Uproot is a library for reading and writing ROOT files in pure Python and NumPy.

Overview

PyPI version Conda-Forge Python 3.6β€’3.10 BSD-3 Clause License Continuous integration tests

Scikit-HEP NSF-1836650 DOI 10.5281/zenodo.4340632 Documentation Gitter

Uproot is a library for reading and writing ROOT files in pure Python and NumPy.

Unlike the standard C++ ROOT implementation, Uproot is only an I/O library, primarily intended to stream data into machine learning libraries in Python. Unlike PyROOT and root_numpy, Uproot does not depend on C++ ROOT. Instead, it uses Numpy to cast blocks of data from the ROOT file as Numpy arrays.

Installation

Uproot can be installed from PyPI using pip. Awkward Array is optional but highly recommended:

pip install uproot awkward

Uproot is also available using conda (in this case, Awkward Array is automatically installed):

conda install -c conda-forge uproot

If you have already added conda-forge as a channel, the -c conda-forge is unnecessary. Adding the channel is recommended because it ensures that all of your packages use compatible versions (see conda-forge docs):

conda config --add channels conda-forge
conda update --all

Getting help

Start with the tutorials and reference documentation.

Installation for developers

Uproot is an ordinary Python library; you can get a copy of the code with

git clone https://github.com/scikit-hep/uproot4.git

and install it locally by calling pip install . in the repository directory.

If you need to develop Awkward Array as well, see its installation for developers.

Dependencies

Uproot's only strict dependency is NumPy. This is the only dependency that pip will automatically install.

Awkward Array is highly recommended. It is not a strict dependency to allow Uproot to be used in restrictive environments. If you're using Uproot without Awkward Array, you'll have to use the library="np" option or globally set uproot.default_library to return arrays as NumPy arrays (see documentation).

  • awkward: be sure to use Awkward Array 1.x.

The following libraries are also useful in conjunction with Uproot, but are not necessary. If you call a function that needs one, you'll be prompted to install it. (Conda installs most of these automatically.)

For ROOT files, compressed different ways:

  • lz4 and xxhash: only if reading ROOT files that have been LZ4-compressed.
  • zstandard: only if reading ROOT files that have been ZSTD-compressed.
  • backports.lzma: only if reading ROOT files that have been LZMA-compressed (in Python 2).

For remote data:

  • xrootd: only if reading files with root:// URLs.

For exporting data to other libraries:

  • pandas: only if library="pd".
  • cupy: only if library="cp" (reads arrays onto GPUs).
  • boost-histogram: only if converting histograms to boost-histogram with histogram.to_boost().
  • hist: only if converting histograms to hist with histogram.to_hist().

Acknowledgements

Support for this work was provided by NSF cooperative agreement OAC-1836650 (IRIS-HEP), grant OAC-1450377 (DIANA/HEP) and PHY-1520942 (US-CMS LHC Ops).

Thanks especially to the gracious help of Uproot contributors (including the original repository).


Jim Pivarski

πŸ’» πŸ“– πŸš‡ 🚧

Pratyush Das

πŸ’» πŸš‡

Chris Burr

πŸ’» πŸš‡

Dmitri Smirnov

πŸ’»

Matthew Feickert

πŸš‡

Tamas Gal

πŸ’»

Luke Kreczko

πŸ’» ⚠️

Nicholas Smith

πŸ’»

Noah Biederbeck

πŸ’»

Oksana Shadura

πŸ’» πŸš‡

Henry Schreiner

πŸ’» πŸš‡ ⚠️

Mason Proffitt

πŸ’» ⚠️

Jonas Rembser

πŸ’»

benkrikler

πŸ’»

Hans Dembinski

πŸ“–

Marcel R.

πŸ’»

Ruggero Turra

πŸ’»

Jonas RΓΌbenach

πŸ’»

bfis

πŸ’»

Raymond Ehlers

πŸ’»

Andrzej Novak

πŸ’»

Josh Bendavid

πŸ’»

Doug Davis

πŸ’»

Chao Gu

πŸ’»

Lukas Koch

πŸ’»

Michele Peresano

πŸ’»

Edoardo

πŸ’»

JMSchoeffmann

πŸ’»

alexander-held

πŸ’»

Giordon Stark

πŸ’»

Ryunosuke O'Neil

πŸ’»

ChristopheRappold

πŸ“–

Cosmin Deaconu

⚠️ πŸ’»

Carlos Pegueros

πŸ“– πŸ’‘ ⚠️ βœ…

Benjamin Tovar

πŸ’»

Duncan Macleod

πŸš‡

mpad

πŸ’»

Peter Fackeldey

πŸ’»

πŸ’» : code, πŸ“– : documentation, πŸš‡ : infrastructure, 🚧 : maintainance, ⚠ : tests and feedback, πŸ€” : foundational ideas.

Comments
  • uproot4 unable to open ROOT file with colons in the name that uproot3 can

    uproot4 unable to open ROOT file with colons in the name that uproot3 can

    Hi. I've come across an issue where if a ROOT file has a colon in the name of it uproot3 can open the file but uproot4 fails. I can't give you the file, but I can show you a minimal failing example and then a reproducible example with public files.

    Minimal Failing Example

    $ tree .
    .
    β”œβ”€β”€ data-tree
    β”‚Β Β  └──  data16_13TeV:data16_13TeV.periodA.physics_Main.PhysCont.DAOD_JETM1.grp16_v01_p4061.root
    β”œβ”€β”€ issue.py
    β”œβ”€β”€ requirements.txt
    
    1 directory, 3 files
    $ cat requirements.txt 
    uproot
    uproot4
    $ docker run --rm -it -v $PWD:/data -w /data python:3.8 /bin/bash
    root@510598a7f4e8:/data# python -m pip install --upgrade pip setuptools wheel
    root@510598a7f4e8:/data# python -m pip install -r requirements.txt
    root@510598a7f4e8:/data# python --version
    Python 3.8.5
    root@510598a7f4e8:/data# python -m pip list
    Package        Version
    -------------- -------
    awkward        0.13.0
    cachetools     4.1.1
    numpy          1.19.1
    pip            20.2.2
    setuptools     49.6.0
    uproot         3.12.0
    uproot-methods 0.7.4
    uproot4        0.0.18
    wheel          0.35.1
    root@510598a7f4e8:/data# cp data-tree/data16_13TeV\:data16_13TeV.periodA.physics_Main.PhysCont.DAOD_JETM1.grp16_v01_p4061.root data-tree/renamed.root
    root@510598a7f4e8:/data# python
    Python 3.8.5 (default, Aug  5 2020, 08:22:02) 
    [GCC 8.3.0] on linux
    Type "help", "copyright", "credits" or "license" for more information.
    >>> import uproot as uproot3
    >>> import uproot4
    >>> from pathlib import Path
    >>> 
    >>> uproot3_file = uproot3.open(
    ...     "data-tree/data16_13TeV:data16_13TeV.periodA.physics_Main.PhysCont.DAOD_JETM1.grp16_v01_p4061.root"
    ... )
    >>> print(f"uproot3 opens file as {uproot3_file}")
    uproot3 opens file as <ROOTDirectory b'/home/feickert/workarea/submitDir/data-tree//data16_13TeV:data16_13TeV.periodA.physics_Main.PhysCont.DAOD_JETM1.grp16_v01_p4061.root' at 0x7fce6da5b5e0>
    >>> 
    >>> # uproot4 fails with the ':' in the filename
    >>> uproot4.open(
    ...     "data-tree/data16_13TeV:data16_13TeV.periodA.physics_Main.PhysCont.DAOD_JETM1.grp16_v01_p4061.root"
    ... )
    Traceback (most recent call last):
      File "/usr/local/lib/python3.8/site-packages/uproot4/source/file.py", line 74, in __init__
        self._file = numpy.memmap(self._file_path, dtype=self._dtype, mode="r")
      File "/usr/local/lib/python3.8/site-packages/numpy/core/memmap.py", line 225, in __new__
        f_ctx = open(os_fspath(filename), ('r' if mode == 'c' else mode)+'b')
    FileNotFoundError: [Errno 2] No such file or directory: 'data-tree/data16_13TeV'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<stdin>", line 1, in <module>
      File "/usr/local/lib/python3.8/site-packages/uproot4/reading.py", line 78, in open
        file = ReadOnlyFile(
      File "/usr/local/lib/python3.8/site-packages/uproot4/reading.py", line 265, in __init__
        self._source = Source(file_path, **self._options)
      File "/usr/local/lib/python3.8/site-packages/uproot4/source/file.py", line 80, in __init__
        self._fallback = uproot4.source.file.FileSource(file_path, opts)
    AttributeError: module 'uproot4.source.file' has no attribute 'FileSource'
    >>> # even if that is inside a pathlib object
    >>> uproot4.open(
    ...     Path(
    ...         "data-tree/data16_13TeV:data16_13TeV.periodA.physics_Main.PhysCont.DAOD_JETM1.grp16_v01_p4061.root"
    ...     )
    ... )
    Traceback (most recent call last):
      File "/usr/local/lib/python3.8/site-packages/uproot4/source/file.py", line 74, in __init__
        self._file = numpy.memmap(self._file_path, dtype=self._dtype, mode="r")
      File "/usr/local/lib/python3.8/site-packages/numpy/core/memmap.py", line 225, in __new__
        f_ctx = open(os_fspath(filename), ('r' if mode == 'c' else mode)+'b')
    FileNotFoundError: [Errno 2] No such file or directory: 'data-tree/data16_13TeV'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<stdin>", line 1, in <module>
      File "/usr/local/lib/python3.8/site-packages/uproot4/reading.py", line 78, in open
        file = ReadOnlyFile(
      File "/usr/local/lib/python3.8/site-packages/uproot4/reading.py", line 265, in __init__
        self._source = Source(file_path, **self._options)
      File "/usr/local/lib/python3.8/site-packages/uproot4/source/file.py", line 80, in __init__
        self._fallback = uproot4.source.file.FileSource(file_path, opts)
    AttributeError: module 'uproot4.source.file' has no attribute 'FileSource'
    >>> # but the file itself is fine
    >>> uproot4.open("data-tree/renamed.root")
    <ReadOnlyDirectory '/' at 0x7fce725e7670>
    
    

    Failing Reproducible Example

    # issue.py
    import uproot as uproot3
    import uproot4
    from pathlib import Path
    
    
    def main():
        # curl -sL https://github.com/scikit-hep/scikit-hep-testdata/raw/master/src/skhep_testdata/data/uproot-HZZ-lz4.root -o uproot-HZZ-lz4.root
        uproot3.open("uproot-HZZ-lz4.root")
        uproot3.open("uproot:HZZ-lz4.root")
        uproot3.open(Path("uproot:HZZ-lz4.root"))
    
        uproot4.open("uproot-HZZ-lz4.root")
        uproot4.open("uproot:HZZ-lz4.root")
    
    
    if __name__ == "__main__":
        main()
    
    root@510598a7f4e8:/data# curl -sL https://github.com/scikit-hep/scikit-hep-testdata/raw/master/src/skhep_testdata/data/uproot-HZZ-lz4.root -o uproot-HZZ-lz4.root
    root@510598a7f4e8:/data# cp uproot-HZZ-lz4.root uproot:HZZ-lz4.root 
    root@510598a7f4e8:/data# python issue.py 
    Traceback (most recent call last):
      File "issue.py", line 17, in <module>
        main()
      File "issue.py", line 9, in main
        uproot3.open("uproot:HZZ-lz4.root")
      File "/usr/local/lib/python3.8/site-packages/uproot/rootio.py", line 63, in open
        raise ValueError("URI scheme not recognized: {0}".format(path))
    ValueError: URI scheme not recognized: uproot:HZZ-lz4.root
    
    

    Comments

    I realize that this is probably because uproot4's open's path is

    https://github.com/scikit-hep/uproot4/blob/b8828069b9ae52c742fb704f07e1a4e179fe7b30/uproot4/reading.py#L43-L46

    and it isn't a good idea to have a file with a colon in it in general. However, there are ATLAS files that do, and it would be nice if uproot3 behavior toward filenames could still be supported. If support for this is firmly out of scope it would be great if there could be some huge warning about this in the docs.

    policy 
    opened by matthewfeickert 38
  • Loading multiple large files (>4GB) onto a lazy array produces deserialization error

    Loading multiple large files (>4GB) onto a lazy array produces deserialization error

    Issue description

    This is an issue regarding the question posted here: https://stackoverflow.com/questions/64565208/how-can-i-load-many-very-large-files-using-uproot

    When loading 3 files of about 9 GB each onto a lazy array, the code crashes when the event loop reaches the borders between the first and second files producing a deserialization error. The code works flawlessly with small (~ 1 GB) files. Way of access (local vs XRootD) also doesn't seem to affect the issue. The error message is the following:

    Traceback (most recent call last):
      File "scripts/plotEventShapes_lazy.py", line 44, in <module>
        tracks_x = events['Tracks.fCoordinates.fX'][ievt]
      File "/Users/chrispap/Library/Python/3.8/lib/python/site-packages/awkward1/highlevel.py", line 946, in __getitem__
        self._layout[where], self._behavior, cache=self._cache
      File "/Users/chrispap/Library/Python/3.8/lib/python/site-packages/awkward1/partition.py", line 366, in __getitem__
        return PartitionedArray.from_ext(self._ext.getitem_at(where))
      File "/Users/chrispap/Library/Python/3.8/lib/python/site-packages/uproot4/behaviors/TBranch.py", line 1621, in array
        _ranges_or_baskets_to_arrays(
      File "/Users/chrispap/Library/Python/3.8/lib/python/site-packages/uproot4/behaviors/TBranch.py", line 518, in _ranges_or_baskets_to_arrays
        uproot4.source.futures.delayed_raise(*obj)
      File "/Users/chrispap/Library/Python/3.8/lib/python/site-packages/uproot4/source/futures.py", line 37, in delayed_raise
        raise exception_value.with_traceback(traceback)
      File "/Users/chrispap/Library/Python/3.8/lib/python/site-packages/uproot4/behaviors/TBranch.py", line 444, in chunk_to_basket
        basket = uproot4.models.TBasket.Model_TBasket.read(
      File "/Users/chrispap/Library/Python/3.8/lib/python/site-packages/uproot4/model.py", line 128, in read
        self.read_members(chunk, cursor, context, file)
      File "/Users/chrispap/Library/Python/3.8/lib/python/site-packages/uproot4/models/TBasket.py", line 55, in read_members
        ) = cursor.fields(chunk, _tbasket_format2, context)
      File "/Users/chrispap/Library/Python/3.8/lib/python/site-packages/uproot4/source/cursor.py", line 168, in fields
        return format.unpack(chunk.get(start, stop, self, context))
      File "/Users/chrispap/Library/Python/3.8/lib/python/site-packages/uproot4/source/chunk.py", line 278, in get
        raise uproot4.deserialization.DeserializationError(
    uproot4.deserialization.DeserializationError: while reading
    
        TBasket version None as uproot4.models.TBasket.Model_TBasket (? bytes)
            fNbytes: -1607368158
            fObjlen: -1243566277
            fDatime: 2634931141
            fKeylen: -27664
            fCycle: 21409
    
    attempting to get bytes 483015:483033
    outside expected range 510698:538758 for this Chunk
    in file /Users/chrispap/QCD/Autumn18.QCD_HT1500to2000_TuneCP5_13TeV-madgraphMLM-pythia8_RA2AnalysisTree.root
    

    Reproduction instructions

    The three very large files (9 GB each) are the following:

    root://cmseos.fnal.gov//store/user/kdipetri/SUEP/Production_v0.2/2018/NTUP/Autumn18.QCD_HT1000to1500_TuneCP5_13TeV-madgraphMLM-pythia8_RA2AnalysisTree.root
    root://cmseos.fnal.gov//store/user/kdipetri/SUEP/Production_v0.2/2018/NTUP/Autumn18.QCD_HT1500to2000_TuneCP5_13TeV-madgraphMLM-pythia8_RA2AnalysisTree.root
    root://cmseos.fnal.gov//store/user/kdipetri/SUEP/Production_v0.2/2018/NTUP/Autumn18.QCD_HT2000toInf_TuneCP5_13TeV-madgraphMLM-pythia8_RA2AnalysisTree.root
    

    Two smaller files (1 GB) for which the code works nicely:

    root://cmseos.fnal.gov//store/user/kdipetri/SUEP/Production_v0.2/2018/NTUP/PrivateSamples.SUEP_2018_mMed-1000_mDark-2_temp-2_decay-darkPho_13TeV-pythia8_n-100_0_RA2AnalysisTree.root
    root://cmseos.fnal.gov//store/user/kdipetri/SUEP/Production_v0.2/2018/NTUP/PrivateSamples.SUEP_2018_mMed-1000_mDark-2_temp-2_decay-darkPhoHad_13TeV-pythia8_n-100_0_RA2AnalysisTree.root
    

    The following code reproduces the issue using the files that I cite above:

    import uproot4 as uproot
    import uproot_methods
    import awkward1 as ak
    import numpy as np
    import matplotlib.pyplot as plt
    
    # Get the file and import using uproot
    base = 'root://cmseos.fnal.gov//store/user/kdipetri/SUEP/Production_v0.2/2018/NTUP/'
    #base = '/Users/chrispap/QCD/'
    datasets = {
        base + 'Autumn18.QCD_HT1000to1500_TuneCP5_13TeV-madgraphMLM-pythia8_RA2AnalysisTree.root': 'TreeMaker2/PreSelection',
        base + 'Autumn18.QCD_HT1500to2000_TuneCP5_13TeV-madgraphMLM-pythia8_RA2AnalysisTree.root': 'TreeMaker2/PreSelection',
        base + 'Autumn18.QCD_HT2000toInf_TuneCP5_13TeV-madgraphMLM-pythia8_RA2AnalysisTree.root': 'TreeMaker2/PreSelection',
    }
    
    events = uproot.lazy(datasets)
    
    multiplicity = np.zeros(len(events['Tracks.fCoordinates.fX']))
    for ievt in range(99000,len(events['Tracks.fCoordinates.fX'])):
        if ievt%1000 == 0:
            print("Processing event %d. Progress: %.2f%%"%(ievt,100*ievt/len(events['Tracks.fCoordinates.fX'])))
        if events['HT'][ievt] < 1200:
            multiplicity[ievt] = -1
            continue
        tracks_x = events['Tracks.fCoordinates.fX'][ievt]
        tracks_y = events['Tracks.fCoordinates.fY'][ievt]
        tracks_z = events['Tracks.fCoordinates.fZ'][ievt]
        tracks_E = np.sqrt(tracks_x**2+tracks_y**2+tracks_z**2+0.13957**2)
        tracks = uproot_methods.TLorentzVectorArray.from_cartesian(ak.to_awkward0(tracks_x),
                                                                   ak.to_awkward0(tracks_y),
                                                                   ak.to_awkward0(tracks_z),
                                                                   ak.to_awkward0(tracks_E))
        tracks_fromPV0 = events['Tracks_fromPV0'][ievt]
        tracks_matchedToPFCandidate = events['Tracks_matchedToPFCandidate'][ievt]
        tracks = tracks[(tracks.pt > 1.) & (tracks.eta < 2.5) &
                        (ak.to_awkward0(tracks_fromPV0) >= 2) &
                        (ak.to_awkward0(tracks_matchedToPFCandidate) > 0)]
        multiplicity[ievt] = tracks.size
    
    # Plot results
    fig = plt.figure(figsize=(8,8))
    ax = plt.gca()
    
    CrossSection = events['CrossSection'][events['HT'] > 1200]
    multiplicity = multiplicity[events['HT'] > 1200]
    
    ax.hist(multiplicity, bins=100, density=True, weights=CrossSection, histtype='step', color='b')
    
    plt.show()
    
    bug (unverified) 
    opened by chrispap95 20
  • Drawing of histograms created in uproot fails in ROOT

    Drawing of histograms created in uproot fails in ROOT

    When saving a histogram in a ROOT file using Uproot, if the content of the last bin in the histogram is negative, ROOT will fail to plot it. The error message is

    TCanvas::ResizePad:0: RuntimeWarning: Inf/NaN propagated to the pad. Check drawn objects.
    TCanvas::ResizePad:0: RuntimeWarning: Canvas_1 height changed from 0 to 10
    

    If the last bin's content is non-negative, plotting works.

    To reproduce, create the histogram

    import numpy as np
    import uproot
    
    with uproot.recreate("test.root") as f:
        f["hist_fail"] = (np.asarray([-3, -2, -1]), np.asarray([0, 1, 2, 3]))
        f["hist_pass"] = (np.asarray([-3, -2, +1]), np.asarray([0, 1, 2, 3]))
    

    Opening test.root using rootbrowser (or just root, getting the histograms, and plotting them using Draw()) results in the hist_pass being drawn, while hist_fail won't be.

    Furthermore, even the hist_pass isn't drawn properly - the y-axis starts at 0. When creating the same histogram in ROOT, the range includes all the events.

    I think the issue is caused by the errors of the histogram bins - ROOT initializes them as sqrt(abs(content)) while uproot uses sqrt(content), leading to nans for negative numbers. Not sure what is special about the last bin, though.

    Uproot 4.3.4 ROOT 6.26/04

    bug 
    opened by dcervenkov 17
  • File access methods performance studies

    File access methods performance studies

    Data provided by @chrisburr; discussion below

    If I'm making a fundamental mistake in these file access methods, then I don't want to design around it. I've been thinking about how I can adequately test that. Do you have a suggestion for a publicly available test file?

    I default to using these three open data files for XRootD:

    $ xrdfs root://eospublic.cern.ch/ ls -l /eos/opendata/lhcb/AntimatterMatters2017/data
    -r-- 2017-03-07 13:53:05   666484974 /eos/opendata/lhcb/AntimatterMatters2017/data/B2HHH_MagnetDown.root
    -r-- 2017-03-07 13:53:08   444723234 /eos/opendata/lhcb/AntimatterMatters2017/data/B2HHH_MagnetUp.root
    -r-- 2017-03-07 13:53:08     2272072 /eos/opendata/lhcb/AntimatterMatters2017/data/PhaseSpaceSimulation.root
    

    I've just copied them to CERN S3 so they can be accessed using standard HTTP(S) as well:

    • https://scikit-hep-test-data.s3.cern.ch/B2HHH_MagnetDown.root
    • https://scikit-hep-test-data.s3.cern.ch/B2HHH_MagnetUp.root
    • https://scikit-hep-test-data.s3.cern.ch/PhaseSpaceSimulation.root

    Would a test through a household ISP mean anything, given that most of these files would be used on university or lab computers or on the GRID?

    It's definitely useful as the quality of institute connections varies a lot in my experience and it's more likely to expose issues with latency, especially given you'll be accessing them from the US. I think a good implementation should only be limited by bandwidth when reading large enough files.

    If you put together a test I can easily try it at a few different institutes as well as pushing a test job to every LHCb grid site.

    Originally posted by @chrisburr in https://github.com/scikit-hep/uproot4/pull/1#issuecomment-627928856

    performance 
    opened by jpivarski 17
  • fix: missing hist flow bins handling

    fix: missing hist flow bins handling

    Currently, when uproot writes hist histograms without flow bins, the property isn't checked and regular edge bins get written as flow bins causing weird issues with reading.

    import uproot
    import hist
    import numpy as np
    import mplhep as hep
    
    h = hist.new.Reg(20, 0, 20, name='msd', flow=False).Weight().fill(np.random.normal(10, 6, 1000))
    
    fout = uproot.recreate('test.root')
    fout['test'] = h
    fout.close()
    
    fin = uproot.open('test.root')
    h_read = fin['test']
    fin.close()
    
    len(h.values()), len(h_read.values()), len(h.axes[0].edges)
    
    >>> (20, 18, 21)
    

    This PR materializes the empty flow bins as Nans when writing and filters them out again when reading to match the current expected behaviour. The caveat is that when only one flow bin exists when storing, it won't be obvious which one it is when reading the TH1 with values(flow=True) Possibly this should return a masked array instead to be clearer, but I didn't want to change the return type here.

    opened by andrzejnovak 16
  • feat: Add TGraphAsymmErrors

    feat: Add TGraphAsymmErrors

    here's a test script to work with

    import uproot
    import os.path
    
    fname = "HEPData-ins1755298-v3-Expected_limit_1lbb.root"
    
    if not os.path.isfile(fname):
        with open(fname, 'wb') as f:
            import requests
            response = requests.get("https://www.hepdata.net/download/table/ins1755298/Expected%20limit%201lbb/3/root")
            response.raise_for_status()
            f.write(response.content)
    
    f = uproot.open(fname)
    graph = f['Expected limit 1lbb/Graph1D_y1']
    graph.values()
    graph.errors()
    
    opened by kratsg 16
  • refactor: modernize setup

    refactor: modernize setup

    This is an attempt to modernize the setup. This fixes the issue with https://github.com/conda-forge/uproot-feedstock/pull/73 - and is generally much cleaner and nicer being declarative.

    opened by henryiii 15
  • fix: working TList serialization

    fix: working TList serialization

    Closes https://github.com/scikit-hep/uproot5/issues/762.

    This PR was motivated because of problems serializing TList.

    • TList serialization was fixed in 4da653fee0f28789fbb20abcad3a4541acd6701a.

    A few other minor improvements were done along the way:

    • TObject should now correctly serialize fUniqueID member (previously it was using only 0).
    • TObject __repr__ is fixed.
    • A method Model_TObject.empty has been added as override to avoid using its parent method in order to simplify code.
    • TObjString now correctly initializes its bases with a TObject with all its members.
    • Updated some tojson calls of above mentined classes.
    • Added / Updated tests for writing and reading TObjString and TList.
    opened by lobis 14
  • Add TGraph, RooCurve, and RooHist behaviours.

    Add TGraph, RooCurve, and RooHist behaviours.

    This adds a behaviour for TGraph (based on that for TGraphAsymmErrors), and behaviours for RooHist and RooCurve based on these. These make it easier to plot RooFit objects on a plot that's otherwise made with Python.

    ~~Draft because I haven't added any tests yet. I thought it would be better to discuss first.~~

    opened by beojan 14
  • feat: support categorical axes on boost histograms

    feat: support categorical axes on boost histograms

    Closes https://github.com/scikit-hep/uproot5/issues/672.

    The logic for setting the fLabels on the axis is pretty straightforward, however to achieve this we need to serialize THashList which is not currently implemented.

    While working on this I found out a problem when serializing TList (which THashList inherits directly from), which is pointed out in https://github.com/scikit-hep/uproot5/issues/762 and is fixed by https://github.com/scikit-hep/uproot5/pull/763.

    Another issue related to weighted histograms was also found and fixed at https://github.com/scikit-hep/uproot5/pull/774.

    Summary of changes:

    • Implement THashList serialization and to_HashList factory method.
    • Add tests for THashList writing. Compare serialization (bytes) to TList as they should be the same except for class name.
    • The name (fName) of all axes is now xaxis, yaxis or zaxis regardless of user definition, as this field should not be modified by the user since it causes problems on histogram drawing. (The text of the axis is fTitle). Tests have been updated accordingly.
    • Add tests for histograms with categorical axes.
    next-release 
    opened by lobis 13
  • Which cycle ReadOnlyDirectory should return when not specified

    Which cycle ReadOnlyDirectory should return when not specified

    Hello,

    I've tried to use uproot to parse *.root files; At the same time, I used c++ to verify.

    In the same root file: For Python:

    import uproot
    uproot.__version__         # (4.0.11)
    
    Coins = uproot.open(input_file + ':Coincidences')
    print(Coins.num_entries)
    

    For C++:

    #include "TFile.h"
    #include "TTree.h"
    
    TFile *rootFile;
    rootFile = TFile::Open(root_filename.c_str());
    TTree *Coins = (TTree*)rootFile->Get("Coincidences");
    
    int nevents = Coins->GetEntries();
    std::cout << nevents << std::endl;
    

    The results:

    • Python: 34393000
    • C++ : 34393400

    Why???

    Best regards,

    Connor,

    bug 
    opened by HeConnor 13
  • DAOD_PHYSLITE works in pure python interpretation, not in awkward-forth (uproot 5.0.0)

    DAOD_PHYSLITE works in pure python interpretation, not in awkward-forth (uproot 5.0.0)

    A test in coffea results in:

    ValueError: 'skip beyond' in AwkwardForth runtime: tried to skip beyond the bounds of an input (0 or length)
    

    when awkward forth is used, and passes when forcing the pure-python interpretation paths to be used. These tests involve iterating over arrays and fully validating the data contained, so the arrays produced within the test are correct (and in fact the same data-wise as uproot4/awkward1).

    To reproduce this:

    $ pip install 'git+https://github.com/CoffeaTeam/coffea.git@awkward2_dev'
    $ python -c 'from coffea.nanoevents import NanoEventsFactory, PHYSLITESchema; NanoEventsFactory.from_root("https://github.com/CoffeaTeam/coffea/blob/master/tests/samples/DAOD_PHYSLITE_21.2.108.0.art.pool.root?raw=true", treepath="CollectionTree", schemaclass=PHYSLITESchema, use_ak_forth=False).events()'
    $ python -c 'from coffea.nanoevents import NanoEventsFactory, PHYSLITESchema; NanoEventsFactory.from_root("https://github.com/CoffeaTeam/coffea/blob/master/tests/samples/DAOD_PHYSLITE_21.2.108.0.art.pool.root?raw=true", treepath="CollectionTree", schemaclass=PHYSLITESchema, use_ak_forth=True).events()'
    
    bug 
    opened by lgray 1
  • Problems when saving jagged arrays

    Problems when saving jagged arrays

    I'm a newbie to uproot and encountered some problems when trying to use uproot. Sorry for possible misunderstandings of the usage, though I think my expectation might be reasonable.

    Create a jagged array

    import uproot
    import awkward as ak
    array = ak.Array({'a': [[1.1, 2.2, 3.3], [], [4.4, 5.5]], 'b': [[1.1, 2.2, 3.3], [], [4.4, 5.5]], 'c': [1, 2, 3]})
    

    and save it to a ROOT file

    with uproot.recreate('data.root') as output_file:
        output_file['tree'] = array
    

    I expect that the saved tree has 3 branches

    name | typename | interpretation
    ---------------------+--------------------------+------------------------------- a | double[] | AsJagged(AsDtype('>f8')) b | double[] | AsJagged(AsDtype('>f8')) c | int64_t | AsDtype('>i8')

    but actually I got errors

    TypeError: fields of a record must be NumPy types, though the record itself may be in a jagged array

    field 'a' has type var * float64

    This situation easily happens when reading a TTree with variable length arrays and then saving it back after some manipulations.

    feature 
    opened by laf070810 2
  • Support for TLeafG

    Support for TLeafG

    I have a tree with TLeafG type. When I try to process it, I get the following:

    name | typename | interpretation
    ---------------------+--------------------------+------------------------------- runNumber | int32_t | AsDtype('>i4') subrunNumber | int32_t | AsDtype('>i4') timestamp | unknown | <UnknownInterpretation 'non...

    Would it be possible to add the support for TLeafG type in identify.py?

    Thanks, Yuri.

    What you're looking for might already be possible as a combination of existing functions, so these requests might get converted into requests for documentation (with a corresponding change in title).

    Here are some links to documentation, to help you in your search.

    feature 
    opened by oksuzian 1
  • How to create an empty tree with several var-length branches that share the var length

    How to create an empty tree with several var-length branches that share the var length

    I want to write several variable length arrays that have the same length to an empty tree. https://uproot.readthedocs.io/en/latest/basic.html#extending-ttrees-with-large-datasets explains

    1. How to generate an empty tree with mktree, which can be extended later, I need this
    2. How to generate a tree with several arrays that share the length and already contain data, with awkward.zip

    What I am missing is the combination of the two. I want to start with an empty tree like in 1) that has branches which share the varlength. Then I want to extend this tree subsequently. Is this possible? If not, may I suggest the following intuitive API:

    Instead of {"x": "var * float32", "y": "var * float32"}, which generates two extra branches "nx" and "ny", please allow this declaration, where the counting branch is explicit:

    {"n": "int32", "x": "n * float32", "y": "n * float32"}

    As the Python of Zen says, explicit is better than implicit.

    docs 
    opened by HDembinski 3
  • uproot.open(filename,

    uproot.open(filename, "w") and uproot.open(filename, mode="w") fail

    uproot 4.3.7

    When opening a root file for writing, the call to uproot.open(filename, mode="w") fails with this error message

    ---------------------------------------------------------------------------
    AttributeError                            Traceback (most recent call last)
    Cell In [15], line 2
          1 with uproot.open("output.root", mode="w") as f:
    ----> 2     f.mktree("tree", {
          3         "px": "var * float32",
          4     })
          5     f["tree"].show()
    
    AttributeError: 'ReadOnlyDirectory' object has no attribute 'mktree'
    

    It looks like mode="w" is ignored. This is not pythonic. By providing uproot.open you are suggesting that you mimic the interface of the open command, which is used in several places in the Python stdlib (builtins open, gzip.open, lzma.open, ...). But then you should also mimics the signature of the stdlib version as much as possible. Calling uproot.open with mode="w" should forward to uproot.recreate.

    uproot.open(filename, "w") fails with a different error, because the next positional argument after path is not mode, but object_cache. To fix this, mode should be added as the second argument after path or uproot.open should reject positional arguments after path with the signature open(path, *, object_cache=...)

    bug (unverified) 
    opened by HDembinski 5
Releases(v5.0.2)
  • v5.0.2(Dec 22, 2022)

    New features

    (none!)

    Bug-fixes and performance

    • fix: uproot.dask: Protect against branches=None in project_columns by @douglasdavis in https://github.com/scikit-hep/uproot5/pull/806
    • fix: AsStridedObjects.awkward_form was still including the '@' members. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/808

    Other

    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/807

    Full Changelog: https://github.com/scikit-hep/uproot5/compare/v5.0.1...v5.0.2

    Source code(tar.gz)
    Source code(zip)
  • v5.0.1(Dec 15, 2022)

    New features

    (none!)

    Bug-fixes and performance

    • fix: protect Uproot's 'project_columns' from Dask node names. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/801

    Other

    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/799
    • docs: update documentation about Pandas; we don't do MultiIndex anymore. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/802
    • chore(deps): bump pypa/gh-action-pypi-publish from 1.6.1 to 1.6.4 by @dependabot in https://github.com/scikit-hep/uproot5/pull/797

    Full Changelog: https://github.com/scikit-hep/uproot5/compare/v5.0.0...v5.0.1

    Source code(tar.gz)
    Source code(zip)
  • v5.0.0(Dec 10, 2022)

    Uproot version 5.0.0

    Uproot version 5 has a few major new features, one removal (uproot.lazy), and is based on Awkward Array version 2 instead of version 1.

    uproot.lazy β†’ uproot.dask

    @kkothari2001 upgraded Uproot from Awkward version 1 to version 2, the major part of which was replacing uproot.lazy, which is based on Awkward 1's virtual and partitioned lazy arrays, with the new Dask collection, dask-awkward. The entry point for this function is uproot.dask.

    @kkothari2001 also simplified Uproot's Pandas backend, which used to "explode" ragged arrays from ROOT into Pandas DataFrames with a non-trivial MultiIndex. Now, it takes advantage of awkward-pandas to put ragged (and more complex) Awkward Arrays directly into Pandas columns.

    If you want the old behavior, you can read data using library="ak" to get an Awkward Array, and use ak.to_dataframe to "explode" the data into a MultiIndex.

    TTree-reading with AwkwardForth

    @aryan26roy added a new code path to the TTree-reading routines to read them with AwkwardForth instead of pure Python. Users won't see any interface changes due to this code, but the performance of reading TBranches with AsObject or AsStrings Interpretations should be orders of magnitude faster. For example, std::vector<std::vector<float>> reading is now 400Γ— faster.

    Reading RNTuples

    @Moelf added a complete reader of RNTuple data with most of an RNTuple-writer in an unmerged pull request (#705). Although the RNTuple format is still in development, this is a very good start at reading RNTuple data, whose structure is a close match to Awkward Arrays (so the translation is more one-to-one than it is for TTrees, for instance).

    New features

    • feat: move to hatchling by @henryiii in https://github.com/scikit-hep/uproot5/pull/688
    • feat: from_map like optimization for dask arrays by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/679
    • feat: Finalizing AwkwardForth reader for Uproot by @aryan26roy in https://github.com/scikit-hep/uproot5/pull/644
    • feat: implemented NON-memberwise deserialization for AsMap. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/746
    • feat: Added column_projection optimization by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/755
    • feat: support categorical axes on boost histograms by @lobis in https://github.com/scikit-hep/uproot5/pull/764
    • feat: warn about TBranch name, alias name conflict. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/776
    • feat: any Mapping assigned to a WritableDirectory is interpreted as a TTree or failure, no fall-through. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/779
    • feat: add 'interp_options' mechanism and ak_add_doc. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/784
    • feat: Use awkward pandas, instead of the existing code that explodes Pandas Dataframes by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/734
    • feat: made 'very optional' arguments keyword-only by @jpivarski in https://github.com/scikit-hep/uproot5/pull/787
    • feat: adjust for name change in scikit-hep/awkward#1919. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/788

    Bug-fixes and performance

    • fix: depend on packaging, not setuptools vendored packaging by @henryiii in https://github.com/scikit-hep/uproot5/pull/684
    • fix: Avoid triggering temporary dask-awkward/awkward incompatibility. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/694
    • fix: Do not write incorrect fSumw2 in histograms (v5). by @jpivarski in https://github.com/scikit-hep/uproot5/pull/698
    • fix: Fixes uproot.dask bug with empty branches by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/700
    • fix: Use from_map optimization for delayed numpy arrays and add tests with empty branches for the same by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/703
    • fix: use ctx manager to ensure resources are freed by @agoose77 in https://github.com/scikit-hep/uproot5/pull/713
    • fix: ReadOnlyDirectory should provide the largest abs(cycle) when cycle is unspecified, not the largest cycle. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/715
    • fix: regularize ROOT type aliases to C fundamental type names. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/717
    • fix: avoid empty TBasket issue in embedded TBasket by @jpivarski in https://github.com/scikit-hep/uproot5/pull/751
    • fix: don't use Awkward in test_0751 that doesn't need it by @jpivarski in https://github.com/scikit-hep/uproot5/pull/753
    • fix: working TList serialization by @lobis in https://github.com/scikit-hep/uproot5/pull/763
    • fix: histogram weights not handled correctly in hist / boost conversion by @lobis in https://github.com/scikit-hep/uproot5/pull/774
    • perf: streamline metadata handling for TBranch name lookup and uproot.dask by @jpivarski in https://github.com/scikit-hep/uproot5/pull/772
    • fix: ensure AwkwardForth fallback path is tested without history. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/780
    • fix: all AwkwardForth Forms now agree with awkward_form method output. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/790
    • fix: Uproot tests now work with Awkward 2.0.0. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/795

    Other

    • Manually add a Model for TMatrixTSym. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/484
    • Updating docs and test in response to the removal of uproot.lazy in Uproot5 by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/615
    • changed arguments for awkward_form by @aryan26roy in https://github.com/scikit-hep/uproot5/pull/617
    • Completed the Forth based AsStrings reader. by @aryan26roy in https://github.com/scikit-hep/uproot5/pull/616
    • Actually pass user-specified 'awkward_form' arguments into context. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/622
    • Fix annoying gaps in test files. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/625
    • Cleaning up string generation in streamers.py by @aryan26roy in https://github.com/scikit-hep/uproot5/pull/629
    • chore: add dependabot for actions by @henryiii in https://github.com/scikit-hep/uproot5/pull/631
    • Bump actions/checkout from 2 to 3 by @dependabot in https://github.com/scikit-hep/uproot5/pull/632
    • Bump actions/upload-artifact from 2 to 3 by @dependabot in https://github.com/scikit-hep/uproot5/pull/633
    • Bump pypa/gh-action-pypi-publish from 1.4.2 to 1.5.0 by @dependabot in https://github.com/scikit-hep/uproot5/pull/634
    • Bump actions/download-artifact from 2 to 3 by @dependabot in https://github.com/scikit-hep/uproot5/pull/635
    • Forth based ROOT reader (revised) by @aryan26roy in https://github.com/scikit-hep/uproot5/pull/636
    • Set up tests for AsObjects, for the AwkwardForth reader by @jpivarski in https://github.com/scikit-hep/uproot5/pull/637
    • Iterate over objects in TDirectory in linear time. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/638
    • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/641
    • Awkward v2 update by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/620
    • docs: add aryan26roy as a contributor for code by @allcontributors in https://github.com/scikit-hep/uproot5/pull/645
    • docs: add kkothari2001 as a contributor for code by @allcontributors in https://github.com/scikit-hep/uproot5/pull/646
    • docs: add Moelf as a contributor for code by @allcontributors in https://github.com/scikit-hep/uproot5/pull/647
    • chore: cleanup flake8 by @henryiii in https://github.com/scikit-hep/uproot5/pull/527
    • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/650
    • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/654
    • Bump pypa/gh-action-pypi-publish from 1.5.0 to 1.5.1 by @dependabot in https://github.com/scikit-hep/uproot5/pull/656
    • Primitive Support for RNTuple by @Moelf in https://github.com/scikit-hep/uproot5/pull/630
    • Set ReadOnlyDirectory attributes when fSeekKeys == 0 by @kakwok in https://github.com/scikit-hep/uproot5/pull/660
    • docs: add kakwok as a contributor for code by @allcontributors in https://github.com/scikit-hep/uproot5/pull/663
    • Dask awkward support for uproot.dask by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/652
    • pathlib.Path drops '//' (naturally), but it's sometimes used for URLs by @jpivarski in https://github.com/scikit-hep/uproot5/pull/670
    • Gets the number of overflow bins for hist.axis.IntCategory, at least. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/671
    • Prevent std::pair from being AsStridedObjects. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/673
    • Implement transformed axis from boost-histogram/hist. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/675
    • AsDynamic has no self._header. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/674
    • Fixed TTree write_anew in a subdirectory (consistent caches). by @jpivarski in https://github.com/scikit-hep/uproot5/pull/677
    • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/657
    • Implement stl containers for RNTuple by @Moelf in https://github.com/scikit-hep/uproot5/pull/662
    • Multiple clusters support for RNTuple by @Moelf in https://github.com/scikit-hep/uproot5/pull/682
    • ci: Get test dependencies from one source by @jpivarski in https://github.com/scikit-hep/uproot5/pull/686
    • ci: autocancel repeated runs by @henryiii in https://github.com/scikit-hep/uproot5/pull/685
    • ci: use mamba by @henryiii in https://github.com/scikit-hep/uproot5/pull/683
    • ci: Lint PR titles according to conventional commits by @jpivarski in https://github.com/scikit-hep/uproot5/pull/689
    • docs: Installation requirements and error text for dask/dask-awkward in extras.py by @jpivarski in https://github.com/scikit-hep/uproot5/pull/690
    • ci: use concurrency group for semantic-pr-title by @agoose77 in https://github.com/scikit-hep/uproot5/pull/691
    • docs: Add image for dask docs by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/708
    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/706
    • chore: dask_awkward.test_utils moved in ContinuumIO/dask-awkward#76 by @jpivarski in https://github.com/scikit-hep/uproot5/pull/714
    • test: adjust for boost-histogram 1.3.2's _storage_type deprecation. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/719
    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/716
    • add veprbl as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/728
    • add nikoladze as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/729
    • add klieret as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/730
    • add dcervenkov as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/731
    • add beojan as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/732
    • add agoose77 as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/733
    • docs: add a CITATION.cff for Uproot. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/726
    • chore: drop Python 3.6. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/742
    • ci: remove GHA workaround for macOS Python 3.11 by @henryiii in https://github.com/scikit-hep/uproot5/pull/743
    • chore: some cleanup inpsired by refurb by @henryiii in https://github.com/scikit-hep/uproot5/pull/745
    • chore(deps): update pre-commit hooks by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/737
    • chore(deps): bump amannn/action-semantic-pull-request from 4 to 5 by @dependabot in https://github.com/scikit-hep/uproot5/pull/757
    • chore: update Uproot to require Awkward 2.0.0rc1. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/765
    • ci: update to Python 3.11 final by @henryiii in https://github.com/scikit-hep/uproot5/pull/766
    • docs: add lobis as a contributor for code by @allcontributors in https://github.com/scikit-hep/uproot5/pull/771
    • refactor: refactor Forth generation by @aryan26roy in https://github.com/scikit-hep/uproot5/pull/710
    • chore: remove Identifier and "uproot" parameter. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/770
    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/773
    • refactor: final refactoring for Forth generation by @aryan26roy in https://github.com/scikit-hep/uproot5/pull/749
    • docs: fix TRef.py doc urls by @veprbl in https://github.com/scikit-hep/uproot5/pull/782
    • ci: pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/783
    • docs: uproot.dask docs by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/702
    • test: make tests parallelizable (custom_classes in uproot.open). by @jpivarski in https://github.com/scikit-hep/uproot5/pull/786
    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/789
    • chore(deps): bump pypa/gh-action-pypi-publish from 1.5.1 to 1.6.1 by @dependabot in https://github.com/scikit-hep/uproot5/pull/792
    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/793

    New Contributors

    • @aryan26roy made their first contribution in https://github.com/scikit-hep/uproot5/pull/617
    • @dependabot made their first contribution in https://github.com/scikit-hep/uproot5/pull/632
    • @Moelf made their first contribution in https://github.com/scikit-hep/uproot5/pull/630
    • @agoose77 made their first contribution in https://github.com/scikit-hep/uproot5/pull/691
    • @lobis made their first contribution in https://github.com/scikit-hep/uproot5/pull/763

    Full Changelog: https://github.com/scikit-hep/uproot5/compare/4.2.4...v5.0.0

    Source code(tar.gz)
    Source code(zip)
  • v5.0.0rc7(Dec 6, 2022)

    New features

    • feat: support categorical axes on boost histograms by @lobis in https://github.com/scikit-hep/uproot5/pull/764
    • feat: warn about TBranch name, alias name conflict. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/776
    • feat: any Mapping assigned to a WritableDirectory is interpreted as a TTree or failure, no fall-through. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/779
    • feat: add 'interp_options' mechanism and ak_add_doc. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/784
    • feat: Use awkward pandas, instead of the existing code that explodes Pandas Dataframes by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/734
    • feat: made 'very optional' arguments keyword-only by @jpivarski in https://github.com/scikit-hep/uproot5/pull/787
    • feat: adjust for name change in scikit-hep/awkward#1919. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/788

    Bug-fixes and performance

    • fix: histogram weights not handled correctly in hist / boost conversion by @lobis in https://github.com/scikit-hep/uproot5/pull/774
    • perf: streamline metadata handling for TBranch name lookup and uproot.dask by @jpivarski in https://github.com/scikit-hep/uproot5/pull/772
    • fix: ensure AwkwardForth fallback path is tested without history. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/780
    • fix: all AwkwardForth Forms now agree with awkward_form method output. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/790

    Other

    • refactor: final refactoring for Forth generation by @aryan26roy in https://github.com/scikit-hep/uproot5/pull/749
    • test: make tests parallelizable (custom_classes in uproot.open). by @jpivarski in https://github.com/scikit-hep/uproot5/pull/786
    • docs: fix TRef.py doc urls by @veprbl in https://github.com/scikit-hep/uproot5/pull/782
    • docs: uproot.dask docs by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/702
    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/773
    • ci: pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/783
    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/789
    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/793
    • chore(deps): bump pypa/gh-action-pypi-publish from 1.5.1 to 1.6.1 by @dependabot in https://github.com/scikit-hep/uproot5/pull/792

    Full Changelog: https://github.com/scikit-hep/uproot5/compare/v5.0.0rc6...v5.0.0rc7

    Source code(tar.gz)
    Source code(zip)
  • v5.0.0rc6(Oct 29, 2022)

    This release is coordinated with Awkward 2.0.0rc2 because it involves a change that had to be applied to both (removal of Identifier/Identities).

    New features

    (none!)

    Bug-fixes and performance

    • fix: working TList serialization by @lobis in https://github.com/scikit-hep/uproot5/pull/763

    Other

    • refactor: refactor Forth generation by @aryan26roy in https://github.com/scikit-hep/uproot5/pull/710
    • docs: add lobis as a contributor for code by @allcontributors in https://github.com/scikit-hep/uproot5/pull/771
    • ci: update to Python 3.11 final by @henryiii in https://github.com/scikit-hep/uproot5/pull/766
    • chore: remove Identifier and "uproot" parameter. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/770

    New Contributors

    • @lobis made their first contribution in https://github.com/scikit-hep/uproot5/pull/763

    Full Changelog: https://github.com/scikit-hep/uproot5/compare/v5.0.0rc5...v5.0.0rc6

    Source code(tar.gz)
    Source code(zip)
  • v5.0.0rc5(Oct 26, 2022)

    This is the first Uproot release that requires awkward>=2.0.0rc1. See Awkward Array v2.0.0rc1.

    New features

    • feat: implemented NON-memberwise deserialization for AsMap. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/746
    • feat: Added column_projection optimization by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/755

    Bug-fixes and performance

    • fix: avoid empty TBasket issue in embedded TBasket by @jpivarski in https://github.com/scikit-hep/uproot5/pull/751
    • fix: don't use Awkward in test_0751 that doesn't need it by @jpivarski in https://github.com/scikit-hep/uproot5/pull/753

    Other

    • ci: remove GHA workaround for macOS Python 3.11 by @henryiii in https://github.com/scikit-hep/uproot5/pull/743
    • chore: some cleanup inpsired by refurb by @henryiii in https://github.com/scikit-hep/uproot5/pull/745
    • chore(deps): update pre-commit hooks by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/737
    • chore(deps): bump amannn/action-semantic-pull-request from 4 to 5 by @dependabot in https://github.com/scikit-hep/uproot5/pull/757
    • chore: update Uproot to require Awkward 2.0.0rc1. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/765

    Full Changelog: https://github.com/scikit-hep/uproot5/compare/v5.0.0rc4...v5.0.0rc5

    Source code(tar.gz)
    Source code(zip)
  • v4.3.7(Oct 7, 2022)

    New features

    (none)

    Bug-fixes and performance

    • fix: avoid empty TBasket issue in embedded TBasket (v4) by @jpivarski in https://github.com/scikit-hep/uproot5/pull/752

    Other

    (none)

    Full Changelog: https://github.com/scikit-hep/uproot5/compare/v4.3.6...v4.3.7

    Source code(tar.gz)
    Source code(zip)
  • v4.3.6(Oct 5, 2022)

    New features

    • feat: implemented NON-memberwise deserialization for AsMap (v4). by @jpivarski in https://github.com/scikit-hep/uproot5/pull/747

    Bug-fixes and performance

    • fix: ReadOnlyDirectory should provide the largest abs(cycle) when cycle is unspecified, not the largest cycle (v4). by @jpivarski in https://github.com/scikit-hep/uproot5/pull/721
    • fix: regularize ROOT type aliases to C fundamental type names (v4). by @jpivarski in https://github.com/scikit-hep/uproot5/pull/718

    Other

    • test: adjust for boost-histogram 1.3.2's _storage_type deprecation (v4). by @jpivarski in https://github.com/scikit-hep/uproot5/pull/720

    Full Changelog: https://github.com/scikit-hep/uproot5/compare/v4.3.5...v4.3.6

    Source code(tar.gz)
    Source code(zip)
  • v5.0.0rc4(Sep 30, 2022)

    New features

    (none)

    Bug-fixes and performance

    (none)

    Other

    • chore: drop Python 3.6. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/742

    Full Changelog: https://github.com/scikit-hep/uproot5/compare/v5.0.0rc3...v5.0.0rc4

    Source code(tar.gz)
    Source code(zip)
  • v5.0.0rc3(Sep 23, 2022)

    New features

    • feat: from_map like optimization for dask arrays by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/679
    • feat: Finalizing AwkwardForth reader for Uproot by @aryan26roy in https://github.com/scikit-hep/uproot5/pull/644

    Bug-fixes and performance

    • fix: Avoid triggering temporary dask-awkward/awkward incompatibility. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/694
    • fix: Do not write incorrect fSumw2 in histograms (v5). by @jpivarski in https://github.com/scikit-hep/uproot5/pull/698
    • fix: Fixes uproot.dask bug with empty branches by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/700
    • fix: Use from_map optimization for delayed numpy arrays and add tests with empty branches for the same by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/703
    • fix: use ctx manager to ensure resources are freed by @agoose77 in https://github.com/scikit-hep/uproot5/pull/713
    • fix: ReadOnlyDirectory should provide the largest abs(cycle) when cycle is unspecified, not the largest cycle. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/715
    • fix: regularize ROOT type aliases to C fundamental type names. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/717

    Other

    • test: adjust for boost-histogram 1.3.2's _storage_type deprecation. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/719
    • ci: Lint PR titles according to conventional commits by @jpivarski in https://github.com/scikit-hep/uproot5/pull/689
    • ci: use concurrency group for semantic-pr-title by @agoose77 in https://github.com/scikit-hep/uproot5/pull/691
    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/706
    • docs: Installation requirements and error text for dask/dask-awkward in extras.py by @jpivarski in https://github.com/scikit-hep/uproot5/pull/690
    • ci: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/uproot5/pull/716
    • docs: Add image for dask docs by @kkothari2001 in https://github.com/scikit-hep/uproot5/pull/708
    • docs: add veprbl as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/728
    • docs: add nikoladze as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/729
    • docs: add klieret as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/730
    • docs: add dcervenkov as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/731
    • docs: add beojan as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/732
    • docs: add agoose77 as a contributor by @allcontributors in https://github.com/scikit-hep/uproot5/pull/733
    • docs: add a CITATION.cff for Uproot. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/726
    • chore: dask_awkward.test_utils moved in ContinuumIO/dask-awkward#76 by @jpivarski in https://github.com/scikit-hep/uproot5/pull/714

    New Contributors

    • @agoose77 made their first contribution in https://github.com/scikit-hep/uproot5/pull/691

    Full Changelog: https://github.com/scikit-hep/uproot5/compare/5.0.0rc2...v5.0.0rc3

    Source code(tar.gz)
    Source code(zip)
  • v4.3.5(Sep 2, 2022)

    Features

    • feat: Implement transformed axis from boost-histogram/hist (v4). by @jpivarski in https://github.com/scikit-hep/uproot5/pull/676

    Bug-fixes

    • fix: Fixed TTree write_anew in a subdirectory (consistent caches). (v4) by @jpivarski in https://github.com/scikit-hep/uproot5/pull/678
    • fix: Do not write incorrect fSumw2 in histograms (v4). by @jpivarski in https://github.com/scikit-hep/uproot5/pull/699

    Other

    • ci: Apply #657 (pre-commit with flake8 v5) to main-v4. by @jpivarski in https://github.com/scikit-hep/uproot5/pull/681

    Full Changelog: https://github.com/scikit-hep/uproot5/compare/4.3.4...v4.3.5

    Source code(tar.gz)
    Source code(zip)
  • 5.0.0rc2(Aug 24, 2022)

    Development of Uproot v5:

    @Moelf reached a first milestone in implementing an RNTuple reader: basic and jagged arrays from all sorts of STL containers: PR #630, #662. Multiple clusters for RNTuple: PR #682.

    @kakwok fixed the RAII state of ReadOnlyDirectory in the corner-case fSeekKeys == 0: PR #660.

    @kkothari2001 added uproot.dask support for Awkward arrays using dask-awkward: PR #652.

    @jpivarski fixed pathlib.Path handling of double slashes in URLs: PR #670. Fixed number of overflow bins in hist.axis.IntCategory: PR #671. Prevented std::pair from being AsStridedObjects (which doesn't work): PR #673. Properly handled transformed axis from boost-histogram: PR #675. Fixed a bug caused by AsDynamic with self._header: PR #674. Fixed WritableTTree's write_anew when in a subdirectory: PR #677.

    @henryiii made many CI updates, concluding with a move to hatchling: PRs #686, #684, #685, #683, #688.

    Source code(tar.gz)
    Source code(zip)
  • 4.3.4(Aug 4, 2022)

  • 5.0.0rc1(Jul 22, 2022)

    This is the first 5.0 (pre) release!

    It should not be considered stable, and it strictly requires Awkward 2.0, so you need to have the latest pre-release of that. This may be reflected in the lazy import of awkward; if not, a subsequent 5.0 pre-release will get that right.

    Changes relative to any 4.x release:

    @kkothari2001 removed the uproot.lazy function (though a stub remains for the sake of keeping the documentation until 5.0 is actually released): PR #615. Updated the entire codebase from Awkward 1.x to Awkward 2.x: PR #620.

    @aryan26roy changed arguments in the awkward_form method: PR #617. (@jpivarski fixed a bug in it: PR #622.) @aryan26roy completed an AwkwardForth-based reader for AsStrings: PR #616. Made the Python code generation in streamers.py more readable: #629. Revised the way that the AwkwardForth code generator would pass through the control flow: PR #636.

    @henryiii added dependabot for GitHub Actions: PR #631. Cleaned up flake8: PR #527.

    @jpivarski fixed a performance bug, to allow linear-time iteration over TDirectory fields: PR #638 (backported to v4 as well). Set up as close as possible to full-coverage tests for AwkwardForth: #637.

    Source code(tar.gz)
    Source code(zip)
  • 4.3.3(Jul 2, 2022)

    @jpivarski fixed an O(nΒ²) scaling bug in getting data from TDirectories. Now it's O(n). (Matters for large TDirectories.)

    PR #638 in main and #639 in main-v4. This release is from main-v4.

    Source code(tar.gz)
    Source code(zip)
  • 4.3.2(Jun 22, 2022)

  • 4.3.1(Jun 22, 2022)

  • 4.3.0(Jun 21, 2022)

    First Uproot 4 release from the bug-fix branch.

    @jpivarski added a TMatrixTSym model (long stalled PR): #484.

    @aryan26roy restored the argument list of Interpretation.awkward_form, a public function: PR #618.

    Source code(tar.gz)
    Source code(zip)
  • 4.2.4(Jun 21, 2022)

    @kkothari2001 implemented uproot.dask (for library="np" only), a new function to provide Uproot data as Dask arrays: PRs #578, #603. Added another new function, uproot.num_entries, for getting the number of TTree entries from a set of files with minimal reading: PR #609.

    @jpivarski removed tests that rely on a ROOT TStreamerInfo behavior: PR #612. Changed awkward_form arguments to (self, file, context) so that new pseudo-arguments can be passed through the context without another major code change: PR #611. This is to prepare for @aryan26roy's AwkwardForth implementation of AsObjects interpretations (see #610, WIP targeting Uproot 5).

    Note: this is the last Uproot 4 release before the repo branches into main (for version 5) and main-v4 (for bug-fixes in Uproot 4, starting with 4.3.0). Uproot 5 will incorporate Awkward version 2, as described in the Awkward road map, but it will have minimal interface changes relative to Uproot 4 (mostly just uproot.lazy β†’ uproot.dask).

    Source code(tar.gz)
    Source code(zip)
  • 4.2.3(May 11, 2022)

    @jpivarski fixed the use of Unicode names for objects in ROOT files: PR #577. Made flow=True mean the same thing for Uproot histograms as hist: PR #582. Added an interpretation for ROOT::VecOps::RVec: PR #593. Replaced an error message in HTTPSource with a fallback to the non-multipart-GET case: PR #594. Put an upper limit on the time KeyInFileError takes to print itself: PR #595.

    Source code(tar.gz)
    Source code(zip)
  • 4.2.2(Mar 14, 2022)

  • 4.2.1(Mar 8, 2022)

    @henryiii removed wheel from pyproject.toml: PR #565.

    @jpivarski added a rule to skip parsing Float16/Double32 TBranch titles if the title is not parsable (and just assume default number of bits): PR #561. Removed references to deprecated distutils and Pandas Int64Index: PR #564. Removed the rule that interpreted fBits as 1 byte (it's 4 bytes everywhere except in some branches of some Delphes files): PR #570.

    Source code(tar.gz)
    Source code(zip)
  • 4.2.0(Feb 14, 2022)

    Dropped support for Pythons 2.7 and 3.5: PR #525. From now on, Uproot only supports Python 3.6 and up.

    @henryiii dropped Python2isms from the codebase: PR #526.

    @jrueb made writing to Python file handles work (fixed a half-finished, forgotten implementation): PR #538.

    @jpivarski fixed cut jagged-array corner-case in library="pd". Fixed a case in which the instance version is 0, but the streamer version is not: PR #537. Fixed uproot.WritableTTree.extend when the metadata needs to be rewritten: PR #547. When checking to see if something in file["name"] = something is an Awkward Array or Pandas DataFrame for creating a TTree, also check for superclasses (the whole mro): PR #557.

    Source code(tar.gz)
    Source code(zip)
  • 4.1.9(Dec 8, 2021)

    The 4.1.x series is the last to support Python 2.7 and Python 3.5. From 4.2.0 onward, only Python 3.6 and above will be supported.

    (Any bug-fixes that absolutely must be used in an old Python environment will need to be versions 4.1.10, 4.1.11, etc., and these won't include features and regular maintenance that go into the main branch, 4.2.x and beyond.)

    In this version:

    @pfackeldey removed an unnecessary copy of memory-mapped data.

    @veprbl exposed the data property of TTable: PR #506.

    @jpivarski added an example of RNTuple header parsing: accidentally as 4bb0f6aedbe7e9a8ba8feb166a16e71274259d26, rather than a formal PR. Added more careful DataFrame-checking code in TTree-writing, to avoid a spurious error message: PR #517. Fixed a picking issue with histograms (just the TAxis) by ensuring that all Behaviors are not Python Abstract Base Classes: PR #521.

    Source code(tar.gz)
    Source code(zip)
  • 4.1.8(Nov 8, 2021)

    @masonproffitt fixed warning message for old versions of XRootD/pyxrootd (before 4.11.1): PR #501.

    @jpivarski fixed conflicts between explicitly specified TBranches and automatically generated counter-TBranches when they have the same name: PR #499. Also, uproot.lazy identifies the only TTree in a file even if there are multiple with the same name, different cycle numbers: PR #500.

    Source code(tar.gz)
    Source code(zip)
  • 4.1.7(Oct 28, 2021)

    @mpad added an AsDtypeInPlace interpretation to read data into a preallocated array (in library="np" mode): PR #487.

    @jpivarski restricted Uproot 4.x to Awkward 1.x in pip install uproot[dev] as well as at runtime.

    Source code(tar.gz)
    Source code(zip)
  • 4.1.6(Oct 28, 2021)

    @duncanmmacleod included the test suite in the source distribution: PR #477.

    @btovar fixed exception handling in XRootD callback threads by passing them on to the main thread: PR #480.

    @jpivarski restricted Uproot 4.x to Awkward 1.x: PR #478. Also fixed some bugs when writing TTrees to preexisting files ("update" mode): PR #488.

    Source code(tar.gz)
    Source code(zip)
  • 4.1.5(Oct 14, 2021)

    @jpivarski fixed another Uproot-writing bug: writing TTrees didn't update the FreeSegments record, which means that writing another TTree (with another file handle, with uproot.update or ROOT) could overwrite the first TTree.

    Like 4.1.4, this is an important bug-fix for anyone creating a robust dataset of ROOT files. (It doesn't affect you if you consider all files to be write-once only, but if you're ever thinking of updating files, this will matter. And besides, correctness is important in principle!)

    Source code(tar.gz)
    Source code(zip)
  • 4.1.4(Oct 13, 2021)

    @jpivarski added TStreamerInfo for TTrees in files written by Uproot. If you're using an older version, you're producing files without TStreamerInfo! (Which means they won't be readable in some older versions of ROOT, and possibly not new ones, either.) PR #472.

    Also corrected the TLeaf fTitle for jagged arrays, which is needed to read jagged arrays back in ROOT's TTree::Draw and TTree::Scan, but not for iteration in PyROOT (which is what we had been using for testing). PR #458.

    Added an implementation of non-split TClonesArray, which makes more files readable: PR #467, and added RNTuple to the must_be_attached list, which enables RNTuple objects to read more data (like TTrees): PR #463. That's just a step in developing RNTuple-reading capabilities.

    Source code(tar.gz)
    Source code(zip)
  • 4.1.3(Sep 29, 2021)

    @nsmith- fixed Awkward Forms for objects: PR #441, and implemented regular array support for TClonesArray: PR #442.

    @jpivarski fixed Pandas representations of leaf-lists (structs) and non-leaf-lists in the same DataFrame: PR #449. Fixed uproot.lazy for empty TTrees and boost-histogram with no title: #451. Fixed issue #439 by checking to see if an array is an Awkward Array before checking to see if it could be NumPy: #453. Fixed both Delphes bugs in issue #438: PR #454.

    Source code(tar.gz)
    Source code(zip)
Dragon Age: Origins toolset to extract/build .erf files, patch language-specific .dlg files, and view the contents of files in the ERF or GFF format

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TemporaryStorage An simple library for temporary storage of small files. Navigation Install Usage In Python console As a standalone application List o

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Python Fstab Generator is a small Python script to write and generate /etc/fstab files based on yaml file on Unix-like systems.

PyFstab Generator PyFstab Generator is a small Python script to write and generate /etc/fstab files based on yaml file on Unix-like systems. NOTE : Th

Mahdi 2 Nov 9, 2021
pydicom - Read, modify and write DICOM files with python code

pydicom is a pure Python package for working with DICOM files. It lets you read, modify and write DICOM data in an easy "pythonic" way.

DICOM in Python 1.5k Jan 4, 2023
Fast Python reader and editor for ASAM MDF / MF4 (Measurement Data Format) files

asammdf is a fast parser and editor for ASAM (Association for Standardization of Automation and Measuring Systems) MDF (Measurement Data Format) files

Daniel Hrisca 440 Dec 31, 2022
Here is some Python code that allows you to read in SVG files and approximate their paths using a Fourier series.

Here is some Python code that allows you to read in SVG files and approximate their paths using a Fourier series. The Fourier series can be animated and visualized, the function can be output as a two dimensional vector for Desmos and there is a method to output the coefficients as LaTeX code.

Alexander 12 Jan 1, 2023
A tool written in python to generate basic repo files from github

A tool written in python to generate basic repo files from github

Riley 7 Dec 2, 2021
FUSE filesystem Python scripts for Nintendo console files

ninfs (formerly fuse-3ds) is a FUSE program to extract data from Nintendo game consoles. It works by presenting a virtual filesystem with the contents of your games, NAND, or SD card contents, and you can browse and copy out just the files that you need.

Ian Burgwin 343 Jan 2, 2023
A python script generate password files in plain text

KeePass (or any desktop pw manager?) Helper WARNING: This script will generate password files in plain text. ITS NOT SECURE. I needed help remembering

Eric Thomas 1 Nov 21, 2021