Merge pull request #100 from kyleaoman/pyproject_toml

Pyproject toml

Author: JBorrow

.gitignore

@@ -14,3 +14,6 @@ dist/*
 
 # MacOS
 *.DS_Store
+
+# autoformatter virtualenv
+black_formatting_env/*

pyproject.toml

@@ -0,0 +1,36 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+packages = ["velociraptor"]
+
+[project]
+name = "velociraptor-python"
+version="0.16.1"
+authors = [
+    { name="Josh Borrow", email="[email protected]" },
+    { name="Kyle Oman", email="[email protected]" },
+]
+description="Velociraptor catalogue reading routines."
+readme = "README.md"
+requires-python = ">3.6.0"
+classifiers = [
+    "License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "numpy",
+    "h5py",
+    "unyt>=2.6.0",
+    "astropy",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/SWIFTSIM/velociraptor-python"
+"Bug Tracker" = "https://github.com/SWIFTSIM/velociraptor-python/issues"
+"Documentation" = "https://velociraptor-python.readthedocs.io/en/latest"
+
+[project.scripts]
+velociraptor-plot = "velociraptor.velociraptor_plot:velociraptor_plot"
+velociraptor-compute-box-size-correction = "velociraptor.velociraptor_compute_box_size_correction:velociraptor_compute_box_size_correction"

tests/__init__.py

@@ -3,7 +3,7 @@
 """
 
 from velociraptor import load
-from helper import requires
+from .helper import requires
 
 
 @requires("cosmo_0000.properties")

tests/test_load_catalogue.py

@@ -0,0 +1,134 @@
+#!/usr/bin/env python
+
+"""
+Compute a box size correction file that can be used as the 'box_size_correction'
+argument for an autoplotter plot.
+
+Usage:
+  velociraptor-compute-box-size-correction \
+    smallbox largebox plotname plottype output
+
+with:
+  - smallbox/largebox: data*.yml output file from a pipeline run
+  - plotname: Name of a particular plot in the data*.yml files
+  - plottype: Type of plot (currently supported: mass_function)
+  - output: Name of an output .yml file. If the .yml extension is missing, it is
+    added.
+"""
+
+import argparse
+import os
+import yaml
+import numpy as np
+import scipy.interpolate as interpol
+
+
+def velociraptor_compute_box_size_correction():
+    argparser = argparse.ArgumentParser("Compute the box size correction for a plot.")
+    argparser.add_argument(
+        "smallbox", help="Pipeline output for the small box that needs to be corrected."
+    )
+    argparser.add_argument(
+        "largebox", help="Pipeline output for the large box that we want to correct to."
+    )
+    argparser.add_argument("plotname", help="Name of the plot that we want to correct.")
+    argparser.add_argument("plottype", help="Type of the plot we want to correct.")
+    argparser.add_argument(
+        "output", help="Name of the output file that will store the correction."
+    )
+    args = argparser.parse_args()
+
+    if not args.plottype in ["mass_function"]:
+        raise AttributeError(
+            f"Cannot compute box size correction for plot type {args.plottype}!"
+        )
+
+    log_x = False
+    log_y = False
+    if args.plottype in ["mass_function"]:
+        log_x = True
+        log_y = True
+
+    small_box = args.smallbox
+    large_box = args.largebox
+    for file in [args.smallbox, args.largebox]:
+        if not os.path.exists(file):
+            raise AttributeError(f"File {file} could not be found!")
+
+    output_file = args.output
+    if not output_file.endswith(".yml"):
+        output_file += ".yml"
+    try:
+        open(output_file, "w").close()
+    except:
+        raise AttributeError(f"Can not write to {output_file}!")
+
+    with open(args.smallbox, "r") as handle:
+        small_box = yaml.safe_load(handle)
+    with open(args.largebox, "r") as handle:
+        large_box = yaml.safe_load(handle)
+
+    try:
+        small_box_data = small_box[args.plotname]["lines"]
+    except:
+        raise AttributeError(f"Could not find {args.plotname} in {args.smallbox}!")
+    try:
+        large_box_data = large_box[args.plotname]["lines"]
+    except:
+        raise AttributeError(f"Could not find {args.plotname} in {args.largebox}!")
+
+    try:
+        small_box_plot_data = small_box_data[args.plottype]
+    except:
+        raise AttributeError(
+            f"{args.plottype} not found in plot {args.plotname} in {args.smallbox}!"
+        )
+    try:
+        large_box_plot_data = large_box_data[args.plottype]
+    except:
+        raise AttributeError(
+            f"{args.plottype} not found in plot {args.plotname} in {args.largebox}!"
+        )
+
+    small_box_x = small_box_plot_data["centers"]
+    small_box_y = small_box_plot_data["values"]
+    large_box_x = large_box_plot_data["centers"]
+    large_box_y = large_box_plot_data["values"]
+
+    if log_x:
+        small_box_x = np.log10(small_box_x)
+        large_box_x = np.log10(large_box_x)
+
+    if log_y:
+        small_box_y = np.log10(small_box_y)
+        large_box_y = np.log10(large_box_y)
+
+    small_spline = interpol.InterpolatedUnivariateSpline(small_box_x, small_box_y)
+    large_spline = interpol.InterpolatedUnivariateSpline(large_box_x, large_box_y)
+
+    xmin = max(small_box_x.min(), large_box_x.min())
+    xmax = min(small_box_x.max(), large_box_x.max())
+    x_range = np.linspace(xmin, xmax, 100)
+    small_y_range = small_spline(x_range)
+    large_y_range = large_spline(x_range)
+
+    if log_y:
+        small_y_range = 10.0 ** small_y_range
+        large_y_range = 10.0 ** large_y_range
+
+    correction = large_y_range / small_y_range
+
+    correction_data = {}
+    correction_data["plot_name"] = args.plotname
+    correction_data["plot_type"] = args.plottype
+    correction_data["is_log_x"] = True
+    correction_data["x_units"] = small_box_plot_data["centers_units"]
+    correction_data["x_limits"] = np.array([xmin, xmax]).tolist()
+    correction_data["x"] = x_range.tolist()
+    correction_data["y"] = correction.tolist()
+    with open(output_file, "w") as handle:
+        yaml.safe_dump(correction_data, handle)
+
+
+if __name__ == "__main__":
+    velociraptor_compute_box_size_correction()

velociraptor-compute-box-size-correction

@@ -109,7 +109,7 @@
 )
 
 
-if __name__ == "__main__":
+def velociraptor_plot():
     # Parse our lovely arguments and pass them to the velociraptor library
     from velociraptor.autoplotter.objects import AutoPlotter
     from velociraptor.autoplotter.metadata import AutoPlotterMetadata
@@ -169,3 +169,7 @@ def print_if_debug(string: str):
         auto_plotter_metadata.write_metadata(args.metadata)
 
     print_if_debug("Done.")
+
+
+if __name__ == "__main__":
+    velociraptor_plot()