Merge branch 'stable' into faster_circular_resistive_wall

.gitlab-ci.yml

+stages:
+  - test
+  - build_docker
+  - build_pip
+
+.python_job:
+  image: gitlab-registry.synchrotron-soleil.fr/pa/collective-effects/python_mpi:latest
+  before_script:
+    - pip install poetry
+    - poetry install
+    - source `poetry env info --path`/bin/activate
+
+include:
+  - template: Jobs/Dependency-Scanning.gitlab-ci.yml
+
+testing:
+  extends: .python_job
+  stage: test
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "stable"'
+    - if: '$CI_COMMIT_BRANCH == "develop"'
+    - if: '$CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "stable"'
+    - if: '$CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "develop"'
+  script:
+    - cd tests
+    - poetry run pytest --junitxml=report.xml
+  artifacts:
+    when: always
+    reports:
+      junit: /builds/PA/collective-effects/mbtrack2/tests/report.xml
+
+formatters:
+  extends: .python_job
+  stage: test
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "stable"'
+    - if: '$CI_COMMIT_BRANCH == "develop"'
+    - if: '$CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "stable"'
+    - if: '$CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "develop"'
+  script:
+    - poetry run isort --check --diff mbtrack2/
+    - poetry run yapf -d -r mbtrack2/
+
+docker_develop:
+  stage: build_docker
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "develop"'
+  image: docker:latest
+  services:
+    - docker:dind
+  variables:
+    CONTAINER_RELEASE_IMAGE: ${CI_REGISTRY_IMAGE}:develop
+  script:
+    - echo "${CI_REGISTRY_PASSWORD}" | docker login -u ${CI_REGISTRY_USER} --password-stdin ${CI_REGISTRY}
+    - docker build --pull -t ${CONTAINER_RELEASE_IMAGE} .
+    - docker push ${CONTAINER_RELEASE_IMAGE}
+
+docker_stable:
+  stage: build_docker
+  rules:
+    - if: '$CI_COMMIT_TAG'
+  image: docker:latest
+  services:
+    - docker:dind
+  variables:
+    CONTAINER_RELEASE_IMAGE: ${CI_REGISTRY_IMAGE}:latest
+    CONTAINER_TAG_IMAGE: ${CI_REGISTRY_IMAGE}:${CI_COMMIT_TAG}
+  script:
+    - echo "${CI_REGISTRY_PASSWORD}" | docker login -u ${CI_REGISTRY_USER} --password-stdin ${CI_REGISTRY}
+    - docker build --pull -t ${CONTAINER_RELEASE_IMAGE} .
+    - docker image tag ${CONTAINER_RELEASE_IMAGE} ${CONTAINER_TAG_IMAGE}
+    - docker push ${CONTAINER_RELEASE_IMAGE}
+    - docker push ${CONTAINER_TAG_IMAGE}
+
+pip_stable:
+  extends: .python_job
+  stage: build_pip
+  rules:
+    - if: '$CI_COMMIT_TAG'
+  script:
+    - poetry config repositories.gitlab ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi
+    - poetry build
+    - poetry publish --repository gitlab -u gitlab-ci-token -p ${CI_JOB_TOKEN}

CONTRIBUTORS.md

@@ -6,4 +6,5 @@ The following people contributed to the developpement of this code (chronologic
 + Naoto Yamamoto
 + David Amorim
 + Antonin Sauret
-+ Vadim Gubaidulin
\ No newline at end of file
++ Vadim Gubaidulin
++ Keon Hee Kim
\ No newline at end of file

Dockerfile

+FROM gitlab-registry.synchrotron-soleil.fr/pa/collective-effects/python_mpi:latest
+LABEL name mbtrack2
+USER dockeruser
+WORKDIR '/home/dockeruser'
+ENV PATH ${PATH}:/home/dockeruser/miniconda3/bin:/home/dockeruser/miniconda3/condabin
+RUN pip3 install accelerator-toolbox==0.5.0
+COPY --chown=dockeruser mbtrack2 /home/dockeruser/mbtrack2
+ENV PYTHONPATH=/home/dockeruser/
\ No newline at end of file

README.md

 mbtrack2
 ========
 
+[![GitLab Release](https://img.shields.io/gitlab/v/release/184?gitlab_url=https%3A%2F%2Fgitlab.synchrotron-soleil.fr%2F)](https://gitlab.synchrotron-soleil.fr/PA/collective-effects/mbtrack2/-/releases) [![PyPI - Version](https://img.shields.io/pypi/v/mbtrack2)](https://pypi.org/project/mbtrack2/)
+[![PyPI - License](https://img.shields.io/pypi/l/mbtrack2)](https://gitlab.synchrotron-soleil.fr/PA/collective-effects/mbtrack2/-/blob/stable/LICENSE)
+[![Read the Docs](https://img.shields.io/readthedocs/mbtrack2)](https://mbtrack2.readthedocs.io/)
+
 mbtrack2 is a coherent object-oriented framework written in python to work on collective effects in synchrotrons.
 
 mbtrack2 is composed of different modules allowing to easily write scripts for single bunch or multi-bunch tracking using MPI parallelization in a transparent way. The base of the tracking model of mbtrack2 is inspired by mbtrack, a C multi-bunch tracking code initially developed at SOLEIL.
@@ -56,14 +60,22 @@ To test your installation run:
 from mbtrack2 import *
 ```
 
+### Using docker
+
+A docker image is available:
+
+```
+docker pull gitlab-registry.synchrotron-soleil.fr/pa/collective-effects/mbtrack2
+```
+
 References
 ----------
 If used in a publication, please cite mbtrack2 paper and the zenodo archive for the corresponding code version (and any other paper in this list for more specific features).
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10871040.svg)](https://doi.org/10.5281/zenodo.10871040)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12749990.svg)](https://doi.org/10.5281/zenodo.12749990)
 
 ### mbtrack2 general features
 A. Gamelin, W. Foosang, and R. Nagaoka, “mbtrack2, a Collective Effect Library in Python”, presented at the 12th Int. Particle Accelerator Conf. (IPAC'21), Campinas, Brazil, May 2021, paper MOPAB070.
 
-### RF cavities with beam loading and RF feedbacks 
-Yamamoto, Naoto, Alexis Gamelin, and Ryutaro Nagaoka. "Investigation of Longitudinal Beam Dynamics With Harmonic Cavities by Using the Code Mbtrack." Proc. 10th International Partile Accelerator Conference (IPAC’19), Melbourne, Australia, 19-24 May 2019. 2019.
\ No newline at end of file
+### RF cavities with beam loading and RF feedbacks
+Yamamoto, Naoto, Alexis Gamelin, and Ryutaro Nagaoka. "Investigation of Longitudinal Beam Dynamics With Harmonic Cavities by Using the Code Mbtrack." Proc. 10th International Partile Accelerator Conference (IPAC’19), Melbourne, Australia, 19-24 May 2019. 2019.

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/build/html/.buildinfo

+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 05f20f44309c0b23df92472b9aade71e
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_modules/index.html

+
+<!DOCTYPE html>
+
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Overview: module code &#8212; mbtrack2 0.6.0 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/nature.css" />
+    <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
+    <script src="../_static/jquery.js"></script>
+    <script src="../_static/underscore.js"></script>
+    <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
+    <script src="../_static/doctools.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+  </head><body>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">mbtrack2 0.6.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Overview: module code</a></li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="mbtrack2/impedance/csr.html">mbtrack2.impedance.csr</a></li>
+<li><a href="mbtrack2/impedance/impedance_model.html">mbtrack2.impedance.impedance_model</a></li>
+<li><a href="mbtrack2/impedance/resistive_wall.html">mbtrack2.impedance.resistive_wall</a></li>
+<li><a href="mbtrack2/impedance/resonator.html">mbtrack2.impedance.resonator</a></li>
+<li><a href="mbtrack2/impedance/tapers.html">mbtrack2.impedance.tapers</a></li>
+<li><a href="mbtrack2/impedance/wakefield.html">mbtrack2.impedance.wakefield</a></li>
+<li><a href="mbtrack2/instability/instabilities.html">mbtrack2.instability.instabilities</a></li>
+<li><a href="mbtrack2/instability/ions.html">mbtrack2.instability.ions</a></li>
+<li><a href="mbtrack2/tracking/aperture.html">mbtrack2.tracking.aperture</a></li>
+<li><a href="mbtrack2/tracking/element.html">mbtrack2.tracking.element</a></li>
+<li><a href="mbtrack2/tracking/feedback.html">mbtrack2.tracking.feedback</a></li>
+<li><a href="mbtrack2/tracking/monitors/monitors.html">mbtrack2.tracking.monitors.monitors</a></li>
+<li><a href="mbtrack2/tracking/monitors/plotting.html">mbtrack2.tracking.monitors.plotting</a></li>
+<li><a href="mbtrack2/tracking/monitors/tools.html">mbtrack2.tracking.monitors.tools</a></li>
+<li><a href="mbtrack2/tracking/parallel.html">mbtrack2.tracking.parallel</a></li>
+<li><a href="mbtrack2/tracking/particles.html">mbtrack2.tracking.particles</a></li>
+<li><a href="mbtrack2/tracking/rf.html">mbtrack2.tracking.rf</a></li>
+<li><a href="mbtrack2/tracking/synchrotron.html">mbtrack2.tracking.synchrotron</a></li>
+<li><a href="mbtrack2/tracking/wakepotential.html">mbtrack2.tracking.wakepotential</a></li>
+<li><a href="mbtrack2/utilities/beamloading.html">mbtrack2.utilities.beamloading</a></li>
+<li><a href="mbtrack2/utilities/misc.html">mbtrack2.utilities.misc</a></li>
+<li><a href="mbtrack2/utilities/optics.html">mbtrack2.utilities.optics</a></li>
+<li><a href="mbtrack2/utilities/read_impedance.html">mbtrack2.utilities.read_impedance</a></li>
+<li><a href="mbtrack2/utilities/spectrum.html">mbtrack2.utilities.spectrum</a></li>
+</ul>
+
+            <div class="clearer"></div>
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<div id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</div>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">mbtrack2 0.6.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Overview: module code</a></li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        &#169; Copyright 2024, A. Gamelin et al.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 5.0.2.
+    </div>
+  </body>
+</html>
\ No newline at end of file