})
 
             val_split = value.split(",")
             if len(val_split) == 1:
                 if "min" in current or "max" in current:
                     raise FilterError("do not mix range and value filters")
-                value = url_unquote(value)
+                value = unquote(value)
                 values = current.setdefault("values", [])
                 values.append(value)
 
             elif len(val_split) == 2:
                 if len(current) > 1:
                     raise FilterError("duplicate range specification")
-                min = url_unquote(val_split[0])
-                max = url_unquote(val_split[1])
+                min = unquote(val_split[0])
+                max = unquote(val_split[1])
                 if min != "*":
                     current["min"] = float(min)
                 if max != "*":
@@ -379,7 +379,7 @@ def summarize_var_helper(request, data_adaptor, key, raw_query):
             HTTPStatus.OK,
             {"Content-Type": "application/octet-stream"},
         )
-    except (ValueError) as e:
+    except ValueError as e:
         return abort(HTTPStatus.NOT_FOUND, description=str(e))
     except (UnsupportedSummaryMethod, FilterError) as e:
         return abort(HTTPStatus.BAD_REQUEST, description=str(e))

server/common/utils/utils.py

@@ -8,7 +8,7 @@ import socket
 from urllib.parse import urlsplit, urljoin
 
 import numpy as np
-from flask import json
+import json
 
 from server.common.errors import ConfigurationError
 
@@ -100,6 +100,7 @@ def custom_format_warning(msg, *args, **kwargs):
 def jsonify_strict(data):
     return StrictJSONEncoder().encode(data)
 
+
 def import_plugins(plugin_module):
     """
     Load optional plugin modules from server.common.plugins

server/data_anndata/anndata_adaptor.py

@@ -92,7 +92,7 @@ class AnndataAdaptor(DataAdaptor):
         """
         self.original_obs_index = self.data.obs.index
 
-        for (ax_name, var_name) in ((Axis.OBS, "obs"), (Axis.VAR, "var")):
+        for ax_name, var_name in ((Axis.OBS, "obs"), (Axis.VAR, "var")):
             config_name = f"single_dataset__{var_name}_names"
             parameter_name = f"{var_name}_names"
             name = getattr(self.server_config, config_name)
@@ -175,10 +175,11 @@ class AnndataAdaptor(DataAdaptor):
             raise DatasetAccessError("Out of memory - file is too large for available memory.")
         except Exception:
             import traceback
+
             message = (
                 "File not found or is inaccessible. File must be an .h5ad object. "
                 "Please check your input and try again."
-                )
+            )
             if self.server_config.app__verbose:
                 message += f"\n{traceback.format_exc()}"
             raise DatasetAccessError(message)
@@ -218,7 +219,7 @@ class AnndataAdaptor(DataAdaptor):
         * with shape (n_obs, >= 2)
         * with all values finite or NaN (no +Inf or -Inf)
         """
-        is_valid = type(arr) == np.ndarray and arr.dtype.kind in "fiu"
+        is_valid = type(arr) is np.ndarray and arr.dtype.kind in "fiu"
         is_valid = is_valid and arr.shape[0] == self.data.n_obs and arr.shape[1] >= 2
         is_valid = is_valid and not np.any(np.isinf(arr)) and not np.all(np.isnan(arr))
         return is_valid
@@ -242,8 +243,10 @@ class AnndataAdaptor(DataAdaptor):
             )
         if self.data.X.dtype < np.float32:
             if self.data.isbacked:
-                raise DatasetAccessError(f"Data matrix in {self.data.X.dtype} format is not supported in backed mode."
-                                         " Please reload without --backed, or convert matrix to float32")
+                raise DatasetAccessError(
+                    f"Data matrix in {self.data.X.dtype} format is not supported in backed mode."
+                    " Please reload without --backed, or convert matrix to float32"
+                )
             warnings.warn(
                 f"Anndata data matrix is in unsupported {self.data.X.dtype} format -- will be cast to float32"
             )
@@ -299,7 +302,7 @@ class AnndataAdaptor(DataAdaptor):
         layouts = self.dataset_config.embeddings__names
 
         if layouts is None or len(layouts) == 0:
-            layouts = [key[2:] for key in self.data.obsm_keys() if type(key) == str and key.startswith("X_")]
+            layouts = [key[2:] for key in self.data.obsm_keys() if type(key) is str and key.startswith("X_")]
 
