Merge branch 'sparkx_devel' into sass/BulkObservables

.github/workflows/code_formatting.yml

@@ -5,22 +5,20 @@ on:
     branches:
       - main
       - sparkx_devel
-    types:
-      - closed  # Trigger when the PR is closed (includes merging)
 
 jobs:
   code-formatting:
-    if: github.event.pull_request.merged == true
     runs-on: ubuntu-latest
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
+    - name: Checkout PR branch
+      uses: actions/checkout@v3
       with:
-        ref: ${{ github.sha }}  # Check out the exact commit of the merged PR
+        ref: ${{ github.head_ref }}
+        fetch-depth: 0  # Ensures full history is available
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.9'
 
@@ -29,22 +27,25 @@ jobs:
         python -m pip install --upgrade pip
         pip install black==24.8.0
 
-    - name: Format code
+    - name: Run black to check formatting
+      id: black-check
       run: |
-        black --line-length 80 src/sparkx tests/
+        black --check --line-length 80 src/sparkx tests/
+      continue-on-error: true
 
-    - name: Commit changes
-      run: |
-        git config --local user.name "GitHub Action"
-        git config --local user.email "[email protected]"
-        git add src/sparkx tests/
-        git commit -m "Automatically format code using black" || echo "No changes to commit"
+    - name: Capture formatting status
+      if: ${{ steps.black-check.outcome == 'failure' }}
+      run: echo "needs_formatting=true" >> $GITHUB_ENV
 
-    - name: Push changes
-      run: |
-        git push origin ${{ github.head_ref }}
+    - name: Format code with black
+      if: env.needs_formatting == 'true'
+      run: black --line-length 80 src/sparkx tests/
 
-    - name: Run format test again
+    - name: Push formatted changes
+      if: env.needs_formatting == 'true'
       run: |
-        # Add your test commands here
-        black --check --line-length 80 src/sparkx tests/
+        git config --global user.name "github-actions[bot]"
+        git config --global user.email "github-actions[bot]@users.noreply.github.com"
+        git add src/sparkx tests/
+        git commit -m "Auto-format code with black"
+        git push origin ${{ github.head_ref }}

CHANGELOG.md

@@ -31,6 +31,7 @@ Date:
 * Added support for the SMASH 3.2 feature of custom output format
 * Add option to add two Oscar/Jetscape/ParticleObjectStorer instances while preserving the event order
 * BulkObservables: Add a class for calculating spectra and integrated yields
+* Oscar: Add function to extract the impact parameters
 
 ### Changed
 * Particle: Rename several methods for a more intuitive naming scheme. Renamed methods are:

pyproject.toml

@@ -6,9 +6,11 @@ build-backend = "setuptools.build_meta"
 name = "sparkx"
 version = "2.0.0"
 authors = [
+    { name="Lucas Constantin", email="[email protected]"},
     { name="Niklas Götz", email="[email protected]"},
     { name="Renata Krupczak", email="[email protected]"},
     { name="Hendrik Roch", email="[email protected]" },
+    { name="Carl Rosenkvist", email="[email protected]"},
     { name="Nils Sass", email="[email protected]" }
 ]
 description = "Software Package for Analyzing Relativistic Kinematics in Collision eXperiments"
@@ -25,11 +27,10 @@ classifiers = [
 ]
 
 dependencies = [
-    "particle==0.23.0",
+    "particle>=0.23.0",
     "numpy>=1.23.5",
     "scipy>=1.10.1",
-    "abc-property==1.0",
-    "fastjet==3.4.1.3",
+    "fastjet>=3.4.2.1",
     "matplotlib>=3.7.1"
 ]
 

requirements.txt

@@ -1,9 +1,8 @@
 # Main dependencies
-particle==0.23.0
+particle>=0.23.0
 numpy>=1.23.5
 scipy>=1.10.1
-abc-property==1.0
-fastjet==3.4.1.3
+fastjet>=3.4.2.1
 matplotlib>=3.7.1
 
