Version 1.3.0 Changes (#104)

Author: fsoubelet

.github/workflows/cron.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, ubuntu-22.04, macos-latest, windows-latest]
+        os: [ubuntu-22.04, macos-latest, windows-latest]
         python-version: [3.8, 3.9, "3.10", "3.11", 3.x]  # crons should always run latest python hence 3.x
         # exclude:
           # - os: windows-latest  # scipy deps issues

.github/workflows/docker.yml

@@ -18,32 +18,32 @@ jobs:
     steps:
 
       - name: Check Out Repo 
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v2
 
       - name: Cache Docker layers
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /tmp/.buildx-cache
           key: ${{ runner.os }}-buildx-${{ github.sha }}
           restore-keys: |
             ${{ runner.os }}-buildx-
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKERHUB_ID }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build and push image
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v4
         with:
           context: ./
           file: ./docker/Dockerfile

.github/workflows/documentation.yml

@@ -16,7 +16,7 @@ jobs:
     name: ${{ matrix.os }} / ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
-      matrix:  # only lowest supported python on ubuntu-latest
+      matrix:
         os: [ubuntu-latest]
         python-version: [3.9]
 
@@ -65,8 +65,8 @@ jobs:
 
       - name: Upload documentation to gh-pages
         if: success() && github.ref == 'refs/heads/master'  # only for pushes to master
-        uses: JamesIves/github-pages-deploy-action@3.7.1
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          BRANCH: gh-pages
-          FOLDER: doc_build
+          folder: doc_build
+          # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Now default
+          # BRANCH: gh-pages  # now default

.github/workflows/tests.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, ubuntu-22.04, macos-latest, windows-latest]
+        os: [ubuntu-22.04, macos-latest, windows-latest]
         python-version: [3.8, 3.9, "3.10", "3.11"]
       fail-fast: false
 
@@ -41,7 +41,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, ubuntu-22.04, macos-latest, windows-latest]
+        os: [ubuntu-22.04, macos-latest, windows-latest]
         python-version: [3.8, 3.9, "3.10", "3.11"]
       fail-fast: false
 

docs/release.rst

@@ -3,6 +3,14 @@ Release Notes
 
 The full list of releases can be found in the GitHub repository's `releases page <https://github.com/fsoubelet/PyhDToolkit/releases>`_.
 
+Version 1.3.0
+-------------
+
+.. toctree::
+    :maxdepth: 2
+
+    releases/v1.3.0
+
 Version 1.2.0
 -------------
 

docs/releases/v1.3.0.rst

@@ -0,0 +1,28 @@
+.. _release_1.3.0:
+
+1.3.0
+-----
+
+Release `1.3.0` brings a few additions and bug fixes.
+
+Enhancements
+~~~~~~~~~~~~
+
+* The `pyhdtoolkit.plotting.aperture.plot_physical_apertures` now has an ``xoffset`` argument similar to the one of the other plotting functions.
+* The `pyhdtoolkit.plotting.envelope.plot_beam_envelope` now has an ``xoffset`` argument similar to the one of the other plotting functions.
+* The `pyhdtoolkit.plotting.layout` module has a new public function, `scale_patches`, to enable easy scaling of the element patches.
+
+Bug Fixes
+~~~~~~~~~
+
+* The `pyhdtoolkit.plotting.layout.plot_machine_layout` function will now plot skew elements too, with a hatching pattern to differentiate them from their normal counterparts.
+
+Maintenance
+~~~~~~~~~~~
+
+* The `pyhdtoolkit.plotting.styles.paper.SINGLE_COLUMN` matplotlib style has been adjusted to be tighter at the edges of the figure when saving to a file.
+* Relaxed the tolerance of some coupling correction tests as the routine seems to perform slightly worse on the new MAD-X version.
+* Removed deprecated workers versions from the CI configuration.
+* Updated the CI configuration to use the latest versions of the docker actions.
+
+See `v1.3.0 release notes on GitHub <https://github.com/fsoubelet/PyhDToolkit/releases/tag/1.3.0>`_ and the `full changes since v1.2.0 <https://github.com/fsoubelet/PyhDToolkit/compare/1.2.0...1.3.0>`_.

