more maintenance stuff

.pre-commit-config.yaml

@@ -2,15 +2,17 @@ ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autofix_commit_msg: "style: pre-commit fixes"
 
+exclude: ^src/pscpy/sample/.*$
+
 repos:
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.16.0"
+    rev: "1.19.1"
     hooks:
       - id: blacken-docs
         additional_dependencies: [black==24.*]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.6.0"
+    rev: "v5.0.0"
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -33,27 +35,27 @@ repos:
       - id: rst-inline-touching-normal
 
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.1.0"
+    rev: "v4.0.0-alpha.8"
     hooks:
       - id: prettier
         types_or: [yaml, markdown, html, css, scss, javascript, json]
         args: [--prose-wrap=always]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.1"
+    rev: "v0.8.4"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: "v18.1.4"
+    rev: "v19.1.5"
     hooks:
       - id: clang-format
         types_or: [c++, c, cuda]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.9.0"
+    rev: "v1.13.0"
     hooks:
       - id: mypy
         files: src|tests
@@ -64,7 +66,7 @@ repos:
           - adios2
 
   - repo: https://github.com/codespell-project/codespell
-    rev: "v2.2.6"
+    rev: "v2.3.0"
     hooks:
       - id: codespell
 
@@ -87,13 +89,13 @@ repos:
       - id: cmake-format
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: "v0.16"
+    rev: "v0.23"
     hooks:
       - id: validate-pyproject
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: "0.28.2"
+    rev: "0.30.0"
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

pyproject.toml

@@ -42,6 +42,8 @@ Homepage = "https://github.com/psc-code/pscpy"
 Discussions = "https://github.com/psc-code/pscpy/discussions"
 Changelog = "https://github.com/psc-code/pscpy/releases"
 
+[project.entry-points."xarray.backends"]
+pscadios2_engine = "pscpy.pscadios2:PscAdios2BackendEntrypoint"
 
 [build-system]
 build-backend = "setuptools.build_meta"

src/pscpy/__init__.py

@@ -6,8 +6,13 @@
 
 from __future__ import annotations
 
+import pathlib
+
 from pscpy import pscadios2  # noqa: F401
 
 from ._version import version as __version__
 
+sample_dir = pathlib.Path(__file__).parent / "sample"
+
+
 __all__ = ["__version__"]

src/pscpy/adios2py/__init__.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import logging
+import os
 from collections.abc import Collection
 from types import TracebackType
 from typing import Any, SupportsInt
@@ -109,10 +110,10 @@ def __repr__(self) -> str:
 class FileState:
     """Collects the state of a `File` to reflect the fact that they are coupled."""
 
-    def __init__(self, filename: str) -> None:
+    def __init__(self, filename: str | os.PathLike[Any]) -> None:
         self.io_name = f"io-{filename}"
         self.io = _ad.declare_io(self.io_name)
-        self.engine = self.io.open(filename, adios2.bindings.Mode.Read)
+        self.engine = self.io.open(str(filename), adios2.bindings.Mode.Read)
 
     @staticmethod
     def is_open(maybe_state: FileState | None) -> TypeGuard[FileState]:
@@ -124,7 +125,7 @@ class File:
 
     _state: FileState | None
 
-    def __init__(self, filename: str, mode: str = "r") -> None:
+    def __init__(self, filename: str | os.PathLike[Any], mode: str = "r") -> None:
         logging.debug("adios2py: __init__ %s", filename)
         assert mode == "r"
         self._state = FileState(filename)

src/pscpy/pscadios2.py

@@ -10,7 +10,6 @@
 from typing_extensions import Never, override
 from xarray.backends import CachingFileManager
 from xarray.backends.common import (
-    BACKEND_ENTRYPOINTS,
     AbstractDataStore,
     BackendArray,
     BackendEntrypoint,
@@ -198,6 +197,3 @@ def guess_can_open(self, filename_or_obj: str | os.PathLike[Any] | ReadBuffer[An
     @override
     def open_datatree(self, filename_or_obj: str | os.PathLike[Any] | ReadBuffer[Any] | AbstractDataStore, **kwargs: Any) -> DataTree:
         raise NotImplementedError()
-
-
-BACKEND_ENTRYPOINTS["pscadios2"] = ("pscpy", PscAdios2BackendEntrypoint)

src/pscpy/sample/pfd.000000400.bp/profiling.json

@@ -0,0 +1,6 @@
+[
+{ "rank": 0, "start": "Tue_Sep_27_10:16:01_2022", "threads": 1, "bytes": 590260, "mkdir_mus": 193, "memcpy_mus": 505340, "aggregation_mus": 0, "meta_sort_merge_mus": 320, "minmax_mus": 148649, "buffering_mus": 668923, "transport_0": { "type": "File_POSIX", "close_mus": 216, "write_mus": 643, "open_mus": 244 },"transport_1": { "type": "File_POSIX", "close_mus": 0, "write_mus": 41, "open_mus": 250 } },
+{ "rank": 1, "start": "Tue_Sep_27_10:16:01_2022", "threads": 1, "bytes": 590193, "mkdir_mus": 201, "memcpy_mus": 505280, "aggregation_mus": 0, "meta_sort_merge_mus": 165, "minmax_mus": 147485, "buffering_mus": 667610,  },
+{ "rank": 2, "start": "Tue_Sep_27_10:16:01_2022", "threads": 1, "bytes": 590193, "mkdir_mus": 205, "memcpy_mus": 472637, "aggregation_mus": 0, "meta_sort_merge_mus": 52, "minmax_mus": 148323, "buffering_mus": 635610,  },
+{ "rank": 3, "start": "Tue_Sep_27_10:16:01_2022", "threads": 1, "bytes": 590193, "mkdir_mus": 201, "memcpy_mus": 484106, "aggregation_mus": 0, "meta_sort_merge_mus": 29, "minmax_mus": 148251, "buffering_mus": 647150,  }
+]

tests/test_adios2py.py

@@ -0,0 +1,8 @@
+from __future__ import annotations
+
+import pscpy
+from pscpy import adios2py
+
+
+def test_adios2py_open():
+    adios2py.File(pscpy.sample_dir / "pfd.000000400.bp")

tests/test_xarray_adios2.py

@@ -0,0 +1,9 @@
+from __future__ import annotations
+
+import xarray as xr
+
+import pscpy
+
+
+def test_open_dataset():
+    xr.open_dataset(pscpy.sample_dir / "pfd.000000400.bp", species_names=[], length=[10, 10, 10], corner=[0, 0, 0])