add formatting and linting python in pre-commit

.github/workflows/pre-commit.yml

@@ -32,7 +32,7 @@ jobs:
  cd $STARTDIR
  python3 -m venv /root/pre-commit-venv
  source /root/pre-commit-venv/bin/activate
- pip install pre-commit
+ pip install pre-commit ruff
  cmake -DENABLE_SIO=ON \
  -DCMAKE_CXX_STANDARD=20 \
  -DCMAKE_CXX_FLAGS=" -fdiagnostics-color=always -Werror "\

.pre-commit-config.yaml

@@ -18,3 +18,13 @@ repos:
  entry: python ./scripts/updateReadmeLinks.py --check
  files: (^README.md$)
  language: system
+ - id: ruff
+ name: ruff
+ entry: ruff check --force-exclude
+ types: [python]
+ language: system
+ - id: ruff-format
+ name: ruff-format
+ entry: ruff format --force-exclude
+ types: [python]
+ language: system

.ruff.toml

@@ -0,0 +1,13 @@
+target-version = "py311"
+
+line-length = 99
+
+[format]
+# Make things format the same way as black
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+
+[lint]
+select = ["F", "E", "W", "PLE", "PLW", "PLC"]

CMakeLists.txt

@@ -73,3 +73,6 @@ add_subdirectory(test)
 
 #--- create uninstall target ---------------------------------------------------
 include(cmake/EDM4HEPUninstall.cmake)
+
+#--- code format targets -------------------------------------------------------
+include(cmake/pythonFormat.cmake)

cmake/pythonFormat.cmake

@@ -0,0 +1,25 @@
+# Additional target to run python linters and formatters on python files
+#
+# Requires ruff to be available in the environment
+
+# Get all our Python files
+file(GLOB_RECURSE ALL_PYTHON_FILES ${PROJECT_SOURCE_DIR}/python/*.py
+ ${PROJECT_SOURCE_DIR}/scripts/*.py ${PROJECT_SOURCE_DIR}/test/*.py)
+
+find_program(RUFF_EXECUTABLE ruff)
+if(RUFF_EXECUTABLE)
+ add_custom_target(
+ ruff
+ COMMAND ${RUFF_EXECUTABLE}
+ check --force-exclude ${ALL_PYTHON_FILES}
+ )
+ set_target_properties(ruff PROPERTIES EXCLUDE_FROM_ALL TRUE)
+ add_custom_target(
+ ruff-format
+ COMMAND ${RUFF_EXECUTABLE}
+ format --force-exclude ${ALL_PYTHON_FILES}
+ )
+ set_target_properties(ruff-format PROPERTIES EXCLUDE_FROM_ALL TRUE)
+else()
+ message(STATUS "Failed to find ruff executable - no target to run ruff can be set")
+endif()

python/edm4hep/__init__.py

@@ -1,34 +1,37 @@
 """Python module for the EDM4HEP datamodel and utilities."""
+
 import sys
 
 from .__version__ import __version__
 import ROOT
-res = ROOT.gSystem.Load('libedm4hepDict')
+
+res = ROOT.gSystem.Load("libedm4hepDict")
 if res < 0:
- raise RuntimeError('Failed to load libedm4hepDict')
+ raise RuntimeError("Failed to load libedm4hepDict")
 
-res = ROOT.gSystem.Load('libedm4hepRDF')
+res = ROOT.gSystem.Load("libedm4hepRDF")
 if res < 0:
- raise RuntimeError('Failed to load libedm4hepRDF')
+ raise RuntimeError("Failed to load libedm4hepRDF")
 
-res = ROOT.gInterpreter.LoadFile('edm4hep/utils/kinematics.h')
+res = ROOT.gInterpreter.LoadFile("edm4hep/utils/kinematics.h")
 if res != 0:
- raise RuntimeError('Failed to load kinematics.h')
+ raise RuntimeError("Failed to load kinematics.h")
 
-res = ROOT.gInterpreter.LoadFile('edm4hep/utils/dataframe.h')
+res = ROOT.gInterpreter.LoadFile("edm4hep/utils/dataframe.h")
 if res != 0:
- raise RuntimeError('Failed to load dataframe.h')
+ raise RuntimeError("Failed to load dataframe.h")
 
