[v1] Update dependencies to latest (#567)

* Update dependencies to latest versions

* Update linter type-checking code to 'TC' in pyproject.toml

https://astral.sh/blog/ruff-v0.8.0#new-error-codes-for-flake8-type-checking-rules

* Refactor: Move Zarr codec imports to top-level

* disable safety in CI (temporary)

* Refactor: Replace Zarr codec imports with numcodecs equivalents

* Refactor: Remove unused numcodecs imports and related methods

* pin zarr due to zarr 3.0.9 bug

Author: tasansal

.github/workflows/tests.yml

@@ -13,7 +13,7 @@ jobs:
       matrix:
         include:
           - { python: "3.13", os: "ubuntu-latest", session: "pre-commit" }
-          - { python: "3.13", os: "ubuntu-latest", session: "safety" }
+          #          - { python: "3.13", os: "ubuntu-latest", session: "safety" }
           #          - { python: "3.13", os: "ubuntu-latest", session: "mypy" }
           #          - { python: "3.12", os: "ubuntu-latest", session: "mypy" }
           #          - { python: "3.11", os: "ubuntu-latest", session: "mypy" }

pyproject.toml

@@ -23,30 +23,30 @@ classifiers = [
 ]
 
 dependencies = [
-    "click (>=8.1.7,<9.0.0)",
+    "click (>=8.2.1,<9.0.0)",
     "click-params (>=0.5.0,<0.6.0)",
-    "dask (>=2024.12.0)",
-    "fsspec (>=2024.10.0)",
-    "pint>=0.24.3,<0.25",
-    "psutil (>=6.1.0,<7.0.0)",
-    "pydantic (>=2.8.2,<3.0.0)",
-    "pydantic-settings (>=2.4.0,<3.0.0)",
-    "rich (>=13.9.4,<14.0.0)",
-    "segy (>=0.4.0,<0.5.0)",
-    "tqdm (>=4.67.0,<5.0.0)",
-    "xarray>=2025.3.1",
-    "zarr (>=3.0.8,<4.0.0)",
+    "dask (>=2025.5.1)",
+    "fsspec (>=2025.5.1)",
+    "pint>=0.24.4,<0.25",
+    "psutil (>=7.0.0,<8.0.0)",
+    "pydantic (>=2.11.7,<3.0.0)",
+    "pydantic-settings (>=2.10.1,<3.0.0)",
+    "rich (>=14.0.0,<15.0.0)",
+    "segy (>=0.4.1.post2,<0.5.0)",
+    "tqdm (>=4.67.1,<5.0.0)",
+    "xarray>=2025.6.1",
+    "zarr (>=3.0.8,<3.0.9)",
 ]
 
 [project.optional-dependencies]
 cloud = [
-    "s3fs == 2024.12.0",
-    "gcsfs (>=2024.10.0)",
-    "adlfs (>=2024.7.0)",
+    "s3fs == 2025.5.1",
+    "gcsfs (>=2025.5.1)",
+    "adlfs (>=2024.12.0)",
 ]
 distributed = [
-    "distributed (>=2024.12.0)",
-    "bokeh (>=3.4.2,<4.0.0)",
+    "distributed (>=2025.5.1)",
+    "bokeh (>=3.7.3,<4.0.0)",
 ]
 lossy = ["zfpy (>=1.0.1,<2.0.0)"]
 
@@ -60,17 +60,17 @@ mdio = "mdio.__main__:main"
 
 [dependency-groups]
 dev = [
-    "ruff (>=0.11.8)",
-    "coverage[toml] (>=7.6.7,<8)",
-    "mypy (>=1.13.0,<2)",
-    "pre-commit (>=4.0.1,<5)",
+    "ruff (>=0.12.1)",
+    "coverage[toml] (>=7.9.1,<8)",
+    "mypy (>=1.16.1,<2)",
+    "pre-commit (>=4.2.0,<5)",
     "pre-commit-hooks (>=5.0.0,<6)",
-    "pytest (>=8.3.3,<9)",
+    "pytest (>=8.4.1,<9)",
     "pytest-dependency (>=0.6.0,<0.7)",
-    "safety (>=3.2.3,<4)",
-    "typeguard (>=4.4.1,<5)",
+#    "safety (>=3.5.2,<4)",  # too tight pydantic and psutil dependency
+    "typeguard (>=4.4.4,<5)",
     "xdoctest[colors] (>=1.2.0,<2)",
-    "Pygments (>=2.18.0,<3)",
+    "Pygments (>=2.19.2,<3)",
 ]
 
 docs = [
@@ -116,7 +116,7 @@ select = [
     "RET", # return
     "SIM", # simplify
     "TID", # tidy-imports
-    "TCH", # type-checking
+    "TC", # type-checking
     "ARG", # unused-arguments
     "PTH", # use-pathlib
     "TD",  # todos

src/mdio/schemas/compressors.py

@@ -53,17 +53,6 @@ class Blosc(CamelCaseStrictModel):
         description="The size of the block to be used for compression.",
     )
 
-    def make_instance(self):  # noqa: ANN201
-        """Translate parameters to compressor kwargs.."""
-        from zarr.codecs import Blosc as _Blosc
-
-        return _Blosc(
-            cname=self.algorithm,
-            clevel=self.level,
-            shuffle=self.shuffle,
-            blocksize=self.blocksize,
-        )
-
 
 zfp_mode_map = {
     "fixed_rate": 2,
@@ -139,17 +128,6 @@ def check_requirements(self) -> ZFP:
 
         return self
 
-    def make_instance(self):  # noqa: ANN201
-        """Translate parameters to compressor kwargs.."""
-        from zarr.codecs import ZFPY as _ZFPY
-
-        return _ZFPY(
-            mode=self.mode.int_code,
-            tolerance=self.tolerance,
-            rate=self.rate,
-            precision=self.precision,
-        )
-
 
 class CompressorModel(CamelCaseStrictModel):
     """Model representing compressor configuration."""