Merge pull request #5 from VirtualPlanetaryLaboratory/dev

windows issue

multiplanet/__init__.py

@@ -14,3 +14,5 @@
 __copyright__ = "Copyright 2020  Caitlyn Wilhelm"
 
 from .multiplanet import *
+
+from .multiplanet_module import *

multiplanet/bp_get.py

@@ -0,0 +1,180 @@
+#!/usr/bin/env python
+
+import os
+import subprocess as sub
+import sys
+
+
+def ReadFile(bplSplitFile,verbose = False):
+
+    includelist = []
+    excludelist = []
+    bodylist = []
+    bpl_file = None
+
+    with open(bplSplitFile, 'r') as input:
+        #first thing we check is if both include and exclude are in the file bc that is bad
+        if 'saKeyInclude' and 'saKeyExclude' in input.read():
+            print("ERROR: saKeyInclude and saKeyExclude are mutually exclusive")
+            exit()
+
+    with open(bplSplitFile, 'r') as input:
+        #now we loop over the file and get the various inputs
+        content = [line.strip().split() for line in input.readlines()]
+        for line in content:
+            if line:
+                #we get the folder where the raw data is stored and have the default output file name set
+                if line[0] == 'sDestFolder':
+                    folder_name = line[1]
+                    outputFile = folder_name.split('/')[-1] + "_filtered.bpl"
+                if line[0] == 'sBigplanetFile':
+                    bpl_file = line[1]
+                if line[0] == 'sOutputName':
+                    outputFile = line[1]
+                if line[0] == 'sPrimaryFile':
+                    primaryFile = line[1]
+                if line[0] == 'bUlysses':
+                    thing = line[1]
+                if line[0] == "saBodyFiles":
+                    bodylist = line[1:]
+                    for i, value in enumerate(bodylist):
+                        bodylist[i] = value.strip("[]")
+                if line[0] == 'saKeyInclude':
+                    includelist = line[1:]
+                    for i, value in enumerate(includelist):
+                        includelist[i] = value.strip("[]")
+                if line[0] == 'saKeyExclude':
+                    excludelist = line[1:]
+                    for i, value in enumerate(excludelist):
+                        excludelist[i] = value.strip("[]")
+
+        if bpl_file == None and includelist == [] and excludelist == []:
+            print("No BPL Archive file or Include/Exclude List detected. This will create the BPL Archive File.")
+            print("WARNING: This may take some time...")
+
+
+        if verbose:
+            print("Folder Name:",folder_name)
+            if bpl_file != None and includelist != [] and excludelist != []:
+                print("BPL Archive File:",bpl_file)
+                print("Include List:",includelist)
+                print("Exclude List:",excludelist)
+                print("Output File:",outputFile)
+            print("Body Files:",bodylist)
+            print("Primary File:",primaryFile)
+
+
+        return folder_name,bpl_file,outputFile,bodylist,primaryFile,includelist,excludelist
+
+
+def GetDir(vspace_file):
+    """ Give it input file and returns name of folder where simulations are located. """
+
+    infiles = []
+    # gets the folder name with all the sims
+    with open(vspace_file, 'r') as vpl:
+        content = [line.strip().split() for line in vpl.readlines()]
+        for line in content:
+            if line:
+                if line[0] == 'destfolder':
+                    folder_name = line[1]
+
+                if line[0] == 'bodyfile' or line[0] == 'primaryfile':
+                    infiles.append(line[1])
+    if folder_name is None:
+        raise IOError("Name of destination folder not provided in file '%s'."
+                      "Use syntax 'destfolder <foldername>'"% vspace_file)
+
+
+    if os.path.isdir(folder_name) == False:
+        print("ERROR: Folder", folder_name, "does not exist in the current directory.")
+        exit()
+
+    return folder_name, infiles
+
+def GetSims(folder_name):
+    """ Pass it folder name where simulations are and returns list of simulation folders. """
+    #gets the list of sims
+    sims = sorted([f.path for f in os.scandir(os.path.abspath(folder_name)) if f.is_dir()])
+    return sims
+
+def GetSNames(in_files,sims):
+    #get system and the body names
+    body_names = []
+
+    for file in in_files:
+        #gets path to infile
+        full_path = os.path.join(sims[0],file)
+        #if the infile is the vpl.in, then get the system name
+        if "vpl.in" in file:
+            with open(full_path, 'r') as vpl:
+                content = [line.strip().split() for line in vpl.readlines()]
+                for line in content:
+                    if line:
+                        if line[0] == 'sSystemName':
+                            system_name = line[1]
+        else:
+            with open(full_path, 'r') as infile:
+                content = [line.strip().split() for line in infile.readlines()]
+                for line in content:
+                    if line:
+                        if line[0] == 'sName':
+                            body_names.append(line[1])
+
+    return system_name,body_names
+
+def GetVplanetHelp():
+    command = "vplanet -H | egrep -v '^$|^\+' | cut -f 2,4 -d '|' | egrep '^ \*\*|^ Cust|^ Type|^ Dim|^ Defa|^Output Parameters'"
+    py_ver = sys.version.split()[0]
+    if '3.6' in py_ver:
+        proc = sub.run(command, shell = True, universal_newlines = True, stdout=sub.PIPE,stderr=sub.PIPE)
+    else:
+        proc = sub.run(command, shell = True, text = True, stdout=sub.PIPE,stderr=sub.PIPE)
+    output = proc.stdout.splitlines()
+
+    vplanet_dict = {}
+
+    for count, line in enumerate(output):
+        if ((line.startswith(' **b') or line.startswith(' **d') or line.startswith(' **i') or line.startswith(' **s')) or line.startswith(' **sa') and len(line.split()) == 1):
+
+            option = line.strip("** ")
+            #print("Option:",option)
+            vplanet_dict[option] = {}
+            num = count + 1
+            while num != count:
+                if "Type" in output[num]:
+                    tp = output[num].rpartition('|')[-1].strip()
+                    vplanet_dict[option]['Type'] = tp
+                    #print("Type:",tp)
+                    num += 1
+
+                elif "Custom unit" in output[num]:
+                    custom_unit = output[num].rpartition('|')[-1].strip()
+                    vplanet_dict[option]['Custom Unit'] = custom_unit
+                    #print("Custom Unit:",custom_unit)
+                    num += 1
+
+                elif "Dimension(s)" in output[num]:
+                    dim = output[num].rpartition('|')[-1].strip()
+                    vplanet_dict[option]['Dimension'] = dim
+                    #print("Dimension:",dim)
+                    num += 1
+
+                elif "Default value" in output[num]:
+                    default = output[num].rpartition('|')[-1].strip()
+                    vplanet_dict[option]['Default Value'] = default
+                    #print("Default Value",default)
+                    #print()
+
+                    num += 1
+
+                elif "**" in output[num]:
+                    num = count
+
+                else:
+                    num += 1
+
+        if "Output Parameters" in line:
+            break
+
+    return vplanet_dict

multiplanet/multiplanet.py

@@ -6,7 +6,7 @@
 import argparse
 import h5py
 import numpy as np
-from bigplanet import CreateHDF5Group, GetSNames, GetSims
+from .bp_get import *
 
 # --------------------------------------------------------------------
 
@@ -62,7 +62,8 @@ def parallel_run_planet(input_file, cores, quiet, bigplanet, email):
             w.join()
 
     if bigplanet == False:
-        sub.run(["rm", master_hdf5_file])
+        if  os.path.isfile(master_hdf5_file) == True:
+            sub.run(["rm", master_hdf5_file])
     if email is not None:
         SendMail(email, folder_name)
 
@@ -117,20 +118,25 @@ def CreateCP(checkpoint_file, input_file, quiet, sims):
 def ReCreateCP(checkpoint_file, input_file, quiet, sims):
     if quiet == False:
         print("WARNING: multi-planet checkpoint file already exists!")
-        print("Checking if checkpoint file is corrupt...")
 
     datalist = []
-
-    with open(checkpoint_file, "r") as f:
-        for newline in f:
+    with open(checkpoint_file, "r") as re:
+        for newline in re:
             datalist.append(newline.strip().split())
-            for l in datalist:
-                if l[1] == "0":
-                    l[1] = "-1"
 
-    with open(checkpoint_file, "w") as f:
+        for l in datalist:
+            if l[1] == "0":
+                l[1] = "-1"
+        if datalist[-1] != ["THE","END"]:
+            lest = datalist[-2][0]
+            idx = sims.index(lest)
+            for f in range(idx+2,len(sims)):
+                datalist.append([sims[f],'-1'])
+            datalist.append(["THE","END"])
+
+    with open(checkpoint_file, "w") as wr:
         for newline in datalist:
-            f.writelines(" ".join(newline) + "\n")
+            wr.writelines(" ".join(newline) + "\n")
 
 
 ## parallel worker to run vplanet ##
@@ -207,19 +213,19 @@ def par_worker(
                     break
             if quiet == False:
                 print(folder, "completed")
-            if bigplanet == True:
-                with h5py.File(h5_file, "w") as Master:
-                    group_name = folder.split("/")[-1]
-                    if group_name not in Master:
-                        CreateHDF5Group(
-                            data,
-                            system_name,
-                            body_list,
-                            log_file,
-                            group_name,
-                            in_files,
-                            h5_file,
-                        )
+            # if bigplanet == True:
+            #     with h5py.File(h5_file, "w") as Master:
+            #         group_name = folder.split("/")[-1]
+            #         if group_name not in Master:
+            #             CreateHDF5Group(
+            #                 data,
+            #                 system_name,
+            #                 body_list,
+            #                 log_file,
+            #                 group_name,
+            #                 in_files,
+            #                 h5_file,
+            #             )
         else:
             for l in datalist:
                 if l[0] == folder:
@@ -259,7 +265,7 @@ def Arguments():
         "-bp",
         "--bigplanet",
         action="store_true",
-        help="Runs bigplanet and creates the HDF5 files alongside running mutlt-planet",
+        help="Runs bigplanet and creates the Bigplanet Archive file alongside running multiplanet",
     )
     parser.add_argument(
         "-m",

multiplanet/multiplanet_module.py

@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+
+import os
+import multiprocessing as mp
+import sys
+import subprocess as sub
+import h5py
+import numpy as np
+import csv
+from scipy import stats
+from multiplanet import parallel_run_planet
+
+"""
+Code for Multi-planet Module
+"""
+
+
+def RunMultiplanet(InputFile,cores, quiet=False, bigplanet=False,email=None):
+    parallel_run_planet(InputFile,cores,bigplanet,email)

setup.py

@@ -29,7 +29,7 @@
     ],
     entry_points={
         "console_scripts": [
-            "multi-planet = multiplanet.multiplanet:Arguments",
+            "multiplanet = multiplanet.multiplanet:Arguments",
             "mpstatus = multiplanet.mpstatus:Arguments",
         ],
     },

tests/Checkpoint/test_multi-planet_checkpoint.py

@@ -23,7 +23,7 @@ def test_mp_checkpoint():
 
         # Run multi-planet
         if not (path / ".MP_Checkpoint").exists():
-            subprocess.check_output(["multi-planet", "vspace.in"], cwd=path)
+            subprocess.check_output(["multiplanet", "vspace.in"], cwd=path)
         #gets list of folders
         folders = sorted([f.path for f in os.scandir(path / "MP_Checkpoint") if f.is_dir()])
 

tests/MpStatus/test_mpstatus.py

@@ -22,7 +22,7 @@ def test_mpstatus():
 
         # Run multi-planet
         if not (path / ".MP_Status").exists():
-            subprocess.check_output(["multi-planet", "vspace.in"], cwd=path)
+            subprocess.check_output(["multiplanet", "vspace.in"], cwd=path)
             subprocess.check_output(["mpstatus", "vspace.in"], cwd=path)
 
         #gets list of folders

tests/Parallel/test_multi-planet_parallel.py

@@ -22,7 +22,7 @@ def test_mp_parallel():
 
         # Run multi-planet
         if not (path / ".MP_Parallel").exists():
-            subprocess.check_output(["multi-planet", "vspace.in"], cwd=path)
+            subprocess.check_output(["multiplanet", "vspace.in"], cwd=path)
 
         folders = sorted([f.path for f in os.scandir(path / "MP_Parallel") if f.is_dir()])
 

tests/Serial/test_multi-planet_serial.py

@@ -15,7 +15,7 @@ def test_mp_serial():
 
     # Run multi-planet
     if not (path / ".MP_Serial").exists():
-        subprocess.check_output(["multi-planet", "vspace.in", "-c", "1"], cwd=path)
+        subprocess.check_output(["multiplanet", "vspace.in", "-c", "1"], cwd=path)
 
     folders = sorted([f.path for f in os.scandir(path / "MP_Serial") if f.is_dir()])