add more tests for adios2py

.pre-commit-config.yaml

@@ -24,15 +24,15 @@ repos:
       - id: mixed-line-ending
       - id: name-tests-test
         args: ["--pytest-test-first"]
-      - id: requirements-txt-fixer
+      # - id: requirements-txt-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: "v1.10.0"
-    hooks:
-      - id: rst-backticks
-      - id: rst-directive-colons
-      - id: rst-inline-touching-normal
+  # - repo: https://github.com/pre-commit/pygrep-hooks
+  #   rev: "v1.10.0"
+  #   hooks:
+  #     - id: rst-backticks
+  #     - id: rst-directive-colons
+  #     - id: rst-inline-touching-normal
 
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v4.0.0-alpha.8"
@@ -48,17 +48,17 @@ repos:
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
 
-  - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: "v19.1.5"
-    hooks:
-      - id: clang-format
-        types_or: [c++, c, cuda]
+  # - repo: https://github.com/pre-commit/mirrors-clang-format
+  #   rev: "v19.1.5"
+  #   hooks:
+  #     - id: clang-format
+  #       types_or: [c++, c, cuda]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: "v1.13.0"
     hooks:
       - id: mypy
-        files: src|tests
+        files: src #|tests
         args: []
         additional_dependencies:
           - pytest
@@ -83,10 +83,10 @@ repos:
         entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
         exclude: .pre-commit-config.yaml
 
-  - repo: https://github.com/cheshirekow/cmake-format-precommit
-    rev: "v0.6.13"
-    hooks:
-      - id: cmake-format
+  # - repo: https://github.com/cheshirekow/cmake-format-precommit
+  #   rev: "v0.6.13"
+  #   hooks:
+  #     - id: cmake-format
 
   - repo: https://github.com/abravalheri/validate-pyproject
     rev: "v0.23"

noxfile.py

@@ -19,7 +19,9 @@ def lint(session: nox.Session) -> None:
     Run the linter.
     """
     session.install("pre-commit")
-    session.run("pre-commit", "run", "--all-files", "--show-diff-on-failure", *session.posargs)
+    session.run(
+        "pre-commit", "run", "--all-files", "--show-diff-on-failure", *session.posargs
+    )
 
 
 @nox.session
@@ -50,7 +52,9 @@ def docs(session: nox.Session) -> None:
 
     parser = argparse.ArgumentParser()
     parser.add_argument("--serve", action="store_true", help="Serve after building")
-    parser.add_argument("-b", dest="builder", default="html", help="Build target (default: html)")
+    parser.add_argument(
+        "-b", dest="builder", default="html", help="Build target (default: html)"
+    )
     args, posargs = parser.parse_known_args(session.posargs)
 
     if args.builder != "html" and args.serve:
@@ -62,7 +66,9 @@ def docs(session: nox.Session) -> None:
     session.chdir("docs")
 
     if args.builder == "linkcheck":
-        session.run("sphinx-build", "-b", "linkcheck", ".", "_build/linkcheck", *posargs)
+        session.run(
+            "sphinx-build", "-b", "linkcheck", ".", "_build/linkcheck", *posargs
+        )
         return
 
     shared_args = (

pyproject.toml

@@ -95,10 +95,6 @@ disallow_untyped_defs = true
 disallow_incomplete_defs = true
 
 
-[tool.ruff]
-src = ["src"]
-line-length = 200
-
 [tool.ruff.lint]
 extend-select = [
   "B",   # flake8-bugbear

src/pscpy/adios2py/__init__.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import itertools
 import logging
 import os
 from collections.abc import Collection
@@ -13,7 +14,7 @@
 from numpy.typing import NDArray
 from typing_extensions import TypeGuard
 
-_ad = Adios()
+logger = logging.getLogger(__name__)
 
 
 class Variable:
@@ -25,10 +26,10 @@ def __init__(self, var: adios2.Variable, engine: adios2.Engine) -> None:
         self.name = self._name()
         self.shape = self._shape()
         self.dtype = self._dtype()
-        logging.debug("variable __init__ var %s engine %s", var, engine)
+        logger.debug("variable __init__ var %s engine %s", var, engine)
 
     def close(self) -> None:
-        logging.debug("adios2py.variable close")
+        logger.debug("adios2py.variable close")
         self._var = None
         self._engine = None
 
@@ -37,7 +38,9 @@ def _assert_not_closed(self) -> None:
             error_message = "adios2py: variable is closed"
             raise ValueError(error_message)
 
-    def _set_selection(self, start: NDArray[np.integer[Any]], count: NDArray[np.integer[Any]]) -> None:
+    def _set_selection(
+        self, start: NDArray[np.integer[Any]], count: NDArray[np.integer[Any]]
+    ) -> None:
         self._assert_not_closed()
 
         self._var.set_selection((start[::-1], count[::-1]))
@@ -57,7 +60,9 @@ def _dtype(self) -> np.dtype[Any]:
 
         return np.dtype(adios2.type_adios_to_numpy(self._var.type()))  # type: ignore[no-any-return]
 
-    def __getitem__(self, args: SupportsInt | slice | tuple[SupportsInt | slice, ...]) -> NDArray[Any]:
+    def __getitem__(
+        self, args: SupportsInt | slice | tuple[SupportsInt | slice, ...]
+    ) -> NDArray[Any]:
         self._assert_not_closed()
 
         if not isinstance(args, tuple):
@@ -99,7 +104,9 @@ def __getitem__(self, args: SupportsInt | slice | tuple[SupportsInt | slice, ...
 
         self._set_selection(sel_start, sel_count)
 
-        arr = np.empty(arr_shape, dtype=self.dtype, order="F")  # FIXME is column-major correct?
+        arr = np.empty(
+            arr_shape, dtype=self.dtype, order="F"
+        )  # FIXME is column-major correct?
         self._engine.get(self._var, arr, adios2.bindings.Mode.Sync)
         return arr
 
@@ -110,11 +117,19 @@ def __repr__(self) -> str:
 class FileState:
     """Collects the state of a `File` to reflect the fact that they are coupled."""
 
+    _ad = Adios()
+    _io_count = itertools.count()
+
     def __init__(self, filename: str | os.PathLike[Any]) -> None:
-        self.io_name = f"io-{filename}"
-        self.io = _ad.declare_io(self.io_name)
+        self.io_name = f"io-adios2py-{next(self._io_count)}"
+        logger.debug("io_name = %s", self.io_name)
+        self.io = self._ad.declare_io(self.io_name)
         self.engine = self.io.open(str(filename), adios2.bindings.Mode.Read)
 
+    def close(self) -> None:
+        self.engine.close()
+        self._ad.remove_io(self.io_name)
+
     @staticmethod
     def is_open(maybe_state: FileState | None) -> TypeGuard[FileState]:
         return maybe_state is not None
@@ -126,43 +141,52 @@ class File:
     _state: FileState | None
 
     def __init__(self, filename: str | os.PathLike[Any], mode: str = "r") -> None:
-        logging.debug("adios2py: __init__ %s", filename)
+        logger.debug("File.__init__(%s, %s)", filename, mode)
         assert mode == "r"
         self._state = FileState(filename)
         self._open_vars: dict[str, Variable] = {}
 
-        self.variable_names: Collection[str] = self._state.io.available_variables().keys()
-        self.attribute_names: Collection[str] = self._state.io.available_attributes().keys()
+        self.variable_names: Collection[str] = (
+            self._state.io.available_variables().keys()
+        )
+        self.attribute_names: Collection[str] = (
+            self._state.io.available_attributes().keys()
+        )
 
     def __enter__(self) -> File:
-        logging.debug("adios2py: __enter__")
+        logger.debug("File.__enter__()")
         return self
 
-    def __exit__(self, exception_type: type[BaseException] | None, exception: BaseException | None, traceback: TracebackType | None) -> None:
-        logging.debug("adios2py: __exit__")
+    def __exit__(
+        self,
+        exception_type: type[BaseException] | None,
+        exception: BaseException | None,
+        traceback: TracebackType | None,
+    ) -> None:
+        logger.debug("File.__exit__()")
         self.close()
 
     def __del__(self) -> None:
-        logging.debug("adios2py: __del__")
+        logger.debug("File.__del__()")
         if FileState.is_open(self._state):
             self.close()
 
     def close(self) -> None:
         assert FileState.is_open(self._state)
 
-        logging.debug("adios2py: close")
-        logging.debug("open vars %s", self._open_vars)
+        logger.debug("File.close(): open vars %s", self._open_vars)
         for var in self._open_vars.values():
             var.close()
 
-        self._state.engine.close()
-        _ad.remove_io(self._state.io_name)
+        self._state.close()
         self._state = None
 
     def get_variable(self, variable_name: str) -> Variable:
         assert FileState.is_open(self._state)
 
-        var = Variable(self._state.io.inquire_variable(variable_name), self._state.engine)
+        var = Variable(
+            self._state.io.inquire_variable(variable_name), self._state.engine
+        )
         self._open_vars[variable_name] = var
         return var
 

src/pscpy/psc.py

@@ -8,7 +8,9 @@
 from .adios2py import File
 
 
-def _get_array_attribute(file: File, attribute_name: str, default: ArrayLike | None) -> NDArray[np.floating[Any]]:
+def _get_array_attribute(
+    file: File, attribute_name: str, default: ArrayLike | None
+) -> NDArray[np.floating[Any]]:
     if attribute_name in file.attribute_names:
         return np.asarray(file.get_attribute(attribute_name))
     if default is not None:
@@ -24,7 +26,12 @@
     TODO: Should also know about timestep, species, whatever...
     """
 
-    def __init__(self, file: File, length: ArrayLike | None = None, corner: ArrayLike | None = None) -> None:
+    def __init__(
+        self,
+        file: File,
+        length: ArrayLike | None = None,
+        corner: ArrayLike | None = None,
+    ) -> None:
         assert len(file.variable_names) > 0
         var = next(iter(file.variable_names))
         self.gdims = np.asarray(file.get_variable(var).shape)[0:3]
@@ -86,7 +93,11 @@
     ]
     for species_idx, species_name in enumerate(species_names):
         for moment_idx, moment in enumerate(moments):
-            field_to_component["all_1st"][f"{moment}_{species_name}"] = moment_idx + 13 * species_idx
-            field_to_component["all_1st_cc"][f"{moment}_{species_name}"] = moment_idx + 13 * species_idx
+            field_to_component["all_1st"][f"{moment}_{species_name}"] = (
+                moment_idx + 13 * species_idx
+            )
+            field_to_component["all_1st_cc"][f"{moment}_{species_name}"] = (
+                moment_idx + 13 * species_idx
+            )
 
     return field_to_component