chore: update pre-commit hooks

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
         additional_dependencies: [black==23.*]
 
   - 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
@@ -40,7 +40,7 @@ repos:
           ]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.5.0"
+    rev: "v0.6.9"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
@@ -72,12 +72,12 @@ repos:
         args: [--prose-wrap=always]
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.18
+    rev: v0.20.2
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.28.6
+    rev: 0.29.3
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

docs/source/notebooks/DataCompression.ipynb

@@ -17,9 +17,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
+    "import numpy as np\n",
+    "\n",
     "import lgdo\n",
-    "from lgdo import lh5\n",
-    "import numpy as np"
+    "from lgdo import lh5"
    ]
   },
   {
@@ -41,7 +44,7 @@
     "    size=1000,\n",
     "    col_dict={\n",
     "        \"col1\": lgdo.Array(np.arange(0, 100, 0.1)),\n",
-    "        \"col2\": lgdo.Array(np.random.rand(1000)),\n",
+    "        \"col2\": lgdo.Array(np.random.default_rng().random(1000)),\n",
     "    },\n",
     ")\n",
     "data"
@@ -281,7 +284,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lgdo.compression import encode, RadwareSigcompress\n",
+    "from lgdo.compression import RadwareSigcompress, encode\n",
     "\n",
     "enc_values = encode(wfs.values, RadwareSigcompress(codec_shift=-32768))\n",
     "enc_values"

docs/source/notebooks/LH5Files.ipynb

@@ -27,6 +27,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "from legendtestdata import LegendTestData\n",
     "\n",
     "ldata = LegendTestData()\n",
@@ -210,7 +212,9 @@
    "source": [
     "from lgdo.lh5 import LH5Store\n",
     "\n",
-    "store = LH5Store(keep_open=True)  # with keep_open=True, files are kept open inside the store\n",
+    "store = LH5Store(\n",
+    "    keep_open=True\n",
+    ")  # with keep_open=True, files are kept open inside the store\n",
     "store.read(\"geds/raw\", lh5_file)  # returns a tuple: (obj, n_rows_read)"
    ]
   },
@@ -456,9 +460,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lgdo import Array, Scalar, WaveformTable\n",
     "import numpy as np\n",
     "\n",
+    "from lgdo import Array, Scalar, WaveformTable\n",
+    "\n",
     "rng = np.random.default_rng(12345)\n",
     "\n",
     "scalar = Scalar(\"made with legend-pydataobj!\")\n",

pyproject.toml

@@ -146,6 +146,7 @@ isort.required-imports = ["from __future__ import annotations"]
 [tool.ruff.lint.per-file-ignores]
 "tests/**" = ["T20"]
 "noxfile.py" = ["T20"]
+"docs/source/notebooks/*" = ["T201", "E402"]
 
 [tool.pylint]
 py-version = "3.8"

src/lgdo/compression/radware.py

@@ -441,15 +441,11 @@ def _radware_sigcompress_encode(
         while (i < sig_in.size) and (i < j + 48):
             si_i = int16(sig_in[i] + shift)
             si_im1 = int16(sig_in[i - 1] + shift)
-            if max1 < si_i:
-                max1 = si_i
-            if min1 > si_i:
-                min1 = si_i
+            max1 = max(max1, si_i)
+            min1 = min(min1, si_i)
             ds = si_i - si_im1
-            if max2 < ds:
-                max2 = ds
-            if min2 > ds:
-                min2 = ds
+            max2 = max(max2, ds)
+            min2 = min(min2, ds)
             nw += 1
             i += 1
         if max1 - min1 <= max2 - min2:  # use absolute values
@@ -460,15 +456,13 @@ def _radware_sigcompress_encode(
                 i < j + 128
             ):  # FIXME: 128 could be tuned better?
                 si_i = int16(sig_in[i] + shift)
-                if max1 < si_i:
-                    max1 = si_i
+                max1 = max(max1, si_i)
                 dd1 = max1 - min1
                 if min1 > si_i:
                     dd1 = max1 - si_i
                 if dd1 > mask[nb1]:
                     break
-                if min1 > si_i:
-                    min1 = si_i
+                min1 = min(min1, si_i)
                 nw += 1
                 i += 1
         else:  # use difference values
@@ -481,15 +475,13 @@ def _radware_sigcompress_encode(
                 si_i = int16(sig_in[i] + shift)
                 si_im1 = int16(sig_in[i - 1] + shift)
                 ds = si_i - si_im1
-                if max2 < ds:
-                    max2 = ds
+                max2 = max(max2, ds)
                 dd2 = max2 - min2
                 if min2 > ds:
                     dd2 = max2 - ds
                 if dd2 > mask[nb2]:
                     break
-                if min2 > ds:
-                    min2 = ds
+                min2 = min(min2, ds)
                 nw += 1
                 i += 1
 

src/lgdo/lh5/_serializers/read/composite.py

@@ -103,8 +103,7 @@ def _h5_read_lgdo(
     if idx is not None:
         # check if idx is just an ordered list of the integers if so can ignore
         if (idx == np.arange(0, len(idx), 1)).all():
-            if n_rows > len(idx):
-                n_rows = len(idx)
+            n_rows = min(n_rows, len(idx))
             idx = None
         else:
             # chop off indices < start_row

src/lgdo/lh5/_serializers/read/ndarray.py

@@ -50,8 +50,7 @@ def _h5_read_ndarray(
         n_rows_to_read = len(idx)
     else:
         n_rows_to_read = ds_n_rows - start_row
-    if n_rows_to_read > n_rows:
-        n_rows_to_read = n_rows
+    n_rows_to_read = min(n_rows_to_read, n_rows)
 
     if idx is None:
         fspace.select_hyperslab(

tests/compression/conftest.py

@@ -5,7 +5,7 @@
 from lgdo import lh5
 
 
-@pytest.fixture()
+@pytest.fixture
 def wftable(lgnd_test_data):
     store = lh5.LH5Store()
     wft, _ = store.read(

tests/lh5/test_lh5_write.py

@@ -11,7 +11,7 @@
 from lgdo import lh5, types
 
 
-def test_write_compressed_lgnd_waveform_table(enc_lgnd_file):  # noqa: ARG001
+def test_write_compressed_lgnd_waveform_table(enc_lgnd_file):
     pass
 
 

tests/types/test_vectorofvectors.py

@@ -16,7 +16,7 @@
 VovColl = namedtuple("VovColl", ["v2d", "v3d", "v4d"])
 
 
-@pytest.fixture()
+@pytest.fixture
 def testvov():
     v2d = VectorOfVectors([[1, 2], [3, 4, 5], [2], [4, 8, 9, 7], [5, 3, 1]])
     v3d = VectorOfVectors([[[1, 2], [3, 4, 5]], [[2], [4, 8, 9, 7]], [[5, 3, 1]]])

tests/types/test_vovutils.py

@@ -12,7 +12,7 @@
 VovColl = namedtuple("VovColl", ["v2d", "v3d", "v4d"])
 
 
-@pytest.fixture()
+@pytest.fixture
 def testvov():
     v2d = VectorOfVectors([[1, 2], [3, 4, 5], [2], [4, 8, 9, 7], [5, 3, 1]])
     v3d = VectorOfVectors([[[1, 2], [3, 4, 5]], [[2], [4, 8, 9, 7]], [[5, 3, 1]]])