tiffslide: drop python 3.7

.github/workflows/run_pytests.yaml

@@ -27,8 +27,6 @@ jobs:
             python-version: "3.9"
           - os: ubuntu-latest
             python-version: "3.8"
-          - os: ubuntu-latest
-            python-version: "3.7"
     steps:
       - name: Checkout TiffSlide
         uses: actions/checkout@v3

.pre-commit-config.yaml

@@ -6,25 +6,25 @@ repos:
   - id: end-of-file-fixer
   - id: check-added-large-files
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.3.1
+  rev: v3.9.0
   hooks:
   - id: pyupgrade
-    args: [--py37-plus]
+    args: [--py38-plus]
 - repo: https://github.com/pycqa/isort
   rev: 5.12.0
   hooks:
   - id: isort
 - repo: https://github.com/psf/black
-  rev: 23.1.0
+  rev: 23.3.0
   hooks:
   - id: black
     language_version: python3
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: 'v1.0.1'
+  rev: 'v1.4.1'
   hooks:
   - id: mypy
     additional_dependencies: ["numpy"]
-    exclude: ^examples/
+    exclude: ^examples/|^tiffslide/tests/
 - repo: https://github.com/PyCQA/flake8
   rev: '6.0.0'
   hooks:
@@ -34,7 +34,7 @@ repos:
     language_version: python3
     exclude: "^(build|docs|setup.py)|tests[/]"
 - repo: https://github.com/PyCQA/bandit
-  rev: '1.7.4'
+  rev: '1.7.5'
   hooks:
   - id: bandit
     args: ["--ini", ".bandit", "-lll"]

setup.cfg

@@ -15,11 +15,11 @@ classifiers =
     License :: OSI Approved :: BSD License
     Programming Language :: Python
     Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
     Topic :: Scientific/Engineering
     Topic :: Scientific/Engineering :: Information Analysis
     Topic :: Scientific/Engineering :: Bio-Informatics
@@ -32,7 +32,7 @@ classifiers =
 
 [options]
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8
 install_requires =
     imagecodecs
     fsspec!=2022.11.0,!=2023.1.0

tiffslide/_compat.py

@@ -13,14 +13,10 @@
 from types import TracebackType
 from typing import TYPE_CHECKING
 from typing import Any
+from typing import Literal
 from typing import Mapping
 from typing import Sequence
 
-if sys.version_info >= (3, 8):
-    from typing import Literal
-else:
-    from typing_extensions import Literal
-
 import numpy as np
 import zarr
 from imagecodecs import __version__ as _imagecodecs_version

tiffslide/_kerchunk.py

@@ -13,11 +13,7 @@
 from io import StringIO
 from typing import TYPE_CHECKING
 from typing import Any
-
-if sys.version_info >= (3, 8):
-    from typing import TypedDict
-else:
-    from typing_extensions import TypedDict
+from typing import TypedDict
 
 import fsspec
 from imagecodecs.numcodecs import register_codecs

tiffslide/_types.py

@@ -6,17 +6,10 @@
 from typing import IO
 from typing import TYPE_CHECKING
 from typing import Any
+from typing import Protocol
+from typing import TypedDict
 from typing import Union
-
-if sys.version_info >= (3, 8):
-    from typing import Protocol
-    from typing import TypedDict
-    from typing import runtime_checkable
-
-else:
-    from typing_extensions import Protocol
-    from typing_extensions import TypedDict
-    from typing_extensions import runtime_checkable
+from typing import runtime_checkable
 
 if sys.version_info >= (3, 10):
     from typing import TypeAlias

tiffslide/_zarr.py

@@ -4,12 +4,10 @@
 from __future__ import annotations
 
 import json
-import sys
 from typing import TYPE_CHECKING
 from typing import Any
 from typing import Iterator
 from typing import Mapping
-from warnings import warn
 
 import numpy as np
 import zarr
@@ -19,8 +17,6 @@
 from zarr.storage import FSStore
 
 from tiffslide._compat import NotTiffFile
-from tiffslide._pycompat import REQUIRES_STORE_FIX
-from tiffslide._pycompat import py37_fix_store
 from tiffslide._types import Point3D
 from tiffslide._types import SeriesCompositionInfo
 from tiffslide._types import Size3D
@@ -42,12 +38,6 @@
     "get_zarr_selection",
 ]
 
-if REQUIRES_STORE_FIX and sys.version_info >= (3, 8):
-    warn(
-        "detected outdated tifffile version on `python>=3.8` with `zarr>=2.11.0`: "
-        "updating tifffile is recommended!"
-    )
-
 
 # --- zarr storage classes --------------------------------------------
 
@@ -120,8 +110,6 @@ def _get_series_zarr(
         zstore = FSStore(f"s{series_idx}", fs=obj)
     else:
         raise NotImplementedError(f"{type(obj).__name__} unsupported")
-    if REQUIRES_STORE_FIX:
-        zstore = py37_fix_store(zstore)
     return zstore  # type: ignore
 
 
@@ -302,7 +290,7 @@ def get_zarr_chunk_sizes(
     except AttributeError:
         raise RuntimeError("probably not supported with your tifffile version")
 
-    chunk_sizes = np.full(chunked, dtype=np.int64, fill_value=-1)
+    chunk_sizes: NDArray[np.int64] = np.full(chunked, dtype=np.int64, fill_value=-1)
 
     # _index = ""
     for indices in np.ndindex(*chunked):

tiffslide/tests/conftest.py

@@ -179,13 +179,10 @@ def gen_im(size_hw):
     mpp = 0.25
     mag = 40
     filename = "ASD"
-    if sys.version_info >= (3, 8):
-        resolution_kw = {
-            "resolution": (10000 / mpp, 10000 / mpp),
-            "resolutionunit": "CENTIMETER",
-        }
-    else:
-        resolution_kw = {"resolution": (10000 / mpp, 10000 / mpp, "CENTIMETER")}
+    resolution_kw = {
+        "resolution": (10000 / mpp, 10000 / mpp),
+        "resolutionunit": "CENTIMETER",
+    }
 
     # write to svs format
     with tifffile.TiffWriter(pth, bigtiff=True) as tif: