Merge pull request #19 from rtesse/develop

Merge develop into master

.github/workflows/ci.yml

@@ -20,8 +20,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-latest ]
-        python: ['3.8', '3.9', '3.10']
+        os: [ubuntu-latest]
+        python: ["3.8", "3.9", "3.10"]
     steps:
       #----------------------------------------------
       #       check-out repo and set-up python
@@ -44,11 +44,13 @@ jobs:
       # install dependencies if cache does not exist
       #----------------------------------------------
       - name: Install dependencies
-        run: poetry install --no-interaction --with dev
+        run: |
+          poetry config virtualenvs.create true --local
+          poetry install --no-interaction --with dev
       #----------------------------------------------
       #              run test suite with Sonar
       #----------------------------------------------
-      - name: Run tox
+      - name: Run pytest
         run: |
           source .venv/bin/activate
-          tox -e py
+          pytest

.github/workflows/code_check.yml

@@ -41,11 +41,13 @@ jobs:
       # install dependencies if cache does not exist
       #----------------------------------------------
       - name: Install dependencies
-        run: poetry install --no-interaction --with dev
+        run: |
+          poetry config virtualenvs.create true --local
+          poetry install --no-interaction --with dev
       #----------------------------------------------
       #              run flake8
       #----------------------------------------------
-      - name: Run tox
+      - name: Run flake8
         run: |
           source .venv/bin/activate
           flake8

.github/workflows/coverage.yml

@@ -41,16 +41,21 @@ jobs:
       # install dependencies if cache does not exist
       #----------------------------------------------
       - name: Install dependencies
-        run: poetry install --no-interaction --with dev
+        run: |
+          poetry config virtualenvs.create true --local
+          poetry install --no-interaction --with dev
       #----------------------------------------------
       #              run test suite with Sonar
       #----------------------------------------------
-      - name: Run tox
+      - name: Run pytest
         run: |
           source .venv/bin/activate
-          tox -e py
+          export NUMBA_DISABLE_JIT=1
+          coverage run -m pytest
+          coverage xml
+
       - name: SonarCloud Scan
         uses: SonarSource/sonarcloud-github-action@master
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

.github/workflows/deploy_doc.yml

@@ -37,7 +37,9 @@ jobs:
           virtualenvs-create: true
           virtualenvs-in-project: true
       - name: Install dependencies
-        run: poetry install --no-interaction --with docs
+        run: |
+          poetry config virtualenvs.create true --local
+          poetry install --no-interaction --with docs
       - name: Run sphinx for html
         run: |
           source .venv/bin/activate

.github/workflows/docker-publish.yml

@@ -0,0 +1,53 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+# https://docs.github.com/en/actions/publishing-packages/publishing-docker-images
+
+name: Create and publish a Docker image
+
+on:
+  push:
+    branches:
+    - master
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/documentation.yml

@@ -38,7 +38,9 @@ jobs:
       # install dependencies if cache does not exist
       #----------------------------------------------
       - name: Install dependencies
-        run: poetry install --no-interaction --with docs
+        run: |
+          poetry config virtualenvs.create true --local
+          poetry install --no-interaction --with docs
 
       #----------------------------------------------
       #              Built the doc

.gitignore

@@ -10,3 +10,6 @@ coverage.xml
 .tox/
 docs/build
 docs/jupyter_execute
+.vscode/
+.conda_config
+dist/

.pre-commit-config.yaml

@@ -8,16 +8,16 @@ repos:
         exclude: 'rst'
       - id: trailing-whitespace
   - repo: https://github.com/asottile/add-trailing-comma
-    rev: v2.3.0
+    rev: v2.4.0
     hooks:
       - id: add-trailing-comma
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
         name: isort (python)
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
     hooks:
       - id: black
   - repo: https://github.com/kynan/nbstripout

Dockerfile

@@ -1,25 +1,24 @@
-FROM python:3.8
+FROM python:3.10
 RUN apt-get update \
     && apt-get install --no-install-recommends -y libgl1
 
