From e4463afceaafba68845c8b90a18467511f3ea35c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 24 Aug 2026 19:45:46 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.15.22 → v0.16.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.22...v0.16.4)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b319afa..8cad56c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
     - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.15.22
+  rev: v0.16.4
   hooks:
     # Run the linter.
     - id: ruff

From 2beee7f291d9eb719a99a954028df18ff44af01c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 24 Aug 2026 19:45:54 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/examples/sic_mo_stephan.ipynb      | 4 ++--
 examples/ruthenium_example.ipynb        | 4 ++--
 examples/silicon_example.py             | 6 +++---
 examples/titanium_example.py            | 8 ++++----
 src/pgdtools/__init__.py                | 2 +-
 src/pgdtools/classify.py                | 2 +-
 src/pgdtools/db/__init__.py             | 3 ++-
 src/pgdtools/db/config.py               | 2 +-
 src/pgdtools/db/management.py           | 8 +++-----
 src/pgdtools/db/setup_local.py          | 2 +-
 src/pgdtools/maintainer/__init__.py     | 4 ++--
 src/pgdtools/maintainer/excel_tools.py  | 4 ++--
 src/pgdtools/sub_tools/filters.py       | 2 +-
 src/pgdtools/sub_tools/format.py        | 1 -
 src/pgdtools/sub_tools/info.py          | 2 +-
 src/pgdtools/sub_tools/techniques.py    | 2 +-
 src/pgdtools/sub_tools/utilities.py     | 2 +-
 tests/conftest.py                       | 2 +-
 tests/test_classify.py                  | 3 ++-
 tests/test_data/test_urls.py            | 1 -
 tests/test_db/test_management.py        | 3 ++-
 tests/test_pgdtools.py                  | 1 -
 tests/test_sub_tools/test_filters.py    | 3 +--
 tests/test_sub_tools/test_references.py | 1 -
 tests/test_sub_tools/test_techniques.py | 1 -
 25 files changed, 34 insertions(+), 39 deletions(-)

diff --git a/docs/examples/sic_mo_stephan.ipynb b/docs/examples/sic_mo_stephan.ipynb
index f5f73e9..0819d1f 100644
--- a/docs/examples/sic_mo_stephan.ipynb
+++ b/docs/examples/sic_mo_stephan.ipynb
@@ -26,10 +26,10 @@
    },
    "outputs": [],
    "source": [
-    "from ceresfit import LinReg  # to calculate linear regression\n",
-    "from ceresfit.unc_calc import error_bar_positions  # to plot correlated error bars\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
+    "from ceresfit import LinReg  # to calculate linear regression\n",
+    "from ceresfit.unc_calc import error_bar_positions  # to plot correlated error bars\n",
     "\n",
     "from pgdtools import pgd"
    ]
diff --git a/examples/ruthenium_example.ipynb b/examples/ruthenium_example.ipynb
index 2b00cf2..5a4f61a 100644
--- a/examples/ruthenium_example.ipynb
+++ b/examples/ruthenium_example.ipynb
@@ -29,11 +29,11 @@
     }
    ],
    "source": [
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "from iniabu import (\n",
     "    inimf,\n",
     ")  # iniabu module with abundances as mass fractions - for models!\n",
-    "import matplotlib.pyplot as plt\n",
-    "import numpy as np\n",
     "\n",
     "import pgdtools\n",
     "\n",
diff --git a/examples/silicon_example.py b/examples/silicon_example.py
index 685cb80..10eb7de 100644
--- a/examples/silicon_example.py
+++ b/examples/silicon_example.py
@@ -1,8 +1,8 @@
 """For Benoit: Compare some Si isotope ratios."""
 
-from iniabu import inimf  # import as mass_fraction values right away
 import matplotlib.pyplot as plt
 import numpy as np
+from iniabu import inimf  # import as mass_fraction values right away
 
 import pgdtools
 
@@ -65,8 +65,8 @@
 ax.set_ylim(ylim)
 
 # labels for axes
-ax.set_xlabel("$\delta^{30}$Si$_{28}$   (‰)")
-ax.set_ylabel("$\delta^{29}$Si$_{28}$   (‰)")
+ax.set_xlabel(r"$\delta^{30}$Si$_{28}$   (‰)")
+ax.set_ylabel(r"$\delta^{29}$Si$_{28}$   (‰)")
 ax.legend()
 
 # aspect and layout
diff --git a/examples/titanium_example.py b/examples/titanium_example.py
index 2b9899b..ea53284 100644
--- a/examples/titanium_example.py
+++ b/examples/titanium_example.py
@@ -1,8 +1,8 @@
 """For Benoit: Compare some Ti isotope ratios."""
 
-from iniabu import inimf  # import as mass_fraction values right away
 import matplotlib.pyplot as plt
 import numpy as np
+from iniabu import inimf  # import as mass_fraction values right away
 
 import pgdtools
 
@@ -79,14 +79,14 @@
     a.set_ylim(ylim)
 
     # labels for axes
-    a.set_xlabel("$\delta^{46}$Ti$_{48}$   (‰)")
+    a.set_xlabel(r"$\delta^{46}$Ti$_{48}$   (‰)")
 
     # aspect and layout
     a.set_aspect("equal")
 
 # y label
-ax[0].set_ylabel("$\delta^{47}$Ti$_{48}$   (‰)")
-ax[1].set_ylabel("$\delta^{49}$Ti$_{48}$   (‰)")
+ax[0].set_ylabel(r"$\delta^{47}$Ti$_{48}$   (‰)")
+ax[1].set_ylabel(r"$\delta^{49}$Ti$_{48}$   (‰)")
 
 fig.tight_layout()
 
diff --git a/src/pgdtools/__init__.py b/src/pgdtools/__init__.py
index 41b90c1..9d342b4 100644
--- a/src/pgdtools/__init__.py
+++ b/src/pgdtools/__init__.py
@@ -11,6 +11,6 @@
     "classify_sic_grain",
     "data",
     "db",
-    "pgd",
     "maintainer",
+    "pgd",
 ]
diff --git a/src/pgdtools/classify.py b/src/pgdtools/classify.py
index c3ec8d1..380ea72 100644
--- a/src/pgdtools/classify.py
+++ b/src/pgdtools/classify.py
@@ -49,7 +49,7 @@ def classify_sic_grain(
         if not ret_probabilities:
             return "U", None  # unclassified
         else:
-            return dict(zip(types, probabilities))  #
+            return dict(zip(types, probabilities))
 
     c12_c13 = _replace_errors(c12_c13)
     n14_n15 = _replace_errors(n14_n15)
diff --git a/src/pgdtools/db/__init__.py b/src/pgdtools/db/__init__.py
index eb27dd5..d6bfdb3 100644
--- a/src/pgdtools/db/__init__.py
+++ b/src/pgdtools/db/__init__.py
@@ -1,6 +1,7 @@
 """Local database management for various PGD versions."""
 
 from pgdtools.data import BIBFILE, DB_JSON, REFERENCES_JSON, TECHNIQUES_JSON
+
 from . import setup_local
 from .config import DataBases
 from .management import current, set_current, update
@@ -14,4 +15,4 @@
 LOCAL_REF_JSON = LOCAL_PATH.joinpath(f"config/{REFERENCES_JSON.split('/')[-1]}")
 LOCAL_TECH_JSON = LOCAL_PATH.joinpath(f"config/{TECHNIQUES_JSON.split('/')[-1]}")
 
-__all__ = ["current", "DataBases", "set_current", "update"]
+__all__ = ["DataBases", "current", "set_current", "update"]
diff --git a/src/pgdtools/db/config.py b/src/pgdtools/db/config.py
index 8f15c56..1cf972e 100644
--- a/src/pgdtools/db/config.py
+++ b/src/pgdtools/db/config.py
@@ -1,7 +1,7 @@
 """Classes to deal with the configuration files."""
 