-res = ROOT.gInterpreter.LoadFile('edm4hep/Constants.h')
+res = ROOT.gInterpreter.LoadFile("edm4hep/Constants.h")
 if res != 0:
- raise RuntimeError('Failed to load Constants.h')
-from ROOT import edm4hep
+ raise RuntimeError("Failed to load Constants.h")
+from ROOT import edm4hep # noqa: E402
+
+from podio.pythonizations import load_pythonizations # noqa: E402
 
-from podio.pythonizations import load_pythonizations
-load_pythonizations('edm4hep')
+load_pythonizations("edm4hep")
 
 # Make TAB completion work for utils
-setattr(edm4hep, 'utils', edm4hep.utils)
+setattr(edm4hep, "utils", edm4hep.utils)
 
 # set package attributes for edm4hep
 edm4hep.__version__ = __version__
@@ -38,4 +41,4 @@
 edm4hep.__file__ = __file__
 
 # Make `import edm4hep` work
-sys.modules['edm4hep'] = edm4hep
+sys.modules["edm4hep"] = edm4hep

scripts/createEDM4hepFile.py

@@ -45,15 +45,9 @@ def create_MCParticleCollection():
  particle.setCharge(next(counter))
  particle.setTime(next(counter))
  particle.setMass(next(counter))
- particle.setVertex(
- edm4hep.Vector3d(next(counter), next(counter), next(counter))
- )
- particle.setEndpoint(
- edm4hep.Vector3d(next(counter), next(counter), next(counter))
- )
- particle.setMomentum(
- edm4hep.Vector3d(next(counter), next(counter), next(counter))
- )
+ particle.setVertex(edm4hep.Vector3d(next(counter), next(counter), next(counter)))
+ particle.setEndpoint(edm4hep.Vector3d(next(counter), next(counter), next(counter)))
+ particle.setMomentum(edm4hep.Vector3d(next(counter), next(counter), next(counter)))
  particle.setMomentumAtEndpoint(
  edm4hep.Vector3d(next(counter), next(counter), next(counter))
  )
@@ -174,9 +168,7 @@ def create_ClusterCollection(vectorsize, calo_hit):
  cluster.setPositionError(create_CovMatrixNf(3))
  cluster.setITheta(next(counter))
  cluster.setPhi(next(counter))
- cluster.setDirectionError(
- edm4hep.Vector3f(next(counter), next(counter), next(counter))
- )
+ cluster.setDirectionError(edm4hep.Vector3f(next(counter), next(counter), next(counter)))
  for j in range(vectorsize):
  cluster.addToShapeParameters(next(counter))
  cluster.addToSubdetectorEnergies(next(counter))
@@ -256,9 +248,7 @@ def create_TrackCollection(vectorsize, tracker_hit):
  state.Z0 = next(counter)
  state.tanLambda = next(counter)
  state.time = next(counter)
- state.referencePoint = edm4hep.Vector3f(
- next(counter), next(counter), next(counter)
- )
+ state.referencePoint = edm4hep.Vector3f(next(counter), next(counter), next(counter))
  state.covMatrix = create_CovMatrixNf(6)
  track.addToTrackStates(state)
 
@@ -292,9 +282,7 @@ def create_ReconstructedParticleCollection(vertex, cluster, track):
  rparticle.setPDG(next(counter))
  rparticle.setEnergy(next(counter))
  rparticle.setMomentum(edm4hep.Vector3f(next(counter), next(counter), next(counter)))
- rparticle.setReferencePoint(
- edm4hep.Vector3f(next(counter), next(counter), next(counter))
- )
+ rparticle.setReferencePoint(edm4hep.Vector3f(next(counter), next(counter), next(counter)))
  rparticle.setCharge(next(counter))
  rparticle.setMass(next(counter))
  rparticle.setGoodnessOfPID(next(counter))
@@ -402,9 +390,7 @@ def create_frame():
  particles = frame.put(create_MCParticleCollection(), "MCParticleCollection")
  particle = particles[0]
 
