[pre-commit.ci] pre-commit autoupdate (#105)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.2.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.2.0...v4.5.0)
- [github.com/PyCQA/isort: 5.12.0 → 5.13.2](PyCQA/isort@5.12.0...5.13.2)
- [github.com/asottile/pyupgrade: v2.32.1 → v3.15.0](asottile/pyupgrade@v2.32.1...v3.15.0)
- [github.com/psf/black: 22.3.0 → 24.1.1](psf/black@22.3.0...24.1.1)
- [github.com/PyCQA/pylint: v2.13.8 → v3.0.3](pylint-dev/pylint@v2.13.8...v3.0.3)
- [github.com/pre-commit/mirrors-mypy: v0.991 → v1.8.0](pre-commit/mirrors-mypy@v0.991...v1.8.0)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Make pre-commit happy about code style

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Michael Osthege <[email protected]>

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: ^(docs|mcbackend/testdata)/
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.2.0
+  rev: v4.5.0
   hooks:
     - id: check-merge-conflict
     - id: check-toml
@@ -10,28 +10,28 @@ repos:
     - id: end-of-file-fixer
     - id: requirements-txt-fixer
 - repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
     - id: isort
       name: isort
       args: ["--profile", "black"]
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.32.1
+  rev: v3.15.0
   hooks:
     - id: pyupgrade
       args: [--py37-plus]
 - repo: https://github.com/psf/black
-  rev: 22.3.0
+  rev: 24.1.1
   hooks:
     - id: black
 - repo: https://github.com/PyCQA/pylint
-  rev: v2.13.8
+  rev: v3.0.3
   hooks:
     - id: pylint
       args: [--rcfile=.pylintrc]
       exclude: (test_*|mcbackend/meta.py|mcbackend/npproto/)
       files: ^mcbackend/
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.991
+    rev: v1.8.0
     hooks:
     -   id: mypy

mcbackend/__init__.py

@@ -1,6 +1,7 @@
 """
 A framework agnostic implementation for storage of MCMC draws.
 """
+
 from .backends.numpy import NumPyBackend
 from .core import Backend, Chain, Run
 from .meta import ChainMeta, Coordinate, DataVariable, ExtendedValue, RunMeta, Variable

mcbackend/backends/clickhouse.py

@@ -1,6 +1,7 @@
 """
 This module implements a backend for sample storage in ClickHouse.
 """
+
 import base64
 import logging
 import time
@@ -45,6 +46,10 @@
 }
 
 
+class ClickHouseBackendError(Exception):
+    """Something bad happened in the ClickHouse backend."""
+
+
 def create_runs_table(client: clickhouse_driver.Client):
     query = """
         CREATE TABLE IF NOT EXISTS runs (
@@ -79,7 +84,7 @@ def create_chain_table(client: clickhouse_driver.Client, meta: ChainMeta, rmeta:
     # Check that it does not already exist
     cid = chain_id(meta)
     if client.execute(f"SHOW TABLES LIKE '{cid}';"):
-        raise Exception(f"A table for {cid} already exists.")
+        raise ClickHouseBackendError(f"A table for {cid} already exists.")
 
     # Create a table with columns corresponding to the model variables
     columns = []
@@ -235,7 +240,7 @@ def _get_row_at(
         query = f"SELECT (`{names}`,) FROM {self.cid} WHERE _draw_idx={idx};"
         data = self._client.execute(query)
         if not data:
-            raise Exception(f"No record found for draw index {idx}.")
+            raise ClickHouseBackendError(f"No record found for draw index {idx}.")
         result = dict(zip(var_names, data[0][0]))
         return result
 
@@ -363,7 +368,10 @@ def __init__(
             raise ValueError("Either a `client` or a `client_fn` must be provided.")
 
         if client_fn is None:
-            client_fn = lambda: client
+
+            def client_fn():
+                return client
+
         if client is None:
             client = client_fn()
 
@@ -381,11 +389,11 @@ def init_run(self, meta: RunMeta) -> ClickHouseRun:
         else:
             created_at = datetime.now().astimezone(timezone.utc)
             query = "INSERT INTO runs (created_at, rid, proto) VALUES"
-            params = dict(
-                created_at=created_at,
-                rid=meta.rid,
-                proto=base64.encodebytes(bytes(meta)).decode("ascii"),
-            )
+            params = {
+                "created_at": created_at,
+                "rid": meta.rid,
+                "proto": base64.encodebytes(bytes(meta)).decode("ascii"),
+            }
             self._client.execute(query, [params])
         return ClickHouseRun(meta, client_fn=self._client_fn, created_at=created_at)
 
@@ -407,7 +415,9 @@ def get_run(self, rid: str) -> ClickHouseRun:
             {"rid": rid},
         )
         if len(rows) != 1:
-            raise Exception(f"Unexpected number of {len(rows)} results for rid='{rid}'.")
+            raise ClickHouseBackendError(
+                f"Unexpected number of {len(rows)} results for rid='{rid}'."
+            )
         data = base64.decodebytes(rows[0][2].encode("ascii"))
         meta = RunMeta().parse(data)
         return ClickHouseRun(

mcbackend/backends/numpy.py

@@ -1,6 +1,7 @@
 """
 This backend holds draws in memory, managing them via NumPy arrays.
 """
+
 import math
 from typing import Dict, List, Mapping, Optional, Sequence, Tuple
 
@@ -110,7 +111,7 @@ class NumPyRun(Run):
     """An MCMC run where samples are kept in memory."""
 
     def __init__(self, meta: RunMeta, *, preallocate: int) -> None:
-        self._settings = dict(preallocate=preallocate)
+        self._settings = {"preallocate": preallocate}
         self._chains: List[NumPyChain] = []
         super().__init__(meta)
 
@@ -128,9 +129,7 @@ class NumPyBackend(Backend):
     """An in-memory backend using NumPy."""
 
     def __init__(self, preallocate: int = 1_000) -> None:
-        self._settings = dict(
-            preallocate=preallocate,
-        )
+        self._settings = {"preallocate": preallocate}
         super().__init__()
 
     def init_run(self, meta: RunMeta) -> NumPyRun:

mcbackend/core.py

@@ -1,6 +1,7 @@
 """
 Module with metadata structures and abstract classes.
 """
+
 import collections
 import logging
 from typing import Dict, List, Mapping, Optional, Sequence, Sized, TypeVar, Union, cast
@@ -26,6 +27,10 @@
 __all__ = ("is_rigid", "chain_id", "Chain", "Run", "Backend")
 
 
+class ChainError(Exception):
+    """Something is not right in one chain."""
+
+
 def is_rigid(nshape: Optional[Shape]):
     """Determines wheather the shape is constant.
 
@@ -118,7 +123,7 @@ def __len__(self) -> int:
         ]:
             for var in items:
                 return len(method(var.name))
-        raise Exception("This chain has no variables or sample stats.")
+        raise ChainError("This chain has no variables or sample stats.")
 
     @property
     def cid(self) -> str:

mcbackend/npproto/utils.py

@@ -1,6 +1,7 @@
 """
 Helper functions such as converters between ``ndarray`` and ``Ndarray``.
 """
+
 import numpy
 
 from . import Ndarray

mcbackend/utils.py

@@ -1,4 +1,5 @@
 """Contains helper functions that are independent of McBackend components."""
+
 from typing import Sequence
 
 import numpy as np

protobufs/generate.py

@@ -2,6 +2,7 @@
 This script regenerates the `meta.py` module
 from protobuf definitions of core metadata structures.
 """
+
 import pathlib
 import shutil
 import subprocess