V3.0

.gitignore

@@ -21,29 +21,6 @@ SeasonalClimateFiles
 *.csv
 *.md5
 
-#files created from running tests
-tests/Bpstatus/BP_Status/
-tests/Bpstatus/.*
-tests/CreateHDF5/BP_CreateHDF5/
-tests/CreateHDF5/.*
-tests/ExtractArchive/BP_Extract/
-tests/ExtractArchive/.*
-tests/Stats/BP_Stats/
-tests/Stats/.*
-tests/ExtractFilterArchive/BP_Extract/
-tests/ExtractFilterArchive/.*
-tests/ExtractFilterRawData/BP_Extract/
-tests/ExtractFilterRawData/.*
-tests/MD5CheckSum/BP_Extract/
-tests/MD5CheckSum/.*
-tests/UlyssesAggregated/BP_Extract/
-tests/UlyssesAggregated/.*
-tests/UlyssesForward/BP_Extract/
-tests/UlyssesForward/.*
-tests/SingleSim/BP_Extract/
-tests/SingleSim/.*
-
-
 .coverage
 
 # Aux files / build info / garbage

bigplanet/bp_extract.py

@@ -40,8 +40,8 @@ def ExtractColumn(hf, k):
     k : str
         the name of the column that is to be extracted
         Example:
-            k = 'earth_Obliquity_final'
-        The syntax of the column names is body_variable_aggregation
+            k = 'earth:Obliquity:final'
+        The syntax of the column names is body:variable:aggregation
         the lists of aggregations (and how to call them) is as follows:
 
             forward file data (forward), initial data (initial),
@@ -532,6 +532,7 @@ def Md5CheckSum(archivefile, ignore_corrupt=False):
     md5file = name + ".md5"
     # if it doesn't exist, we need to create it
     if os.path.isfile(md5file) == False:
+        print(md5file+" file not found. Generating.")
         with open(md5file, "w") as md5:
             with open(bpa, "rb") as f:
                 file_hash = hashlib.md5()
@@ -560,11 +561,14 @@ def Md5CheckSum(archivefile, ignore_corrupt=False):
             new_md5 = file_hash.hexdigest()
             # print("MD5 from " + name + ".bpa: " + new_md5)
         if md5_old == new_md5:
-            print("MD5 Checksum verified")
+            print("MD5 Checksum verified.")
         else:
             if ignore_corrupt == True:
-                print("WARNING: MD5 Checksum failed")
+                print("WARNING: MD5 Checksum failed!")
             else:
-                print("ERROR: MD5 Checksum failed")
-                print("set flag --ignorecorrupt to still use corrupted data")
+                print("ERROR: MD5 Checksum failed!")
+                print("MD5 from " + md5file + ":", md5_old)
+                print("MD5 from " + name + ".bpa: " + new_md5)
+                print("set flag -ignorecorrupt to still use corrupted data")
+                print("INFO: MD5Checksumming is not functioning as ov v3.0, so you should probably set this flag!")
                 exit()

bigplanet/bp_get.py

@@ -252,10 +252,15 @@ def GetVplanetHelp():
         ):
 
             option = line.strip("** ")
-            # print("Option:",option)
+            # print("Option: ",option,repr(count))
             vplanet_dict[option] = {}
             num = count + 1
             while num != count:
+                #print("num,count: ",repr(num),repr(len(output)))
+                #print("Output[num]: ",repr(output[num]))
+                if (num >= len(output)):
+                    print("ERROR: Unable to gather VPLanet help information!")
+                    assert(0)
                 if "Type" in output[num]:
                     tp = output[num].rpartition("|")[-1].strip()
                     vplanet_dict[option]["Type"] = tp

