uproot 5.4.0__tar.gz → 5.4.2__tar.gz

{uproot-5.4.0 → uproot-5.4.2}/.all-contributorsrc

@@ -587,6 +587,24 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "MatousVozak",
+      "name": "MatousVozak",
+      "avatar_url": "https://avatars.githubusercontent.com/u/33348191?v=4",
+      "profile": "https://github.com/MatousVozak",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "rossodisera",
+      "name": "Andrea Serafini",
+      "avatar_url": "https://avatars.githubusercontent.com/u/46961664?v=4",
+      "profile": "https://github.com/rossodisera",
+      "contributions": [
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 7,

{uproot-5.4.0 → uproot-5.4.2}/.github/workflows/build-test.yml

@@ -34,9 +34,12 @@ jobs:
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
-          miniforge-variant: Mambaforge
+          miniforge-version: latest
           use-mamba: true
 
+      - name: Check active Python version
+        run: python -c "import sys; assert '.'.join(str(s) for s in sys.version_info[:2]) == '${{ matrix.python-version }}', f'{version} incorrect!'"
+
       - name: Install ROOT
         if: matrix.python-version == 3.8  &&  runner.os != 'macOS'  &&  runner.os != 'Windows'
         run: |
@@ -45,7 +48,7 @@ jobs:
           conda list
 
       - name: Install sshd for fsspec ssh tests
-        if: runner.os != 'macOS'  &&  runner.os != 'Windows'
+        if: runner.os != 'macOS' && runner.os != 'Windows'
         run: |
           sudo apt-get install -y openssh-server
           sudo service ssh restart
@@ -56,7 +59,7 @@ jobs:
           ssh -o StrictHostKeyChecking=no localhost echo "ssh connection successful"
 
       - name: Install XRootD
-        if: runner.os != 'macOS'  &&  runner.os != 'Windows'
+        if: runner.os != 'macOS' && runner.os != 'Windows'
         run: |
           conda env list
           mamba install xrootd
@@ -74,7 +77,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [windows-latest, ubuntu-latest, macos-latest]
-        python-version: ['3.11']
+        python-version: ['3.13']
 
     runs-on: ${{ matrix.platform }}
     timeout-minutes: 30
@@ -85,9 +88,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - uses: astral-sh/setup-uv@v3
 
       - name: Pip install the package
-        run: python -m pip install .[test,dev]
+        run: uv pip install --system .[test,dev]
 
       - name: Run pytest
         run: |
@@ -160,13 +166,13 @@ jobs:
           rm -rf dependencies/
 
       - name: Download Pyodide
-        uses: pyodide/pyodide-actions/download-pyodide@v1
+        uses: pyodide/pyodide-actions/download-pyodide@v2
         with:
           version: ${{ env.PYODIDE_VERSION }}
           to: pyodide-dist
 
       - name: Install browser
-        uses: pyodide/pyodide-actions/install-browser@v1
+        uses: pyodide/pyodide-actions/install-browser@v2
         with:
           runner: selenium
           browser: chrome
@@ -179,3 +185,14 @@ jobs:
       - name: Run pytest
         run: |
           pytest -vv --dist-dir=./pyodide-dist/ --runner=selenium --runtime=chrome tests-wasm
+
+  pass:
+    if: always()
+    needs: [build, vanilla-build, numpy1-build, pyodide-build]
+    runs-on: ubuntu-latest
+    timeout-minutes: 2
+    steps:
+      - name: Decide whether the needed jobs succeeded or failed
+        uses: re-actors/alls-green@release/v1
+        with:
+          jobs: ${{ toJSON(needs) }}

{uproot-5.4.0 → uproot-5.4.2}/.github/workflows/upload-nightly-wheels.yml

@@ -33,7 +33,7 @@ jobs:
         run: ls -lha dist/*.whl
 
       - name: Upload wheel to Anaconda Cloud as nightly
-        uses: scientific-python/upload-nightly-action@b67d7fcc0396e1128a474d1ab2b48aa94680f9fc # 0.5.0
+        uses: scientific-python/upload-nightly-action@82396a2ed4269ba06c6b2988bb4fd568ef3c3d6b # 0.6.1
         with:
           artifacts_path: dist
           anaconda_nightly_upload_token: ${{ secrets.ANACONDA_ORG_UPLOAD_TOKEN }}

