Increase ubuntu version & python version for azure CI (#2447)

* Increase ubuntu version & python version for azure CI

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Set minimum Python version to 3.8

* Remove compatibility code

Signed-off-by: zethson <lukas.heumos@posteo.net>

* Replace Literal typings

Signed-off-by: zethson <lukas.heumos@posteo.net>

---------

Signed-off-by: zethson <lukas.heumos@posteo.net>

.azure-pipelines.yml

@@ -11,11 +11,11 @@ variables:
 jobs:
 - job: PyTest
   pool:
-    vmImage: 'ubuntu-18.04'
+    vmImage: 'ubuntu-22.04'
   strategy:
     matrix:
-      Python37:
-        python.version: '3.7'
+      Python38:
+        python.version: '3.8'
       Python39: {}
       minimal_tests:
         TEST_EXTRA: 'test-min'

pyproject.toml

@@ -10,7 +10,7 @@ requires = [
 [project]
 name = "scanpy"
 description = "Single-Cell Analysis in Python."
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 license = {file = "LICENSE"}
 authors = [
     {name = "Alex Wolf"},
@@ -44,9 +44,9 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Visualization",
 ]
@@ -71,7 +71,6 @@ dependencies = [
     "packaging",
     "session-info",
     # for getting the stable version
-    "importlib_metadata>=0.7; python_version < '3.8'",
 ]
 dynamic = ["version"]
 
@@ -109,7 +108,6 @@ test-full = [
 doc = [
     "sphinx>=4.4,<5", # remove upper bound when theme supports dark mode
     "scanpydoc[typehints]>=0.7.7",
-    "typing_extensions; python_version < '3.8'",  # for `Literal`
     "myst-parser",
     "myst-nb",
     "sphinx-book-theme",
@@ -162,7 +160,7 @@ omit = ["*/tests/*"]
 
 [tool.black]
 line-length = 88
-target-version = ["py37"]
+target-version = ["py38"]
 skip-string-normalization = true
 exclude = """
 /build/.*

scanpy/_compat.py

@@ -1,33 +1,13 @@
 from packaging import version
 
-try:
-    from typing import Literal
-except ImportError:
-    try:
-        from typing_extensions import Literal
-    except ImportError:
-
-        class LiteralMeta(type):
-            def __getitem__(cls, values):
-                if not isinstance(values, tuple):
-                    values = (values,)
-                return type('Literal_', (Literal,), dict(__args__=values))
-
-        class Literal(metaclass=LiteralMeta):
-            pass
-
 
 def pkg_metadata(package):
-    try:
-        from importlib.metadata import metadata as m
-    except ImportError:  # < Python 3.8: Use backport module
-        from importlib_metadata import metadata as m
+    from importlib.metadata import metadata as m
+
     return m(package)
 
 
 def pkg_version(package):
-    try:
-        from importlib.metadata import version as v
-    except ImportError:  # < Python 3.8: Use backport module
-        from importlib_metadata import version as v
+    from importlib.metadata import version as v
+
     return version.parse(v(package))

scanpy/_settings.py

@@ -5,12 +5,11 @@
 from pathlib import Path
 from time import time
 from logging import getLevelName
-from typing import Any, Union, Optional, Iterable, TextIO
+from typing import Any, Union, Optional, Iterable, TextIO, Literal
 from typing import Tuple, List, ContextManager
 
 from . import logging
 from .logging import _set_log_level, _set_log_file, _RootLogger
-from ._compat import Literal
 
 _VERBOSITY_TO_LOGLEVEL = {
     'error': 'ERROR',

scanpy/_utils/__init__.py

@@ -13,7 +13,7 @@
 from collections import namedtuple
 from functools import partial, wraps
 from types import ModuleType, MethodType
-from typing import Union, Callable, Optional, Mapping, Any, Dict, Tuple
+from typing import Union, Callable, Optional, Mapping, Any, Dict, Tuple, Literal
 
 import numpy as np
 from numpy import random
@@ -23,7 +23,6 @@
 from packaging import version
 
 from .._settings import settings
-from .._compat import Literal
 from .. import logging as logg
 
 from .compute.is_constant import is_constant

scanpy/datasets/_datasets.py

@@ -1,14 +1,12 @@
 from pathlib import Path
-from typing import Optional
+from typing import Optional, Literal
 import warnings
 
 import numpy as np
 import pandas as pd
 import anndata as ad
-from packaging import version
 
