fsoubelet · fsoubelet · Aug 13, 2025 · Jun 26, 2025 · Jun 26, 2025 · Jun 26, 2025
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,8 @@
+# Run this command to always ignore formatting commits in `git blame`
+# git config blame.ignoreRevsFile .git-blame-ignore-revs
+
+# Ruff rules refactoring, part 1
+# insert_commit_sha_and_uncomment
+
+# Ruff rules refactoring, part 1
+# insert_commit_sha_and_uncomment
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -18,7 +18,7 @@ jobs:
         python-version: "3.13"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Install uv and Python ${{ env.python-version }}
         uses: astral-sh/setup-uv@v6
@@ -38,6 +38,6 @@ jobs:
         run: make tests
 
       - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Install uv and Python ${{ matrix.python-version }}
         uses: astral-sh/setup-uv@v6

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -17,8 +17,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-      - name: Check Out Repo 
-        uses: actions/checkout@v4
+      - name: Check Out Repo
+        uses: actions/checkout@v5
 
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -18,7 +18,7 @@ jobs:
         python-version: "3.13"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Update apt
         run: sudo apt-get update

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -17,7 +17,7 @@ jobs:
 
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Install uv and Python ${{ env.python-version }}
         uses: astral-sh/setup-uv@v6

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Install uv and Python ${{ matrix.python-version }}
         uses: astral-sh/setup-uv@v6

diff --git a/docs/conf.py b/docs/conf.py
@@ -42,7 +42,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "PyhDToolkit"
-copyright = f"2019, {pyhdtoolkit.__author__}"
+copyright_ = f"2019, {pyhdtoolkit.__author__}"
 author = pyhdtoolkit.__author__
 
 rst_prolog = f""":github_url: {pyhdtoolkit.__url__}"""
@@ -175,7 +175,7 @@
     "capture_repr": ("_repr_html_",),
     "compress_images": ("images", "thumbnails", "-o1"),
     "only_warn_on_example_error": True,  # keep the build going if an example fails, important for doc workflow
-    "parallel": -1,  # number of jobs to use to build the gallery
+    "parallel": 1,  # number of jobs to use to build the gallery
     "write_computation_times": False,  # do not write time to run example in the output
 }
 

diff --git a/examples/demo_acd_tracking_spectra.py b/examples/demo_acd_tracking_spectra.py
@@ -34,7 +34,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-
 from cpymad.madx import Madx
 
 from pyhdtoolkit.cpymadtools import lhc, matching, track

diff --git a/examples/demo_aperture.py b/examples/demo_aperture.py
@@ -23,7 +23,6 @@
 """
 
 import matplotlib.pyplot as plt
-
 from cpymad.madx import Madx
 
 from pyhdtoolkit.cpymadtools import lhc

diff --git a/examples/demo_beam_enveloppe.py b/examples/demo_beam_enveloppe.py
@@ -15,7 +15,6 @@
 # sphinx_gallery_thumbnail_number = 1
 import matplotlib.pyplot as plt
 import numpy as np
-
 from cpymad.madx import Madx
 
 from pyhdtoolkit.plotting.envelope import plot_beam_envelope
@@ -29,7 +28,7 @@
 ###############################################################################
 # Define relevant constants.
 
-pc_GeV = 19  # Beam momentum [GeV]
+pc_GeV = 19  # Beam momentum [GeV]  # noqa: N816
 B_rho_Tm = pc_GeV / 0.3  # Magnetic rigidity [Tm]
 E_0_GeV = 0.9382720813  # proton rest mass [GeV]
 E_tot_GeV = np.sqrt(pc_GeV**2 + E_0_GeV**2)

diff --git a/examples/demo_ir_errors.py b/examples/demo_ir_errors.py
@@ -28,7 +28,6 @@
 # sphinx_gallery_thumbnail_number = 1
 import matplotlib.pyplot as plt
 import numpy as np
-
 from cpymad.madx import Madx
 
 from pyhdtoolkit.cpymadtools import lhc, matching
@@ -51,10 +50,11 @@
 
 ###############################################################################
 # Importantly in ``MAD-X``, when dealing with RNG one should set a generator and
-# seed, which we do below:
+# seed, which we will do below. Make sure to respect numpy's RNG recommendations
 
-madx.option(rand="best", randid=np.random.randint(1, 11))  # random number generator
-madx.eoption(seed=np.random.randint(1, 999999999))  # not using default seed
+rng = np.random.default_rng()
+madx.option(rand="best", randid=rng.integers(1, 11))  # random number generator
+madx.eoption(seed=rng.integers(1, 999999999))  # not using default seed
 
 ###############################################################################
 # We can now install errors in the IR quadrupoles. Note that this function accepts

diff --git a/examples/demo_lattice.py b/examples/demo_lattice.py
@@ -14,7 +14,6 @@
 """
 
 import matplotlib.pyplot as plt
-
 from cpymad.madx import Madx
 
 from pyhdtoolkit.cpymadtools import lhc, matching

diff --git a/examples/demo_lhc_crossing_schemes.py b/examples/demo_lhc_crossing_schemes.py
@@ -14,7 +14,6 @@
 """
 
 import matplotlib.pyplot as plt
-
 from cpymad.madx import Madx
 
 from pyhdtoolkit.cpymadtools import lhc

diff --git a/examples/demo_lhc_rigid_waist_shift.py b/examples/demo_lhc_rigid_waist_shift.py
@@ -44,7 +44,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import tfs
-
 from cpymad.madx import Madx
 from joblib import Parallel, delayed
 

diff --git a/examples/demo_lhc_setup.py b/examples/demo_lhc_setup.py
@@ -27,7 +27,6 @@
 
 # sphinx_gallery_thumbnail_number = 4
 import matplotlib.pyplot as plt
-
 from cpymad.madx import Madx
 
 from pyhdtoolkit.cpymadtools import coupling, lhc, twiss

diff --git a/examples/demo_machine_survey.py b/examples/demo_machine_survey.py
@@ -12,7 +12,6 @@
 
 # sphinx_gallery_thumbnail_number = 2
 import matplotlib.pyplot as plt
-
 from cpymad.madx import Madx
 
 from pyhdtoolkit.cpymadtools._generators import LatticeGenerator

diff --git a/examples/demo_phase_space.py b/examples/demo_phase_space.py
@@ -18,7 +18,6 @@
 # sphinx_gallery_thumbnail_number = 2
 import matplotlib.pyplot as plt
 import numpy as np
-
 from cpymad.madx import Madx
 
 from pyhdtoolkit.cpymadtools._generators import LatticeGenerator

diff --git a/pyhdtoolkit/cpymadtools/constants.py b/pyhdtoolkit/cpymadtools/constants.py
@@ -127,7 +127,7 @@
     [f"kqs.l{ip}b1" for ip in [2, 4, 6, 8]] + \
     [f"kqs.a{sector}{sector+1 if sector < _MAX_SECTOR_VALUE else 1}b1" for sector in [2, 4, 6, 8]] + \
     [f"kqs.r{ip}b2" for ip in [2, 4, 6, 8]] + \
-    [f"kqs.l" f"{ip}b2" for ip in [3, 5, 7, 1]] + \
+    [f"kqs.l{ip}b2" for ip in [3, 5, 7, 1]] + \
     [f"kqs.a{sector}{sector+1 if sector < _MAX_SECTOR_VALUE else 1}b2" for sector in [1, 3, 5, 7]]
 # fmt: on
 LHC_KSF_KNOBS: list[str] = [  # sextupole correctors

diff --git a/pyhdtoolkit/cpymadtools/coupling.py b/pyhdtoolkit/cpymadtools/coupling.py
@@ -15,7 +15,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from loguru import logger
 from optics_functions.coupling import check_resonance_relation, closest_tune_approach, coupling_via_cmatrix
 from scipy import stats

diff --git a/pyhdtoolkit/cpymadtools/lhc/_misc.py b/pyhdtoolkit/cpymadtools/lhc/_misc.py
@@ -90,7 +90,7 @@ def reset_lhc_bump_flags(madx: Madx, /) -> None:
         + LHC_PARALLEL_SEPARATION_FLAGS
     )
     with madx.batch():
-        madx.globals.update({bump: 0 for bump in all_bumps})
+        madx.globals.update(dict.fromkeys(all_bumps, 0))
 
 
 def get_lhc_tune_and_chroma_knobs(

diff --git a/pyhdtoolkit/cpymadtools/lhc/_routines.py b/pyhdtoolkit/cpymadtools/lhc/_routines.py
@@ -13,7 +13,6 @@
 
 import numpy as np
 import tfs
-
 from loguru import logger
 
 from pyhdtoolkit.cpymadtools.lhc._twiss import get_ir_twiss

diff --git a/pyhdtoolkit/cpymadtools/ptc.py b/pyhdtoolkit/cpymadtools/ptc.py
@@ -14,7 +14,6 @@
 from typing import TYPE_CHECKING
 
 import tfs
-
 from loguru import logger
 
 from pyhdtoolkit.cpymadtools.utils import get_table_tfs
@@ -23,7 +22,6 @@
     from collections.abc import Sequence
 
     import pandas as pd
-
     from cpymad.madx import Madx
 
 _MAX_PTC_AMPDET_ORDER: int = 2

diff --git a/pyhdtoolkit/cpymadtools/track.py b/pyhdtoolkit/cpymadtools/track.py
@@ -18,7 +18,6 @@
     from collections.abc import Sequence
 
     import pandas as pd
-
     from cpymad.madx import Madx
 
 # ----- Utlites ----- #

diff --git a/pyhdtoolkit/cpymadtools/tune.py b/pyhdtoolkit/cpymadtools/tune.py
@@ -12,15 +12,13 @@
 
 import math
 import sys
-
 from pathlib import Path
 from typing import TYPE_CHECKING
 
 import matplotlib.collections
 import matplotlib.patches
 import numpy as np
 import tfs
-
 from loguru import logger
 
 if TYPE_CHECKING:

diff --git a/pyhdtoolkit/cpymadtools/twiss.py b/pyhdtoolkit/cpymadtools/twiss.py
@@ -13,7 +13,6 @@
 from typing import TYPE_CHECKING
 
 import tfs
-
 from loguru import logger
 
 from pyhdtoolkit.cpymadtools.constants import DEFAULT_TWISS_COLUMNS

diff --git a/pyhdtoolkit/cpymadtools/utils.py b/pyhdtoolkit/cpymadtools/utils.py
@@ -15,7 +15,6 @@
 
 import pandas as pd
 import tfs
-
 from loguru import logger
 
 if TYPE_CHECKING:

diff --git a/pyhdtoolkit/maths/stats_fitting.py b/pyhdtoolkit/maths/stats_fitting.py
@@ -11,14 +11,12 @@
 from __future__ import annotations
 
 import warnings
-
 from typing import TYPE_CHECKING
 
 import matplotlib.pyplot as plt  # noqa: F401 | if omitted, get AttributeError: module 'matplotlib' has no attribute 'axes'
 import numpy as np
 import pandas as pd
 import scipy.stats as st
-
 from loguru import logger
 
 if TYPE_CHECKING:

diff --git a/pyhdtoolkit/maths/utils.py b/pyhdtoolkit/maths/utils.py
@@ -13,7 +13,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from loguru import logger
 
 if TYPE_CHECKING:

diff --git a/pyhdtoolkit/optics/beam.py b/pyhdtoolkit/optics/beam.py
@@ -9,7 +9,6 @@
 """
 
 import numpy as np
-
 from scipy import constants
 
 from pyhdtoolkit.models.beam import BeamParameters

diff --git a/pyhdtoolkit/plotting/aperture.py b/pyhdtoolkit/plotting/aperture.py
@@ -15,7 +15,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-
 from loguru import logger
 
 from pyhdtoolkit.plotting.layout import plot_machine_layout

diff --git a/pyhdtoolkit/plotting/crossing.py b/pyhdtoolkit/plotting/crossing.py
@@ -13,7 +13,6 @@
 from typing import TYPE_CHECKING
 
 import matplotlib.pyplot as plt
-
 from loguru import logger
 
 if TYPE_CHECKING:

diff --git a/pyhdtoolkit/plotting/envelope.py b/pyhdtoolkit/plotting/envelope.py
@@ -13,7 +13,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-
 from loguru import logger
 
 from pyhdtoolkit.plotting.utils import maybe_get_ax

diff --git a/pyhdtoolkit/plotting/lattice.py b/pyhdtoolkit/plotting/lattice.py
@@ -13,7 +13,6 @@
 from typing import TYPE_CHECKING
 
 import matplotlib.pyplot as plt
-
 from loguru import logger
 
 from pyhdtoolkit.plotting.layout import _ylim_from_input, plot_machine_layout
@@ -222,7 +221,7 @@ def plot_latwiss(
     dispertion_axis.legend(loc=1)
     dispertion_axis.set_ylabel("$D_{x,y}$ $[m]$", color="brown")
     dispertion_axis.tick_params(axis="y", labelcolor="brown")
-    dispertion_axis.grid(False)
+    dispertion_axis.grid(visible=False)
 
     if beta_ylim:
         logger.debug("Setting ylim for betatron functions plot")
-Original file line number
+Diff line change
@@ Expand Up / @@ -23,7 +23,6 @@ @@
     """
     import matplotlib.pyplot as plt
     from cpymad.madx import Madx
     from pyhdtoolkit.cpymadtools import lhc
@@ Expand Down @@