-from datetime import datetime
 import json
+from datetime import datetime
 from typing import Any, List
 
 from pgdtools import db
diff --git a/src/pgdtools/db/management.py b/src/pgdtools/db/management.py
index cd0d9de..37dbad6 100644
--- a/src/pgdtools/db/management.py
+++ b/src/pgdtools/db/management.py
@@ -6,8 +6,7 @@
 
 import requests
 
-from pgdtools import data
-from pgdtools import db
+from pgdtools import data, db
 
 
 def current() -> Dict[str, Path]:
@@ -33,7 +32,7 @@ def current() -> Dict[str, Path]:
     try:
         curr = json.load(open(db.LOCAL_CURRENT, "r"))
     except json.JSONDecodeError as err:
-        raise IOError(file_io_error) from err
+        raise OSError(file_io_error) from err
 
     # turn values of keys into paths
     curr_ret = {k: Path(v) for k, v in curr.items()}
@@ -166,5 +165,4 @@ def _download_file(url: str, local_file: Path) -> None:
             raise ConnectionError(f"Connection error {rin.status_code} for url {url}.")
 
         with open(local_file, "wb") as floc:
-            for chunk in rin.iter_content(chunk_size=8192):
-                floc.write(chunk)
+            floc.writelines(rin.iter_content(chunk_size=8192))
diff --git a/src/pgdtools/db/setup_local.py b/src/pgdtools/db/setup_local.py
index 7243cfe..3d3578a 100644
--- a/src/pgdtools/db/setup_local.py
+++ b/src/pgdtools/db/setup_local.py
@@ -1,7 +1,7 @@
 """Set up the local path for the database based on OS."""
 
-from pathlib import Path
 import sys
+from pathlib import Path
 
 
 def setup_path() -> Path:
diff --git a/src/pgdtools/maintainer/__init__.py b/src/pgdtools/maintainer/__init__.py
index 927d7f2..98ac488 100644
--- a/src/pgdtools/maintainer/__init__.py
+++ b/src/pgdtools/maintainer/__init__.py
@@ -1,9 +1,9 @@
 """Tools and routines for maintaining the PGD database."""
 
 from .excel_tools import (
-    append_to_db_json,
     append_reference_json,
     append_techniques_json,
+    append_to_db_json,
 )
 
-__all__ = ["append_to_db_json", "append_reference_json", "append_techniques_json"]
+__all__ = ["append_reference_json", "append_techniques_json", "append_to_db_json"]
diff --git a/src/pgdtools/maintainer/excel_tools.py b/src/pgdtools/maintainer/excel_tools.py
index a938f92..80f58b8 100644
--- a/src/pgdtools/maintainer/excel_tools.py
+++ b/src/pgdtools/maintainer/excel_tools.py
@@ -4,11 +4,11 @@
 used with `pgdtools`.
 """
 
-from datetime import datetime
 import json
+import warnings
+from datetime import datetime
 from pathlib import Path
 from typing import Union
-import warnings
 
 import numpy as np
 import pandas as pd
diff --git a/src/pgdtools/sub_tools/filters.py b/src/pgdtools/sub_tools/filters.py
index 99c3e75..f70b502 100644
--- a/src/pgdtools/sub_tools/filters.py
+++ b/src/pgdtools/sub_tools/filters.py
@@ -1,6 +1,6 @@
 """Sub tool to add filtering capabilities."""
 
-from typing import List, Union, Tuple
+from typing import List, Tuple, Union
 
 import pgdtools
 import pgdtools.sub_tools.utilities as utl
diff --git a/src/pgdtools/sub_tools/format.py b/src/pgdtools/sub_tools/format.py
index 8a0fe74..6dc82f1 100644
--- a/src/pgdtools/sub_tools/format.py
+++ b/src/pgdtools/sub_tools/format.py
@@ -2,7 +2,6 @@
 
 from typing import Tuple
 
-
 import pgdtools
 import pgdtools.sub_tools.utilities as utl
 
diff --git a/src/pgdtools/sub_tools/info.py b/src/pgdtools/sub_tools/info.py
index c0a8447..bfee5a7 100644
--- a/src/pgdtools/sub_tools/info.py
+++ b/src/pgdtools/sub_tools/info.py
@@ -1,6 +1,6 @@
 """Sub tool to add information querying capabilities."""
 
-from typing import List, Union, Set, Tuple
+from typing import List, Set, Tuple, Union
 
 import pgdtools
 import pgdtools.sub_tools.utilities as utl
diff --git a/src/pgdtools/sub_tools/techniques.py b/src/pgdtools/sub_tools/techniques.py
index 2bfb469..f7f61a4 100644
--- a/src/pgdtools/sub_tools/techniques.py
+++ b/src/pgdtools/sub_tools/techniques.py
@@ -2,8 +2,8 @@
 
 import itertools
 import json
-from typing import List, Set
 import re
+from typing import List, Set
 
 import pandas as pd
 
diff --git a/src/pgdtools/sub_tools/utilities.py b/src/pgdtools/sub_tools/utilities.py
index 872054e..846790e 100644
--- a/src/pgdtools/sub_tools/utilities.py
+++ b/src/pgdtools/sub_tools/utilities.py
@@ -1,6 +1,6 @@
 """Utilities for all tool modules in pgdtools."""
 
