diff --git a/docs/conf.py b/docs/conf.py
index 1f21a6f..bd47e1c 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -12,9 +12,6 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
-import os
-
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
diff --git a/src/mopdb/__init__.py b/src/mopdb/__init__.py
index 2a413df..e69de29 100644
--- a/src/mopdb/__init__.py
+++ b/src/mopdb/__init__.py
@@ -1 +0,0 @@
-from mopdb import *
diff --git a/src/mopdb/mopdb.py b/src/mopdb/mopdb.py
index 40757b2..561e728 100644
--- a/src/mopdb/mopdb.py
+++ b/src/mopdb/mopdb.py
@@ -19,19 +19,16 @@
 # last updated 08/04/2024
 
 import click
-import sqlite3
 import logging
 import sys
-import csv
 import json
 
 from importlib.resources import files as import_files
 from pathlib import Path
 
 from mopdb.mopdb_utils import (mapping_sql, cmorvar_sql, read_map,
-    read_map_app4, map_update_sql, create_table, write_cmor_table,
-    check_varlist, update_db) 
-from mopdb.utils import *
+    read_map_app4, create_table, write_cmor_table, update_db) 
+from mopdb.utils import (config_log, db_connect, query, delete_record)
 from mopdb.mopdb_map import (write_varlist, write_map_template,
     write_catalogue, map_variables, load_vars, get_map_obj)
 
@@ -112,7 +109,7 @@ def mopdb(ctx, debug):
     ctx.obj={}
     # set up a default value for flow if none selected for logging
     ctx.obj['debug'] = debug
-    mopdb_log = config_log(debug, logname='mopdb_log')
+    #mopdb_log = config_log(debug, logname='mopdb_log')
 
 
 @mopdb.command(name='check')
@@ -200,7 +197,7 @@ def cmor_table(ctx, dbname, fname, alias, label):
     # extract cmor_var,units,dimensions,frequency,realm,cell_methods
     var_list = []
     for v in vlist[1:]:
-        vid = (v[0], v[5], v[6])
+        #vid = (v[0], v[5], v[6])
         # This was adding variables to the table just if they didn't exists in other tables
         if v[0][:4] != 'fld_':
             if v[0] not in cmor_vars:
@@ -353,17 +350,6 @@ def map_template(ctx, fpath, match, dbname, version, alias):
         fname, vobjs, fobjs = write_varlist(conn, fpath, match, version, alias)
     if alias == '':
         alias = fname.split(".")[0]
-# also from here on it should be called by separate function I can call from intake too
-# without repeating steps
-    # read list of vars from file
-    # this should now spit out fobjs, vobjs to pass to template 
-    #with open(fname, 'r') as csvfile:
-    #    reader = csv.DictReader(csvfile, delimiter=';')
-    #    rows = list(reader)
-    #check_varlist(rows, fname)
-    # return lists of fully/partially matching variables and stash_vars 
-    # these are input_vars for calculation defined in already in mapping db
-    #parsed = map_variables(conn, rows, version)
     parsed = map_variables(conn, vobjs, version)
     # potential vars have always duplicates: 1 for each input_var
     write_map_template(conn, parsed, alias)
@@ -425,11 +411,6 @@ def write_intake(ctx, fpath, match, filelist, dbname, version, alias):
         map_file, vobjs, fobjs = load_vars(flist, indir=fpath)
     if alias == '':
         alias = fname.split(".")[0]
-    # read list of vars from file
-    #with open(fname, 'r') as csvfile:
-    #    reader = csv.DictReader(csvfile, delimiter=';')
-    #    rows = list(reader)
-    #check_varlist(rows, fname)
     # return lists of fully/partially matching variables and stash_vars 
     # these are input_vars for calculation defined in already in mapping db
     if map_file is False:
@@ -527,7 +508,7 @@ def model_vars(ctx, fpath, match, dbname, version, alias):
     if dbname == 'default':
         dbname = import_files('mopdata').joinpath('access.db')
     conn = db_connect(dbname, logname='mopdb_log')
-    mopdb_log = logging.getLogger('mopdb_log')
+    #mopdb_log = logging.getLogger('mopdb_log')
     fname, vobjs, fobjs = write_varlist(conn, fpath, match, version, alias)
     conn.close()
     return None
diff --git a/src/mopdb/mopdb_class.py b/src/mopdb/mopdb_class.py
index d044eaa..a36a6a4 100644
--- a/src/mopdb/mopdb_class.py
+++ b/src/mopdb/mopdb_class.py
@@ -85,11 +85,6 @@ class Variable():
        and the one added by mapping.
     """ 
 
-  #  __slots__ = ('name', 'pattern', 'files', 'frequency', 'realm',
-  #      'cmor_var', 'cmor_table', 'version', 'units', 'dimensions',
-  #      'cell_methods', 'positive', 'long_name', 'standard_name',
-  #      'vtype', 'size', 'nsteps')
-
     def __init__(self, varname: str, fobj: FPattern):
         self.name = varname
         # path object
@@ -148,7 +143,7 @@ def get_match(self):
             cmor_var = self.cmor_var
         else:
             cmor_var = self.name
-        match = (self.cmor_var, self.name, '', self.frequency,
+        match = (cmor_var, self.name, '', self.frequency,
             self.realm, self.version, '', self.positive, self.units)
         return match
 
diff --git a/src/mopdb/mopdb_map.py b/src/mopdb/mopdb_map.py
index b88ea7c..135a960 100644
--- a/src/mopdb/mopdb_map.py
+++ b/src/mopdb/mopdb_map.py
@@ -33,9 +33,9 @@
 #from access_nri_intake.source.builders import AccessEsm15Builder
 
 from mopdb.mopdb_class import FPattern, Variable, MapVariable
-from mopdb.utils import *
+from mopdb.utils import query, read_yaml
 from mopdb.mopdb_utils import (get_cell_methods, remove_duplicate,
-    get_realm, check_realm_units, get_date_pattern, check_varlist)
+    get_realm, check_realm_units, get_date_pattern)
 
 
 def get_cmorname(conn, vobj, version):
@@ -111,13 +111,12 @@ def get_file_frq(ds, fnext, int2frq):
     # so we open also next file but get only time axs
     if max_len == 1:
         if fnext is None:
-            mopdb_log.info(f"Only 1 file cannot determine frequency for: {fpattern}")
+            mopdb_log.info(f"Only 1 file with 1 tstep cannot determine frequency")
         else:
             dsnext = xr.open_dataset(fnext, decode_times = False)
             time_axs2 = [d for d in dsnext.dims if 'time' in d]
             ds = xr.concat([ds[time_axs], dsnext[time_axs2]], dim='time')
             time_axs = [d for d in ds.dims if 'time' in d]
-            time_axs_len = set(len(ds[d]) for d in time_axs)
             time_axs.sort(key=lambda x: len(ds[x]), reverse=True)
     if max_len > 0:
         for t in time_axs: 
@@ -232,7 +231,7 @@ def match_stdname(conn, vobj, stdn):
     in cmorvar table that match the standard name passed as input.
     It also return a False/True found_match boolean.
     """
-    mopdb_log = logging.getLogger('mopdb_log')
+    #mopdb_log = logging.getLogger('mopdb_log')
     found_match = False
     sql = f"""SELECT name FROM cmorvar where 
         standard_name='{vobj.standard_name}'"""
@@ -451,7 +450,7 @@ def write_vars(vlist, fwriter, div, conn=None, sortby='cmor_var'):
     """
     """
 
-    mopdb_log = logging.getLogger('mopdb_log')
+    #mopdb_log = logging.getLogger('mopdb_log')
     if len(vlist) > 0:
         if type(div) is str:
             divrow = {x:'' for x in vlist[0].attrs()}
@@ -503,6 +502,7 @@ def get_map_obj(parsed):
 def write_catalogue(conn, vobjs, fobjs, alias):
     """Write intake-esm catalogue and returns name
     """
+
     mopdb_log = logging.getLogger('mopdb_log')
     # read template json file 
     jfile = import_files('mopdata').joinpath('intake_cat_template.json')
@@ -510,7 +510,7 @@ def write_catalogue(conn, vobjs, fobjs, alias):
         template = json.load(f)
     # write updated json to file
     for k,v in template.items():
-        if type(v) == str:
+        if type(v) is str:
             template[k] = v.replace("<experiment>", alias)
     jout = f"intake_{alias}.json"
     with open(jout, 'w') as f:
@@ -542,7 +542,7 @@ def write_catalogue(conn, vobjs, fobjs, alias):
 def create_file_dict(fobjs, alias):
     """
     """
-    mopdb_log = logging.getLogger('mopdb_log')
+    #mopdb_log = logging.getLogger('mopdb_log')
     lines = []
     for pat_obj in fobjs:
         var_list = [v.name for v in pat_obj.varlist]
@@ -574,7 +574,7 @@ def create_file_dict(fobjs, alias):
 def add_mapvars(vobjs, lines, path_list, alias):
     """
     """
-    mopdb_log = logging.getLogger('mopdb_log')
+    #mopdb_log = logging.getLogger('mopdb_log')
     for vobj in vobjs:
         if vobj.cmor_var != "" or vobj.standard_name != "":
             mapvar = vobj.cmor_var
@@ -598,7 +598,7 @@ def add_mapvars(vobjs, lines, path_list, alias):
 def load_vars(fname, indir=None):
     """Returns Variable and FPattern objs from varlist or map file.
     """
-    mopdb_log = logging.getLogger('mopdb_log')
+    #mopdb_log = logging.getLogger('mopdb_log')
     vobjs = []
     fobjs = {}
     if indir is not None:
diff --git a/src/mopdb/mopdb_utils.py b/src/mopdb/mopdb_utils.py
index 0f80b6d..6de2ddf 100644
--- a/src/mopdb/mopdb_utils.py
+++ b/src/mopdb/mopdb_utils.py
@@ -19,7 +19,6 @@
 # last updated 10/04/2024
 #
 
-import sqlite3
 import logging
 import sys
 import csv
@@ -28,7 +27,7 @@
 from datetime import date
 from collections import Counter
 
-from mopdb.utils import *
+from mopdb.utils import query 
 
 
 def mapping_sql():
@@ -236,7 +235,7 @@ def get_cell_methods(attrs, dims):
        `time: point`
        If `area` not specified is added at start of string as `area: `
     """
-    mopdb_log = logging.getLogger('mopdb_log')
+    #mopdb_log = logging.getLogger('mopdb_log')
     frqmod = ''
     val = attrs.get('cell_methods', "") 
     if 'area' not in val: 
@@ -252,7 +251,7 @@ def get_cell_methods(attrs, dims):
 
 def read_map_app4(fname):
     """Reads APP4 style mapping """
-    mopdb_log = logging.getLogger('mopdb_log')
+    #mopdb_log = logging.getLogger('mopdb_log')
     # old order
     #cmor_var,definable,input_vars,calculation,units,axes_mod,positive,ACCESS_ver[CM2/ESM/both],realm,notes
     var_list = []
@@ -404,7 +403,7 @@ def get_date_pattern(fname, fpattern):
     """Try to build a date range for each file pattern based
        on its filename
     """
-    mopdb_log = logging.getLogger('mopdb_log')
+    #mopdb_log = logging.getLogger('mopdb_log')
     # assign False to any character which is not a digit
     date_pattern = [True if c.isdigit() else False for c in fname]
     # assign False to fpattern
diff --git a/src/mopdb/utils.py b/src/mopdb/utils.py
index 1a6ff11..c71dc71 100644
--- a/src/mopdb/utils.py
+++ b/src/mopdb/utils.py
@@ -22,8 +22,6 @@
 import sqlite3
 import logging
 import os
-import csv
-import json
 import stat
 import yaml
 
@@ -57,7 +55,7 @@ def config_log(debug, logname):
     logname = f"{logname}_{day}.txt"
     flog = logging.FileHandler(logname)
     try:
-        os.chmod(logname, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO);
+        os.chmod(logname, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO)
     except OSError:
         pass
     flog.setLevel(flevel)
@@ -112,7 +110,7 @@ def query(conn, sql, tup=(), first=True, logname='__name__'):
     result : tuple/list(tuple)
         tuple or a list of, representing row/s returned by query 
     """
-    log = logging.getLogger(logname)
+    #log = logging.getLogger(logname)
     with conn:
         c = conn.cursor()
         c.execute(sql, tup)
@@ -127,7 +125,7 @@ def query(conn, sql, tup=(), first=True, logname='__name__'):
 def get_columns(conn, table, logname='__name__'):
     """Gets list of columns from db table
     """
-    log = logging.getLogger(logname)
+    #log = logging.getLogger(logname)
     sql = f'PRAGMA table_info({table});'
     table_data = query(conn, sql, first=False, logname=logname)
     columns = [x[1] for x in table_data]
@@ -205,6 +203,7 @@ def write_yaml(data, fname, logname='__name__'):
     try:
         with open(fname, 'w') as f:
             yaml.dump(data, f)
-    except:
-        log.error(f"Check that {data} exists and it is an object compatible with yaml")
+    except Exception as e:
+        log.error(f"Exception: {e}")
+        log.error(f"Check {data} exists and is yaml object")
     return
diff --git a/src/mopper/__init__.py b/src/mopper/__init__.py
index 2c52bb9..e69de29 100644
--- a/src/mopper/__init__.py
+++ b/src/mopper/__init__.py
@@ -1 +0,0 @@
-from mopper import *
diff --git a/src/mopper/calculations.py b/src/mopper/calculations.py
index ed9ae92..ab8462c 100644
--- a/src/mopper/calculations.py
+++ b/src/mopper/calculations.py
@@ -33,7 +33,6 @@
 import click
 import xarray as xr
 import os
-import yaml
 import json 
 import numpy as np
 import dask
@@ -233,7 +232,7 @@ def transAcrossLine(self, var, i_start, i_end, j_start, j_end):
                 #sum each axis apart from time (3d)
                 #trans = var.isel(yu_ocean=slice(271, 271+1), xt_ocean=slice(292, 300+1))
                 trans = var[..., j_start:j_end+1, i_start:i_end+1].sum(dim=['st_ocean', f'{y_ocean}', f'{x_ocean}']) #4D
-            except:
+            except Exception as e:
                 trans = var[..., j_start:j_end+1, i_start:i_end+1].sum(dim=[f'{y_ocean}', f'{x_ocean}']) #3D
             
             return trans
@@ -665,25 +664,6 @@ def calc_hemi_seaice_extent(self, hemi):
 
         return vout.item()
 
-
-def ocean_floor(var):
-    """Not sure.. 
-
-    Parameters
-    ----------
-    var : Xarray dataset
-        pot_temp variable
-
-    Returns
-    -------
-    vout : Xarray dataset
-        ocean floor temperature?
-    """
-    lv = (~var.isnull()).sum(dim='st_ocean') - 1
-    vout = var.take(lv, dim='st_ocean').squeeze()
-    return vout
-
-
 def maskSeaIce(var, sic):
     """Mask seaice.
 
@@ -702,7 +682,6 @@ def maskSeaIce(var, sic):
     vout = var.where(sic != 0)
     return vout
 
-
 def sithick(hi, aice):
     """Calculate seaice thickness.
 
@@ -722,7 +701,6 @@ def sithick(hi, aice):
     vout = hi / aice
     return vout
 
-
 def sisnconc(sisnthick):
     """Calculate seas ice?
 
@@ -807,7 +785,7 @@ def calc_global_ave_ocean(var, rho_dzt, area_t):
     
     try:
         vnew = var.weighted(mass).mean(dim=('st_ocean', 'yt_ocean', 'xt_ocean'), skipna=True)
-    except:
+    except Exception as e:
         vnew = var.weighted(mass[:, 0, :, :]).mean(dim=('x', 'y'), skipna=True)
     
     return vnew
@@ -1267,7 +1245,7 @@ def calc_global_ave_ocean(ctx, var, rho_dzt):
     mass = rho_dzt * area_t
     try: 
         vnew=np.average(var,axis=(1,2,3),weights=mass)
-    except: 
+    except Exception as e:
         vnew=np.average(var,axis=(1,2),weights=mass[:,0,:,:])
 
     return vnew
@@ -1437,7 +1415,7 @@ def calc_depositions(ctx, var, weight=None):
     (personal communication from M. Woodhouse)
     """
 
-    var_log = logging.getLogger(ctx.obj['var_log'])
+    #var_log = logging.getLogger(ctx.obj['var_log'])
     varlist = []
     for v in var:
         v0 = v.sel(model_theta_level_number=1).squeeze(dim='model_theta_level_number')
diff --git a/src/mopper/cmip_utils.py b/src/mopper/cmip_utils.py
index dd7674c..161e55f 100755
--- a/src/mopper/cmip_utils.py
+++ b/src/mopper/cmip_utils.py
@@ -25,7 +25,6 @@
 import json
 import csv
 import ast
-import copy
 import click
 from collections import OrderedDict
 
@@ -39,7 +38,7 @@ def find_cmip_tables(dreq):
     with dreq.open(mode='r') as f:
         reader = csv.reader(f, delimiter='\t')
         for row in reader:
-            if not row[0] in tables:
+            if row[0] not in tables:
                 if (row[0] != 'Notes') and (row[0] != 'MIP table') and (row[0] != '0'):
                     tables.append(f"CMIP6_{row[0]}")
     f.close()
@@ -137,9 +136,9 @@ def read_dreq_vars(ctx, table_id, activity_id):
                             years = ast.literal_eval(row[31])
                             years = reallocate_years(years, ctx.obj['reference_date'])
                             years = f'"{years}"'
-                        except:
+                        except Exception as e:
                             years = 'all'
-                except:
+                except Exception as e:
                     years = 'all'
                 dreq_variables[cmorname] = years
     f.close()
diff --git a/src/mopper/mop_setup.py b/src/mopper/mop_setup.py
index 5c1e04b..02132bb 100755
--- a/src/mopper/mop_setup.py
+++ b/src/mopper/mop_setup.py
@@ -24,7 +24,6 @@
 import os
 import sys
 import shutil
-import yaml
 import json
 import csv
 import click
@@ -33,7 +32,9 @@
 from json.decoder import JSONDecodeError
 from importlib.resources import files as import_files
 
-from mopper.setup_utils import *
+from mopper.setup_utils import (define_timeshot, adjust_nsteps,
+    find_custom_tables, write_var_map, write_table)
+from mopper.cmip_utils import find_cmip_tables, read_dreq_vars
 from mopdb.utils import read_yaml
 
 
@@ -99,10 +100,10 @@ def find_matches(table, var, realm, frequency, varlist):
         match['timeshot'] = timeshot
         match['table'] = table
         match['frequency'] = frequency
-        if match['realm'] == 'land':
-            realmdir = 'atmos'
-        else:
-            realmdir = match['realm']
+        #if match['realm'] == 'land':
+        #    realmdir = 'atmos'
+        #else:
+        #    realmdir = match['realm']
         in_fname = match['fpattern'].split()
         match['file_structure'] = ''
         for f in in_fname:
@@ -253,8 +254,8 @@ def var_map(ctx, activity_id=None):
         else:
             sublist = ctx.obj['appdir'] / sublist
 # Custom mode vars
-    if ctx.obj['mode'].lower() == 'custom':
-        access_version = ctx.obj['access_version']
+    #if ctx.obj['mode'].lower() == 'custom':
+    #    access_version = ctx.obj['access_version']
     if ctx.obj['force_dreq'] is True:
         if ctx.obj['dreq'] == 'default':
             ctx.obj['dreq'] = import_files('mopdata').joinpath( 
@@ -272,7 +273,7 @@ def var_map(ctx, activity_id=None):
             create_var_map(table, masters, selection=selection[table])
     elif tables.lower() == 'all':
         mop_log.info(f"Experiment {ctx.obj['exp']}: processing all tables")
-        if ctx.obj['force_dreq'] == True:
+        if ctx.obj['force_dreq']:
             tables = find_cmip_tables(ctx.obj['dreq'])
         else:
             tables = find_custom_tables()
diff --git a/src/mopper/mop_utils.py b/src/mopper/mop_utils.py
index 6ed8b60..315afec 100755
--- a/src/mopper/mop_utils.py
+++ b/src/mopper/mop_utils.py
@@ -22,19 +22,17 @@
 # last updated 15/05/2024
 
 import numpy as np
-import glob
 import re
-import os,sys
+import os
 import stat
 import yaml
 import xarray as xr
 import cmor
-import calendar
 import click
 import logging
 import cftime
-import itertools
 import copy
+import json
 from functools import partial
 from pathlib import Path
 
@@ -71,7 +69,7 @@ def config_log(debug, path, stream_level=logging.WARNING):
     logname = f"{path}/mopper_log.txt"
     flog = logging.FileHandler(logname)
     try:
-        os.chmod(logname, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO);
+        os.chmod(logname, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO)
     except OSError:
         pass
     flog.setLevel(level)
@@ -93,7 +91,7 @@ def config_varlog(debug, logname, pid):
     logger.setLevel(level)
     flog = logging.FileHandler(logname)
     try:
-        os.chmod(logname, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO);
+        os.chmod(logname, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO)
     except OSError:
         pass
     flog.setLevel(level)
@@ -147,7 +145,7 @@ def get_files(ctx):
                 inrange_files.append( check_in_range(paths, time_dim) )
             else:
                 inrange_files.append( check_timestamp(paths) )
-    except:
+    except Exception as e:
         for i,paths in enumerate(all_files):
             inrange_files.append( check_in_range(paths, time_dim) )
 
@@ -205,7 +203,7 @@ def check_vars_in_file(ctx, invars, fname):
     """Check that all variables needed for calculation are in file
     else return extra filenames
     """
-    var_log = logging.getLogger(ctx.obj['var_log'])
+    #var_log = logging.getLogger(ctx.obj['var_log'])
     ds = xr.open_dataset(fname, decode_times=False)
     tofind = [v for v in invars if v not in ds.variables]
     found = [v for v in invars if v not in tofind]
@@ -457,7 +455,6 @@ def pseudo_axis(ctx, axis):
         cmor_name = 'vegtype'
     return cmor_name, p_vals, p_len
 
-
 #PP this should eventually just be generated directly by defining the dimension using the same terms 
 # in calculation for meridional overturning
 @click.pass_context
@@ -480,11 +477,13 @@ def create_axis(ctx, axis, table):
     var_log.info(f"setup of {axis.name} axis complete")
     return axis_id
 
-
-def hybrid_axis(lev, z_ax_id, z_ids):
+@click.pass_context
+def hybrid_axis(ctx, lev, z_ax_id, z_ids):
     """Setting up additional hybrid axis information
+     PP this needs fixing can't possible work now without b_vals, b_bnds??
+    lev is cmor_zName?
     """
-    var_log = logging.getLogger(ctx.obj['var_log'])
+    #var_log = logging.getLogger(ctx.obj['var_log'])
     hybrid_dict = {'hybrid_height': 'b',
                    'hybrid_height_half': 'b_half'}
     orog_vals = getOrog()
@@ -503,31 +502,26 @@ def hybrid_axis(lev, z_ax_id, z_ids):
             zfactor_values=orog_vals)
     return zfactor_b_id, zfactor_orog_id
 
-
 @click.pass_context
 def ij_axis(ctx, ax, ax_name, table):
     """
     """
-    var_log = logging.getLogger(ctx.obj['var_log'])
+    #var_log = logging.getLogger(ctx.obj['var_log'])
     cmor.set_table(table)
     ax_id = cmor.axis(table_entry=ax_name,
         units='1',
         coord_vals=ax.values)
     return ax_id
 
-
 @click.pass_context
 def ll_axis(ctx, ax, ax_name, ds, table, bounds_list):
     """
     """
     var_log = logging.getLogger(ctx.obj['var_log'])
-    var_log.debug(f"in ll_axis")
+    var_log.debug("in ll_axis")
     cmor.set_table(table)
     cmor_aName = get_cmorname(ax_name, ax)
-    try:
-        ax_units = ax.units
-    except:
-        ax_units = 'degrees'
+    ax_units = ax.attrs.get('units', 'degrees')
     a_bnds = None
     var_log.debug(f"got cmor name: {cmor_aName}")
     if cmor_aName in bounds_list:
@@ -606,10 +600,10 @@ def get_axis_dim(ctx, var):
             'lat_ax': None, 'lon_ax': None, 'j_ax': None,
             'i_ax': None, 'p_ax': None, 'e_ax': None}
     for dim in var.dims:
-        try:
+        if dim in var.coords:
             axis = var[dim]
             var_log.debug(f"axis found: {axis}")
-        except:
+        else:
             var_log.warning(f"No coordinate variable associated with the dimension {dim}")
             axis = None
         # need to file to give a value then???
@@ -694,7 +688,7 @@ def bnds_change(ctx, axis):
     """Returns True if calculation/resample changes bnds of specified
        dimension.
     """
-    var_log = logging.getLogger(ctx.obj['var_log'])
+    #var_log = logging.getLogger(ctx.obj['var_log'])
     dim = axis.name
     calculation = ctx.obj['calculation']
     changed_bnds = False
@@ -707,7 +701,6 @@ def bnds_change(ctx, axis):
             changed_bnds = True
     return changed_bnds
 
-
 @click.pass_context
 def get_bounds(ctx, ds, axis, cmor_name, ax_val=None):
     """Returns bounds for input dimension, if bounds are not available
@@ -800,10 +793,10 @@ def get_bounds_values(ctx, ds, bname):
     calc = False
     var_log = logging.getLogger(ctx.obj['var_log'])
     var_log.debug(f"Getting bounds values for {bname}")
+    ancil_file =  ctx.obj[f"grid_{ctx.obj['realm']}"]
     if bname in ds.variables:
         bnds_val = ds[bname].values
     elif ancil_file != "":     
-        ancil_file =  ctx.obj[f"grid_{ctx.obj['realm']}"]
         fname = f"{ctx.obj['ancils_path']}/{ancil_file}"
         ancil = xr.open_dataset(fname)
         if bname in ancil.variables:
@@ -902,7 +895,7 @@ def extract_var(ctx, input_ds, tdim, in_missing):
     if array.dtype.kind == 'i':
         try:
             in_missing = int(in_missing)
-        except:
+        except Eception as e:
             in_missing = int(-999)
     else:
         array = array.fillna(in_missing)
@@ -925,7 +918,7 @@ def define_attrs(ctx):
     listed in notes file, this is indicated by precending any function
     in file with a ~. For other fields it checks equality.
     """
-    var_log = logging.getLogger(ctx.obj['var_log'])
+    #var_log = logging.getLogger(ctx.obj['var_log'])
     attrs = ctx.obj['attrs']
     notes = attrs.get('notes', '')
     # open file containing notes
diff --git a/src/mopper/mopper.py b/src/mopper/mopper.py
index 4b08c5a..2c155a3 100644
--- a/src/mopper/mopper.py
+++ b/src/mopper/mopper.py
@@ -25,17 +25,22 @@
 
 import click
 import logging
-import sqlite3
 import concurrent.futures
-import os,sys
+import os
+import subprocess
+import sys
 import warnings
 import yaml
 import cmor
-import numpy as np
-import xarray as xr
-
-from mopper.mop_utils import *
-from mopper.mop_setup import *
+import cftime
+
+from mopper.mop_utils import (config_log, config_varlog, get_files,
+    load_data, get_cmorname, pseudo_axis, create_axis, hybrid_axis,
+    ij_axis, ll_axis, define_grid, get_coords, get_axis_dim,
+    require_bounds, get_bounds, get_attrs, extract_var, define_attrs)
+from mopper.mop_setup import setup_env, var_map, manage_env
+from mopper.setup_utils import create_exp_json, edit_json_cv, write_config,
+    populate_db, count_rows, sum_file_sizes, filelist_sql, write_job 
 from mopdb.mopdb_utils import db_connect, create_table, query
 
 warnings.simplefilter(action='ignore', category=FutureWarning)
@@ -359,7 +364,7 @@ def mop_process(ctx):
     # Set up additional hybrid coordinate information
     if (axes['z_ax'] is not None and cmor_zName in 
         ['hybrid_height', 'hybrid_height_half']):
-        zfactor_b_id, zfactor_orog_id = hybrid_axis(lev_name, z_ax_id, z_ids)
+        zfactor_b_id, zfactor_orog_id = hybrid_axis(cmor_zName, z_ax_id, z_ids)
 
     # Freeing up memory 
     del dsin
@@ -382,11 +387,11 @@ def mop_process(ctx):
         mop_log.error(f"Unable to define the CMOR variable {ctx.obj['filename']}")
         var_log.error(f"Unable to define the CMOR variable {e}")
         return 2
-    var_log.info('Writing...')
+    var_log.info("Writing...")
     var_log.info(f"Variable shape is {ovar.shape}")
     status = None
     # Write timesteps separately if variable potentially exceeding memory
-    if float(ctx.obj['file_size']) > 4000.0 and time_dim != None:
+    if float(ctx.obj['file_size']) > 4000.0 and time_dim is not None:
         for i in range(ovar.shape[0]):
             data = ovar.isel({time_dim: i}).values
             status = cmor.write(variable_id, data, ntimes_passed=1)
@@ -395,10 +400,10 @@ def mop_process(ctx):
         status = cmor.write(variable_id, ovar.values)
     if status != 0:
         mop_log.error(f"Unable to write the CMOR variable: {ctx.obj['filename']}\n")
-        var_log.error(f"Unable to write the CMOR variable to file\n"
+        var_log.error("Unable to write the CMOR variable to file\n"
                       + f"See cmor log, status: {status}")
         return 2
-    var_log.info(f"Finished writing")
+    var_log.info("Finished writing")
     
     # Close the CMOR file.
     path = cmor.close(variable_id, file_name=True)
@@ -508,14 +513,12 @@ def process_row(ctx, row):
               'json_file_path', 'reference_date', 'version', 'rowid']  
     for i,val in enumerate(header):
         record[val] = row[i]
-    table = record['table'].split('_')[1]
     # call logging 
-    trange = record['filename'].replace('.nc.','').split("_")[-1]
     varlog_file = (f"{ctx.obj['var_logs']}/{record['variable_id']}"
                  + f"_{record['table']}_{record['tstart']}.txt")
     var_log = config_varlog(ctx.obj['debug'], varlog_file, pid) 
     ctx.obj['var_log'] = var_log.name 
-    var_log.info(f"Start processing")
+    var_log.info("Start processing")
     var_log.debug(f"Process id: {pid}")
     msg = process_file(record)
     var_log.handlers[0].close()
diff --git a/src/mopper/setup_utils.py b/src/mopper/setup_utils.py
index ff1e082..2bc293d 100755
--- a/src/mopper/setup_utils.py
+++ b/src/mopper/setup_utils.py
@@ -21,28 +21,18 @@
 #
 # last updated 08/04/2024
 
-import os
 import sys
-import shutil
-import calendar
-import yaml
 import json
-import csv
 import sqlite3
-import subprocess
-import ast
 import copy
-import re
 import click
 import pathlib
 import logging
 
-from collections import OrderedDict
 from datetime import datetime#, timedelta
 from dateutil.relativedelta import relativedelta
-from json.decoder import JSONDecodeError
 
-from mopdb.utils import query, write_yaml, read_yaml
+from mopdb.utils import query, write_yaml
 from mopper.cmip_utils import fix_years
 
 
@@ -129,12 +119,11 @@ def write_config(ctx, fname='exp_config.yaml'):
 
 
 @click.pass_context
-def find_custom_tables(ctx):
+def find_custom_tables(ctx, cmip=False):
     """Returns list of tables files in custom table path
     """
     mop_log = logging.getLogger('mop_log')
     tables = []
-    path = ctx.obj['tables_path']
     table_files = ctx.obj['tables_path'].rglob("*_*.json")
     for f in table_files:
         f = str(f).replace(".json", "")
@@ -411,10 +400,10 @@ def adjust_size(opts, insize):
     resample = opts['resample']
     grid_size = insize
     if 'plevinterp' in calc:
-        try:
+        if "," in calc:
             plevnum = calc.split(',')[-1]
-        except:
-            raise('check plevinterp calculation definition plev probably missing')
+        else:
+            raise('check plevinterp calculation def plev probably missing')
         plevnum = float(plevnum.replace(')',''))
         grid_size = float(insize)/float(opts['levnum'])*plevnum
     return grid_size
@@ -437,7 +426,7 @@ def compute_fsize(ctx, opts, grid_size, frequency):
     Returns
     -------
     """
-    mop_log = logging.getLogger('mop_log')
+    #mop_log = logging.getLogger('mop_log')
     # set small number for fx frequency so it always create only one file
     nstep_day = {'10min': 144, '30min': 48, '1hr': 24, '3hr': 8, 
                  '6hr': 4, 'day': 1, '10day': 0.1, 'mon': 1/30, 
@@ -557,10 +546,6 @@ def process_vars(ctx, maps, opts, cursor):
     Returns
     -------
     """
-    tstep_dict = {'10min': 'minutes=10', '30min': 'minutes=30',
-        '1hr': 'hours=1', '3hr': 'hours=3', '6hr': 'hours=6',
-        'day': 'days=1', '10day': 'days=10', 'mon': 'months=1',
-        'yr': 'years=1', 'dec': 'years=10'}
     unchanged = ['frequency', 'realm', 'table', 'calculation',
                  'resample', 'positive', 'timeshot']  
     for mp in maps:
@@ -620,7 +605,6 @@ def define_files(ctx, cursor, opts, mp):
          finish = start + relativedelta(days=1)
          tstep_dict['fx'] = tstep_dict['day']
     while (start < finish):
-        tstep = eval(f"relativedelta({tstep_dict[frq][0]})")
         half_tstep = eval(f"relativedelta({tstep_dict[frq][1]})")
         delta = eval(f"relativedelta({interval})")
         newtime = min(start+delta, finish)
@@ -633,6 +617,7 @@ def define_files(ctx, cursor, opts, mp):
         opts['filepath'], opts['filename'] = build_filename(opts,
             start, newtime, half_tstep)
         rowid = add_row(opts, cursor, update)
+        mop_log.debug(f"Last added row id: {rowid}")
         start = newtime
     return