         # remove invalid layouts
         valid_layouts = []

server/data_common/data_adaptor.py

@@ -154,7 +154,7 @@ class DataAdaptor(metaclass=ABCMeta):
         parameters.update(self.parameters)
 
     def _index_filter_to_mask(self, filter, count):
-        mask = np.zeros((count,), dtype=np.bool)
+        mask = np.zeros((count,), dtype="bool")
         for i in filter:
             if isinstance(i, list):
                 mask[i[0] : i[1]] = True
@@ -163,7 +163,7 @@ class DataAdaptor(metaclass=ABCMeta):
         return mask
 
     def _axis_filter_to_mask(self, axis, filter, count):
-        mask = np.ones((count,), dtype=np.bool)
+        mask = np.ones((count,), dtype="bool")
         if "index" in filter:
             mask = np.logical_and(mask, self._index_filter_to_mask(filter["index"], count))
         if "annotation_value" in filter:
@@ -172,7 +172,7 @@ class DataAdaptor(metaclass=ABCMeta):
         return mask
 
     def _annotation_filter_to_mask(self, axis, filter, count):
-        mask = np.ones((count,), dtype=np.bool)
+        mask = np.ones((count,), dtype="bool")
         for v in filter:
             name = v["name"]
             if axis == Axis.VAR:

server/data_common/matrix_loader.py

@@ -12,7 +12,7 @@ class MatrixDataType(Enum):
 
 class MatrixDataLoader(object):
     def __init__(self, location, matrix_data_type=None, app_config=None):
-        """ location can be a string or DataLocator """
+        """location can be a string or DataLocator"""
         region_name = None if app_config is None else app_config.server_config.data_locator__s3__region_name
         self.location = DataLocator(location, region_name=region_name)
         if not self.location.exists():

server/requirements-annotate.txt

@@ -1,2 +1,2 @@
-mlflow
+mlflow==1.27.0
 scanpy

server/requirements-dev.txt

@@ -5,6 +5,6 @@ parameterized>=0.7.0
 pytest>=3.6.3
 python-jose>=3.2.0
 twine>=1.12.1
+aiohttp>=3.9.1
 -r requirements.txt
 -r requirements-prepare.txt
--r requirements-annotate.txt

server/requirements.txt

@@ -1,25 +1,22 @@
-# NOTE: If you update 'anndata' min version, also update the 'anndata_version'
-# matrix value in .github/workflows/compatibility_tests.yml
-anndata>=0.7.6 # we need to_memory(), added in 0.7.6
-boto3>=1.12.18
-click>=7.1.2
-Flask>=1.0.2,<2.3.0
-Flask-Compress>=1.4.0
-Flask-Cors>=3.0.9  # CVE-2020-25032
-Flask-RESTful>=0.3.6
-flask-server-timing>=0.1.2
-flask-talisman>=0.7.0
-flatbuffers>=1.11.0,<2.0.0 # cellxgene is not compatible with 2.0.0. Requires migration
-flatten-dict>=0.2.0
-fsspec>=0.4.4,<0.8.0
-gunicorn>=20.0.4
-h5py>=3.0.0
-numba>=0.51.2
-numpy>=1.17.5,<=1.22
-packaging>=20.0
-pandas>=1.0,!=1.1  # pandas 1.1 breaks tests, https://github.com/pandas-dev/pandas/issues/35446
-PyYAML>=5.4  # CVE-2020-14343
-scipy>=1.4
-requests>=2.22.0
+anndata==0.10.3
+boto3==1.29.5
+click==8.1.7
+Flask==3.0.0
+Flask-Compress==1.14
+Flask-Cors==4.0.0
+Flask-RESTful==0.3.10
+flask-server-timing==0.1.2
+flask-talisman==1.1.0
+flatbuffers==1.12
+flatten-dict==0.4.2
+fsspec==2023.10.0
+gunicorn==21.2.0
+h5py==3.10.0
+numba==0.58.1
+numpy==1.26.2
+packaging==23.2
+pandas<2.0.0
+PyYAML==6.0.1
+requests==2.31.0
 s3fs==0.4.2
-# Werkzeug>=2.2.0,<3.0.0 # our version of flask doesn't support 3.0.0
+scipy==1.11.4