Add Jyputer formatting and fix GAMP writing

This will be the 3.2 release. This _should_ fix all issues with gamp,
as well as add some HTML formatting for Four Vector and Particles.

CHANGELOG.md

@@ -5,15 +5,15 @@ All changes important to the user will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/)
 
-## [Unreleased]
+## [3.2.0] - 2021-6-1
 ### Added
 - Vectors now support iPython and Jupyter Pretty printing
 ### Changed
 - Vector sanitization function has improved handling of non-array inputs
-### Removed
 ### Fixed
 - FourVectors variable order is now in the correct order
 - Vectors now work with inputs that aren't arrays
+- Patched issue with GAMP failing to write to file
 
 ## [3.1.0] - 2020-10-2
 ### Added
@@ -189,7 +189,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/)
 - PySim plugin
 - Packaging
 
-[Unreleased]: https://github.com/JeffersonLab/PyPWA/compare/v3.1.0...development
+[Unreleased]: https://github.com/JeffersonLab/PyPWA/compare/v3.2.0...main
+[3.2.0]: https://github.com/JeffersonLab/PyPWA/compare/v3.1.0...v3.2.0
 [3.1.0]: https://github.com/JeffersonLab/PyPWA/compare/v3.0.0...v3.1.0
 [3.0.0]: https://github.com/JeffersonLab/PyPWA/compare/v3.0.0a1...v3.0.0
 [3.0.0a1]: https://github.com/JeffersonLab/PyPWA/compare/v2.2.1...v3.0.0a1

PyPWA/libs/vectors/four_vector.py

@@ -20,6 +20,7 @@
 from typing import List, Union, Optional as Opt
 
 import numpy as np
+import pandas
 import pandas as pd
 from . import _base_vector, three_vector
 
@@ -73,6 +74,13 @@ def __init__(
     def __repr__(self):
         return f"FourVector(e={self.e}, x={self.x}, y={self.y}, z={self.z})"
 
+    def _repr_html_(self):
+        df = pandas.DataFrame()
+        df['Θ'] = self.get_theta()
+        df['̅ϕ'] = self.get_phi()
+        df['Mass'] = self.get_mass()
+        return df._repr_html_()
+
     def _repr_pretty_(self, p, cycle):
         if cycle:
             p.text("FourVector( ?.)")
@@ -102,6 +110,12 @@ def _get_repr_data(self):
             mass = self.get_mass()
         return theta, phi, mass
 
+    def display_raw(self):
+        df = pandas.DataFrame()
+        df['e'], df['x'] = self.e, self.x
+        df['y'], df['z'] = self.y, self.z
+        print(df)
+
     def __eq__(self, vector: "FourVector") -> bool:
         return self._compare_vectors(vector)
 

PyPWA/libs/vectors/particle.py

@@ -26,10 +26,16 @@
 from typing import List, Union, Tuple, Optional as Opt
 
 import numpy as np
-import pandas
+import pandas as pd
 from PyPWA.libs.vectors import FourVector
 from PyPWA import info as _info
 
+try:
+    from IPython.display import display
+except ImportError:
+    display = print
+
+
 __credits__ = ["Mark Jones"]
 __author__ = _info.AUTHOR
 __version__ = _info.VERSION
@@ -96,10 +102,10 @@ class Particle(FourVector):
     def __init__(
             self,
             particle_id: int,
-            e: Union[int, np.ndarray, float, pandas.DataFrame],
-            x: Opt[Union[float, pandas.Series, np.ndarray]] = None,
-            y: Opt[Union[float, pandas.Series, np.ndarray]] = None,
-            z: Opt[Union[float, pandas.Series, np.ndarray]] = None
+            e: Union[int, np.ndarray, float, pd.DataFrame],
+            x: Opt[Union[float, pd.Series, np.ndarray]] = None,
+            y: Opt[Union[float, pd.Series, np.ndarray]] = None,
+            z: Opt[Union[float, pd.Series, np.ndarray]] = None
     ):
         super(Particle, self).__init__(e, x, y, z)
         self.__particle_id = particle_id
@@ -130,9 +136,27 @@ def _repr_pretty_(self, p, cycle):
                 f" x̅Mass={mass})"
             )
 
+    def _repr_html_(self):
+        df = pd.DataFrame()
+        df['Θ'], df['ϕ'] = self.get_theta(), self.get_phi()
+        df['Mass'] = self.get_mass()
+        return (
+            f'<h2>{self.__particle_id}: {self.__particle_name}</h2>'
+            f'{df._repr_html_()}'
+        )
+
+    def display_raw(self):
+        df = pd.DataFrame()
+        df['e'], df['x'], df['y'], df['z'] = self.e, self.x, self.y, self.z
+
+        display(
+            f'{self.__particle_id}: {self.__particle_name}', raw=True
+        )
+        display(df)
+
     def __getitem__(
             self, item: Union[int, str, slice]
-    ) -> Union["Particle", pandas.Series]:
+    ) -> Union["Particle", pd.Series]:
         if isinstance(item, (int, slice)) or \
                 isinstance(item, np.ndarray) and item.dtype == bool:
             return Particle(
@@ -281,6 +305,23 @@ def __repr__(self) -> str:
                 string += repr(particle) + ","
         return f"ParticlePool({string})"
 
+    def _repr_pretty_(self, p, cycle):
+        if cycle:
+            return 'ParticlePool( ?.)'
+        else:
+            for particle in self.__particle_list:
+                particle._repr_pretty_(p, cycle)
+
+    def _repr_html_(self):
+        html = ""
+        for p in self.__particle_list:
+            html += p._repr_html_()
+        return html
+
+    def display_raw(self):
+        for p in self.__particle_list:
+            p.display_raw()
+
     def __len__(self):
         return len(self.__particle_list)
 

PyPWA/plugins/data/gamp.py

@@ -197,7 +197,7 @@ def write(self, data: vectors.ParticlePool):
         for p in data.iter_particles():
             self.__file_handle.write(
                 "%d %d %.20f %.20f %.20f %.20f\n" % (
-                    p.id, p.charge, p.x, p.y, p.z, p.e
+                    p.id, p.charge, p.x[0], p.y[0], p.z[0], p.e[0]
                 )
             )
 

setup.py

@@ -16,19 +16,7 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-import os
 import setuptools
-from distutils.extension import Extension
-from pathlib import Path
-
-import numpy as np
-
-try:
-    from Cython.Distutils import build_ext
-except ImportError:
-    print("Install Cython before building!")
-    raise
-
 
 __author__ = "PyPWA Team and Contributors"
 __license__ = "GPLv3"
@@ -37,75 +25,60 @@
 __status__ = "development"
 
 
-"""
-Why are these entry points disable?
-
-So PyPWA 2.0 had support for running scripts directly from the local
-directory, and these entry points were that functionality. With PyPWA 3
-though we dumped these scripts and instead moved almost entirely to
-Jupyter notebooks since they offer a solid amount of flexibility for
-physicists without the complicated overhead of importing Python scripts
-into an already running interpreter. Maybe eventually we'll fully remove
-them, bring them back if the physicists want them, or roll out other
-helping utilities like pymask if they need it.
-"""
-
-
 progs = "PyPWA.progs"
+
 entry_points = {
     "console_scripts": [
         f"pymask = {progs}.masking:start_masking",
-#        f"pybin = {progs}.binner:start_binning",
+        f"pybin = {progs}.binner:start_binning",
 #        f"pysimulate = {progs}.simulation:simulation",
 #        f"pyfit = {progs}.pyfit:start_fitting"
     ]
 }
 
-extension_kwargs = {
-    "sources": [],
-    "language": "c++",
-    "extra_compile_args": {
-        "gcc": ["-Wall", "-std=c++11", "-fPIC"],
-        "include_dirs": [np.get_include()]
-    }
+requires = [
+    "tqdm",        # Progress Bars
+    "iminuit<2",   # Default minimizer
+    "scipy",       # Needed for Nestle with multiple ellipsoids.
+    "numpy",       # Arrays and optimizations
+    "pyyaml",      # YAML Parser
+    "tabulate",    # Tables for iminuit
+    "appdirs",     # Attempts to find data locations
+    "tables",      # Stores table in a specialized table format
+    "pandas",      # A powerful statistics package that's used everywhere
+    "openpyxl",    # Provides support for XLXS, used for resonance,
+    "matplotlib",  # Adds support for plotting
+    "numexpr"      # Accelerates numpy by removing intermediate steps
+]
+
+extras = {
+    # Adds value correction to users configuration file
+    "fuzzing": ["fuzzywuzzy", "python-Levenshtein"]
 }
 
