Bump min Python version to 3.8; CI update

.github/workflows/conda.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10"]
         os: ["ubuntu-latest", "macos-latest"]
 
     steps:
@@ -27,7 +27,7 @@ jobs:
           miniforge-variant: Mambaforge
           miniforge-version: latest
           channels: conda-forge,bioconda
-          channel-priority: strict 
+          channel-priority: strict
           python-version: ${{ matrix.python-version }}
 
       - name: install conda build

.github/workflows/pythonpublish.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v1
         with:
-          python-version: "3.8"
+          python-version: "3.9"
       - name: Install dependencies
         run: |
           # https://github.com/pypa/pip/issues/11110

.github/workflows/test.yml

@@ -16,10 +16,11 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { python-version: 3.7, os: ubuntu-latest }
           - { python-version: 3.8, os: ubuntu-latest }
           - { python-version: 3.9, os: ubuntu-latest }
           - { python-version: "3.10", os: ubuntu-latest }
+          # as of 2023-02-17 not yet supported by numba (ETA 2023-03, https://github.com/numba/numba/issues/8304)
+          # - { python-version: "3.11", os: ubuntu-latest }
           #           - { python-version: 3.9, os: macos-latest }
           - { python-version: 3.9, os: windows-latest }
 
@@ -61,9 +62,6 @@ jobs:
         run: |
           pip install .[test]
 
-      - name: Check black formatting
-        run: |
-          black --check .
       - name: Test with pytest (Linux)
         if: matrix.config.os == 'ubuntu-latest'
         run: pytest

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/ambv/black
-    rev: 22.3.0
+    rev: 23.1.0
     hooks:
       - id: black
         language_version: python3.10

pyproject.toml

@@ -23,7 +23,7 @@ classifiers = [
     'Programming Language :: Python :: 3',
     'Programming Language :: R'
 ]
-requires-python = '>= 3.7'
+requires-python = '>= 3.8'
 dependencies = [
     'anndata>=0.7.6',
     'scanpy>=1.6.0',

scirpy/_compat.py

@@ -1,33 +1,18 @@
 from packaging import version
 
 try:
-    from typing import Literal
+    pass
 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
+    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))

scirpy/io/_io.py

@@ -28,7 +28,7 @@
     _check_upgrade_schema,
     _read_airr_rearrangement_df,
 )
-from .._compat import Literal
+from typing import Literal
 from airr import RearrangementSchema
 import itertools
 import re

scirpy/io/_tracerlib/core.py

@@ -45,7 +45,6 @@ def __init__(
         receptor=None,
         loci=None,
     ):
-
         self.name = cell_name
         self.bgcolor = None
         self.recombinants = self._process_recombinants(recombinants, receptor, loci)
@@ -170,7 +169,6 @@ def html_style_label_dna(self, receptor, loci, colours):
         # return(self.name)
 
     def html_style_label_for_circles(self, receptor, loci, colours):
-
         # colours = {'A': {'productive': '#E41A1C', 'non-productive': "#ff8c8e"},
         #           'B': {'productive': '#377eb8', 'non-productive': "#95c1e5"},
         #           'G': {'productive': '#4daf4a', 'non-productive': "#aee5ac"},

scirpy/ir_dist/__init__.py

@@ -1,7 +1,7 @@
 """Compute distances between immune receptor sequences"""
 from anndata import AnnData
 from typing import Optional, Sequence, Union
-from .._compat import Literal
+from typing import Literal
 import numpy as np
 from scanpy import logging
 from ..util import _is_na, deprecated

scirpy/ir_dist/_clonotype_neighbors.py

@@ -2,7 +2,7 @@
 from typing import Dict, Mapping, Tuple, Union, Sequence, Optional
 from anndata import AnnData
 from scanpy import logging
-from .._compat import Literal
+from typing import Literal
 import numpy as np
 import scipy.sparse as sp
 import itertools

scirpy/ir_dist/_util.py

@@ -4,7 +4,7 @@
 import scipy.sparse as sp
 from scipy.sparse.coo import coo_matrix
 from scipy.sparse.csr import csr_matrix
-from .._compat import Literal
+from typing import Literal
 import warnings
 from functools import reduce
 from operator import mul

scirpy/ir_dist/metrics.py

@@ -384,7 +384,6 @@ def _compute_block(self, seqs1, seqs2, origin):
 
         result = []
         for (row, s1), (col, s2) in coord_iterator:
-
             # require identical length of sequences
             if len(s1) != len(s2):
                 continue

scirpy/pl/_cdr_convergence.py

@@ -1,5 +1,5 @@
 import matplotlib.pyplot as plt
-from .._compat import Literal
+from typing import Literal
 from anndata import AnnData
 import pandas as pd
 from .. import tl

scirpy/pl/_clonal_expansion.py

@@ -2,7 +2,7 @@
 from anndata import AnnData
 from . import base
 from typing import Union
-from .._compat import Literal
+from typing import Literal
 from ..io._util import _check_upgrade_schema
 