-from typing import Iterable
+from collections.abc import Iterable
 
 
 class Isotope:
diff --git a/tests/conftest.py b/tests/conftest.py
index 056cc23..b90c05c 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -51,7 +51,7 @@ def pgd_setup(tmpdir_home, data_files_dir):
 
     current_file = tmpdir_home.joinpath("current.json")
     current_file.write_text(
-        f'{{"sic": "{str(sic_db.absolute())}", "gra": "{str(gra_db.absolute())}"}}'
+        f'{{"sic": "{sic_db.absolute()!s}", "gra": "{gra_db.absolute()!s}"}}'
     )  # noqa: B907
 
 
diff --git a/tests/test_classify.py b/tests/test_classify.py
index d1f7e55..d4ec50d 100644
--- a/tests/test_classify.py
+++ b/tests/test_classify.py
@@ -3,7 +3,8 @@
 import numpy as np
 import pytest
 
-from pgdtools import classify as cl, classify_sic_grain, PresolarGrains
+from pgdtools import PresolarGrains, classify_sic_grain
+from pgdtools import classify as cl
 
 # grains to test, following definitions:
 # [
diff --git a/tests/test_data/test_urls.py b/tests/test_data/test_urls.py
index 79d3053..208319b 100644
--- a/tests/test_data/test_urls.py
+++ b/tests/test_data/test_urls.py
@@ -11,7 +11,6 @@
 
 from pgdtools import data
 
-
 ALL_URLS = [data.BIBFILE, data.DB_JSON, data.REFERENCES_JSON, data.TECHNIQUES_JSON]
 
 
diff --git a/tests/test_db/test_management.py b/tests/test_db/test_management.py
index 559a8e1..0687097 100644
--- a/tests/test_db/test_management.py
+++ b/tests/test_db/test_management.py
@@ -6,7 +6,8 @@
 import requests_mock
 
 from pgdtools import db
-from pgdtools.db import DataBases, management as mgmt
+from pgdtools.db import DataBases
+from pgdtools.db import management as mgmt
 
 
 def test_current_no_file():
diff --git a/tests/test_pgdtools.py b/tests/test_pgdtools.py
index 7880000..f60fec3 100644
--- a/tests/test_pgdtools.py
+++ b/tests/test_pgdtools.py
@@ -5,7 +5,6 @@
 import pgdtools.sub_tools.headers
 import pgdtools.sub_tools.utilities as utl
 
-
 # ISOTOPE CLASS #
 
 
diff --git a/tests/test_sub_tools/test_filters.py b/tests/test_sub_tools/test_filters.py
index 03d0739..7fc4a74 100644
--- a/tests/test_sub_tools/test_filters.py
+++ b/tests/test_sub_tools/test_filters.py
@@ -4,9 +4,8 @@
 import pytest
 
 from pgdtools import PresolarGrains
-from pgdtools.sub_tools import filters as flt
 from pgdtools.sub_tools import Filters
-
+from pgdtools.sub_tools import filters as flt
 
 # DUNDER METHODS #
 
diff --git a/tests/test_sub_tools/test_references.py b/tests/test_sub_tools/test_references.py
index bb52b3e..0182489 100644
--- a/tests/test_sub_tools/test_references.py
+++ b/tests/test_sub_tools/test_references.py
@@ -4,7 +4,6 @@
 
 from pgdtools.sub_tools import References
 
-
 # DUNDER METHODS #
 
 
diff --git a/tests/test_sub_tools/test_techniques.py b/tests/test_sub_tools/test_techniques.py
index 639ba09..9f3adbb 100644
--- a/tests/test_sub_tools/test_techniques.py
+++ b/tests/test_sub_tools/test_techniques.py
@@ -4,7 +4,6 @@
 
 from pgdtools.sub_tools import Techniques
 
-
 # DUNDER METHODS #