pyhdtoolkit/plotting/aperture.py

@@ -188,7 +188,13 @@ def plot_aperture(
 
 
 def plot_physical_apertures(
-    madx, /, plane: str, scale: float = 1, xlimits: Tuple[float, float] = None, **kwargs
+    madx,
+    /,
+    plane: str,
+    scale: float = 1,
+    xoffset: float = 0,
+    xlimits: Tuple[float, float] = None,
+    **kwargs,
 ) -> None:
     """
     .. versionadded:: 1.2.0
@@ -213,6 +219,11 @@ def plot_physical_apertures(
         scale (float): a scaling factor to apply to the beam orbit and beam
             enveloppe, for the user to adjust to their wanted scale. Defaults
             to 1 (values in [m]).
+        xoffset (float): An offset applied to the ``S`` coordinate before
+            plotting. This is useful if you want to center a plot around a
+            specific point or element, which would then become located
+            at :math:`s = 0`. Beware this offset is applied before applying
+            the *xlimits*. Defaults to 0.
         xlimits (Tuple[float, float]): will implement xlim (for the ``s``
             coordinate) if this is not ``None``, using the tuple passed.
             Defaults to ``None``.
@@ -249,10 +260,9 @@ def plot_physical_apertures(
     logger.debug("Plotting real element apertures")
     axis, kwargs = maybe_get_ax(**kwargs)
 
-    if xlimits is not None:
-        axis.set_xlim(xlimits)
-
-    positions, apertures = _get_positions_and_real_apertures(madx, plane, xlimits, **kwargs)
+    positions, apertures = _get_positions_and_real_apertures(madx, plane, **kwargs)
+    logger.trace(f"Applying scale ({scale}) and offset ({xoffset})")
+    positions = positions - xoffset
     apertures = apertures * scale
 
     logger.trace("Plotting apertures")
@@ -262,12 +272,16 @@ def plot_physical_apertures(
     axis.plot(positions, apertures, "k", label="_nolegend_")
     axis.plot(positions, -1 * apertures, "k", label="_nolegend_")
 
+    if xlimits:
+        logger.trace("Setting xlim for longitudinal coordinate")
+        axis.set_xlim(xlimits)
+
 
 # ----- Helpers ----- #
 
 
 def _get_positions_and_real_apertures(
-    madx, /, plane: str, xlimits: Tuple[float, float] = None, **kwargs
+    madx, /, plane: str, xoffset: float = 0, xlimits: Tuple[float, float] = None, **kwargs
 ) -> Tuple[np.ndarray, np.ndarray]:
     """
     .. versionadded:: 1.2.0
@@ -288,6 +302,11 @@ def _get_positions_and_real_apertures(
             Positional only.
         plane (str): the physical plane to plot for, should be either `x`,
             `horizontal`, `y` or `vertical`, and is case-insensitive.
+        xoffset (float): An offset applied to the ``S`` coordinate before
+            plotting. This is useful if you want to center a plot around a
+            specific point or element, which would then become located
+            at :math:`s = 0`. Beware this offset is applied before applying
+            the *xlimits*. Defaults to 0.
         xlimits (Tuple[float, float]): will implement xlim (for the ``s``
             coordinate) if this is not ``None``, using the tuple passed.
             Defaults to ``None``.
@@ -303,6 +322,7 @@ def _get_positions_and_real_apertures(
     madx.command.select(flag="twiss", column=["aper_1", "aper_2"])  # make sure we to get these two
     twiss_df = madx.twiss(**kwargs).dframe()
     madx.command.select(flag="twiss", clear=True)  # clean up
+    twiss_df.s = twiss_df.s - xoffset
 
     logger.trace("Determining aperture column to use")
     plane_number = 1 if plane.lower() in ("x", "horizontal") else 2
@@ -325,7 +345,7 @@ def _get_positions_and_real_apertures(
     indices = list(reversed(indices))
 