{uproot-5.4.0 → uproot-5.4.2}/.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - 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
@@ -18,19 +18,19 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.5
+    rev: v0.7.2
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
 
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.19.0
     hooks:
       - id: pyupgrade
         args: [--py38-plus]

{uproot-5.4.0 → uproot-5.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: uproot
-Version: 5.4.0
+Version: 5.4.2
 Summary: ROOT I/O in pure Python and NumPy.
 Project-URL: Download, https://github.com/scikit-hep/uproot5/releases
 Project-URL: Homepage, https://github.com/scikit-hep/uproot5
@@ -23,6 +23,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Information Analysis
 Classifier: Topic :: Scientific/Engineering :: Mathematics
@@ -67,6 +68,7 @@ Requires-Dist: pytest-pyodide; extra == 'test-pyodide'
 Requires-Dist: pytest-timeout; extra == 'test-pyodide'
 Requires-Dist: pytest>=6; extra == 'test-pyodide'
 Requires-Dist: scikit-hep-testdata; extra == 'test-pyodide'
+Requires-Dist: selenium<=4.25.0; extra == 'test-pyodide'
 Provides-Extra: xrootd
 Requires-Dist: fsspec-xrootd; extra == 'xrootd'
 Description-Content-Type: text/markdown
@@ -263,6 +265,10 @@ Thanks especially to the gracious help of Uproot contributors (including the [or
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/Pepesob"><img src="https://avatars.githubusercontent.com/u/113636251?v=4?s=100" width="100px;" alt="Piotr Sobczyński"/><br /><sub><b>Piotr Sobczyński</b></sub></a><br /><a href="https://github.com/scikit-hep/uproot5/commits?author=Pepesob" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/giedrius2020"><img src="https://avatars.githubusercontent.com/u/71819123?v=4?s=100" width="100px;" alt="Giedrius Juškevičius"/><br /><sub><b>Giedrius Juškevičius</b></sub></a><br /><a href="https://github.com/scikit-hep/uproot5/commits?author=giedrius2020" title="Code">💻</a></td>
     </tr>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/MatousVozak"><img src="https://avatars.githubusercontent.com/u/33348191?v=4?s=100" width="100px;" alt="MatousVozak"/><br /><sub><b>MatousVozak</b></sub></a><br /><a href="https://github.com/scikit-hep/uproot5/commits?author=MatousVozak" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/rossodisera"><img src="https://avatars.githubusercontent.com/u/46961664?v=4?s=100" width="100px;" alt="Andrea Serafini"/><br /><sub><b>Andrea Serafini</b></sub></a><br /><a href="https://github.com/scikit-hep/uproot5/commits?author=rossodisera" title="Code">💻</a></td>
+    </tr>
   </tbody>
 </table>
 

{uproot-5.4.0 → uproot-5.4.2}/README.md

@@ -190,6 +190,10 @@ Thanks especially to the gracious help of Uproot contributors (including the [or
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/Pepesob"><img src="https://avatars.githubusercontent.com/u/113636251?v=4?s=100" width="100px;" alt="Piotr Sobczyński"/><br /><sub><b>Piotr Sobczyński</b></sub></a><br /><a href="https://github.com/scikit-hep/uproot5/commits?author=Pepesob" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/giedrius2020"><img src="https://avatars.githubusercontent.com/u/71819123?v=4?s=100" width="100px;" alt="Giedrius Juškevičius"/><br /><sub><b>Giedrius Juškevičius</b></sub></a><br /><a href="https://github.com/scikit-hep/uproot5/commits?author=giedrius2020" title="Code">💻</a></td>
     </tr>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/MatousVozak"><img src="https://avatars.githubusercontent.com/u/33348191?v=4?s=100" width="100px;" alt="MatousVozak"/><br /><sub><b>MatousVozak</b></sub></a><br /><a href="https://github.com/scikit-hep/uproot5/commits?author=MatousVozak" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/rossodisera"><img src="https://avatars.githubusercontent.com/u/46961664?v=4?s=100" width="100px;" alt="Andrea Serafini"/><br /><sub><b>Andrea Serafini</b></sub></a><br /><a href="https://github.com/scikit-hep/uproot5/commits?author=rossodisera" title="Code">💻</a></td>
+    </tr>
   </tbody>
 </table>
 

