More removal of owmeta/pyopenworm...

c302/__init__.py

@@ -41,19 +41,6 @@
 
 import collections
 
-try:
-    from owmeta_core import __version__ as owc_version
-    from owmeta_core.bundle import Bundle
-    from owmeta_core.context import Context
-    from owmeta import __version__ as owmeta_version
-    from owmeta.cell import Cell
-    from owmeta.neuron import Neuron
-    from owmeta.muscle import Muscle
-
-    owmeta_installed = True
-except:
-    print("owmeta not installed! Proceeding anyway...")
-    owmeta_installed = False
 
 try:
     from urllib2 import URLError  # Python 2
@@ -108,7 +95,7 @@ def get_str_from_expnotation(num):
 def get_muscle_position(muscle, data_reader="SpreadsheetDataReader"):
     if muscle == "MANAL" or muscle == "MVULVA":
         return 0, 0, 0
-    # TODO: Pull these positions from openworm/owmeta-data
+        
     pat1 = r"M([VD])([LR])(\d+)"
     pat2 = r"([VD])([LR])(\d+)"
     md = re.fullmatch(pat1, muscle)
@@ -512,24 +499,24 @@ def elem_in_coll_matches_conn(coll, conn):
 cached_owmeta_data = None
 
 
-def _get_cell_info(bnd, cells):
+def _get_cell_info(cells):
     global cached_owmeta_data
     # print('------ Getting the cell info for %s'%cells)
     all_neuron_info = collections.OrderedDict()
     all_muscle_info = collections.OrderedDict()
 
-    if bnd is None:
-        if cached_owmeta_data == None:
-            print_("Loading owmeta cached data from: %s" % OWMETA_CACHED_DATA_FILE)
-            with open(OWMETA_CACHED_DATA_FILE) as f:
-                cached_owmeta_data = json.load(f)
+    if cached_owmeta_data == None:
+        print_("Loading owmeta cached data from: %s" % OWMETA_CACHED_DATA_FILE)
+        with open(OWMETA_CACHED_DATA_FILE) as f:
+            cached_owmeta_data = json.load(f)
 
-        for cell in cells:
-            if is_muscle(cell):
-                all_muscle_info[cell] = cached_owmeta_data["muscle_info"][cell]
-            else:
-                all_neuron_info[cell] = cached_owmeta_data["neuron_info"][cell]
+    for cell in cells:
+        if is_muscle(cell):
+            all_muscle_info[cell] = cached_owmeta_data["muscle_info"][cell]
+        else:
+            all_neuron_info[cell] = cached_owmeta_data["neuron_info"][cell]
 
+    '''
     else:
         ctx = bnd(Context)(ident="http://openworm.org/data").stored
         # Go through our list and get the neuron object associated with each name.
@@ -590,6 +577,7 @@ def _get_cell_info(bnd, cells):
                 all_muscle_info[cell.name()] = info
             elif isinstance(cell, Neuron):
                 all_neuron_info[cell.name()] = info
+    '''
 
     # print('==== Returning %s; %s'%(all_neuron_info, all_muscle_info))
     return all_neuron_info, all_muscle_info
@@ -705,10 +693,6 @@ def generate(
         "\n\nParameters and setting used to generate this network:\n\n"
         + "    Data reader:                    %s\n" % data_reader
         + "    c302 version:                   %s\n" % __version__
-        + "    owmeta version:                 %s\n"
-        % ("- not installed -" if not owmeta_installed else owmeta_version)
-        + "    owmeta_core version:            %s\n"
-        % ("- not installed -" if not owmeta_installed else owc_version)
         + "    Cells:                          %s\n"
         % (cells if cells is not None else "All cells")
         + "    Cell stimulated:                %s\n"
@@ -843,12 +827,7 @@ def generate(
 
     count = 0
 
-    try:
-        with Bundle("openworm/owmeta-data", version=6) as bnd:
-            all_neuron_info, all_muscle_info = _get_cell_info(bnd, set(cell_names))
-    except Exception as e:
-        print_('Unable to open "openworm/owmeta-data" bundle: %s' % e)
-        all_neuron_info, all_muscle_info = _get_cell_info(None, set(cell_names))
+    all_neuron_info, all_muscle_info = _get_cell_info(set(cell_names))
 
     for cell in cell_names:
         if cells is None or cell in cells:

c302/__version__.py

@@ -1 +1 @@
-__version__ = "0.8.1"
+__version__ = "0.9.0"

c302/backers.py

@@ -1,7 +1,7 @@
 """
     This method reads a generated list of cells vs. names as assigned by OpenWorm backers
 
-    This information will eventually be moved to owmeta/elsewhere...
+    This information will eventually be moved elsewhere...
 """
 
 import os

c302/bioparameters.py

@@ -3,7 +3,7 @@
 from neuroml import ExpTwoSynapse, GapJunction, GradedSynapse
 
 """
-    Subject to much change & refactoring once owmeta is stable...
+    Subject to much change & refactoring...
 """
 
 

c302/c302_info.py

@@ -52,27 +52,7 @@ def generate_c302_info(nml_doc, verbose=False):
 
     all_cells = sorted(all_cells)
 
-    try:
-        from PyOpenWorm import (
-            connect as pyow_connect,
-            __version__ as pyow_version,
-            ConnectionFailError,
-        )
-
-        pow_conn = pyow_connect("./pyopenworm.conf")
-        all_neuron_info, all_muscle_info = c302._get_cell_info(pow_conn, all_cells)
-        ver_info = "PyOpenWorm v%s" % pyow_version
-    except Exception as e:
-        c302.print_("Unable to connect to PyOpenWorm database: %s" % e)
-        from owmeta_core.bundle import Bundle
-
-        from owmeta_core import __version__ as owc_version
-        from owmeta import __version__ as owmeta_version
-
-        ver_info = "owmeta v%s (owmeta core v%s)" % (owmeta_version, owc_version)
-
-        with Bundle("openworm/owmeta-data", version=6) as bnd:
-            all_neuron_info, all_muscle_info = c302._get_cell_info(bnd, all_cells)
+    all_neuron_info, all_muscle_info = c302._get_cell_info(all_cells)
 
     all_neurons = []
     all_muscles = []

c302/c302_utils.py

@@ -516,17 +516,7 @@ def generate_conn_matrix(
         else:
             all_neurons.append(c)
 
-    try:
-        from owmeta_core.bundle import Bundle
-
-        with Bundle("openworm/owmeta-data", version=6) as bnd:
-            all_neuron_info, all_muscle_info = c302._get_cell_info(bnd, all_cells)
-    except Exception as e:
-        traceback.print_exc()
-        c302.print_(
-            "Unable to connect to the owmeta bundle: %s\n Proceeding anyway..." % e
-        )
-        all_neuron_info, all_muscle_info = c302._get_cell_info(None, all_cells)
+    all_neuron_info, all_muscle_info = c302._get_cell_info(all_cells)
 
     """
     if order_by_type:

examples/LEMS_c302_A_Full.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          All cells
     Cell stimulated:                ['PLML', 'PLMR']
     Connection:                     []

examples/LEMS_c302_A_IClamp.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['ADAL', 'PVCL']
     Cell stimulated:                []
     Connection:                     []

examples/LEMS_c302_A_Muscles.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR']
     Cell stimulated:                ['AVBL', 'AVBR']
     Connection:                     []

examples/LEMS_c302_A_Oscillator.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR']
     Cell stimulated:                ['AVBL', 'AVBR']
     Connection:                     []

examples/LEMS_c302_A_Pharyngeal.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR']
     Cell stimulated:                ['M1', 'M3R', 'M4', 'M5', 'I1L', 'I4', 'I5', 'I6', 'MCL', 'MCR']
     Connection:                     []

examples/LEMS_c302_A_Social.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR']
     Cell stimulated:                []
     Connection:                     []

examples/LEMS_c302_A_Syns.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2']
     Cell stimulated:                []
     Connection:                     []

examples/LEMS_c302_B_Full.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          All cells
     Cell stimulated:                ['PLML', 'PLMR']
     Connection:                     []

examples/LEMS_c302_B_IClamp.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['ADAL', 'PVCL']
     Cell stimulated:                []
     Connection:                     []

examples/LEMS_c302_B_Muscles.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR']
     Cell stimulated:                ['AVBL', 'AVBR']
     Connection:                     []

examples/LEMS_c302_B_Oscillator.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR']
     Cell stimulated:                ['AVBL', 'AVBR']
     Connection:                     []

examples/LEMS_c302_B_Pharyngeal.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR']
     Cell stimulated:                ['M1', 'M3R', 'M4', 'M5', 'I1L', 'I4', 'I5', 'I6', 'MCL', 'MCR']
     Connection:                     []

examples/LEMS_c302_B_Social.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR']
     Cell stimulated:                []
     Connection:                     []

examples/LEMS_c302_B_Syns.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL']
     Cell stimulated:                []
     Connection:                     []

examples/LEMS_c302_C0_Full.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          All cells
     Cell stimulated:                ['PLML', 'PLMR']
     Connection:                     []

examples/LEMS_c302_C0_IClamp.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['ADAL', 'PVCL']
     Cell stimulated:                []
     Connection:                     []

examples/LEMS_c302_C0_Muscles.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR']
     Cell stimulated:                ['AVBL', 'AVBR']
     Connection:                     []

examples/LEMS_c302_C0_Oscillator.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR']
     Cell stimulated:                ['AVBL', 'AVBR']
     Connection:                     []

examples/LEMS_c302_C0_Pharyngeal.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR']
     Cell stimulated:                ['M1', 'M3R', 'M4', 'M5', 'I1L', 'I4', 'I5', 'I6', 'MCL', 'MCR']
     Connection:                     []

examples/LEMS_c302_C0_Social.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR']
     Cell stimulated:                []
     Connection:                     []

examples/LEMS_c302_C0_Syns.xml

@@ -6,9 +6,7 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.8.0
-    owmeta version:                 0.12.3
-    owmeta_core version:            0.13.5
+    c302 version:                   0.9.0
     Cells:                          ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL']
     Cell stimulated:                []
     Connection:                     []