     logger.trace("Extrapolating data at beginning of elements")
-    counter = 0# Keep track of exact position in new array with counter
+    counter = 0  # Keep track of exact position in new array with counter
     for j in indices:
         new_pos.insert(j + counter, (twiss_df.s[j] - twiss_df.l[j]))
         counter += 1
@@ -334,5 +354,4 @@ def _get_positions_and_real_apertures(
     apertures = np.array(new_aper)
     apertures[apertures == 0] = np.nan
     positions = np.array(new_pos)
-
     return positions, apertures

pyhdtoolkit/plotting/envelope.py

@@ -23,6 +23,7 @@ def plot_beam_envelope(
     plane: str,
     nsigma: float = 1,
     scale: float = 1,
+    xoffset: float = 0,
     xlimits: Tuple[float, float] = None,
     **kwargs,
 ) -> None:
@@ -48,6 +49,11 @@ def plot_beam_envelope(
         scale (float): a scaling factor to apply to the beam orbit and beam
             enveloppe, for the user to adjust to their wanted scale. Defaults
             to 1 (values in [m]).
+        xoffset (float): An offset applied to the ``S`` coordinate before
+            plotting. This is useful if you want to center a plot around a
+            specific point or element, which would then become located
+            at :math:`s = 0`. Beware this offset is applied before applying
+            the *xlimits*. Defaults to 0.
         xlimits (Tuple[float, float]): will implement xlim (for the ``s``
             coordinate) if this is not ``None``, using the tuple passed.
             Defaults to ``None``.
@@ -87,6 +93,8 @@ def plot_beam_envelope(
     logger.debug("Getting Twiss dframe from MAD-X")
     plane_letter = "x" if plane.lower() in ("x", "horizontal") else "y"
     twiss_df = madx.twiss(**kwargs).dframe()
+    twiss_df.s = twiss_df.s - xoffset
+
     if xlimits is not None:
         axis.set_xlim(xlimits)
         twiss_df = twiss_df[twiss_df.s.between(*xlimits)]

pyhdtoolkit/plotting/layout.py

@@ -12,6 +12,7 @@
 import matplotlib
 import matplotlib.axes
 import matplotlib.patches as patches
+import numpy as np
 import pandas as pd
 
 from cpymad.madx import Madx
@@ -172,7 +173,8 @@ def plot_machine_layout(
     dipole_patches_axis = axis.twinx()
     dipole_patches_axis.set_ylabel("$\\theta=K_{0}L$ $[rad]$", color="royalblue")  # dipoles in blue
     dipole_patches_axis.tick_params(axis="y", labelcolor="royalblue")
-    dipole_patches_axis.set_ylim(k0l_lim)
+    if not np.nan in k0l_lim:
+        dipole_patches_axis.set_ylim(k0l_lim) 
     dipole_patches_axis.grid(False)
 
     if plot_dipoles:  # beware 'sbend' and 'rbend' have an 'angle' value and not a 'k0l'
@@ -210,12 +212,14 @@ def plot_machine_layout(
         plotted_elements = 0
         for quadrupole_name, quadrupole in quadrupoles_df.iterrows():
             logger.trace(f"Plotting quadrupole element '{quadrupole_name}'")
+            element_k = quadrupole.k1l if quadrupole.k1l != 0 else quadrupole.k1sl  # can be skew quadrupole
             _plot_lattice_series(
                 axis,
                 quadrupole,
-                height=quadrupole.k1l,
-                v_offset=quadrupole.k1l / 2,
+                height=element_k,
+                v_offset=element_k / 2,
                 color="r",
+                hatch=None if quadrupole.k1l != 0 else "///",  # hatch skew quadrupoles
                 label="MQ" if plotted_elements == 0 else None,  # avoid duplicating legend labels
                 **kwargs,
             )
@@ -235,12 +239,14 @@ def plot_machine_layout(
         plotted_elements = 0
         for sextupole_name, sextupole in sextupoles_df.iterrows():
             logger.trace(f"Plotting sextupole element '{sextupole_name}'")
+            element_k = sextupole.k2l if sextupole.k2l != 0 else sextupole.k2sl  # can be skew sextupole
             _plot_lattice_series(
                 sextupoles_patches_axis,
                 sextupole,
-                height=sextupole.k2l,
-                v_offset=sextupole.k2l / 2,
+                height=element_k,
+                v_offset=element_k / 2,
                 color="goldenrod",
+                hatch=None if sextupole.k2l != 0 else "\\\\\\",  # hatch skew sextupoles
                 label="MS" if plotted_elements == 0 else None,  # avoid duplicating legend labels
                 **kwargs,
             )
@@ -263,12 +269,14 @@ def plot_machine_layout(
         plotted_elements = 0
         for octupole_name, octupole in octupoles_df.iterrows():
             logger.trace(f"Plotting octupole element '{octupole_name}'")
+            element_k = octupole.k3l if octupole.k3l else octupole.k3sl  # can be skew octupole
             _plot_lattice_series(
                 octupoles_patches_axis,
                 octupole,
                 height=octupole.k3l,
                 v_offset=octupole.k3l / 2,
                 color="forestgreen",
+                hatch=None if octupole.k3l != 0 else "xxx",  # hatch skew octupoles
                 label="MO" if plotted_elements == 0 else None,  # avoid duplicating legend labels
                 **kwargs,
             )
@@ -314,6 +322,35 @@ def plot_machine_layout(
         bpm_patches_axis.grid(False)
 
 
+def scale_patches(scale: float, ylabel: str, **kwargs) -> None:
+    """
+    .. versionadded:: 1.3.0
+
+    This is a convenience function to update the scale of the elements layout
+    patches as well as the corresponding y-axis label.
+
+    Args:
+        scale (float): the scale factor to apply to the patches. The new 
+            height of the patches will be ``scale * original_height``.
+        ylabel (str): the new label for the y-axis.
+        **kwargs: If either `ax` or `axis` is found in the kwargs, the
+            corresponding value is used as the axis object to plot on,
+            otherwise the current axis is used.
+    
+    Example:
+        .. code-block:: python
+
+            >>> fig, ax = plt.subplots(figsize=(6, 2))
+            >>> plot_machine_layout(madx, title="Machine Elements", lw=3)
+            >>> scale_patches(ax=fig.axes[0], scale=100, ylabel=r"$K_{1}L$ $[10^{-2} m^{-1}]$")
+    """
+    axis, kwargs = maybe_get_ax(**kwargs)
+    axis.set_ylabel(ylabel)
+    for patch in axis.patches:
+        h = patch.get_height()
+        patch.set_height(scale * h)
+
+
 # ----- Helpers ----- #
 
 
@@ -399,7 +436,7 @@ def _determine_default_knl_lim(df: pd.DataFrame, col: str, coeff: float) -> Tupl
 
     Determine the default limits for the ``knl`` axis, when plotting machine
     layout. This is in case `None` are provided by the user, to make sure the
-    plot still looks coherent and symmetric in 
+    plot still looks coherent and symmetric in
     `~.plotting.utils.plot_machine_layout`.
 
     The limits are determined symmetric, using the maximum absolute value of

pyhdtoolkit/plotting/styles/paper.py

@@ -59,8 +59,8 @@
     "figure.figsize": (11, 7),  # Size of the figure
     "figure.titlesize": 20,  # Size of the figure title
     "figure.subplot.left": 0.13,  # Left side limit of the subplots of the figure
-    "figure.subplot.top": 0.92,  # Top side limit of the subplots of the figure
-    "figure.subplot.bottom": 0.15,  # Bottom side limit of the subplots of the figure
+    "figure.subplot.top": 0.9,  # Top side limit of the subplots of the figure
+    "figure.subplot.bottom": 0.1,  # Bottom side limit of the subplots of the figure
     # ------ Saving ------ #
     "savefig.dpi": 400,  # Saved figure dots per inch
     "savefig.format": "pdf",  # Saved figure file format

pyhdtoolkit/version.py

@@ -1,4 +1,4 @@
-VERSION = "1.2.0"
+VERSION = "1.3.0"
 
 
 def version_info() -> str: