Remove old merger tree (#93)

* Edit docs

* Delete merger tree files

* Edit README

* Edit docs

csiborgtools/read/paths.py

@@ -12,7 +12,9 @@
 # You should have received a copy of the GNU General Public License along
 # with this program; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-"""CSiBORG paths manager."""
+"""
+CSiBORG paths manager.
+"""
 from glob import glob, iglob
 from os import makedirs
 from os.path import isdir, join
@@ -312,26 +314,6 @@ class Paths:
             nsnap = str(nsnap).zfill(3)
             return join(simpath, f"snapdir_{nsnap}", f"snap_{nsnap}")
 
-    def merger_tree_file(self, nsnap, nsim):
-        """
-        Path to the CSiBORG on-the-fly generated merger tree file.
-
-        Parameters
-        ----------
-        nsnap : int
-            Snapshot index.
-        nsim : int
-            IC realisation index.
-
-        Returns
-        -------
-        str
-        """
-        nsim = str(nsim)
-        nsnap = str(nsnap).zfill(5)
-        return join(self.srcdir, f"ramses_out_{nsim}",
-                    f"output_{nsnap}", f"mergertree_{nsnap}.dat")
-
     def processed_output(self, nsim, simname, halo_finder):
         """
         Path to the files containing all particles of a CSiBORG realisation at
@@ -378,23 +360,6 @@ class Paths:
         try_create_directory(fdir)
         return join(fdir, f"phew_{str(nsim).zfill(5)}.hdf5")
 
-    def processed_merger_tree(self, nsim):
-        """
-        Path to the files containing the processed original merger tree files.
-
-        Parameters
-        ----------
-        nsim : int
-            IC realisation index.
-
-        Returns
-        -------
-        str
-        """
-        fdir = join(self.postdir, "processed_output")
-        try_create_directory(fdir)
-        return join(fdir, f"merger_{str(nsim).zfill(5)}.hdf5")
-
     def halomaker_particle_membership(self, nsnap, nsim, halo_finder):
         """
         Path to the HaloMaker particle membership file (CSiBORG only).

csiborgtools/read/readsim.py

@@ -145,8 +145,6 @@ class CSiBORGReader(BaseReader):
     ----------
     paths : py:class`csiborgtools.read.Paths`
     """
-    # _snapshot_cache = {}
-
     def __init__(self, paths):
         self.paths = paths
 
@@ -433,37 +431,6 @@ class CSiBORGReader(BaseReader):
 
         return parent_arr, parent_mass
 
-    def read_merger_tree(self, nsnap, nsim):
-        """
-        Read in the raw merger tree file.
-
-        Parameters
-        ----------
-        nsnap : int
-            Snapshot index.
-        nsim : int
-            IC realisation index.
-
-        Returns
-        -------
-        data : 2-dimensional array
-        """
-        fname = self.paths.merger_tree_file(nsnap, nsim)
-        # Do some checks if the file exists or is empty
-        if not isfile(fname) or getsize(fname) == 0:
-            raise FileExistsError(f"Merger file `{fname}` does not exist.")
-
-        data = numpy.genfromtxt(fname)
-
-        if data.ndim == 1:
-            raise FileExistsError(f"Invalid merger file `{fname}`.")
-
-        # Convert to Msun / h and cMpc / h but keep velocity in box units.
-        data[:, 3] *= 2.6543271649678946e+19
-        data[:, 5:8] *= 677.7
-
-        return data
-
 
 ###############################################################################
 #                         Quijote particle reader                             #

csiborgtools/utils.py

@@ -12,7 +12,9 @@
 # You should have received a copy of the GNU General Public License along
 # with this program; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-"""Collection of stand-off utility functions used in the scripts."""
+"""
+Collection of stand-off utility functions used in the scripts.
+"""
 import numpy
 from numba import jit
 from datetime import datetime