Documentation updates

.github/workflows/coverage.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       matrix:  # only lowest supported python on ubuntu-latest
         os: [ubuntu-latest]
-        python-version: [3.9]
+        python-version: [3.11]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/documentation.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.9]
+        python-version: [3.11]
 
     steps:
       - uses: actions/checkout@v3
@@ -32,6 +32,12 @@ jobs:
       - name: Install optipng, dvipng and cm-super
         run: sudo apt-get install -y optipng dvipng cm-super
 
+      - name: Get acc-models-lhc
+        run: git clone -b 2022 https://gitlab.cern.ch/acc-models/acc-models-lhc.git --depth 1
+
+      - name: Move acc-models-lhc to examples folder
+        run: mv acc-models-lhc examples/
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
@@ -42,18 +48,10 @@ jobs:
       - name: Install package with doc dependencies
         run: python -m pip install ".[docs]"
 
-      # Sometimes the minrpc client will close while documentation builds and I don't know why
-      # Forcing several successive builds here and hoping it works out (sphinx-gallery 
-      # checks for the existence of already built examples to avoid re-running them, so
-      # once the gallery is built successive builds will just re-generate the html, very quickly)
       - name: Build documentation
         continue-on-error: true
         run: make docs
 
-      # - name: Build documentation (2/n)
-      #   continue-on-error: true
-      #   run: make docs
-
       # 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@v3
@@ -63,10 +61,9 @@ jobs:
           path: doc_build
           retention-days: 7
 
+      # Upload the doc to github pages branch and publish if from a push to master
       - name: Upload documentation to gh-pages
         if: success() && github.ref == 'refs/heads/master'  # only for pushes to master
         uses: JamesIves/github-pages-deploy-action@v4
         with:
           folder: doc_build
-          # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Now default
-          # BRANCH: gh-pages  # now default

.github/workflows/publish.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:  # only lowest supported python on ubuntu-latest
         os: [ubuntu-latest]
-        python-version: [3.9]
+        python-version: [3.11]
 
 
     steps:

docs/conf.py

@@ -90,7 +90,7 @@ def __call__(self, *args, **kwargs):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs/contributing.rst

@@ -33,13 +33,13 @@ Please include the following items in a bug report:
 
     .. code-block:: python
 
-        >>> import pyhdtoolkit
-        >>> print(pyhdtoolkit.version.version_info())
-            PyhDToolkit version: 0.21.0
-                   Install path: /Users/felixsoubelet/Repositories/Work/PyhDToolkit/pyhdtoolkit
-                 Python version: 3.10.6
-          Python implementation: 3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:41:54) [Clang 13.0.1 ]
-                       Platform: macOS-12.5.1-x86_64-i386-64bit
+        import pyhdtoolkit
+        print(pyhdtoolkit.version.version_info())
+        #    PyhDToolkit version: 0.21.0
+        #           Install path: /Users/felixsoubelet/Repositories/Work/PyhDToolkit/pyhdtoolkit
+        #         Python version: 3.10.6
+        #  Python implementation: 3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:41:54) [Clang 13.0.1 ]
+        #               Platform: macOS-12.5.1-x86_64-i386-64bit
 
 Enhancement Proposals
 ---------------------

docs/quickstart.rst

@@ -51,14 +51,14 @@ Any jupyter notebook or Python files in the mounted directory can then be used o
 
 One can use the library by simply importing it:
 
-.. prompt:: python >>>
+.. prompt:: python
 
     import pyhdtoolkit
 
 This will include only the core components of ``PyhDToolkit``.
 The different sub-packages must be imported separately, depending on your needs:
 
-.. prompt:: python >>>
+.. prompt:: python
 
     import pyhdtoolkit.cpymadtools
     import pyhdtoolkit.maths
@@ -78,14 +78,14 @@ All the public apis in the `~pyhdtoolkit.cpymadtools` work in the same fashion:
 `~cpymad.madx.Madx` instance, and then any `args` and `kwargs` relevant to the functionality at hand.
 Let's say one has initiated their ``MAD-X`` simulation through `~cpymad.madx.Madx` as follows:
 
-.. prompt:: python >>>
+.. prompt:: python
 
     from cpymad.madx import Madx
     madx = Madx()
 
 Then using the `~pyhdtoolkit.cpymadtools` apis goes as:
 
-.. prompt:: python >>>
+.. prompt:: python
 
     from pyhdtoolkit.cpymadtools import super_cool_function  # pretend it exists ;)
     super_cool_function(madx, *args, **kwargs)
@@ -111,7 +111,7 @@ Using the `~pyhdtoolkit.plotting` apis goes as:
 
 .. tabbed:: Standalone
 
-    .. prompt:: python >>>
+    .. prompt:: python
 
         from pyhdtoolkit.plotting.tune import plot_tune_diagram  # for instance
         plot_tune_diagram(max_order=6, differentiate_orders=True)  # and enjoy the result!
@@ -120,15 +120,15 @@ Using the `~pyhdtoolkit.plotting` apis goes as:
 
     Let's say one has initiated their ``MAD-X`` simulation through `~cpymad.madx.Madx` as follows:
 
-    .. prompt:: python >>>
+    .. prompt:: python
 
         from cpymad.madx import Madx
         madx = Madx()
         # do some simulation with this instance
 
     Then using the api goes as:
 
-    .. prompt:: python >>>
+    .. prompt:: python
 
         from pyhdtoolkit.plotting.aperture import plot_aperture  # for instance
         plot_aperture(madx, *args, **kwargs)  # and enjoy the result!
@@ -145,14 +145,14 @@ functions, or perform many convenient :ref:`operations <utils-operations>` on mi
 
 For instance, one can safely run an input at the commandline with:
 
-.. prompt:: python >>>
+.. prompt:: python
 
     from pyhdtoolkit.utils.cmdline import CommandLine
     CommandLine.run("sleep 5")
 
 Alternatively one can easily parallelise an I/O-intensive function through multithreading with:
 
-.. prompt:: python >>>
+.. prompt:: python
 
     from pyhdtoolkit.utils.executors import MultiThreader
     Threader = MultiThreader()
@@ -165,7 +165,7 @@ Alternatively one can easily parallelise an I/O-intensive function through multi
 .. tip::
     A useful tidbit is the following which sets up the logging level for functions in the package:
 
-    .. prompt:: python >>>
+    .. prompt:: python
 
         from pyhdtoolkit.utils import logging
         logging.config_logger(level="trace")  # the lowest level used, will give ALL logging

docs/references.bib

@@ -90,4 +90,15 @@ @article{Carlier:AccuracyFeasibilityMeasurement2017
   journaltitle = {Physical Review Accelerators and Beams},
   title        = {Accuracy and Feasibility of the β * Measurement for {{LHC}} and {{High Luminosity LHC}} Using k Modulation},
   year         = {2017}
+}
+
+@article{PRAB:Soubelet:Rigid_Waist_Shift_Method_Local_Coupling_Correction_LHC_IR,
+  author    = {F. Soubelet and T. Persson and R. Tomás and O. Apsimon and C.P. Welsch},
+  doi       = {10.1103/PhysRevAccelBeams.26.051001},
+  journal   = {{Phys. Rev. ST Accel. Beams}},
+  month     = May,
+  publisher = {{American Physical Society}},
+  title     = {{Rigid Waist Shift: A New Method for Local Coupling Corrections in the LHC Interaction Regions}},
+  volume    = {26},
+  year      = 2023
 }

docs/releases/v1.3.2.rst

@@ -1,4 +1,4 @@
-.. _release_1.3.1:
+.. _release_1.3.2:
 
 1.3.2
 -----

examples/README.rst

@@ -26,7 +26,7 @@ submodules, or plots made from results of convenient functions available in `~py
 
         Update the ``rcParams`` at runtime with:
 
-            .. prompt:: python >>>
+            .. prompt:: python
 
                 from matplotlib import pyplot as plt
                 from pyhdtoolkit.plotting.styles.thesis import MEDIUM
@@ -36,7 +36,7 @@ submodules, or plots made from results of convenient functions available in `~py
 
         Or, for a temporary update of the ``rcParams``:
 
-            .. prompt:: python >>>
+            .. prompt:: python
 
                 from matplotlib import pyplot as plt
                 from pyhdtoolkit.plotting.styles.thesis import MEDIUM
@@ -48,7 +48,7 @@ submodules, or plots made from results of convenient functions available in `~py
 
         Do a one-time install of the styles as **.mplstyle** files to use in `~matplotlib`:
 
-            .. prompt:: python >>>
+            .. prompt:: python
 
                 from matplotlib import pyplot as plt
                 from pyhdtoolkit.plotting.styles import install_mpl_styles