 from .. import logging as logg, _utils
-from .._compat import Literal
 from .._settings import settings
 from ..readwrite import read, read_visium
 from ._utils import check_datasetdir_exists, filter_oldformatwarning

scanpy/experimental/pp/_highly_variable_genes.py

@@ -1,6 +1,6 @@
 from multiprocessing.sharedctypes import Value
 import warnings
-from typing import Optional
+from typing import Optional, Literal
 
 import numpy as np
 import pandas as pd
@@ -12,7 +12,6 @@
 from scanpy._settings import settings, Verbosity
 from scanpy._utils import check_nonnegative_integers, view_to_actual
 from scanpy.get import _get_obs_rep
-from scanpy._compat import Literal
 from scanpy._utils import _doc_params
 from scanpy.preprocessing._utils import _get_mean_var
 from scanpy.preprocessing._distributed import materialize_as_ndarray

scanpy/external/pp/_dca.py

@@ -1,9 +1,8 @@
 from types import MappingProxyType
-from typing import Optional, Sequence, Union, Mapping, Any
+from typing import Optional, Sequence, Union, Mapping, Any, Literal
 
 from anndata import AnnData
 
-from ..._compat import Literal
 from ..._utils import AnyRandom
 
 

scanpy/external/pp/_magic.py

@@ -1,14 +1,13 @@
 """\
 Denoise high-dimensional data using MAGIC
 """
-from typing import Union, Sequence, Optional
+from typing import Union, Sequence, Optional, Literal
 
 from anndata import AnnData
 from packaging import version
 
 from ... import logging as logg
 from ..._settings import settings
-from ..._compat import Literal
 from ..._utils import AnyRandom
 
 

scanpy/external/pp/_mnn_correct.py

@@ -1,11 +1,10 @@
-from typing import Union, Collection, Optional, Any, Sequence, Tuple, List
+from typing import Union, Collection, Optional, Any, Sequence, Tuple, List, Literal
 
 import numpy as np
 import pandas as pd
 from anndata import AnnData
 
 from ..._settings import settings
-from ..._compat import Literal
 
 
 def mnn_correct(

scanpy/external/tl/_phate.py

@@ -1,12 +1,11 @@
 """\
 Embed high-dimensional data using PHATE
 """
-from typing import Optional, Union
+from typing import Optional, Union, Literal
 
 from anndata import AnnData
 
 from ..._settings import settings
-from ..._compat import Literal
 from ... import logging as logg
 from ..._utils import AnyRandom
 

scanpy/external/tl/_phenograph.py

@@ -1,14 +1,13 @@
 """\
 Perform clustering using PhenoGraph
 """
-from typing import Union, Tuple, Optional, Type, Any
+from typing import Union, Tuple, Optional, Type, Any, Literal
 
 import numpy as np
 import pandas as pd
 from anndata import AnnData
 from scipy.sparse import spmatrix
 
-from ..._compat import Literal
 from ...tools._leiden import MutableVertexPartition
 from ... import logging as logg
 

scanpy/external/tl/_sam.py

@@ -1,12 +1,11 @@
 """\
 Run the Self-Assembling Manifold algorithm
 """
-from typing import Optional, Union, Tuple, Any
+from typing import Optional, Union, Tuple, Any, Literal
 
 from anndata import AnnData
 
 from ... import logging as logg
-from ..._compat import Literal
 
 try:
     from samalg import SAM

scanpy/external/tl/_trimap.py

@@ -1,13 +1,12 @@
 """\
 Embed high-dimensional data using TriMap
 """
-from typing import Optional, Union
+from typing import Optional, Union, Literal
 
 from anndata import AnnData
 import scipy.sparse as scp
 
 from ..._settings import settings
-from ..._compat import Literal
 from ... import logging as logg
 