tests/CreateHDF5/test_CreateHDF5.py

@@ -0,0 +1,56 @@
+import multiprocessing as mp
+import os
+import pathlib
+import subprocess
+import sys
+import warnings
+import shutil
+
+import numpy as np
+
+
+def test_CreateHDF5():
+    # gets current path
+    path = pathlib.Path(__file__).parents[0].absolute()
+    sys.path.insert(1, str(path.parents[0]))
+
+    # gets the number of cores on the machine
+    cores = mp.cpu_count()
+    if cores == 1:
+        warnings.warn("There is only 1 core on the machine", stacklevel=3)
+    else:
+        # Remove anything from previous tests
+        if (path / "BP_CreateHDF5").exists():
+            shutil.rmtree(path / "BP_CreateHDF5")
+        if (path / ".BP_CreateHDF5").exists():
+            os.remove(path / ".BP_CreateHDF5")
+        if (path / ".BP_CreateHDF5_BPL").exists():
+            os.remove(path / ".BP_CreateHDF5_BPL")
+        if (path / "BP_CreateHDF5.bpa").exists():
+            os.remove(path / "BP_CreateHDF5.bpa")
+        if (path / "BP_CreateHDF5.md5").exists():
+            os.remove(path / "BP_CreateHDF5.md5")
+
+        # Run vspace
+        print("Running vspace.")
+        sys.stdout.flush()
+        subprocess.check_output(["vspace", "vspace.in"], cwd=path)
+
+        # Run multi-planet
+        print("Running MultiPlanet.")
+        sys.stdout.flush()
+        subprocess.check_output(["multiplanet", "vspace.in"], cwd=path)
+
+        # Run bigplanet
+        print("Running BigPlanet.")
+        sys.stdout.flush()
+        subprocess.check_output(["bigplanet", "bpl.in", "-a"], cwd=path)
+
+        file = path / "BP_CreateHDF5.bpa"
+
+        # checks if the bpl files exist
+        assert os.path.isfile(file) == True
+
+
+if __name__ == "__main__":
+    test_CreateHDF5()

tests/ExtractArchive/test_ExtractArchive.py

@@ -0,0 +1,67 @@
+import multiprocessing as mp
+import os
+import pathlib
+import subprocess
+import sys
+import warnings
+import shutil
+import numpy as np
+import bigplanet as bp
+
+
+def test_ExtractArchive():
+    # gets current path
+    path = pathlib.Path(__file__).parents[0].absolute()
+    sys.path.insert(1, str(path.parents[0]))
+
+    # gets the number of cores on the machine
+    cores = mp.cpu_count()
+    if cores == 1:
+        warnings.warn("There is only 1 core on the machine", stacklevel=3)
+    else:
+        # Remove anything from previous tests
+        if (path / "BP_Extract").exists():
+            shutil.rmtree(path / "BP_Extract")
+        if (path / ".BP_Extract").exists():
+            os.remove(path / ".BP_Extract")
+        if (path / ".BP_Extract_BPL").exists():
+            os.remove(path / ".BP_Extract_BPL")
+        if (path / "BP_Extract.bpa").exists():
+            os.remove(path / "BP_Extract.bpa")
+        if (path / "../BP_Extract.md5").exists():
+            os.remove(path / "../BP_Extract.md5")
+        if (path / "BP_Extract.md5").exists():
+            os.remove(path / "BP_Extract.md5")
+
+        # Run vspace
+        print("Running vspace.")
+        sys.stdout.flush()
+        subprocess.check_output(["vspace", "vspace.in"], cwd=path)
+
+        # Run multi-planet
+        print("Running MultiPlanet.")
+        sys.stdout.flush()
+        subprocess.check_output(["multiplanet", "vspace.in"], cwd=path)
+
+        # Run bigplanet
+        print("Running BigPlanet.")
+        sys.stdout.flush()
+
+        ######## SOMETHING IS WRONG WITH MD5CHECKSUMS! #######
+        subprocess.check_output(["bigplanet", "-ignorecorrupt", "bpl.in", "-a"], cwd=path)
+
+        file = bp.BPLFile(path / "BP_Extract.bpa")
+
+        earth_Instellation_final = bp.ExtractColumn(
+            file, "earth:Instellation:final"
+        )
+        sun_RotPer_initial = bp.ExtractColumn(file, "sun:RotPer:initial")
+
+        assert np.isclose(earth_Instellation_final[0], 1367.635318)
+        assert np.isclose(earth_Instellation_final[1], 341.90883)
+
+        assert np.isclose(sun_RotPer_initial[0], 86400.0)
+
+
+if __name__ == "__main__":
+    test_ExtractArchive()