{uproot-5.4.0 → uproot-5.4.2}/pyproject.toml

@@ -29,6 +29,7 @@ classifiers = [
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Topic :: Scientific/Engineering",
   "Topic :: Scientific/Engineering :: Information Analysis",
   "Topic :: Scientific/Engineering :: Mathematics",
@@ -82,6 +83,7 @@ test = [
 ]
 test-pyodide = [
   "pytest>=6",
+  "selenium<=4.25.0",  # unpin once >4.26.0 is available
   "pytest-pyodide",
   "pytest-timeout",
   "scikit-hep-testdata"

{uproot-5.4.0 → uproot-5.4.2}/src/uproot/behaviors/TBranch.py

@@ -210,10 +210,16 @@ def iterate(
                             arrays, report = item
                             arrays = library.global_index(arrays, global_offset)
                             report = report.to_global(global_offset)
-                            yield arrays, report
+                            popper = [arrays]
+                            del arrays
+                            del item
+                            yield popper.pop(), report
+
                         else:
-                            arrays = library.global_index(item, global_offset)
-                            yield arrays
+                            popper = [library.global_index(item, global_offset)]
+                            del item
+                            yield popper.pop()
+
                 except uproot.exceptions.KeyInFileError:
                     if allow_missing:
                         continue
@@ -1111,6 +1117,9 @@ class HasBranches(Mapping):
                     ak_add_doc,
                 )
 
+                # no longer needed; save memory
+                del output
+
                 next_baskets = {}
                 for branch, basket_num, basket in ranges_or_baskets:
                     basket_entry_start, basket_entry_stop = basket.entry_start_stop
@@ -1119,10 +1128,14 @@ class HasBranches(Mapping):
 
                 previous_baskets = next_baskets
 
+                # no longer needed; save memory
+                popper = [out]
+                del out
+
                 if report:
-                    yield out, Report(self, sub_entry_start, sub_entry_stop)
+                    yield popper.pop(), Report(self, sub_entry_start, sub_entry_stop)
                 else:
-                    yield out
+                    yield popper.pop()
 
     def keys(
         self,
@@ -2959,6 +2972,9 @@ def _regularize_expressions(
     return arrays, expression_context, branchid_interpretation
 
 
+_basket_arrays_lock = threading.Lock()
+
+
 def _ranges_or_baskets_to_arrays(
     hasbranches,
     ranges_or_baskets,
@@ -3057,7 +3073,7 @@ def _ranges_or_baskets_to_arrays(
             context = dict(branch.context)
             context["forth"] = forth_context[branch.cache_key]
 
-            basket_arrays[basket.basket_num] = interpretation.basket_array(
+            basket_array = interpretation.basket_array(
                 basket.data,
                 basket.byte_offsets,
                 basket,
@@ -3067,16 +3083,21 @@ def _ranges_or_baskets_to_arrays(
                 library,
                 interp_options,
             )
-            if basket.num_entries != len(basket_arrays[basket.basket_num]):
+            if basket.num_entries != len(basket_array):
                 raise ValueError(
                     f"""basket {basket.basket_num} in tree/branch {branch.object_path} has the wrong number of entries """
-                    f"""(expected {basket.num_entries}, obtained {len(basket_arrays[basket.basket_num])}) when interpreted as {interpretation}
+                    f"""(expected {basket.num_entries}, obtained {len(basket_array)}) when interpreted as {interpretation}
     in file {branch.file.file_path}"""
                 )
 
+            basket_num = basket.basket_num
             basket = None
 
-            if len(basket_arrays) == branchid_num_baskets[branch.cache_key]:
+            with _basket_arrays_lock:
+                basket_arrays[basket_num] = basket_array
+                len_basket_arrays = len(basket_arrays)
+
+            if len_basket_arrays == branchid_num_baskets[branch.cache_key]:
                 arrays[branch.cache_key] = interpretation.final_array(
                     basket_arrays,
                     entry_start,
@@ -3086,8 +3107,9 @@ def _ranges_or_baskets_to_arrays(
                     branch,
                     interp_options,
                 )
-                # no longer needed, save memory
-                basket_arrays.clear()
+                with _basket_arrays_lock:
+                    # no longer needed, save memory
+                    basket_arrays.clear()
 
         except Exception:
             notifications.put(sys.exc_info())

{uproot-5.4.0 → uproot-5.4.2}/src/uproot/const.py

@@ -5,7 +5,7 @@ This module defines integer constants used by serialization and deserialization
 """
 from __future__ import annotations
 
-import struct
+from enum import IntEnum
 
 import numpy
 
@@ -118,8 +118,6 @@ kGenerateOffsetMap = numpy.uint8(1)
 kStreamedMemberWise = numpy.uint16(1 << 14)
 
 ############ RNTuple https://github.com/root-project/root/blob/master/tree/ntuple/v7/doc/specifications.md
-_rntuple_frame_format = struct.Struct("<Q")
-rntuple_env_header = _rntuple_frame_format.pack(0)  # TODO: need to check this
 rntuple_col_num_to_dtype_dict = {
     1: "uint64",
     2: "uint32",
@@ -149,6 +147,8 @@ rntuple_col_num_to_dtype_dict = {
     26: "int64",  # split + zigzag encoding
     27: "int32",  # split + zigzag encoding
     28: "int16",  # split + zigzag encoding
+    29: "float32trunc",
+    30: "float32quant",
 }
 rntuple_col_num_to_size_dict = {
     1: 64,
@@ -179,6 +179,8 @@ rntuple_col_num_to_size_dict = {
     26: 64,  # split + zigzag encoding
     27: 32,  # split + zigzag encoding
     28: 16,  # split + zigzag encoding
+    29: 32,  # TODO: variable size
+    30: 32,  # TODO: variable size
 }
 
 rntuple_col_type_to_num_dict = {
@@ -212,7 +214,49 @@ rntuple_col_type_to_num_dict = {
     "splitzigzagint16": 28,
 }
 
-rntuple_role_leaf = 0
-rntuple_role_vector = 1
-rntuple_role_struct = 2
-rntuple_role_union = 3
+
+class RNTupleLocatorType(IntEnum):
+    STANDARD = 0x00
+    LARGE = 0x01
+    DAOS = 0x02
+
+
+class RNTupleEnvelopeType(IntEnum):
+    RESERVED = 0x00
+    HEADER = 0x01
+    FOOTER = 0x02
+    PAGELIST = 0x03
+
+
+class RNTupleFieldRole(IntEnum):
+    LEAF = 0x00
+    VECTOR = 0x01
+    STRUCT = 0x02
+    UNION = 0x03
+    UNSPLIT = 0x04
+
+
+class RNTupleFieldFlag(IntEnum):
+    REPETITIVE = 0x01
+    PROJECTED = 0x02
+    CHECKSUM = 0x04
+
+
+class RNTupleColumnFlag(IntEnum):
+    DEFERRED = 0x08
+    RANGE = 0x10
+
+
+class RNTupleExtraTypeIdentifier(IntEnum):
+    ROOT = 0x00
+
+
+class RNTupleUserMetadataType(IntEnum):
+    INT = 0x01
+    BOOL = 0x02
+    DOUBLE = 0x03
+    STRING = 0x04
+
+
+class RNTupleClusterFlag(IntEnum):
+    SHARDED = 0x01

{uproot-5.4.0 → uproot-5.4.2}/src/uproot/containers.py

@@ -1541,7 +1541,7 @@ class ROOTRVec(Container, Sequence):
             return False
 
     def __array__(self, *args, **kwargs):
-        return numpy.asarray(self._vector, *args, **kwargs)
+        return numpy.asarray(self._values, *args, **kwargs)
 
     def tolist(self):
         return [
@@ -1656,7 +1656,7 @@ class STLVector(Container, Sequence):
             return False
 
     def __array__(self, *args, **kwargs):
-        return numpy.asarray(self._vector, *args, **kwargs)
+        return numpy.asarray(self._values, *args, **kwargs)
 
     def tolist(self):
         return [

{uproot-5.4.0 → uproot-5.4.2}/src/uproot/interpretation/identify.py

@@ -607,6 +607,8 @@ def _parse_node(tokens, i, typename, file, quote, header, inner_header):
         return i + 1, _parse_maybe_quote('numpy.dtype("u1")', quote)
     elif has2 and tokens[i].group(0) == "unsigned" and tokens[i + 1].group(0) == "char":
         return i + 2, _parse_maybe_quote('numpy.dtype("u1")', quote)
+    elif has2 and tokens[i].group(0) == "signed" and tokens[i + 1].group(0) == "char":
+        return i + 2, _parse_maybe_quote('numpy.dtype(">i1")', quote)
 
     elif _simplify_token(tokens[i]) == "UChar_t*":
         return (
@@ -639,6 +641,8 @@ def _parse_node(tokens, i, typename, file, quote, header, inner_header):
         has2 and tokens[i].group(0) == "unsigned" and tokens[i + 1].group(0) == "short"
     ):
         return i + 2, _parse_maybe_quote('numpy.dtype(">u2")', quote)
+    elif has2 and tokens[i].group(0) == "signed" and tokens[i + 1].group(0) == "short":
+        return i + 2, _parse_maybe_quote('numpy.dtype(">i2")', quote)
 
     elif _simplify_token(tokens[i]) == "Short_t*":
         return (
@@ -685,6 +689,8 @@ def _parse_node(tokens, i, typename, file, quote, header, inner_header):
         return i + 1, _parse_maybe_quote('numpy.dtype(">u4")', quote)
     elif has2 and tokens[i].group(0) == "unsigned" and tokens[i + 1].group(0) == "int":
         return i + 2, _parse_maybe_quote('numpy.dtype(">u4")', quote)
+    elif has2 and tokens[i].group(0) == "signed" and tokens[i + 1].group(0) == "int":
+        return i + 2, _parse_maybe_quote('numpy.dtype(">i4")', quote)
 
     elif _simplify_token(tokens[i]) == "Int_t*":
         return (
@@ -744,6 +750,8 @@ def _parse_node(tokens, i, typename, file, quote, header, inner_header):
         return i + 1, _parse_maybe_quote('numpy.dtype(">u8")', quote)
     elif has2 and tokens[i].group(0) == "unsigned" and tokens[i + 1].group(0) == "long":
         return i + 2, _parse_maybe_quote('numpy.dtype(">u8")', quote)
+    elif has2 and tokens[i].group(0) == "signed" and tokens[i + 1].group(0) == "long":
+        return i + 2, _parse_maybe_quote('numpy.dtype(">i8")', quote)
 
     elif (
         has2

{uproot-5.4.0 → uproot-5.4.2}/src/uproot/interpretation/library.py

@@ -919,7 +919,12 @@ class Pandas(Library):
             )
 
         else:
-            index = arrays.index.arrays
+            # arrays.index.values before Pandas 0.24 and again now;
+            # arrays.index.arrays from Pandas 0.24 through some time ago.
+            if hasattr(arrays.index, "values"):
+                index = arrays.index.values
+            else:
+                index = arrays.index.arrays
             numpy.add(index, global_offset, out=index)
 
         return arrays

{uproot-5.4.0 → uproot-5.4.2}/src/uproot/language/python.py

@@ -516,6 +516,10 @@ class PythonLanguage(uproot.language.Language):
                 else:
                     output[name] = output[name][cut]
 
+        # clear dicts to get rid of big arrays.
+        # note: without this these arrays are not properly released from memory!
+        values.clear()
+        scope.clear()
         return output