Release 1.2.0 (#101)

.github/workflows/README.md

@@ -1,4 +1,4 @@
-# Continous Integration Workflows
+# Continuous Integration Workflows
 
 This package implements different workflows for CI.
 They are organised as follows.

.github/workflows/coverage.yml

@@ -34,7 +34,7 @@ jobs:
         run: python -m pip install ".[test]"
 
       - name: Get acc-models-lhc
-        run: git clone https://gitlab.cern.ch/acc-models/acc-models-lhc.git --depth 1
+        run: git clone -b 2022 https://gitlab.cern.ch/acc-models/acc-models-lhc.git --depth 1
 
       - name: Run all tests
         run: make alltests

.github/workflows/cron.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04, ubuntu-22.04, macos-latest, windows-latest]
-        python-version: [3.8, 3.9, "3.10", 3.x]  # crons should always run latest python hence 3.x
+        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
           #   python-version: "3.10"
@@ -42,7 +42,7 @@ jobs:
         run: python -m pip install ".[test]"
 
       - name: Get acc-models-lhc
-        run: git clone https://gitlab.cern.ch/acc-models/acc-models-lhc.git --depth 1
+        run: git clone -b 2022 https://gitlab.cern.ch/acc-models/acc-models-lhc.git --depth 1
 
       - name: Run Tests
         run: make alltests

.github/workflows/documentation.yml

@@ -56,7 +56,7 @@ jobs:
 
       # Upload artifacts if in PR so reviewers can have a quick look without building documentation from the branch locally
       - name: Upload build artifacts
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         if: success() && github.event_name == 'pull_request'  # only for pushes in PR
         with:
           name: site-build

.github/workflows/tests.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04, ubuntu-22.04, macos-latest, windows-latest]
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: [3.8, 3.9, "3.10", "3.11"]
       fail-fast: false
 
     steps:
@@ -42,7 +42,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04, ubuntu-22.04, macos-latest, windows-latest]
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: [3.8, 3.9, "3.10", "3.11"]
       fail-fast: false
 
     steps:
@@ -59,7 +59,7 @@ jobs:
         run: python -m pip install ".[test]"
 
       - name: Get acc-models-lhc
-        run: git clone https://gitlab.cern.ch/acc-models/acc-models-lhc.git --depth 1
+        run: git clone -b 2022 https://gitlab.cern.ch/acc-models/acc-models-lhc.git --depth 1
 
       - name: Run Tests
         run: make slowtests

docs/conf.py

@@ -36,6 +36,10 @@
 
 import pyhdtoolkit
 
+# This is to tell Sphinx how to print some specific type annotations
+# See: https://stackoverflow.com/a/67483317
+# See: https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#confval-autodoc_type_aliases
+autodoc_type_aliases = {"ArrayLike": "ArrayLike"}
 
 # To use SVG outputs when scraping matplotlib figures for the sphinx-gallery
 class matplotlib_svg_scraper(object):
@@ -144,6 +148,7 @@ def __call__(self, *args, **kwargs):
     "sphinx_panels",  # Create panels in a grid layout or as drop-downs
     "matplotlib.sphinxext.plot_directive",  # Include a Matplotlib plot in a Sphinx document
     "sphinx-prompt",  # prompt symbols will not be copy-pastable
+    "sphinx_codeautolink",  # Automatically link example code to documentation source
 ]
 
 # Config for autosectionlabel extension

docs/release.rst

@@ -3,22 +3,30 @@ Release Notes
 
 The full list of releases can be found in the GitHub repository's `releases page <https://github.com/fsoubelet/PyhDToolkit/releases>`_.
 
+Version 1.2.0
+-------------
+
+.. toctree::
+    :maxdepth: 2
+
+    releases/v1.2.0
+
 Version 1.1.1
 -------------
 
 .. toctree::
     :maxdepth: 2
 
     releases/v1.1.1
-    
+
 Version 1.1.0
 -------------
 
 .. toctree::
     :maxdepth: 2
 
     releases/v1.1.0
-    
+
 Version 1.0.0
 -------------
 

docs/releases/v1.1.1.rst

@@ -13,4 +13,4 @@ Bug Fixes
 * A few values in the available plotting settings were changed.
 
 
-See `v1.1.1 release notes on GitHub <https://github.com/fsoubelet/PyhDToolkit/releases/tag/1.1.1>`_ and the `full changes since v1.0.0 <https://github.com/fsoubelet/PyhDToolkit/compare/1.1.0...1.1.1>`_.
+See `v1.1.1 release notes on GitHub <https://github.com/fsoubelet/PyhDToolkit/releases/tag/1.1.1>`_ and the `full changes since v1.1.0 <https://github.com/fsoubelet/PyhDToolkit/compare/1.1.0...1.1.1>`_.

docs/releases/v1.2.0.rst

@@ -0,0 +1,45 @@
+.. _release_1.2.0:
+
+1.2.0
+-----
+
+Release `1.2.0` brings some new features and dependency changes.
+
+Changes
+~~~~~~~
+
+* The `pyhdtoolkit.plotting.envelope` functions `plot_envelope` and `plot_stay_clear` have been removed. They are replaced by a new one, `plot_beam_envelope`, which handles all enveloppe calculations directly from the `MAD-X` instance. Documentation and examples have been updated.
+
+Enhancements
+~~~~~~~~~~~~
+
+* The `pyhdtoolkit.plotting.aperture` module has a new function, `~pyhdtoolkit.plotting.aperture.plot_physical_apertures`, to try and plot the physical apertures of elements on the given axis.
+* The `pyhdtoolkit.plotting.utils` module has a new function, `~pyhdtoolkit.plotting.utils.draw_confidence_ellipse`, to plot the covariance ellipse of two arrays.
+* The `pyhdtoolkit.plotting.layout.plot_machine_layout` function (and those relying on it) can now plot octupole patches.
+* The `pyhdtoolkit.plotting.layout.plot_machine_layout` function (and those relying on it) can now handle single values given for ylimits of different elements in the machine layout. For instance now `k1l_lim=5e-2` is valid and equivalent to `k1l_lim=(-5e-2, 5e-2)`.
+* An experimental utility function was added to split a complex-valued columns from a dataframe into two real-valued ones. It might join the public API in a future release, and is for now available as `~pyhdtoolkit.utils._misc.split_complex_columns`.
+* An experimental utility function was added to add noise to the ``LHC`` *IR* BPMs in a given dataframe column. It might join the public API in a future release, and is for now available as `~pyhdtoolkit.utils._misc.add_noise_to_ir_bpms`.
+* An experimental utility function was added to add noise to the ``LHC`` *arc* BPMs in a given dataframe column. It might join the public API in a future release, and is for now available as `~pyhdtoolkit.utils._misc.add_noise_to_arc_bpms`. 
+* The functions in the `pyhdtoolkit.cpymadtools.ptc` module can now be given values for the ``PTC`` universe creation and called commands parameters through keyword arguments. The documentation has been updated with information on the available parameters.
+
+Bug Fixes
+~~~~~~~~~
+
+* The `pyhdtoolkit.plotting.layout.plot_machine_layout` function now only adds a legend for element patches of a certain type if at least one element was drawn.
+* The `pyhdtoolkit.plotting.layout.plot_machine_layout` function now tries to properly determine legend locations based on which elements were drawn.
+
+Documentation
+~~~~~~~~~~~~~
+
+* The documentation generated by `Sphinx` should now properly display short type hints instead of the full expanded ones.
+* Some example pages have been updated to use the minimal requirement of provided **args** for the functions in `~pyhdtoolkit.cpymadtools.matching`.
+* Some typos that were left in a few docstrings have been corrected.
+
+Maintenance
+~~~~~~~~~~~
+
+* The `madx` argument is now positional only in all APIs involving it (APIs in `~pyhdtoolkit.cpymadtools` and `~pyhdtoolkit.plotting`).
+* The `~numpy` dependency is now capped at version `<1.24.0`, as when using this new version some `~matplotlib` functions are broken.
+* Various type hints from the `typing` module, such as `Dict` or `List`, have been superseeded by the default, now-standard builtins (such as `dict` or `list`).
+
+See `v1.2.0 release notes on GitHub <https://github.com/fsoubelet/PyhDToolkit/releases/tag/1.2.0>`_ and the `full changes since v1.1.1 <https://github.com/fsoubelet/PyhDToolkit/compare/1.1.1...1.2.0>`_.

examples/acc-models-lhc/operation/optics/R2022a_A11mC11mA10mL10m.madx

@@ -0,0 +1,10 @@
+! JMad export of model LHC 2022 optic R2022a_A11mC11mA10mL10m
+
+
+call, file="acc-models-lhc/toolkit/zero-strengths.madx";
+call, file="acc-models-lhc/strengths/ATS_Nominal/2022/ramp/ats_11m.madx";
+call, file="acc-models-lhc/toolkit/reset-bump-flags.madx";
+call, file="acc-models-lhc/toolkit/match-lumiknobs.madx";
+call, file="acc-models-lhc/toolkit/generate-op-tune-knobs-ats.madx";
+call, file="acc-models-lhc/toolkit/generate-op-chroma-knobs-ats.madx";
+call, file="acc-models-lhc/toolkit/generate-op-coupling-knobs-ats.madx";