Fix cibuildwheel with patch (#131)

* Fix cibuildwheel with patch

* Add link to PR for more info

* add cp311, drop cp36

* formally drop python 3.6

* test in 3.7, 3.11

* Implement warning for exclusive jets

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* More consistent naming for patches

* Rename patch files

Co-authored-by: Lindsey Gray <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

.github/workflows/ci.yml

@@ -33,7 +33,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.6', '3.10']
+        python-version: ['3.7', '3.11']
         runs-on: [ubuntu-latest]   # , macos-latest
 
         # include:
@@ -58,7 +58,7 @@ jobs:
       run: sudo apt-get update && sudo apt-get install -y libboost-dev libmpfr-dev swig autoconf libtool
 
     - name: Install package
-      run: python -m pip install .[test] -v
+      run: python -m pip install '.[test]' -v
 
     - name: Test package
       run: python -m pytest -vv -rs -Wd
@@ -72,10 +72,10 @@ jobs:
       with:
         submodules: recursive
 
-    - uses: pypa/cibuildwheel@v2.1.2
+    - uses: pypa/cibuildwheel@v2.11.2
       env:
         CIBW_ARCHS: auto64
-        CIBW_BUILD: cp310-*
+        CIBW_BUILD: cp311-*
         CIBW_BUILD_VERBOSITY: 2
 
     - name: Upload wheels

.github/workflows/wheels.yml

@@ -28,7 +28,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-build-version: ["cp36-*", "cp37-*", "cp38-*", "cp39-*", "cp310-*"]
+        python-build-version: ["cp37-*", "cp38-*", "cp39-*", "cp310-*", "cp311-*"]
         os: [ubuntu-latest]   # , macos-latest
 
     steps:
@@ -40,7 +40,7 @@ jobs:
       if: runner.os == 'macOS'
       run: brew install automake
 
-    - uses: pypa/cibuildwheel@v2.1.2
+    - uses: pypa/cibuildwheel@v2.11.2
       env:
         CIBW_ARCHS: auto64
         CIBW_BUILD: ${{ matrix.python-build-version }}

MANIFEST.in

@@ -3,4 +3,4 @@ graft tests
 graft fastjet-core
 graft pybind11
 global-exclude .git .gitmodules
-include LICENSE README.md pyproject.toml setup.py setup.cfg patch.txt .clang-format
+include LICENSE README.md pyproject.toml setup.py setup.cfg patch_fastjet_i.txt patch_clustersequence.txt

patch_clustersequence.txt

@@ -0,0 +1,18 @@
+--- ClusterSequence_old.cc	2022-11-02 01:34:43.387347058 +0000
++++ ClusterSequence.cc	2022-11-02 01:36:31.518212219 +0000
+@@ -1017,6 +1017,7 @@
+   // Native algorithm that support it are: kt, ee_kt, Cambridge/Aachen,
+   //   genkt and ee_genkt (both with p>=0)
+   // For plugins, we check Plugin::exclusive_sequence_meaningful()
++  /*
+   if (( _jet_def.jet_algorithm() != kt_algorithm) &&
+       ( _jet_def.jet_algorithm() != cambridge_algorithm) &&
+       ( _jet_def.jet_algorithm() != ee_kt_algorithm) &&
+@@ -1027,6 +1028,7 @@
+        (!_jet_def.plugin()->exclusive_sequence_meaningful()))) {
+     _exclusive_warnings.warn("dcut and exclusive jets for jet-finders other than kt, C/A or genkt with p>=0 should be interpreted with care.");
+   }
++  */
+
+
+   // calculate the point where we have to stop the clustering.

patch.txt renamed to patch_fastjet_i.txt

@@ -21,3 +21,5 @@ before-all = [
     "tar --bzip2 -xf boost_1_80_0.tar.bz2",
     "mv boost_1_80_0/boost /usr/include/boost",
 ]
+# Skip musllinux builds for the moment
+skip = "*-musllinux_*"

pyproject.toml

@@ -34,7 +34,7 @@ install_requires =
     awkward>=1
     numpy>=1.13.3
     vector
-python_requires = >=3.6
+python_requires = >=3.7
 include_package_data = True
 package_dir =
     =src
@@ -64,6 +64,7 @@ ignore =
     docs/**
     .pre-commit-config.yaml
     .readthedocs.yml
+    .clang-format
     src/*/version.py
 
 [tool:isort]

setup.cfg

@@ -56,7 +56,14 @@ def build_extensions(self):
             # Patch for FastJet core version 3.4.0
             # To be removed when https://gitlab.com/fastjet/fastjet/-/merge_requests/1 is merged upstream
             subprocess.run(
-                ["patch", "pyinterface/fastjet.i", DIR / "patch.txt"],
+                ["patch", "pyinterface/fastjet.i", DIR / "patch_fastjet_i.txt"],
+                cwd=FASTJET,
+            )
+
+            # Patch for segfault of LimitedWarning
+            # For more info see https://github.com/scikit-hep/fastjet/pull/131
+            subprocess.run(
+                ["patch", "src/ClusterSequence.cc", DIR / "patch_clustersequence.txt"],
                 cwd=FASTJET,
             )
 

setup.py

@@ -547,3 +547,8 @@ class multi_inheritor(
 ):  # class that inherits both the custom ClusterSequence and swig ClusterSequence and acts as a trampoline
     def __init__(self):
         pass
+
+
+def formatwarning(message, category, filename, lineno, line=None):
+    """Make warnings resemble the ones from fastjet-core"""
+    return f"{category.__name__}: {message}\n"

src/fastjet/__init__.py

@@ -1,3 +1,5 @@
+import warnings
+
 import awkward as ak
 import numpy as np
 
@@ -555,6 +557,25 @@ def replace(self, layout, cluster, level):
         else:
             raise AssertionError(layout)
 
+    def _warn_for_exclusive(self):
+        if (
+            self.jetdef
+            not in [
+                fastjet.kt_algorithm,
+                fastjet.cambridge_algorithm,
+                fastjet.ee_kt_algorithm,
+                fastjet.plugin_algorithm,
+            ]
+        ) and (
+            (self.jetdef not in [fastjet.kt_algorithm, fastjet.cambridge_algorithm])
+            or self.jetdef.extra_param() < 0
+        ):
+            warnings.formatwarning = fastjet.formatwarning
+            warnings.warn(
+                "dcut and exclusive jets for jet-finders other than kt, C/A or genkt with p>=0 should be interpreted with care."
+            )
+        return
+
     def inclusive_jets(self, min_pt):
         self._out = []
         self._input_flag = 0
@@ -727,6 +748,7 @@ def jets(self):
         return res
 
     def exclusive_jets(self, n_jets, dcut):
+        self._warn_for_exclusive()
         self._out = []
         self._input_flag = 0
         for i in range(len(self._clusterable_level)):
@@ -764,6 +786,7 @@ def exclusive_jets(self, n_jets, dcut):
         return res
 
     def exclusive_jets_ycut(self, ycut):
+        self._warn_for_exclusive()
         self._out = []
         self._input_flag = 0
         for i in range(len(self._clusterable_level)):

src/fastjet/_generalevent.py

@@ -1,3 +1,5 @@
+import warnings
+
 import awkward as ak
 import numpy as np
 
@@ -61,6 +63,25 @@ def single_to_jagged(self, array):
         )
         return single
 
+    def _warn_for_exclusive(self):
+        if (
+            self.jetdef
+            not in [
+                fastjet.kt_algorithm,
+                fastjet.cambridge_algorithm,
+                fastjet.ee_kt_algorithm,
+                fastjet.plugin_algorithm,
+            ]
+        ) and (
+            (self.jetdef not in [fastjet.kt_algorithm, fastjet.cambridge_algorithm])
+            or self.jetdef.extra_param() < 0
+        ):
+            warnings.formatwarning = fastjet.formatwarning
+            warnings.warn(
+                "dcut and exclusive jets for jet-finders other than kt, C/A or genkt with p>=0 should be interpreted with care."
+            )
+        return
+
     def inclusive_jets(self, min_pt):
         np_results = self._results.to_numpy(min_pt)
         of = np_results[-1]
@@ -102,6 +123,7 @@ def unclustered_particles(self):
         )
 
     def exclusive_jets(self, n_jets, dcut):
+        self._warn_for_exclusive()
         of = 0
         np_results = 0
         if n_jets == 0:

src/fastjet/_multievent.py

@@ -1,3 +1,5 @@
+import warnings
+
 import awkward as ak
 import numpy as np
 
@@ -66,6 +68,25 @@ def single_to_jagged(self, array):
         )
         return single
 
+    def _warn_for_exclusive(self):
+        if (
+            self.jetdef
+            not in [
+                fastjet.kt_algorithm,
+                fastjet.cambridge_algorithm,
+                fastjet.ee_kt_algorithm,
+                fastjet.plugin_algorithm,
+            ]
+        ) and (
+            (self.jetdef not in [fastjet.kt_algorithm, fastjet.cambridge_algorithm])
+            or self.jetdef.extra_param() < 0
+        ):
+            warnings.formatwarning = fastjet.formatwarning
+            warnings.warn(
+                "dcut and exclusive jets for jet-finders other than kt, C/A or genkt with p>=0 should be interpreted with care."
+            )
+        return
+
     def inclusive_jets(self, min_pt):
         np_results = self._results.to_numpy(min_pt)
         return ak.Array(
@@ -99,6 +120,7 @@ def unclustered_particles(self):
         )
 
     def exclusive_jets(self, n_jets, dcut):
+        self._warn_for_exclusive()
         np_results = 0
         if n_jets == 0:
             raise ValueError("Njets cannot be 0") from None
@@ -123,6 +145,7 @@ def exclusive_jets(self, n_jets, dcut):
         )
 
     def exclusive_jets_ycut(self, ycut):
+        self._warn_for_exclusive()
         np_results = self._results.to_numpy_exclusive_ycut(ycut)
         return ak.Array(
             ak.layout.RecordArray(