 ENV GIT_SSL_NO_VERIFY=1
 
 # Configure Poetry
-ENV POETRY_VERSION=1.2.0
 ENV POETRY_HOME=/opt/poetry
 ENV POETRY_VENV=/opt/poetry-venv
 ENV POETRY_CACHE_DIR=/opt/.cache
 
 # Install poetry separated from system interpreter
 RUN python3 -m venv $POETRY_VENV \
     && $POETRY_VENV/bin/pip install -U pip setuptools \
-    && $POETRY_VENV/bin/pip install poetry==${POETRY_VERSION}
+    && $POETRY_VENV/bin/pip install poetry
 
 # Add `poetry` to PATH
 ENV PATH="${PATH}:${POETRY_VENV}/bin"
 
 WORKDIR /home
-RUN git clone --recurse-submodules --branch develop https://github.com/rtesse/georges-core.git
+RUN git clone --branch master https://github.com/ULB-Metronu/georges-core.git
 RUN poetry config virtualenvs.in-project true
 WORKDIR /home/georges-core
 RUN poetry install

README.md

@@ -1,4 +1,4 @@
-# georges-core
+# Georges' accelerator physics library - Core
 
 [![ci](https://github.com/ULB-Metronu/georges-core/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/ULB-Metronu/georges-core/actions/workflows/ci.yml)
 [![documentation](https://github.com/ULB-Metronu/georges-core/actions/workflows/documentation.yml/badge.svg?branch=master)](https://github.com/ULB-Metronu/georges-core/actions/workflows/documentation.yml)
@@ -13,4 +13,35 @@
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 [![Gitter](https://badges.gitter.im/ULB-Metronu/georges-core.svg)](https://gitter.im/ULB-Metronu/georges-core?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 
-Georges' accelerator physics library - Core
+
+Georges-core is a Python3 library that provides a lot of basic functionalities for other libraries such as Zgoubidoo or Georges. Among the different modules, we have :
+
+* The Kinematics module
+* The beam's distribution generator
+* The Twiss computation
+* The plotting module
+* The sequence converter
+
+## Design
+The aim of this library is to unify the description of particle accelerator beamlines for different tools
+(MAD-X, MAD-NG and BDSIM at this stage) in a unique Python library.
+
+The library design strongly follows conventions and typical uses of the *Pandas* library:
+beamlines are naturally described as *Dataframes*.
+A functional approach is also one of the design goal of the library, something which fits well with
+*Pandas*.
+
+Beamlines are loaded and converted using functions split in packages (one package per beam physics code, *e.g.* MAD-X or BDSIM)
+in a unique format (`georges-core.Sequence`). This object serves as an input for other tracking code such as Manzoni or Zgoubidoo.
+
+Twiss computation is also provided especially in coupled Twiss computation.
+
+Support tools are also provided, notably a plotting library (based on *Matplotlib* or *Plotly*)
+
+## Installation
+
+`georges-core` is available from PyPI with pip::
+
+    pip install georges-core
+
+For a custom installation, please read the installation section in the [documentation](https://ulb-metronu.github.io/georges-core/installation.html).

docs/api/georges_core.sequences.rst

@@ -15,7 +15,7 @@ georges\_core.sequences.betablock module
 georges\_core.sequences.elements module
 ---------------------------------------
 
-.. automodule:: georges_core.sequences.elements
+.. automodule:: Elements
    :members:
    :undoc-members:
    :show-inheritance:

docs/changelog.rst

@@ -4,12 +4,21 @@ Changelog
 
 * 2023-xx
 
+    * Write the documentation for Twiss module
+    * Adapt the Twiss module for 13 particles
+    * Add installation section for Conda
+    * Remove tox and add doctesting
+    * Write a README file
+    * Fix small issues in sequences/BDSIMSequence
+    * Update pybdsim in pyproject.toml
+    * Fix in the documentation
+
 .. todolist::
 
-* 2022-1
 
+* 2022-1
     * Write the documentation
     * Refactor entire library
     * Implement tests
     * Add geometry module
-    * Improve bean distribution generation
+    * Improve beam distribution generation

docs/contributing.rst

@@ -31,8 +31,8 @@ to ensure consistent Python code. All the parameters are described in the `pypro
 
