temet 0.9.1__tar.gz → 0.9.2__tar.gz

{temet-0.9.1 → temet-0.9.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: temet
-Version: 0.9.1
+Version: 0.9.2
 Summary: temet simulation analysis framework.
 Keywords: astronomy,simulation,cosmology,astrophysics
 Author-Email: Dylan Nelson <dnelson@uni-heidelberg.de>

{temet-0.9.1 → temet-0.9.2}/docs/installation.rst

@@ -45,7 +45,7 @@ Or, if you would like to install the most up-to-date version directly from the r
 
 .. code-block:: bash
 
-    pip install git+ssh://git@github.com/dnelson/temet.git
+    pip install git+https://git@github.com/dnelson/temet.git
 
 If you plan on editing, making changes, and adding functionality to this package (**recommended choice**), then first 
 clone the repository, then install the package in 'editable' mode. This means that the files in this directory are not copied 

{temet-0.9.1 → temet-0.9.2}/pyproject.toml

@@ -14,7 +14,7 @@ temet = ["temet/plot/mpl.style", "temet/util/*.cpp", "temet/tables/fonts/*.ttf"]
 
 [project]
 name = "temet"
-version = "0.9.1"
+version = "0.9.2"
 authors = [
     { name="Dylan Nelson", email="dnelson@uni-heidelberg.de" },
 ]

{temet-0.9.1 → temet-0.9.2}/temet/cosmo/cloudyGrid.py

@@ -12,11 +12,12 @@ import h5py
 import numpy as np
 
 from ..cosmo import hydrogen
+from ..util.extern import tables_path
 from ..util.helper import closest, logZeroNaN, num_cpus, rootPath
 from ..util.simParams import simParams
 
 
-basePath = rootPath + "tables/cloudy/"
+basePath = tables_path + "cloudy/"
 basePathTemp = expanduser("~") + "/data/cloudy_tables/"
 
 # emission lines recorded (must redo Cloudy grid to add lines)
@@ -386,7 +387,7 @@ def _loadExternalUVB(redshifts=None, hm12=False, puchwein19=False):
     if hm12:
         filePath = rootPath + "data/haardt.madau/hm2012.uvb.txt"
     if puchwein19:
-        filePath = rootPath + "/data/puchwein/p19.uvb.txt"
+        filePath = rootPath + "data/puchwein/p19.uvb.txt"
 
     sP = simParams(res=1820, run="tng")  # for units
 

{temet-0.9.1 → temet-0.9.2}/temet/cosmo/mergertree.py

@@ -531,7 +531,7 @@ def plot_tree(sP, subhaloID, saveFilename, treeName=treeName_default, dpi=100, c
 
     if tree is None:
         # subhalo not in tree
-        return None
+        return False
 
     nrows = tree["count"]
 
@@ -652,8 +652,6 @@ def plot_tree(sP, subhaloID, saveFilename, treeName=treeName_default, dpi=100, c
     if saveFilename is not None:
         fig.savefig(saveFilename, format=output_fmt, dpi=dpi)
         plt.close(fig)
-
-        return True
     else:
         # return image array itself, i.e. draw the canvas then extract the (Nx,Ny,3) array
         canvas = FigureCanvasAgg(fig)

{temet-0.9.1 → temet-0.9.2}/temet/cosmo/stellarPop.py

@@ -12,7 +12,8 @@ from numba import jit
 from scipy.interpolate import interp1d
 from scipy.ndimage import map_coordinates
 
-from ..util.helper import iterable, logZeroMin, logZeroNaN, num_cpus, rootPath, trapsum
+from ..util.extern import tables_path
+from ..util.helper import iterable, logZeroMin, logZeroNaN, num_cpus, trapsum
 from ..util.rotation import rotateCoordinateArray, rotationMatrixFromVec
 from ..util.simParams import simParams
 from ..util.sphMap import sphMap
@@ -315,7 +316,7 @@ def _dust_tau_model_lum_indiv(
 class sps:
     """Use pre-computed FSPS stellar photometrics tables to derive magnitudes for simulation stars."""
 
