Merge pull request #172 from smash-transport/sparkx_devel

Push to version 1.1.0-Newton

.github/workflows/GitHub_tests.yml

@@ -0,0 +1,40 @@
+name: Run Tests
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+  push:
+    branches:
+      - main
+      - sparkx_devel
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Run tests
+        run: |
+          python -m pytest tests/
+
+      - name: Check test results
+        run: |
+          if [ $? -ne 0 ]; then
+            echo "Tests failed. Blocking pull request merge."
+            exit 1
+          fi

.github/workflows/PyPI_release.yml

@@ -0,0 +1,32 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+
+    - name: Build and publish
+      run: |
+        python setup.py sdist bdist_wheel
+        python -m twine upload --skip-existing dist/*
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/docs.yml

@@ -2,8 +2,8 @@ name: Build and Deploy Documentation
 
 on:
   push:
-    tags:
-      - 'v**'  # specify the pattern for release tags
+    branches:
+      - main
 
 permissions:
   contents: write
@@ -23,14 +23,14 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: "3.9"  # adjust the Python version if needed
+        python-version: "3.9"
         cache: "pip"
         architecture: "x64"
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt  # adjust the path if needed
+        pip install -r requirements.txt
 
     - name: Build documentation
       run: |
@@ -41,4 +41,4 @@ jobs:
       uses: peaceiris/actions-gh-pages@v3
       with:
         github_token: ${{ secrets.ACCESS_TOKEN }}
-        publish_dir: docs/build/html  # adjust the path if needed
+        publish_dir: docs/build/html

.gitignore

@@ -0,0 +1,2 @@
+__pycache__/
+docs/build/

CHANGELOG.md

@@ -0,0 +1,96 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The versioning of the codebase is inspired by [Semantic Versioning](https://semver.org/spec/v2.0.0.html) with a version number `X.Y.Z`, where
+
+* `X` is incremented for major changes (e.g. large backwards incompatible updates),
+* `Y` is incremented for minor changes (e.g. external pull-request that adds one feature) and
+* `Z` is incremented for the indication of a bug fix or other very small changes that are not backwards incompatible.
+
+The main categories for changes in this file are:
+
+* `Input / Output` for all, in particular breaking, changes, fixes and additions to the in- and output files;
+* `Added` for new features;
+* `Changed` for changes in existing functionality;
+* `Fixed` for any bug fixes;
+* `Removed` for now removed features.
+
+A `Deprecated` section could be added if needed for soon-to-be removed features.
+
+## v1.1.0-Newton
+
+### Added
+
+* Import with `from sparkx import *` is now possible
+* EventCharacteristics: Possibility to smear (Gaussian or covariant) energy, baryon, charge and strangeness densities in Milne and Minkowski coordinates with writing to a file for subsequent hydro evolution
+* Histogram: Method to set the systematic error
+* Lattice3D: Add covariant smearing of densities for particles
+* Oscar: Add option to apply filters while read-in to improve RAM usage
+* Oscar: Add spacetime cut
+* Particle: Add strangeness, spin and spin_degeneracy functions 
+* Tests: Add automatic tests for the Particle class
+* GenerateFlow: Add functionality to generate flow with k-particle correlations
+* LeeYangZeroFlow: Add beta version of integrated and differential flow analysis with the Lee-Yang zero method
+* QCumulantFlow: Add beta version of integrated flow analysis with the Q-Cumulant method
+* PCAFlow: Add flow analysis with PCA method
+* CentralityClasses: Class to determine the centrality classes from a set of events
+
+### Fixed
+
+* Histogram: Correct error handling when reweighting or averaging over histograms
+* Oscar/Jetscape: Fix bug when reading in a single event from input file
+* Jetscape: Fix asymmetric pseudorapidity cut
+
+### Changed
+
+* Histogram: Can write multiple histograms to file now
+* Oscar/Jetscape: Handling of PDG id's which are not present in the `particle` package is moved to the Particle class
+* Oscar/Jetscape: Improved writing to file
+* Particle: Particle construction is now done within the constructor by providing a format and an array of values
+* Particle: Internal structure is now a numpy float array
+* Particle: Functions using `PDGID` from the `particle` package handle now the case if the PDG ID is unknown to the package
+* Particle: Returns `nan` if the quantity is not known or can not be computed
+
+# Removed
+
+
+## v1.0.2-Newton
+Date: 2023-06-26
+
+### Fixed
+
+* Bug fix in Histogram class for values outside the bin range
+
+### Changed
+
+* Histogram printout to the terminal
+
+[Link to diff from previous version](https://github.com/smash-transport/sparkx/compare/v1.0.1...v1.0.2)
+
+## v1.0.1-Newton
+Date: 2023-06-19
+
+### Added
+
+* Read in of X-SCAPE hadron output
+
+### Fixed
+
+* JetAnalysis class can be imported now
+* Jet analysis can be performed with different jet finding algorithms without throwing errors
+
+[Link to diff from previous version](https://github.com/smash-transport/sparkx/compare/v1.0.0...v1.0.1)
+
+## v1.0.0-Newton
+Date: 2023-06-14
+
+**[First public version of SPARKX](https://github.com/smash-transport/sparkx/releases/tag/v1.0.0)**
+
+### Added
+
+* SMASH / Jetscape particle data read in and processing
+* Anisotropic flow analysis (reaction plane, event plane, scalar product methods)
+* Jet analysis (wrapper for fastjet)
+* Initial state characterization via eccentricities
+* Histogram class

CONTRIBUTORS.md

@@ -1,8 +1,12 @@
 Credits
 =======
 
-Contributors
-------------
-- Hendrik Roch <[email protected]>
-- Nils Sass <[email protected]>
-- Niklas Götz <[email protected]>
+The SPARKX Team
+---------------
+
+Author  |  &ensp;E-Mail&ensp; | Copyright © 
+:----:  |  :----: | :---------: |
+Niklas Götz | [✉️](mailto:[email protected]) | `2023 -` |
+Hendrik Roch | [✉️](mailto:[email protected]) | `2023 -` |
+Nils Sass | [✉️](mailto:[email protected]) | `2023 -` |
+

docs/source/classes/CentralityClasses/index.rst

@@ -0,0 +1,10 @@
+.. _centrality_classes:
+
+CentralityClasses
+=================
+
+.. currentmodule:: CentralityClasses
+.. autoclass:: CentralityClasses
+
+.. automethod:: CentralityClasses.get_centrality_class
+.. automethod:: CentralityClasses.output_centrality_classes

docs/source/classes/EventCharacteristics/index.rst

@@ -7,4 +7,6 @@ EventCharacteristics
 .. autoclass:: EventCharacteristics
 
 .. automethod:: EventCharacteristics.set_event_data
-.. automethod:: EventCharacteristics.eccentricity
+.. automethod:: EventCharacteristics.eccentricity
+.. automethod:: EventCharacteristics.generate_eBQS_densities_Milne_from_OSCAR_IC
+.. automethod:: EventCharacteristics.generate_eBQS_densities_Minkowski_from_OSCAR_IC

docs/source/classes/Histogram/index.rst

@@ -20,6 +20,7 @@ Histogram
 .. automethod:: Histogram.average_weighted
 .. automethod:: Histogram.standard_error
 .. automethod:: Histogram.statistical_error
+.. automethod:: Histogram.set_systematic_error
 .. automethod:: Histogram.scale_histogram
 .. automethod:: Histogram.set_error
 .. automethod:: Histogram.print_histogram

docs/source/classes/Jetscape/index.rst

@@ -21,4 +21,5 @@ Jetscape
 .. automethod:: Jetscape.rapidity_cut
 .. automethod:: Jetscape.pseudorapidity_cut
 .. automethod:: Jetscape.multiplicity_cut
+.. automethod:: Jetscape.particle_status
 .. automethod:: Jetscape.print_particle_lists_to_file

docs/source/classes/Lattice3D/index.rst

@@ -9,7 +9,9 @@ Lattice3D
 .. automethod:: Lattice3D.set_value_by_index
 .. automethod:: Lattice3D.get_value_by_index
 .. automethod:: Lattice3D.set_value
+.. automethod:: Lattice3D.set_value_nearest_neighbor
 .. automethod:: Lattice3D.get_value
+.. automethod:: Lattice3D.get_value_nearest_neighbor
 .. automethod:: Lattice3D.get_coordinates
 .. automethod:: Lattice3D.find_closest_indices
 .. automethod:: Lattice3D.interpolate_value
@@ -23,4 +25,5 @@ Lattice3D
 .. automethod:: Lattice3D.interpolate_to_lattice
 .. automethod:: Lattice3D.interpolate_to_lattice_new_extent
 .. automethod:: Lattice3D.reset
+.. automethod:: Lattice3D.add_same_spaced_grid
 .. automethod:: Lattice3D.add_particle_data

docs/source/classes/Particle/index.rst

@@ -7,9 +7,6 @@ Particle
 .. autoclass:: Particle
 
 .. automethod:: Particle.print_particle
-.. automethod:: Particle.set_quantities_OSCAR2013
-.. automethod:: Particle.set_quantities_OSCAR2013Extended
-.. automethod:: Particle.set_quantities_JETSCAPE
 .. automethod:: Particle.angular_momentum
 .. automethod:: Particle.momentum_rapidity_Y
 .. automethod:: Particle.p_abs
@@ -26,3 +23,5 @@ Particle
 .. automethod:: Particle.is_hadron
 .. automethod:: Particle.is_strange
 .. automethod:: Particle.is_heavy_flavor
+.. automethod:: Particle.spin
+.. automethod:: Particle.spin_degeneracy

docs/source/classes/flow/EventPlaneFlow/index.rst

@@ -1,7 +1,7 @@
 .. _event_plane_flow:
 
 EventPlaneFlow
-=================
+==============
 
 .. currentmodule:: EventPlaneFlow
 .. autoclass:: EventPlaneFlow

docs/source/classes/flow/GenerateFlow/index.rst

@@ -8,5 +8,9 @@ GenerateFlow
 
 .. automethod:: GenerateFlow.generate_dummy_JETSCAPE_file
 .. automethod:: GenerateFlow.generate_dummy_JETSCAPE_file_realistic_pt_shape
+.. automethod:: GenerateFlow.generate_dummy_JETSCAPE_file_multi_particle_correlations
+.. automethod:: GenerateFlow.generate_dummy_JETSCAPE_file_realistic_pt_shape_multi_particle_correlations    
 .. automethod:: GenerateFlow.generate_dummy_OSCAR_file
 .. automethod:: GenerateFlow.generate_dummy_OSCAR_file_realistic_pt_shape
+.. automethod:: GenerateFlow.generate_dummy_OSCAR_file_multi_particle_correlations
+.. automethod:: GenerateFlow.generate_dummy_OSCAR_file_realistic_pt_shape_multi_particle_correlations

docs/source/classes/flow/LeeYangZeroFlow/index.rst

@@ -0,0 +1,10 @@
+.. _Lee_Yang_zero_flow:
+
+LeeYangZeroFlow
+===============
+
+.. currentmodule:: LeeYangZeroFlow
+.. autoclass:: LeeYangZeroFlow
+
+.. automethod:: LeeYangZeroFlow.integrated_flow
+.. automethod:: LeeYangZeroFlow.differential_flow

docs/source/classes/flow/PCAFlow/index.rst

@@ -0,0 +1,10 @@
+.. _PCA_flow:
+
+PCAFlow
+=======
+
+.. currentmodule:: PCAFlow
+.. autoclass:: PCAFlow
+
+.. automethod:: PCAFlow.differential_flow
+.. automethod:: PCAFlow.Pearson_correlation

docs/source/classes/flow/QCumulantFlow/index.rst

@@ -0,0 +1,10 @@
+.. _QCumulant_flow:
+
+QCumulantFlow
+=============
+
+.. currentmodule:: QCumulantFlow
+.. autoclass:: QCumulantFlow
+
+.. automethod:: QCumulantFlow.integrated_flow
+.. automethod:: QCumulantFlow.differential_flow

docs/source/classes/flow/index.rst

@@ -6,8 +6,11 @@ Flow
 .. toctree::
    :maxdepth: 2
 
+   ReactionPlaneFlow/index
    ScalarProductFlow/index
    EventPlaneFlow/index
-   ReactionPlaneFlow/index
+   LeeYangZeroFlow/index
+   QCumulantFlow/index
+   PCAFlow/index
    GenerateFlow/index
 

docs/source/classes/index.rst

@@ -14,3 +14,4 @@ Classes
    flow/index
    Lattice3D/index
    EventCharacteristics/index
+   CentralityClasses/index

docs/source/conf.py

@@ -31,7 +31,6 @@
     'sphinx.ext.coverage',
     'numpydoc',
     'sphinx.ext.viewcode',
-    'sphinx.ext.autosummary',
     'myst_parser', # for markdown parsing (needs myst-parser package)
     'sphinx_rtd_theme'
 ]

docs/source/requirements.txt

@@ -1,9 +1,8 @@
 particle
 numpy
 scipy
-matplotlib
-sphinx
 fastjet
+sphinx
 numpydoc
 myst-parser
 sphinx-rtd-theme