 

scanpy/get/get.py

@@ -1,12 +1,11 @@
 """This module contains helper functions for accessing data."""
-from typing import Optional, Iterable, Tuple, Union, List
+from typing import Optional, Iterable, Tuple, Union, List, Literal
 
 import numpy as np
 import pandas as pd
 from scipy.sparse import spmatrix
 
 from anndata import AnnData
-from .._compat import Literal
 
 # --------------------------------------------------------------------------------
 # Plotting data helpers

scanpy/neighbors/__init__.py

@@ -1,5 +1,15 @@
 from types import MappingProxyType
-from typing import Union, Optional, Any, Mapping, Callable, NamedTuple, Generator, Tuple
+from typing import (
+    Union,
+    Optional,
+    Any,
+    Mapping,
+    Callable,
+    NamedTuple,
+    Generator,
+    Tuple,
+    Literal,
+)
 import warnings
 
 import numpy as np
@@ -11,7 +21,6 @@
 from .. import logging as logg
 from .. import _utils
 from .._utils import _doc_params, AnyRandom, NeighborsView
-from .._compat import Literal
 from ..tools._utils import _choose_representation, doc_use_rep, doc_n_pcs
 from .. import settings
 

scanpy/plotting/_anndata.py

@@ -3,7 +3,7 @@
 import collections.abc as cabc
 from itertools import product
 from collections import OrderedDict
-from typing import Optional, Union, Mapping  # Special
+from typing import Optional, Union, Mapping, Literal  # Special
 from typing import Sequence, Collection, Iterable  # ABCs
 from typing import Tuple, List  # Classes
 
@@ -24,7 +24,6 @@
 from .. import logging as logg
 from .._settings import settings
 from .._utils import sanitize_anndata, _doc_params, _check_use_raw
-from .._compat import Literal
 from . import _utils
 from ._utils import scatter_base, scatter_group, setup_axes, check_colornorm
 from ._utils import ColorLike, _FontWeight, _FontSize

scanpy/plotting/_baseplot_class.py

@@ -2,7 +2,7 @@
 """
 import collections.abc as cabc
 from collections import namedtuple
-from typing import Optional, Union, Mapping  # Special
+from typing import Optional, Union, Mapping, Literal  # Special
 from typing import Sequence, Iterable  # ABCs
 from typing import Tuple  # Classes
 
@@ -15,7 +15,6 @@
 from warnings import warn
 
 from .. import logging as logg
-from .._compat import Literal
 from ._utils import make_grid_spec, check_colornorm
 from ._utils import ColorLike, _AxesSubplot
 from ._anndata import _plot_dendrogram, _get_dendrogram_key, _prepare_dataframe

scanpy/plotting/_dotplot.py

@@ -1,4 +1,4 @@
-from typing import Optional, Union, Mapping  # Special
+from typing import Optional, Union, Mapping, Literal  # Special
 from typing import Sequence  # ABCs
 from typing import Tuple  # Classes
 
@@ -11,7 +11,6 @@
 
 from .. import logging as logg
 from .._utils import _doc_params
-from .._compat import Literal
 from ._utils import make_grid_spec, fix_kwds, check_colornorm
 from ._utils import ColorLike, _AxesSubplot
 from ._utils import savefig_or_show

scanpy/plotting/_matrixplot.py

@@ -1,4 +1,4 @@
-from typing import Optional, Union, Mapping  # Special
+from typing import Optional, Union, Mapping, Literal  # Special
 from typing import Sequence  # ABCs
 from typing import Tuple  # Classes
 
@@ -11,7 +11,6 @@
 
 from .. import logging as logg
 from .._utils import _doc_params
-from .._compat import Literal
 from ._utils import fix_kwds, check_colornorm
 from ._utils import ColorLike, _AxesSubplot
 from ._utils import savefig_or_show

scanpy/plotting/_stacked_violin.py

@@ -1,4 +1,4 @@
-from typing import Optional, Union, Mapping  # Special
+from typing import Optional, Union, Mapping, Literal  # Special
 from typing import Sequence  # ABCs
 from typing import Tuple  # Classes
 
@@ -9,7 +9,6 @@
 from matplotlib.colors import is_color_like, Normalize
 from .. import logging as logg
 from .._utils import _doc_params
-from .._compat import Literal
 from ._utils import make_grid_spec, check_colornorm
 from ._utils import _AxesSubplot
 from ._utils import savefig_or_show

scanpy/plotting/_tools/__init__.py

@@ -9,11 +9,10 @@
 from matplotlib import pyplot as pl
 from matplotlib import rcParams, cm
 from anndata import AnnData
-from typing import Union, Optional, List, Sequence, Iterable, Mapping
+from typing import Union, Optional, List, Sequence, Iterable, Mapping, Literal
 
 from .._utils import savefig_or_show
 from ..._utils import _doc_params, sanitize_anndata, subsample
-from ..._compat import Literal
 from ... import logging as logg
 from .._anndata import ranking
 from .._utils import timeseries, timeseries_subplot, timeseries_as_heatmap