- hits = frame.put(
- create_SimTrackerHitCollection(particle), "SimTrackerHitCollection"
- )
+ hits = frame.put(create_SimTrackerHitCollection(particle), "SimTrackerHitCollection")
  simtracker_hit = hits[0]
 
  calo_contribs = frame.put(
@@ -422,9 +408,7 @@ def create_frame():
  hits = frame.put(create_CalorimeterHitCollection(), "CalorimeterHitCollection")
  calo_hit = hits[0]
 
- clusters = frame.put(
- create_ClusterCollection(VECTORSIZE, calo_hit), "ClusterCollection"
- )
+ clusters = frame.put(create_ClusterCollection(VECTORSIZE, calo_hit), "ClusterCollection")
  cluster = clusters[0]
 
  hits = frame.put(create_TrackerHit3DCollection(), "TrackerHit3DCollection")
@@ -433,9 +417,7 @@ def create_frame():
 
  frame.put(create_RawTimeSeriesCollection(VECTORSIZE), "RawTimeSeriesCollection")
 
- tracks = frame.put(
- create_TrackCollection(VECTORSIZE, tracker_hit), "TrackCollection"
- )
+ tracks = frame.put(create_TrackCollection(VECTORSIZE, tracker_hit), "TrackCollection")
  track = tracks[0]
 
  pids, pid = create_ParticleIDCollection(VECTORSIZE)
@@ -456,9 +438,7 @@ def create_frame():
 
  put_link_collection(frame, "RecoMCParticleLink", reco_particle, particle)
  put_link_collection(frame, "CaloHitSimCaloHitLink", calo_hit, simcalo_hit)
- put_link_collection(
- frame, "TrackerHitSimTrackerHitLink", tracker_hit, simtracker_hit
- )
+ put_link_collection(frame, "TrackerHitSimTrackerHitLink", tracker_hit, simtracker_hit)
  put_link_collection(frame, "CaloHitMCParticleLink", calo_hit, particle)
  put_link_collection(frame, "ClusterMCParticleLink", cluster, particle)
  put_link_collection(frame, "TrackMCParticleLink", track, particle)
@@ -481,9 +461,7 @@ def create_frame():
  parser.add_argument(
  "--rntuple", action="store_true", help="Use a ROOT ntuple instead of EDM4hep"
  )
- parser.add_argument(
- "--output-file", type=str, help="Output file name", default="edm4hep.root"
- )
+ parser.add_argument("--output-file", type=str, help="Output file name", default="edm4hep.root")
  args = parser.parse_args()
  output_file = args.output_file
 

scripts/updateReadmeLinks.py

@@ -5,46 +5,70 @@
 
 parser = argparse.ArgumentParser()
 parser.add_argument("inputfile", help="The README file to run on", default="README.md")
-parser.add_argument("--check", action='store_true', help='Use if you want to just check the links without actually changing the file')
+parser.add_argument(
+ "--check",
+ action="store_true",
+ help="Use if you want to just check the links without actually changing the file",
+)
 args = parser.parse_args()
 