 # Documentation dependencies
@@ -15,7 +14,7 @@ setuptools>=68.0.0
 
 # Development and testing dependencies
 pytest>=7.4.3
-black>=24.8.0
+black==24.8.0
 
 # Editable Sparkx install
 -e .

setup.py

@@ -5,18 +5,17 @@
     packages=find_packages(where='src'),
     package_dir={'': 'src'},
     install_requires=[
-        "particle==0.23.0",
+        "particle>=0.23.0",
         "numpy>=1.23.5",
         "scipy>=1.10.1",
-        "abc-property==1.0",
-        "fastjet==3.4.1.3",
+        "fastjet>=3.4.2.1",
         "matplotlib>=3.7.1",
     ],
     version='2.0.0',
     description='Software Package for Analyzing Relativistic Kinematics in Collision eXperiments',
     long_description=open("README.md").read(),
     long_description_content_type="text/markdown",
-    author='Niklas Götz, Renata Krupczak, Hendrik Roch, Nils Sass',
+    author='Lucas Constantin, Niklas Götz, Renata Krupczak, Hendrik Roch, Carl Rosenkvist, Nils Sass',
     author_email="[email protected], [email protected], [email protected]",
     url="https://smash-transport.github.io/sparkx/",
     download_url="https://github.com/smash-transport/sparkx",

src/sparkx/BaseStorer.py

@@ -23,7 +23,7 @@ class BaseStorer(ABC):
     ----------
     num_output_per_event_ : numpy.array
         Array containing the event number and the number of particles in this
-        event as :code:`num_output_per_event_[event i][num_output in event i]` 
+        event as :code:`num_output_per_event_[event i][num_output in event i]`
         (updated when filters are applied)
     num_events_ : int
         Number of events contained in the Oscar object (updated when filters
@@ -105,11 +105,11 @@ def __init__(
                 self.particle_list_,
                 self.num_events_,
                 self.num_output_per_event_,
-                self.custom_attr_list
+                self.custom_attr_list,
             ) = self.loader_.load(**kwargs)
         else:
             raise ValueError("Loader has not been created properly")
-        
+
     def __add__(self, other: "BaseStorer") -> "BaseStorer":
         """
         Adds two BaseStorer objects by combining their particle lists and updating num_output_per_event accordingly.
@@ -134,12 +134,14 @@ def __add__(self, other: "BaseStorer") -> "BaseStorer":
         """
         if not isinstance(other, BaseStorer):
             raise TypeError("Can only add BaseStorer objects")
-        
+
         # Ensure that both instances are of the same class
         if type(self) is not type(other):
             raise TypeError("Can only add objects of the same class")
 
-        combined_particle_list: list = self.particle_list_ + other.particle_list_
+        combined_particle_list: list = (
+            self.particle_list_ + other.particle_list_
+        )
 
         # Ensure num_output_per_event_ is not None
         if self.num_output_per_event_ is None:
@@ -156,18 +158,22 @@ def __add__(self, other: "BaseStorer") -> "BaseStorer":
         )
 
         # Adjust event_number for the parts that originally belonged to other
-        combined_num_output_per_event[self.num_events_:, 0] += self.num_events_
+        combined_num_output_per_event[self.num_events_ :, 0] += self.num_events_
 
         combined_storer: BaseStorer = self.__class__.__new__(self.__class__)
-        combined_storer.__dict__.update(self.__dict__)  # Inherit all properties from self
+        combined_storer.__dict__.update(
+            self.__dict__
+        )  # Inherit all properties from self
         combined_storer._update_after_merge(other)
         combined_storer.particle_list_ = combined_particle_list
         combined_storer.num_output_per_event_ = combined_num_output_per_event
         combined_storer.num_events_ = self.num_events_ + other.num_events_
-        combined_storer.loader_ = None  # Loader is not applicable for combined object
+        combined_storer.loader_ = (
+            None  # Loader is not applicable for combined object
+        )
 
         return combined_storer
-    
+
     @abstractmethod
     def _update_after_merge(self, other: "BaseStorer") -> None:
         """
@@ -203,7 +209,7 @@ def num_output_per_event(self) -> Optional[np.ndarray]:
 
         :code:`num_output_per_event[event_n, number_of_particles_in_event_n]`
 
-        :code:`num_output_per_event` is updated with every manipulation e.g. 
+        :code:`num_output_per_event` is updated with every manipulation e.g.
         after applying cuts.
 
         Returns
@@ -336,7 +342,7 @@ def particle_species(
         Returns
         -------
         self : BaseStorer object
-            Containing only particle species specified by :code:`pdg_list` for 
+            Containing only particle species specified by :code:`pdg_list` for
             every event
         """
         self.particle_list_ = particle_species(self.particle_list_, pdg_list)
@@ -348,7 +354,7 @@ def remove_particle_species(
         self, pdg_list: Union[int, Union[Tuple[int], List[int], np.ndarray]]
     ) -> "BaseStorer":
         """
-        Remove particle species from :code:`particle_list` by their PDG ID in 
+        Remove particle species from :code:`particle_list` by their PDG ID in
         every event.
 
         Parameters
@@ -409,7 +415,7 @@ def lower_event_energy_cut(
         Parameters
         ----------
         minimum_event_energy : int or float
-            The minimum event energy threshold. Should be a positive integer or 
+            The minimum event energy threshold. Should be a positive integer or
             float.
 
         Returns
@@ -421,10 +427,10 @@ def lower_event_energy_cut(
         Raises
         ------
         TypeError
-            If the :code:`minimum_event_energy` parameter is not an integer or 
+            If the :code:`minimum_event_energy` parameter is not an integer or
             float.
         ValueError
-            If the :code:`minimum_event_energy` parameter is less than or 
+            If the :code:`minimum_event_energy` parameter is less than or
             equal to 0.
         """
         self.particle_list_ = lower_event_energy_cut(
@@ -502,7 +508,7 @@ def rapidity_cut(
         cut_value : float
             If a single value is passed, the cut is applied symmetrically
             around 0.
-            For example, if :code:`cut_value = 1`, only particles with rapidity 
+            For example, if :code:`cut_value = 1`, only particles with rapidity
             in :code:`[-1.0, 1.0]` are kept.
 
         cut_value : tuple
@@ -556,7 +562,7 @@ def spacetime_rapidity_cut(
     ) -> "BaseStorer":
         """
         Apply spacetime rapidity (space-time rapidity) cut to all events and
-        remove all particles with spacetime rapidity not complying with 
+        remove all particles with spacetime rapidity not complying with
         cut_value.
 
         Parameters
@@ -587,7 +593,7 @@ def spacetime_rapidity_cut(
 
     def multiplicity_cut(
         self, cut_value_tuple: Tuple[Union[float, None], Union[float, None]]
-        ) -> "BaseStorer":
+    ) -> "BaseStorer":
         """
         Apply multiplicity cut. Remove all events with a multiplicity not
         complying with cut_value.
@@ -596,7 +602,7 @@ def multiplicity_cut(
         ----------
         cut_value_tuple : tuple
             Upper and lower bound for multiplicity. If the multiplicity of an event is
-            not in this range, the event is discarded. The range is inclusive on the 
+            not in this range, the event is discarded. The range is inclusive on the
             lower bound and exclusive on the upper bound.
 
         Returns
@@ -634,7 +640,7 @@ def spacetime_cut(
         Returns
         -------
         self : BaseStorer object
-            Containing only particles complying with the spacetime cut for all 
+            Containing only particles complying with the spacetime cut for all
             events
         """
         self.particle_list_ = spacetime_cut(
@@ -662,7 +668,7 @@ def particle_status(
         Returns
         -------
         self : BaseStorer object
-            Containing only hadrons with status specified by 
+            Containing only hadrons with status specified by
             :code:`status_list` for every event
         """
         self.particle_list_ = particle_status(self.particle_list_, status_list)
@@ -848,9 +854,13 @@ def _update_num_output_per_event_after_filter(self) -> None:
             self.num_output_per_event_[1] = len(self.particle_list_[0])
         elif self.num_output_per_event_.ndim == 2:
             # Handle the case where num_output_per_event_ is a two-dimensional array
-            updated_num_output_per_event : np.ndarray = np.ndarray((len(self.particle_list_),2), dtype=int)
+            updated_num_output_per_event: np.ndarray = np.ndarray(
+                (len(self.particle_list_), 2), dtype=int
+            )
             for event in range(len(self.particle_list_)):
-                updated_num_output_per_event[event][0] = event + self.num_output_per_event_[0][0]
+                updated_num_output_per_event[event][0] = (
+                    event + self.num_output_per_event_[0][0]
+                )
                 updated_num_output_per_event[event][1] = len(
                     self.particle_list_[event]
                 )
@@ -869,7 +879,7 @@ def print_particle_lists_to_file(self, output_file: str) -> None:
         Prints the particle lists to a specified file.
 
         This method should be implemented by subclasses to print the particle
-        lists to the specified output file. The method raises a 
+        lists to the specified output file. The method raises a
         :code:`NotImplementedError` if it is not overridden by a subclass.
 
         Parameters