 Testing and metrics
 ###################
-All the tests are available in the georges-cores's test repository. We use `pytest <https://docs.pytest.org/en/7.2.x/>`_ as a tool for testing and
-through `tox <https://tox.wiki/en/latest/>`_ and the results are then passed to `coverage` and uploaded to `sonar <https://www.sonarsource.com/products/sonarcloud/>`_
+All the tests are available in the georges-cores's test repository. We use `pytest <https://docs.pytest.org/en/7.2.x/>`_ as a tool for testing
+and the results are then passed to `coverage` and uploaded to `sonar <https://www.sonarsource.com/products/sonarcloud/>`_
 to compute metrics such as:
 
 * Bugs

docs/examples/converters.rst

@@ -2,7 +2,13 @@
 Conversion of a sequence
 ************************
 
-Blabla.
+Georges-core can convert different output files into an object of type sequence. As an example,
+the user can provide an output file from:
+* MAD-X
+* MAD-NG
+* TRANSPORT
+* BDSIM
+* CSV File (SURVEY)
 
 .. jupyter-execute::
     :hide-output:
@@ -54,7 +60,8 @@ Load a Transport file
 
 Load a CSV file (survey file)
 #############################
-Structure du fichier csv, ...
+A survey file is a `.csv` file containing the elements' information as the NAME or the TYPE of
+the element. The user can provide a survey in a global reference frame (`X, Y, Z`) or in a Frenet-Serret (`S, L`)
 
 .. jupyter-execute::
     :hide-output:

docs/index.rst

@@ -2,18 +2,22 @@
 Welcome to Georges-core's documentation!
 ****************************************
 
-|Actions Status| |Documentation Status|
+|Actions Status| |Documentation Status| |Python version| |version| |Bugs| |Coverage| |Reliability|
+|License| |Code Style|
 
 Introduction
 ############
-Georges_core is a Python3 library that provides a lot of basic functionalities for other libraries such as Zgoubidoo or Georges. Among the different modules, we have :
+Georges-core is an open source project hosted on Github under the GNU General Public Licence (GPL) version 3. It is a Python3 library that provides a lot of basic functionalities for other libraries such as Zgoubidoo or Georges. Among the different modules, we have :
 
 * The Kinematics module
 * The beam's distribution generator
 * The Twiss computation
 * The plotting module
 * The sequence converter
 
+Georges-core's documentation
+============================
+
 The documentation is part of the Georges-core repository itself and is made available *via* `Github Pages <https://pages.github.com>`_ .
 It is hosted at `ulb-metronu.github.io/georges-core/ <https://ulb-metronu.github.io/georges-core/>`_
 
@@ -63,4 +67,23 @@ Indices and tables
    :target: https://github.com/ULB-Metronu/georges-core/actions
 
 .. |Documentation Status| image:: https://github.com/ULB-Metronu/georges-core/actions/workflows/documentation.yml/badge.svg?branch=master
-   :target: https://github.com/ULB-Metronu/georges-core/actions
+   :target: https://github.com/ULB-Metronu/georges-core/actions
+
+.. |Python version| image:: _static/python_versions.svg
+
+.. |version| image:: https://img.shields.io/badge/version-2022.1-blue
+
+.. |Bugs| image:: https://sonarcloud.io/api/project_badges/measure?project=ULB-Metronu_georges-core&metric=bugs
+   :target: https://sonarcloud.io/summary/new_code?id=ULB-Metronu_georges-core
+
+.. |Coverage| image:: https://sonarcloud.io/api/project_badges/measure?project=ULB-Metronu_georges-core&metric=coverage
+   :target: https://sonarcloud.io/summary/new_code?id=ULB-Metronu_georges-core
+
+.. |Reliability| image:: https://sonarcloud.io/api/project_badges/measure?project=ULB-Metronu_georges-core&metric=reliability_rating
+   :target: https://sonarcloud.io/summary/new_code?id=ULB-Metronu_georges-core
+
+.. |License| image:: https://img.shields.io/badge/License-GPLv3-blue.svg
+   :target: https://www.gnu.org/licenses/gpl-3.0
+
+.. |Code Style| image:: https://img.shields.io/badge/codestyle-black-000000.svg
+   :target: https://github.com/ambv/black