+
 def check_readme_links():
- edm4hep_yaml_content = ""
- with open("edm4hep.yaml") as edm4hep_yaml:
- edm4hep_yaml_content = edm4hep_yaml.readlines()
-
- readme_content = ""
- with open("README.md", "r") as readme:
- readme_content = readme.readlines()
-
- new_readme_content = ""
-
- links_are_ok = True
- for readme_line in readme_content:
- edm4hep_objects = re.findall("\[(.*?)\]\(https:\/\/github.com\/key4hep\/EDM4hep\/blob\/main\/edm4hep\.yaml#L(\d+?)\)", readme_line)
- if edm4hep_objects:
- for edm4hep_object, original_line_number in edm4hep_objects:
- regex = f".*edm4hep::{edm4hep_object} *: *"
- # find in which line it appears in edm4hep.yaml
- edm4hep_yaml_line_numbers_with_match = [str(i + 1) for i, line in enumerate(edm4hep_yaml_content) if re.match(regex, line)]
- if len(edm4hep_yaml_line_numbers_with_match) != 1:
- print(f"Error: failed to replace line number for {edm4hep_object}, either no or several matches were found in edm4hep.yaml with the regex '{regex}'")
- sys.exit(1)
- if edm4hep_yaml_line_numbers_with_match[0] != original_line_number:
- links_are_ok = False
- readme_line = readme_line.replace(f"[{edm4hep_object}](https://github.com/key4hep/EDM4hep/blob/main/edm4hep.yaml#L{original_line_number})", f"[{edm4hep_object}](https://github.com/key4hep/EDM4hep/blob/main/edm4hep.yaml#L{edm4hep_yaml_line_numbers_with_match[0]})")
- print(f"{edm4hep_object} is wrongly linked (line {original_line_number} --> {edm4hep_yaml_line_numbers_with_match[0]})")
- new_readme_content += readme_line
- return links_are_ok, new_readme_content
+ edm4hep_yaml_content = ""
+ with open("edm4hep.yaml") as edm4hep_yaml:
+ edm4hep_yaml_content = edm4hep_yaml.readlines()
+
+ readme_content = ""
+ with open("README.md", "r") as readme:
+ readme_content = readme.readlines()
+
+ new_readme_content = ""
+
+ links_are_ok = True
+ for readme_content_line in readme_content:
+ readme_line = readme_content_line
+ edm4hep_objects = re.findall(
+ r"\[(.*?)\]\(https:\/\/github.com\/key4hep\/EDM4hep\/blob\/main\/edm4hep\.yaml#L(\d+?)\)",
+ readme_line,
+ )
+ if edm4hep_objects:
+ for edm4hep_object, original_line_number in edm4hep_objects:
+ regex = f".*edm4hep::{edm4hep_object} *: *"
+ # find in which line it appears in edm4hep.yaml
+ edm4hep_yaml_line_numbers_with_match = [
+ str(i + 1)
+ for i, line in enumerate(edm4hep_yaml_content)
+ if re.match(regex, line)
+ ]
+ if len(edm4hep_yaml_line_numbers_with_match) != 1:
+ print(
+ f"Error: failed to replace line number for {edm4hep_object}, either no "
+ f"or several matches were found in edm4hep.yaml with the regex '{regex}'"
+ )
+ sys.exit(1)
+ if edm4hep_yaml_line_numbers_with_match[0] != original_line_number:
+ links_are_ok = False
+ readme_line = readme_line.replace(
+ f"[{edm4hep_object}](https://github.com/key4hep/EDM4hep/blob/main/edm4hep.yaml#L{original_line_number})",
+ f"[{edm4hep_object}](https://github.com/key4hep/EDM4hep/blob/main/edm4hep.yaml#L{edm4hep_yaml_line_numbers_with_match[0]})",
+ )
+ print(
+ f"{edm4hep_object} is wrongly linked (line {original_line_number} --> {edm4hep_yaml_line_numbers_with_match[0]})" # noqa: E501
+ )
+ new_readme_content += readme_line
+ return links_are_ok, new_readme_content
+
 
 links_are_ok, new_readme_content = check_readme_links()
 if links_are_ok:
- print("README.md links are fine, nothing to change")
+  print("README.md links are fine, nothing to change")
 else:
- if not args.check:
- with open("README.md", "w") as readme:
- readme.write(new_readme_content)
- print("README.md links updated.")
- else:
- print("README.md links should be updated. (Run ./scripts/updateReadmeLinks.py to fix them)")
- sys.exit(1)
+ if not args.check:
+ with open("README.md", "w") as readme:
+ readme.write(new_readme_content)
+ print("README.md links updated.")
+ else:
+ print(
+ "README.md links should be updated. (Run ./scripts/updateReadmeLinks.py to fix them)"
+ )
+ sys.exit(1)

test/conftest.py

@@ -14,5 +14,5 @@ def pytest_addoption(parser):
 def pytest_configure(config):
  """This is a slighty hacky solution to make the pytest configuration
  available in test modules outside of fixtures"""
- global options
+ global options # noqa: PLW0603
  options = config.option