 

scirpy/pl/_clonotype_imbalance.py

@@ -4,7 +4,7 @@
 import seaborn as sns
 import scanpy as sc
 from typing import Union
-from .._compat import Literal
+from typing import Literal
 from .. import tl
 from .base import volcano
 from ..io._util import _check_upgrade_schema

scirpy/pl/_clonotype_modularity.py

@@ -1,6 +1,6 @@
 from numpy.core.fromnumeric import amax
 from .styling import _init_ax, apply_style_to_axes
-from .._compat import Literal
+from typing import Literal
 from ._clonotypes import _plot_size_legend
 from typing import Tuple, Union, Optional, Sequence
 import numpy as np

scirpy/pl/_diversity.py

@@ -1,5 +1,5 @@
 from anndata import AnnData
-from .._compat import Literal
+from typing import Literal
 from . import base
 from .. import tl
 import numpy as np

scirpy/pl/_group_abundance.py

@@ -1,5 +1,5 @@
 import matplotlib.pyplot as plt
-from .._compat import Literal
+from typing import Literal
 from anndata import AnnData
 from .. import tl
 from . import base

scirpy/pl/_spectratype.py

@@ -1,6 +1,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
-from .._compat import Literal
+from typing import Literal
 from anndata import AnnData
 from .. import tl
 from . import base

scirpy/pl/base.py

@@ -1,6 +1,6 @@
 """Base plotting functions"""
 from typing import Union, Sequence, Tuple, Optional
-from .._compat import Literal
+from typing import Literal
 import matplotlib.pyplot as plt
 import pandas as pd
 import numpy as np

scirpy/pl/styling.py

@@ -1,4 +1,4 @@
-from .._compat import Literal
+from typing import Literal
 import matplotlib.pyplot as plt
 from typing import Union, Sequence, Dict
 from scanpy.plotting._utils import (

scirpy/tl/_clonal_expansion.py

@@ -2,7 +2,7 @@
 from ..util import _is_na, _normalize_counts
 import numpy as np
 from typing import Union, List
-from .._compat import Literal
+from typing import Literal
 import pandas as pd
 from ..io._util import _check_upgrade_schema
 

scirpy/tl/_clonotype_imbalance.py

@@ -114,12 +114,8 @@ def clonotype_imbalance(
     for hue, cases, controls, ncase, ncontrol in case_control_groups:
         if hue is None:
             hue = "All"
-        tdf1 = clonotype_presence.loc[
-            cases,
-        ]
-        tdf2 = clonotype_presence.loc[
-            controls,
-        ]
+        tdf1 = clonotype_presence.loc[cases,]
+        tdf2 = clonotype_presence.loc[controls,]
         suspects = set(
             tdf1.loc[:, tdf1.sum() > 0].columns.values.tolist()
             + tdf2.loc[:, tdf2.sum() > 0].columns.values.tolist()
@@ -156,7 +152,6 @@ def clonotype_imbalance(
     clt_stats = clt_stats.sort_values(by="pValue")
 
     if inplace:
-
         # Store calculated data
         adata.uns[key_added] = {"abundance": clt_freq, "pvalues": clt_stats}
         return

scirpy/tl/_clonotype_modularity.py

@@ -4,7 +4,7 @@
 import numpy as np
 from ..util.graph import _get_igraph_from_adjacency
 from ..util._negative_binomial import fit_nbinom
-from .._compat import Literal
+from typing import Literal
 import scipy.stats
 import scipy.sparse
 from statsmodels.stats.multitest import fdrcorrection

scirpy/tl/_clonotypes.py

@@ -9,7 +9,7 @@
 from scanpy import logging
 import scipy.sparse as sp
 
-from .._compat import Literal
+from typing import Literal
 from ..pp import ir_dist
 from ..ir_dist import MetricType, _get_metric_key
 from ..ir_dist._clonotype_neighbors import ClonotypeNeighbors

scirpy/tl/_group_abundance.py

@@ -4,7 +4,7 @@
 import pandas as pd
 from ..util import _is_na, _normalize_counts
 from typing import Sequence
-from .._compat import Literal
+from typing import Literal
 from ..io._util import _check_upgrade_schema
 
 

scirpy/tl/_ir_query.py

@@ -1,6 +1,6 @@
 from typing import Counter, Optional, Union, Sequence
 
-from .._compat import Literal
+from typing import Literal
 from anndata import AnnData
 import pandas as pd
 import itertools

scirpy/tl/_repertoire_overlap.py

@@ -90,7 +90,6 @@ def repertoire_overlap(
     linkage = sc_hierarchy.linkage(distM)
 
     if inplace:
-
         # Store calculated data
         adata.uns[added_key] = {
             "weighted": df,

scirpy/util/graph/__init__.py

@@ -2,7 +2,7 @@
 import igraph as ig
 import numpy as np
 from scipy import sparse
-from ..._compat import Literal
+from typing import Literal
 from scipy.sparse import spmatrix, csr_matrix
 import itertools
 from ._component_layout import layout_components

scirpy/util/graph/_component_layout.py

@@ -1,7 +1,7 @@
 from typing import Optional
 import igraph as ig
 import numpy as np
-from ..._compat import Literal
+from typing import Literal
 from ._fr_size_aware_layout import layout_fr_size_aware
 
 

scirpy/util/graph/_fr_size_aware_layout.py

@@ -218,7 +218,6 @@ def _is_within_bbox(points, origin, scale):
 def _get_temperature_decay(
     initial_temperature, total_iterations, mode="quadratic", eps=1e-9
 ):
-
     x = np.linspace(0.0, 1.0, total_iterations)
     if mode == "quadratic":
         y = (x - 1.0) ** 2 + eps
@@ -336,7 +335,6 @@ def _get_unique_nodes(edge_list):
 
 
 def _edge_list_to_adjacency_matrix(edge_list, edge_weights=None):
-
     sources = [s for (s, _) in edge_list]
     targets = [t for (_, t) in edge_list]
     if edge_weights: