Merge branch 'master' into dependabot/github_actions/pypa/gh-action-p…

…ypi-publish-1.12.3

CITATION.cff

@@ -44,4 +44,4 @@ title: "coffea"
 version: 0.7.21
 doi: 10.5281/zenodo.7733568
 date-released: 2023-03-14
-url: "https://github.com/CoffeaTeam/coffea"
+url: "https://github.com/scikit-hep/coffea"

CONTRIBUTING.md

@@ -2,9 +2,9 @@
 
 #### **Did you find a bug?**
 
-* **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/CoffeaTeam/coffea/issues).
+* **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/scikit-hep/coffea/issues).
 
-* If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/CoffeaTeam/coffea/issues/new). Be sure to include a **title and clear description**, as much relevant information as possible, and a **code sample** or an **executable test case** demonstrating the expected behavior that is not occurring.
+* If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/scikit-hep/coffea/issues/new). Be sure to include a **title and clear description**, as much relevant information as possible, and a **code sample** or an **executable test case** demonstrating the expected behavior that is not occurring.
 
 #### **Do you want to write a patch that fixes a bug?**
 
@@ -22,11 +22,11 @@ Changes that are cosmetic in nature and do not add anything substantial to the s
 
 #### **Do you intend to add a new feature or change an existing one?**
 
-* Suggest your change either in a new GitHub feature request [issue](https://github.com/CoffeaTeam/coffea/issues) or in the [Discussions](https://github.com/CoffeaTeam/coffea/discussions) section!
+* Suggest your change either in a new GitHub feature request [issue](https://github.com/scikit-hep/coffea/issues) or in the [Discussions](https://github.com/scikit-hep/coffea/discussions) section!
 
 #### **Do you have questions about the source code?**
 
-* Ask any question about how to use coffea in the [coffea iris-hep slack channel](https://iris-hep.slack.com) or in the [Discussions](https://github.com/CoffeaTeam/coffea/discussions) section.
+* Ask any question about how to use coffea in the [coffea iris-hep slack channel](https://iris-hep.slack.com) or in the [Discussions](https://github.com/scikit-hep/coffea/discussions) section.
 
 #### **Do you want to contribute to the coffea documentation?**
 

README.rst

@@ -10,11 +10,11 @@ coffea - Columnar Object Framework For Effective Analysis
 .. image:: https://zenodo.org/badge/159673139.svg
    :target: https://zenodo.org/badge/latestdoi/159673139
 
-.. image:: https://github.com/CoffeaTeam/coffea/actions/workflows/ci.yml/badge.svg
-    :target: https://github.com/CoffeaTeam/coffea/actions?query=workflow%3ACI%2FCD+event%3Aschedule+branch%3Amaster
+.. image:: https://github.com/scikit-hep/coffea/actions/workflows/ci.yml/badge.svg
+    :target: https://github.com/scikit-hep/coffea/actions?query=workflow%3ACI%2FCD+event%3Aschedule+branch%3Amaster
 
-.. image:: https://codecov.io/gh/CoffeaTeam/coffea/branch/master/graph/badge.svg?event=schedule
-    :target: https://codecov.io/gh/CoffeaTeam/coffea
+.. image:: https://codecov.io/gh/scikit-hep/coffea/branch/master/graph/badge.svg?event=schedule
+    :target: https://codecov.io/gh/scikit-hep/coffea
 
 .. image:: https://badge.fury.io/py/coffea.svg
     :target: https://badge.fury.io/py/coffea
@@ -25,11 +25,11 @@ coffea - Columnar Object Framework For Effective Analysis
 .. image:: https://img.shields.io/conda/vn/conda-forge/coffea.svg
     :target: https://anaconda.org/conda-forge/coffea
 
-.. image:: https://badges.gitter.im/CoffeaTeam/coffea.svg
+.. image:: https://badges.gitter.im/scikit-hep/coffea.svg
     :target: https://matrix.to/#/#coffea-hep_community:gitter.im
 
 .. image:: https://mybinder.org/badge_logo.svg
-   :target: https://mybinder.org/v2/gh/CoffeaTeam/coffea/master?filepath=binder/
+   :target: https://mybinder.org/v2/gh/scikit-hep/coffea/master?filepath=binder/
 
 .. inclusion-marker-1-do-not-remove
 
@@ -58,7 +58,7 @@ the need to alter or otherwise adapt the analysis code itself.
 coffea is a HEP community project collaborating with `iris-hep <http://iris-hep.org/>`_
 and is currently a prototype. We welcome input to improve its quality as we progress towards
 a sensible refactorization into the scientific python ecosystem and a first release. Please
-feel free to contribute at our `github repo <https://github.com/CoffeaTeam/coffea>`_!
+feel free to contribute at our `github repo <https://github.com/scikit-hep/coffea>`_!
 
 .. inclusion-marker-2-do-not-remove
 

binder/applying_corrections.ipynb

@@ -46,7 +46,7 @@
     "\n",
     "NanoAODSchema.warn_missing_crossrefs = False\n",
     "\n",
-    "fname = \"https://raw.githubusercontent.com/CoffeaTeam/coffea/master/tests/samples/nano_dy.root\"\n",
+    "fname = \"https://raw.githubusercontent.com/scikit-hep/coffea/master/tests/samples/nano_dy.root\"\n",
     "events = NanoEventsFactory.from_root(\n",
     "    {fname: \"Events\"},\n",
     "    schemaclass=NanoAODSchema,\n",
@@ -91,7 +91,7 @@
     "# download some sample correction sources\n",
     "mkdir -p data\n",
     "pushd data\n",
-    "PREFIX=https://raw.githubusercontent.com/CoffeaTeam/coffea/master/tests/samples\n",
+    "PREFIX=https://raw.githubusercontent.com/scikit-hep/coffea/master/tests/samples\n",
     "curl -Os $PREFIX/testSF2d.histo.root\n",
     "curl -Os $PREFIX/Fall17_17Nov2017_V32_MC_L2Relative_AK4PFPuppi.jec.txt\n",
     "curl -Os $PREFIX/Fall17_17Nov2017_V32_MC_Uncertainty_AK4PFPuppi.junc.txt\n",
@@ -105,7 +105,7 @@
    "source": [
     "### Opening a root file and using it as a lookup table\n",
     "\n",
-    "In [tests/samples](https://github.com/CoffeaTeam/coffea/tree/master/tests/samples), there is an example file with a `TH2F` histogram named `scalefactors_Tight_Electron`. The following code reads that histogram into an [evaluator](https://coffeateam.github.io/coffea/api/coffea.lookup_tools.evaluator.html#coffea.lookup_tools.evaluator) instance, under the key `testSF2d` and applies it to some electrons."
+    "In [tests/samples](https://github.com/scikit-hep/coffea/tree/master/tests/samples), there is an example file with a `TH2F` histogram named `scalefactors_Tight_Electron`. The following code reads that histogram into an [evaluator](https://coffeateam.github.io/coffea/api/coffea.lookup_tools.evaluator.html#coffea.lookup_tools.evaluator) instance, under the key `testSF2d` and applies it to some electrons."
    ]
   },
   {

binder/mltools.ipynb

@@ -73,8 +73,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!wget --quiet -O model.pt https://github.com/CoffeaTeam/coffea/raw/master/tests/samples/triton_models_test/pn_test/1/model.pt\n",
-    "!wget --quiet -O pfnano.root https://github.com/CoffeaTeam/coffea/raw/master/tests/samples/pfnano.root"
+    "!wget --quiet -O model.pt https://github.com/scikit-hep/coffea/raw/master/tests/samples/triton_models_test/pn_test/1/model.pt\n",
+    "!wget --quiet -O pfnano.root https://github.com/scikit-hep/coffea/raw/master/tests/samples/pfnano.root"
    ]
   },
   {

binder/nanoevents.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Reading data with coffea NanoEvents\n",
     "\n",
-    "This is a rendered copy of [nanoevents.ipynb](https://github.com/CoffeaTeam/coffea/blob/master/binder/nanoevents.ipynb). You can optionally run it interactively on [binder at this link](https://mybinder.org/v2/gh/coffeateam/coffea/master?filepath=binder%2Fnanoevents.ipynb)\n",
+    "This is a rendered copy of [nanoevents.ipynb](https://github.com/scikit-hep/coffea/blob/master/binder/nanoevents.ipynb). You can optionally run it interactively on [binder at this link](https://mybinder.org/v2/gh/coffeateam/coffea/master?filepath=binder%2Fnanoevents.ipynb)\n",
     "\n",
     "NanoEvents is a Coffea utility to wrap flat nTuple structures (such as the CMS [NanoAOD](https://www.epj-conferences.org/articles/epjconf/pdf/2019/19/epjconf_chep2018_06021.pdf) format) into a single awkward array with appropriate object methods (such as Lorentz vector methods$^*$), cross references, and nested objects, all lazily accessed$^\\dagger$ from the source ROOT TTree via uproot. The interpretation of the TTree data is configurable via [schema objects](https://coffeateam.github.io/coffea/modules/coffea.nanoevents.html#classes), which are community-supplied  for various source file types. These schema objects allow a richer interpretation of the file contents than the [uproot.lazy](https://uproot4.readthedocs.io/en/latest/uproot4.behaviors.TBranch.lazy.html) methods. Currently available schemas include:\n",
     "\n",
@@ -38,7 +38,7 @@
     "\n",
     "NanoAODSchema.warn_missing_crossrefs = False\n",
     "\n",
-    "fname = \"https://raw.githubusercontent.com/CoffeaTeam/coffea/master/tests/samples/nano_dy.root\"\n",
+    "fname = \"https://raw.githubusercontent.com/scikit-hep/coffea/master/tests/samples/nano_dy.root\"\n",
     "events = NanoEventsFactory.from_root(\n",
     "    {fname: \"Events\"},\n",
     "    schemaclass=NanoAODSchema,\n",
@@ -379,7 +379,7 @@
    "source": [
     "The assignment of methods classes to collections is done inside the schema object during the initial creation of the array, governed by the awkward array's `__record__` parameter and the associated behavior. See [ak.behavior](https://awkward-array.readthedocs.io/en/latest/ak.behavior.html) for a more detailed explanation of array behaviors.\n",
     "\n",
-    "Additional methods provide convenience functions for interpreting some branches, e.g. CMS NanoAOD packs several jet identification flag bits into a single integer, `jetId`. By implementing the bit-twiddling in the [Jet mixin](https://github.com/CoffeaTeam/coffea/blob/7045c06b9448d2be4315e65d432e6d8bd117d6d7/coffea/nanoevents/methods/nanoaod.py#L279-L282), the analsyis code becomes more clear:"
+    "Additional methods provide convenience functions for interpreting some branches, e.g. CMS NanoAOD packs several jet identification flag bits into a single integer, `jetId`. By implementing the bit-twiddling in the [Jet mixin](https://github.com/scikit-hep/coffea/blob/7045c06b9448d2be4315e65d432e6d8bd117d6d7/coffea/nanoevents/methods/nanoaod.py#L279-L282), the analsyis code becomes more clear:"
    ]
   },
   {

binder/nanoevents_pq.ipynb

@@ -252,7 +252,7 @@
    "source": [
     "## Define a Processor instance\n",
     "\n",
-    "The processor implementation given below has been taken from [here](https://github.com/CoffeaTeam/coffea/blob/master/binder/nanoevents.ipynb)."
+    "The processor implementation given below has been taken from [here](https://github.com/scikit-hep/coffea/blob/master/binder/nanoevents.ipynb)."
    ]
   },
   {

binder/processor.ipynb

@@ -5,7 +5,7 @@
    "metadata": {},
    "source": [
     "# Coffea Processors\n",
-    "This is a rendered copy of [processor.ipynb](https://github.com/CoffeaTeam/coffea/blob/master/binder/processor.ipynb). You can optionally run it interactively on [binder at this link](https://mybinder.org/v2/gh/coffeateam/coffea/master?filepath=binder%2Fprocessor.ipynb)\n",
+    "This is a rendered copy of [processor.ipynb](https://github.com/scikit-hep/coffea/blob/master/binder/processor.ipynb). You can optionally run it interactively on [binder at this link](https://mybinder.org/v2/gh/coffeateam/coffea/master?filepath=binder%2Fprocessor.ipynb)\n",
     "\n",
     "Coffea relies mainly on [uproot](https://github.com/scikit-hep/uproot) to provide access to ROOT files for analysis.\n",
     "As a usual analysis will involve processing tens to thousands of files, totalling gigabytes to terabytes of data, there is a certain amount of work to be done to build a parallelized framework to process the data in a reasonable amount of time. Of course, one can work directly within uproot to achieve this, as we'll show in the beginning, but coffea provides the `coffea.processor` module, which allows users to worry just about the actual analysis code and not about how to implement efficient parallelization, assuming that the parallization is a trivial map-reduce operation (e.g. filling histograms and adding them together). The module provides the following key features:\n",

docker/skyhook/README.md

@@ -8,7 +8,7 @@ We added a new executor API called the [`run_parquet_job`](../../coffea/processo
 
 1. Clone the repository.
 ```bash
-git clone https://github.com/CoffeaTeam/coffea
+git clone https://github.com/scikit-hep/coffea
 cd coffea/
 ```
 

docs/source/conf.py

@@ -83,7 +83,7 @@ def linkcode_resolve(domain, info):
     except TypeError:
         # skip property or other type that inspect doesn't like
         return None
-    return "http://github.com/CoffeaTeam/coffea/blob/{}/{}#L{}".format(
+    return "http://github.com/scikit-hep/coffea/blob/{}/{}#L{}".format(
         githash, relpath, lineno
     )
 

docs/source/installation.rst

@@ -6,7 +6,7 @@ Installing coffea
 Quick start
 -----------
 To try coffea now, without installing anything, you can experiment with our
-`hosted tutorial notebooks <https://mybinder.org/v2/gh/CoffeaTeam/coffea/master?filepath=binder/>`_.
+`hosted tutorial notebooks <https://mybinder.org/v2/gh/scikit-hep/coffea/master?filepath=binder/>`_.
 
 Platform support
 ----------------
@@ -196,7 +196,7 @@ For Developers
 
   .. code-block:: bash
 
-    git clone https://github.com/CoffeaTeam/coffea
+    git clone https://github.com/scikit-hep/coffea
 
 2. Install with development dependencies:
 

src/coffea/lookup_tools/root_converters.py

@@ -35,7 +35,7 @@ def convert_histo_root_file(file):
         elif rootclass in graphTypes:
             deprecate(
                 RuntimeError(
-                    "The support for TGraph-types will be removed in a future coffea release. In case you need support for TGraph-type, please submit an issue to `https://github.com/CoffeaTeam/coffea/issues`."  # noqa: E501
+                    "The support for TGraph-types will be removed in a future coffea release. In case you need support for TGraph-type, please submit an issue to `https://github.com/scikit-hep/coffea/issues`."  # noqa: E501
                 ),
                 "<unknown>",
             )

src/coffea/nanoevents/methods/nanoaod.py

@@ -163,7 +163,7 @@ def distinctChildrenDeep(self):
         """
         Accessor to distinct child particles with different PDG id, or last ones in the chain.
         Note that this does not always find the correct children, since this sometimes depends
-        on the MC generator! See `here <https://github.com/CoffeaTeam/coffea/pull/698>` for more
+        on the MC generator! See `here <https://github.com/scikit-hep/coffea/pull/698>` for more
         information.
         """
         warnings.warn(

src/coffea/nanoevents/schemas/treemaker.py

@@ -180,7 +180,7 @@ def uproot_writeable(cls, events):
         Converting a TreeMakerSchema event into something that is uproot
         writeable. Based off the discussion thread here [1], but added specific
         cased to handled the nested structures define for TreeMaker n-tuples.
-        [1] https://github.com/CoffeaTeam/coffea/discussions/735
+        [1] https://github.com/scikit-hep/coffea/discussions/735
 
         Parameters
         ----------

tests/test_lumi_tools.py

@@ -65,7 +65,7 @@ def test_lumidata():
     "jsonfile",
     [
         "tests/samples/Cert_294927-306462_13TeV_EOY2017ReReco_Collisions17_JSON.txt",
-        "https://raw.githubusercontent.com/CoffeaTeam/coffea/master/tests/samples/Cert_294927-306462_13TeV_EOY2017ReReco_Collisions17_JSON.txt",
+        "https://raw.githubusercontent.com/scikit-hep/coffea/master/tests/samples/Cert_294927-306462_13TeV_EOY2017ReReco_Collisions17_JSON.txt",
     ],
 )
 def test_lumimask(jsonfile):