-
-setup_kargs = {
-    "name": "PyPWA",
-    "version": __version__,
-    "author": __author__,
-    "author_email": __email__,
-    "packages": setuptools.find_packages(),
-    "url": "http://pypwa.jlab.org",
-    "license": __license__,
-    "ext_module": [Extension("_lib", **extension_kwargs)],
-    "description": "General Partial Wave Analysis",
-    "test_suite": "tests",
-    "entry_points": entry_points,
-    "keywords": "PyPWA GeneralFitting Partial Wave Analysis Minimization",
-    "install_requires": [
-        "cython",      # C/C++ Optimizations
-        "tqdm",        # Progress Bars
-        "iminuit<2",     # Default minimizer
-        "scipy",       # Needed for Nestle with multiple ellipsoids.
-        "numpy",       # Arrays and optimizations
-        "pyyaml",      # YAML Parser
-        "tabulate",    # Tables for iminuit
-        "appdirs",     # Attempts to find data locations
-        "tables",      # Stores table in a specialized table format
-        "pandas",      # A powerful statistics package that's used everywhere
-        "openpyxl",    # Provides support for XLXS, used for resonance,
-        "matplotlib",  # Adds support for plotting
-        "numexpr"      # Accelerates numpy by removing intermediate steps
-    ],
-    "test_require": [
-        'pytest',
-        'pytest-runner',
-        "pytest-cov"
-    ],
-    "extras_requires": {"fuzzing": ["fuzzywuzzy", "python-Levenshtein"]},
-    "classifiers": [
+tests = [
+    'pytest',
+    'pytest-runner',
+    "pytest-cov"
+]
+
+
+setuptools.setup(
+    name="PyPWA",
+    version=__version__,
+    author=__author__,
+    author_email=__email__,
+    packages=setuptools.find_packages(),
+    url="http//pypwa.jlab.org",
+    license=__license__,
+    description="General Partial Wave Analysis",
+    test_suite="tests",
+    entry_points=entry_points,
+    keywords="PyPWA GeneralFitting Partial Wave Analysis Minimization",
+    install_requires=requires,
+    tests_require=tests,
+    extras_require=extras,
+    classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Environment :: Console",
         "Intended Audience :: Science/Research",
@@ -119,63 +92,5 @@
         "Programming Language :: Python :: 3.8",
         "Topic :: Scientific/Engineering :: Mathematics",
         "Topic :: Scientific/Engineering :: Physics"
-    ],
-    "zip_safe": False
-}
-
-
-"""
-Anaconda doesn't have NVCC, but it does supply all the other
-required libraries. Also, if there are no CUDA libs on the system
-(No NVIDIA GPU) then CUDA integration will be disabled.
-"""
-
-base_dir = None
-for directory in os.environ["PATH"].split(os.pathsep):
-    if Path(directory + "/nvcc").exists():
-        nvcc_location = Path(directory + "/nvcc")
-        base_dir = Path(os.environ["CONDA_PREFIX"])
-        break
-
-if base_dir and base_dir.exists() and False:
-    print("Compiling with CUDA support.")
-
-    class custom_build_extension(build_ext):
-
-        def build_extensions(self):
-            self.src_extensions.append(".cu")
-            default_compiler_so = self.compiler_so
-            comp = self._compile
-
-            def _compile(obj, src, ext, cc_args, extra_postargs, pp_opts):
-                if os.path.splitext(src)[1] == '.cu':
-                    self.set_executable('compiler_so', str(nvcc_location))
-                    postargs = extra_postargs["nvcc"]
-                else:
-                    postargs = extra_postargs["gcc"]
-
-                comp(obj, src, ext, cc_args, postargs, pp_opts)
-                self.compile_so = default_compiler_so
-
-            self._compile = _compile
-            build_ext.build_extensions(self)
-
-    extension_kwargs["sources"] = []
-    extension_kwargs["libraries"] = ["cudart"]
-    extension_kwargs["runtime_library_dirs"] = base_dir / "lib64"
-    extension_kwargs["extra_compile_args"]["nvcc"] = [
-        "-fPIC", "--ccbin gcc", "-shared", "-arch=sm_61",
-        "-gencode=arch=compute_61,code=sm_61",
-        "-gencode=arch=compute_70,code=sm_70",
-        "-gencode=arch=compute_70,code=compute_70",
-        "-gencode=arch=compute_75,code=sm_75",
-        "-gencode=arch=compute_75,code=compute_75"
     ]
-    extension_kwargs["extra_compile_args"]["include_dirs"].append(
-        base_dir / "include"
-    )
-    setup_kargs["ext_module"].append(Extension("_cuda", **extension_kwargs))
-    setup_kargs["cmdclass"] = {"build_ext": custom_build_extension}
-
-
-setuptools.setup(**setup_kargs)
+)