-    basePath = rootPath + "/tables/fsps/"
+    basePath = tables_path + "fsps/"
 
     imfTypes = {"salpeter": 0, "chabrier": 1, "kroupa": 2}
     isoTracks = ["mist", "padova07", "parsec", "basti", "geneva"]
@@ -1559,8 +1560,8 @@ def debug_check_rawspec():
     redshift = 0.8
 
     paths = [
-        rootPath + "/tables/fsps/mags_padova07_chabrier_cf00_bands-143_z=0.5.hdf5",
-        rootPath + "/tables/fsps/mags_padova07_chabrier_cf00_bands-143_z=0.5_em.hdf5",
+        tables_path + "fsps/mags_padova07_chabrier_cf00_bands-143_z=0.5.hdf5",
+        tables_path + "fsps/mags_padova07_chabrier_cf00_bands-143_z=0.5_em.hdf5",
     ]
 
     # start plot

{temet-0.9.1 → temet-0.9.2}/temet/cosmo/xray.py

@@ -11,11 +11,12 @@ from scipy.integrate import cumulative_trapezoid
 from scipy.ndimage import map_coordinates
 
 from ..plot.util import contourf, plothist, plotxy, sampleColorTable
-from ..util.helper import closest, rootPath
+from ..util.extern import tables_path
+from ..util.helper import closest
 from ..util.simParams import simParams
 
 
-basePath = rootPath + "tables/xray/"
+basePath = tables_path + "xray/"
 
 # fmt: off
 apec_elem_names = ["H","He","Li","Be","B","C","N","O","F","Ne","Na","Mg","Al","Si","P","S","Cl","Ar","K","Ca",

temet-0.9.2/temet/plot/__init__.py

@@ -0,0 +1,67 @@
+"""Plotting routines."""
+
+import logging
+import pathlib
+import sys
+from importlib import resources
+
+import matplotlib
+import matplotlib.pyplot as plt
+
+from . import (
+    clustering,
+    cosmoMisc,
+    drivers,
+    driversObs,
+    driversSizes,
+    meta,
+    perf,
+    quantities,
+    snapshot,
+    subhalos,
+    subhalos_evo,
+    util,
+)
+
+
+# check if we are in a Jupyter notebook
+def in_notebook():
+    """Determine if we are inside a Jupyter notebook (or similar), or not."""
+    if "IPython" in sys.modules:
+        IPython = sys.modules["IPython"]
+        ipython = IPython.core.getipython.get_ipython()
+
+        try:
+            shell = ipython.__class__.__name__
+            if shell == "ZMQInteractiveShell":
+                return True  # Jupyter notebook or qtconsole
+            elif shell == "TerminalInteractiveShell":
+                return False  # Terminal running IPython
+            else:
+                return False  # Other type (?)
+        except NameError:
+            return False  # Probably standard Python interpreter
+
+    return False  # no ipython
+
+
+in_notebook = in_notebook()
+
+# set default (non-interactive) backend
+if not in_notebook:
+    matplotlib.use("Agg")
+
+# set default style
+style_path = pathlib.Path(__file__).parent.resolve()
+plt.style.use(str(style_path / "mpl.style"))
+
+# add fonts
+try:
+    font_path = resources.files("temet") / "tables" / "fonts"
+    for font_file in font_path.iterdir():
+        matplotlib.font_manager.fontManager.addfont(font_file)
+except FileNotFoundError:
+    pass
+
+# disable fontTools timestamp warnings
+logging.getLogger("fontTools.ttLib.tables").setLevel(logging.ERROR)

{temet-0.9.1 → temet-0.9.2}/temet/plot/cloudy.py

@@ -15,12 +15,13 @@ from ..cosmo.cloudy import cloudyIon
 from ..cosmo.cloudyGrid import loadUVB
 from ..cosmo.hydrogen import photoCrossSecGray, photoRate, uvbEnergyDensity
 from ..plot.config import figsize, linestyles
-from ..plot.util import contourf, loadColorTable, sampleColorTable
-from ..util.helper import closest, evenlySample, logZeroNaN, rootPath
+from ..plot.util import _finish_plot, contourf, loadColorTable, sampleColorTable
+from ..util.extern import tables_path
+from ..util.helper import closest, evenlySample, logZeroNaN
 from ..util.simParams import simParams
 
 
-def plotUVB(uvb="FG11"):
+def plotUVB(uvb="FG11", saveFilename=None):
     """Debug plots of the UVB(nu) as a function of redshift."""
     # config
     redshifts = [0.0, 2.0, 4.0, 6.0, 7.0, 8.0, 9.0]
@@ -104,8 +105,7 @@ def plotUVB(uvb="FG11"):
     cb.ax.set_ylabel(r"log J$_{\nu}(\nu)$ [ 4 $\pi$ erg / s / cm$^2$ / Hz ]")
 
     # finish
-    fig.savefig("uvb_%s.pdf" % uvb)
-    plt.close(fig)
+    _finish_plot(fig, saveFilename, saveNameDefault="uvb_%s.pdf" % uvb)
 
 
 def plotIonAbundances(res="lg_c17", elements=("Magnesium",)):
@@ -291,7 +291,7 @@ def grackleTable():
     # filename2 = 'grid_cooling_UVB=FG11.hdf5' # my new version (testing)
     ##filename2 = 'CloudyData_UVB=FG2011_shielded.h5' # orig
 
-    filepath = rootPath + "tables/cloudy/"
+    filepath = tables_path + "cloudy/"
     # filename1 = 'grid_cooling_UVB=FG20_unshielded.hdf5'
     filename1 = "grid_cooling_UVB=FG20.hdf5"
     filename2 = "grid_cooling_UVB=FG20_ext.hdf5"

{temet-0.9.1 → temet-0.9.2}/temet/plot/clustering.py

@@ -21,7 +21,7 @@ def galaxyTwoPoint(sPs, cenSatSelects=("all", "cen", "sat"), colorBin=None, cTyp
     rMinMax = [0.01, 100.0]  # log Mpc
     yMinMax = [1e-2, 5e4]
 
-    rLabel = "r [ Mpc ]"
+    rLabel = r"r [ Mpc ]"
     yLabel = r"$\xi(r \pm \Delta r)$  [ real space two-point autocorr ]"
 
     # load/calculate
@@ -35,8 +35,7 @@ def galaxyTwoPoint(sPs, cenSatSelects=("all", "cen", "sat"), colorBin=None, cTyp
             cfs.append({"rad": rad, "xi": xi, "xi_err": xi_err, "css": cenSatSelect, "sP": sP})
 
     # start plot
-    fig = plt.figure(figsize=figsize)
-    ax = fig.add_subplot(111)
+    fig, ax = plt.subplots()
     setAxisColors(ax)
 
     ax.set_xlim(rMinMax)
@@ -99,8 +98,8 @@ def galaxyTwoPointQuantBounds(
     drawSymbols = True
     symSize = 7.0
 
-    rLabel = "r [ log Mpc ]"
-    yLabel = "log %s$\\xi(r)$"
+    rLabel = r"r [ log Mpc ]"
+    yLabel = r"log %s$\xi(r)$"
 
     # load/calculate
     cfs = OrderedDict()
@@ -406,9 +405,7 @@ def conformityWithRedFrac(sP, cenSatSelectSec="all"):
             confs[label][colorLabel] = conf
 
     # start plot
-    fig = plt.figure(figsize=figsize)
-    gs = gridspec.GridSpec(1, 1)
-    ax = fig.add_subplot(gs[0])
+    fig, ax = plt.subplots()
     setAxisColors(ax)
 
     ax.set_xlim(rMinMax)

{temet-0.9.1 → temet-0.9.2}/temet/plot/driversSizes.py

@@ -12,6 +12,7 @@ from scipy.signal import savgol_filter
 
 from ..cosmo.util import cenSatSubhaloIndices
 from ..plot.config import binSize, colors, figsize, linestyles, sKn, sKo
+from ..plot.util import _finish_plot
 from ..util.helper import logZeroNaN, running_median
 from ..util.simParams import simParams
 
@@ -26,6 +27,7 @@ def galaxySizes(
     markersize=12.0,
     xlim=None,
     ylim=None,
+    saveFilename=None,
     pdf=None,
 ):
     """Galaxy sizes (half mass radii) vs stellar mass or halo mass, compared to data.
@@ -41,8 +43,8 @@ def galaxySizes(
       markersize (float): if ``scatterPoints`` then override the default marker size.
       xlim (2-tuple): plot x-limits.
       ylim (2-tuple): plot y-limits.
-      pdf (PdfPages or None): if None, an actual PDF file is written to disk with the figure.
-        If not None, then the figure is added to this existing pdf collection.
+      saveFilename (str): name (and extension, setting format) of output plot. Automatic if None.
+      pdf (PdfPages or None): If not None, then the figure is added to this existing pdf collection.
     """
     from ..load.data import baldry2012SizeMass, lange2016SizeMass, shen2003SizeMass
 
@@ -285,21 +287,18 @@ def galaxySizes(
     # legend
     ax.legend(loc="lower right")
 
-    # finish figure
-    if pdf is not None:
-        pdf.savefig(facecolor=fig.get_facecolor())
-    else:
-        saveFilename = "sizes_%s_z%.1f_halomass=%s_halflight=%s.pdf" % (
-            "-".join([str(sim) for sim in sPs]),
-            simRedshift,
-            vsHaloMass,
-            "-".join([str(s) for s in addHalfLightRad]) if addHalfLightRad is not None else "None",
-        )
-        fig.savefig(saveFilename, facecolor=fig.get_facecolor())
-    plt.close(fig)
+    # finish plot and save
+    saveNameDefault = "sizes_%s_z%.1f_halomass=%s_halflight=%s.pdf" % (
+        "-".join([str(sim) for sim in sPs]),
+        simRedshift,
+        vsHaloMass,
+        "-".join([str(s) for s in addHalfLightRad]) if addHalfLightRad is not None else "None",
+    )
+
+    _finish_plot(fig, saveFilename, saveNameDefault, pdf)
 
 
-def galaxyHISizeMass(sPs, pdf, simRedshift=0.0):
+def galaxyHISizeMass(sPs, simRedshift=0.0, saveFilename=None, pdf=None):
     """Galaxy HI size-mass relation, at redshift zero."""
     # plot setup
     fig, ax = plt.subplots()
@@ -366,13 +365,10 @@ def galaxyHISizeMass(sPs, pdf, simRedshift=0.0):
     handles, labels = ax.get_legend_handles_labels()
     ax.legend(handles, labels, loc="lower right")
 
-    # finish figure
-    if pdf is not None:
-        pdf.savefig(facecolor=fig.get_facecolor())
-    else:
-        saveFilename = "sizes_HI_%s_z%.1f.pdf" % ("-".join([str(sim) for sim in sPs]), simRedshift)
-        fig.savefig(saveFilename, facecolor=fig.get_facecolor())
-    plt.close(fig)
+    # finish plot and save
+    saveNameDefault = "sizes_HI_%s_z%.1f.pdf" % ("-".join([str(sim) for sim in sPs]), simRedshift)
+
+    _finish_plot(fig, saveFilename, saveNameDefault, pdf)
 
 
 def sizeModelsRatios():
@@ -656,7 +652,7 @@ def clumpSizes(sP):
     plt.close(fig)
 
 
-def characteristicSizes(sP, vsHaloMass=False):
+def characteristicSizes(sP, vsHaloMass=False, saveFilename=None):
     """Compare many different 'characteristic' halo/galaxy sizes as a function of mass."""
     from ..load.data import baldry2012SizeMass
 
@@ -792,6 +788,7 @@ def characteristicSizes(sP, vsHaloMass=False):
 
     ax.legend(loc="upper left", ncol=2)
 
-    # finish figure
-    fig.savefig("characteristic_sizes_%s_%d.pdf" % (sP.simName, sP.snap))
-    plt.close(fig)
+    # finish plot and save
+    saveNameDefault = "characteristic_sizes_%s_%d.pdf" % (sP.simName, sP.snap)
+
+    _finish_plot(fig, saveFilename, saveNameDefault)

{temet-0.9.1 → temet-0.9.2}/temet/plot/mpl.style

@@ -290,7 +290,7 @@ legend.scatterpoints : 1 # number of scatter points
 #figure.titlesize : medium     # size of the figure title
 #figure.titleweight : normal   # weight of the figure title
 figure.figsize   : 11.2, 8    # figure size in inches
-figure.dpi       : 150      # figure dots per inch
+figure.dpi       : 100      # figure dots per inch
 figure.facecolor : white    # figure facecolor; 0.75 is scalar gray
 #figure.edgecolor : white   # figure edgecolor
 figure.autolayout : False   # When True, automatically adjust subplot