Merge remote-tracking branch 'origin' into auto_dt_bunch

Conflicts: wake_t/beamline_elements/field_element.py wake_t/beamline_elements/plasma_stage.py
AngelFP · Jul 5, 2024 · 80173ae · 80173ae
2 parents 3bf9eb5 + ed57f5a
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diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -7,29 +7,29 @@ on:
 jobs:
   build-n-publish:
     name: Build and publish package to PyPI
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
     steps:
-    - uses: actions/checkout@master
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install pypa/build
       run: >-
-        python -m
+        python3 -m
         pip install
         build
         --user
     - name: Build a binary wheel and a source tarball
       run: >-
-        python -m
+        python3 -m
         build
         --sdist
         --wheel
         --outdir dist/
         .
-    - name: Publish distribution to PyPI
-      if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        password: ${{ secrets.PYPI_API_TOKEN }}
+    - name: Publish package distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/test-package.yml b/.github/workflows/test-package.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9, '3.10', 3.11]
 
     steps:
     - uses: actions/checkout@v2

diff --git a/.gitignore b/.gitignore
@@ -10,6 +10,9 @@ __pycache__
 /examples/tests.py
 /old_stuff
 
+# Test output
+/tests_output
+
 # IDEs
 /.vscode
 

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.7"
+    python: "3.8"
     nodejs: "16"
 
 # Build documentation in the docs/ directory with Sphinx

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -2,10 +2,10 @@ numpy
 numba
 scipy
 matplotlib
-aptools>=0.1.23
-openpmd-api~=0.14.0
+aptools~=0.2.0
+openpmd-api
 openpmd-viewer>=1.2.0
 pydata-sphinx-theme
-sphinx-panels
+sphinx-design
 sphinx-gallery
 numpydoc
diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst
@@ -1,7 +1,8 @@
 API reference
 =============
 
-🚧🚧 Page under construction 🚧🚧
+This section contains the detailed documentation of the main classes and
+methods needed to perform simulations with Wake-T.
 
 .. toctree::
    :maxdepth: 3

diff --git a/docs/source/api/laser/laser_pulses/index.rst b/docs/source/api/laser/laser_pulses/index.rst
@@ -10,3 +10,4 @@ Laser pulses
    LaguerreGaussPulse
    FlattenedGaussianPulse
    SummedPulse
+   OpenPMDPulse
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -38,8 +38,8 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'sphinx.ext.coverage',
-    # 'sphinx.ext.intersphinx',
-    'sphinx_panels',
+    'sphinx.ext.viewcode',
+    'sphinx_design',
     'sphinx_gallery.gen_gallery',
     'numpydoc'
 ]
@@ -75,18 +75,25 @@
         {
             "name": "GitHub",
             "url": "https://github.com/AngelFP/Wake-T",
-            "icon": "fab fa-github-square",
+            "icon": "fa-brands fa-github",
         },
         {
             "name": "Slack",
             "url": "https://wake-t.slack.com/",
-            "icon": "fab fa-slack",
+            "icon": "fa-brands fa-slack",
         },
-    ]
+    ],
+    "use_edit_page_button": True,    
+    "pygment_light_style": "default",
+    "pygment_dark_style": "monokai",
 }
 
-# Prevent panels extension from modifying page style.
-panels_add_bootstrap_css = False
+html_context = {
+    "github_user": "AngelFP",
+    "github_repo": "Wake-T",
+    "github_version": "dev",
+    "doc_path": "docs/source",
+}
 
 # Do not show type hints.
 autodoc_typehints = 'none'

diff --git a/docs/source/development.rst b/docs/source/development.rst
diff --git a/docs/source/examples/index.rst b/docs/source/examples/index.rst
@@ -1,7 +1,7 @@
 Examples
 ========
 
-🚧🚧 Page under construction 🚧🚧
+Example scripts ready to run basic simulations.
 
 .. toctree::
    :maxdepth: 2

diff --git a/docs/source/getting_started/index.rst b/docs/source/getting_started/index.rst
@@ -0,0 +1,46 @@
+Getting started
+===============
+
+Installation
+------------
+Wake-T is available on PyPI and can be simply installed with
+
+.. code::
+
+    pip install Wake-T
+
+for more detailed instructions, including guides for installing Wake-T in HPC
+clusters, check the :ref:`installation_ref` section.
+
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+   installation
+
+
+Citing Wake-T
+-------------
+If your usage of Wake-T leads to a scientific publication, please consider
+citing the original `publication <https://dx.doi.org/10.1088/1742-6596/1350/1/012056>`_:
+
+    A Ferran Pousa, R Assmann, A Martinez de la Ossa, Wake-T: a fast particle tracking code for plasma-based accelerators, *J. Phys.: Conf. Ser.* **1350** 012056 (2019)
+
+Bibtex:
+
+.. code::
+
+    @article{FerranPousa_2019,
+      doi = {10.1088/1742-6596/1350/1/012056},
+      url = {https://dx.doi.org/10.1088/1742-6596/1350/1/012056},
+      year = {2019},
+      month = {nov},
+      publisher = {IOP Publishing},
+      volume = {1350},
+      number = {1},
+      pages = {012056},
+      author = {Ferran Pousa, A and Assmann, R and Martinez de la Ossa, A},
+      title = {Wake-{T}: a fast particle tracking code for plasma-based accelerators},
+      journal = {Journal of Physics: Conference Series}
+    }
diff --git a/docs/source/user_guide/installation.rst → docs/source/getting_started/installation.rst b/docs/source/user_guide/installation.rst → docs/source/getting_started/installation.rst
@@ -1,6 +1,8 @@
+.. _installation_ref:
+
 Installation
 ============
-Wake-T is tested on Python 3.7 and above, so make sure to have an up-to-date version
+Wake-T is tested on Python 3.8 and above, so make sure to have an up-to-date version
 in order to avoid potential issues. It is recommended to install Wake-T in its
 own virtual environment, either using ``venv`` or ``conda``. The installation should be
 carried out with ``pip``, since Wake-T is available on `PyPI <https://pypi.org/project/Wake-T/>`_
@@ -32,8 +34,8 @@ using ``pip``::
     
 Latest (development) version from GitHub
 ----------------------------------------
-.. image:: https://travis-ci.org/AngelFP/Wake-T.svg?branch=dev
-   :target: https://travis-ci.org/AngelFP/Wake-T
+.. image:: https://github.com/AngelFP/Wake-T/actions/workflows/test-package.yml/badge.svg
+   :target: https://github.com/AngelFP/Wake-T/actions
 
 The latest release on PyPI might not be fully up to date with the newest additions
 to the code. If you want to stay at the bleeding edge of new features and bug fixes

diff --git a/...source/user_guide/installation_juwels.rst → ...e/getting_started/installation_juwels.rst b/...source/user_guide/installation_juwels.rst → ...e/getting_started/installation_juwels.rst
diff --git a/...ource/user_guide/installation_maxwell.rst → .../getting_started/installation_maxwell.rst b/...ource/user_guide/installation_maxwell.rst → .../getting_started/installation_maxwell.rst
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -6,8 +6,8 @@
 Wake-T |release| documentation
 ==============================
 
-.. |travis| image:: https://travis-ci.org/AngelFP/Wake-T.svg?branch=dev
-   :target: https://travis-ci.org/AngelFP/Wake-T
+.. |tests| image:: https://github.com/AngelFP/Wake-T/actions/workflows/test-package.yml/badge.svg
+   :target: https://github.com/AngelFP/Wake-T/actions
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/Wake-T.svg?logo=python&logoColor=white
    :target: https://pypi.org/project/Wake-T/
@@ -18,93 +18,84 @@ Wake-T |release| documentation
 .. |license| image:: https://img.shields.io/github/license/AngelFP/Wake-T
    :target: https://github.com/AngelFP/Wake-T/blob/master/LICENSE
 
-|travis| |codefactor| |PyPI| |license|
+|tests| |codefactor| |PyPI| |license|
 
-.. panels::
-    :card: + intro-card text-center
-    :column: col-lg-6 col-md-6 col-sm-6 col-xs-12 p-2 d-flex
+.. grid:: 1 2 2 2
+    :gutter: 2
 
-    ---
+    .. grid-item-card:: Getting started
+        :text-align: center
 
-    **User guide**
-    ^^^^^^^^^^^^^^
+        :octicon:`book;3em`
 
-    Instructions for getting the code up and running and basic information of
-    the key concepts behind Wake-T.
+        Get the code up and running.
 
-    +++
+        +++
 
-    .. link-button:: user_guide/index
-            :type: ref
-            :text: To the user guide
-            :classes: btn-outline-primary btn-block stretched-link
+        .. button-ref:: getting_started/index
+            :expand:
+            :color: primary
+            :click-parent:
 
-    ---
+            To the guide
 
-    **Tutorials**
-    ^^^^^^^^^^^^
+    .. grid-item-card:: Tutorials
+        :text-align: center
 
-    Step-by-step tutorials covering the functionality of Wake-T.
+        :octicon:`mortar-board;3em`
+
+        Step-by-step tutorials covering the functionality of Wake-T.
 
-    +++
+        +++
 
-    .. link-button:: tutorials/index
-            :type: ref
-            :text: To the tutorials
-            :classes: btn-outline-primary btn-block stretched-link
+        .. button-ref:: tutorials/index
+            :expand:
+            :color: primary
+            :click-parent:
 
-    ---
+            To the tutorials
 
-    **Examples**
-    ^^^^^^^^^^^^
+    .. grid-item-card:: Examples
+        :text-align: center
 
-    Explore quick examples showcasing how to use the code.
+        :octicon:`light-bulb;3em`
 
-    +++
+        Explore quick examples showcasing how to use the code.
 
-    .. link-button:: examples/index
-            :type: ref
-            :text: To the examples
-            :classes: btn-outline-primary btn-block stretched-link
+        +++
 
-    ---
+        .. button-ref:: examples/index
+            :expand:
+            :color: primary
+            :click-parent:
 
-    **API reference**
-    ^^^^^^^^^^^^^^^^^
+            To the examples
 
-    Detailed documentation of the Wake-T API.
+    .. grid-item-card:: API reference
+        :text-align: center
 
-    +++
+        :octicon:`code;3em`
+
+        Detailed documentation of the Wake-T API.
 
-    .. link-button:: api/index
-            :type: ref
-            :text: To the reference guide
-            :classes: btn-outline-primary btn-block stretched-link
+        +++
 
-    ---
+        .. button-ref:: api/index
+            :expand:
+            :color: primary
+            :click-parent:
 
-    **Development**
-    ^^^^^^^^^^^^^^^
-
-    Guidelines for contributing to Wake-T.
-
-    +++
-
-    .. link-button:: development
-            :type: ref
-            :text: To the development guide
-            :classes: btn-outline-primary btn-block stretched-link
+            To the reference guide
 
 
 .. toctree::
    :hidden:
    :maxdepth: 4
 
-   user_guide/index
+   getting_started/index
    tutorials/index
    examples/index
    api/index
-   development
 
 
 
diff --git a/docs/source/user_guide/index.rst b/docs/source/user_guide/index.rst
diff --git a/setup.cfg b/setup.cfg
@@ -21,12 +21,12 @@ classifiers =
 packages = find:
 install_requires =
     numpy
-    numba<0.57
+    numba!=0.57.0
     scipy
     aptools~=0.2.0
     openpmd-api
     tqdm
-python_requires = >=3.7
+python_requires = >=3.8
 
 [options.extras_require]
 test =