Merge pull request #1008 from PCMDI/feature/1007_lee1043_stringConstr…

…uctor

string constructor

cmec/scripts/climatologies.py

@@ -2,7 +2,7 @@
 import subprocess
 import sys
 
-import genutil
+from pcmdi_metrics.utils import StringConstructor
 
 
 def make_climatologies(settings, model_dir, wk_dir):
@@ -12,7 +12,7 @@ def make_climatologies(settings, model_dir, wk_dir):
     realization = settings.get("realization", "")
     period = settings.get("period", "")
     tmp = os.path.join(model_dir, filename_template)
-    model_file = genutil.StringConstructor(tmp)
+    model_file = StringConstructor(tmp)
     model_file.period = period
     model_file.realization = realization
     out_base = os.path.join(wk_dir, "AC")

doc/jupyter/Demo/Demo_2a_monsoon_wang.ipynb

@@ -82,7 +82,8 @@
       "results_dir = 'demo_output/monsoon_wang'\n",
       "\n",
       "# Threshold\n",
-      "threshold = 2.5 / 86400\n"
+      "threshold = 2.5 / 86400\n",
+      "\n"
      ]
     }
    ],
@@ -110,7 +111,6 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Deprecation warning: please use 'import pcmdi_metrics.driver.pmp_parser.PMPParser'\n",
       "******************************************************************************************\n",
       "demo_data/CMIP5_demo_clims/cmip5.historical.CanCM4.r1i1p1.mon.pr.198101-200512.AC.v20200426.nc\n"
      ]
@@ -119,7 +119,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO::2021-11-15 14:52::pcmdi_metrics:: Results saved to a json file: /Users/ordonez4/Documents/git/pcmdi_metrics/doc/jupyter/Demo/demo_output/monsoon_wang/monsoon_wang.json\n"
+      "/Users/lee1043/mambaforge/envs/pmp_devel_20230223/lib/python3.9/site-packages/cdms2/avariable.py:1289: Warning: \n",
+      "avariable.regrid: regridTool = 'esmf' but your version does not\n",
+      "seems to be built with esmf, will switch to regridTool = 'libcf'\n",
+      "                  \n",
+      "  warnings.warn(message, Warning)\n",
+      "INFO::2023-12-18 12:39::pcmdi_metrics:: Results saved to a json file: /Users/lee1043/Documents/Research/git/pcmdi_metrics_20230620_pcmdi/pcmdi_metrics/doc/jupyter/Demo/demo_output/monsoon_wang/monsoon_wang.json\n",
+      "2023-12-18 12:39:49,908 [INFO]: base.py(write:250) >> Results saved to a json file: /Users/lee1043/Documents/Research/git/pcmdi_metrics_20230620_pcmdi/pcmdi_metrics/doc/jupyter/Demo/demo_output/monsoon_wang/monsoon_wang.json\n",
+      "2023-12-18 12:39:49,908 [INFO]: base.py(write:250) >> Results saved to a json file: /Users/lee1043/Documents/Research/git/pcmdi_metrics_20230620_pcmdi/pcmdi_metrics/doc/jupyter/Demo/demo_output/monsoon_wang/monsoon_wang.json\n"
      ]
     }
    ],
@@ -148,42 +155,42 @@
       "  \"CanCM4\": {\n",
       "    \"AllMW\": {\n",
       "      \"cor\": \"0.754\",\n",
-      "      \"rmsn\": \"0.692\",\n",
-      "      \"threat_score\": \"0.477\"\n",
+      "      \"rmsn\": \"0.691\",\n",
+      "      \"threat_score\": \"0.479\"\n",
       "    },\n",
       "    \"AllM\": {\n",
       "      \"cor\": \"0.757\",\n",
-      "      \"rmsn\": \"0.691\",\n",
-      "      \"threat_score\": \"0.477\"\n",
+      "      \"rmsn\": \"0.689\",\n",
+      "      \"threat_score\": \"0.479\"\n",
       "    },\n",
       "    \"NAMM\": {\n",
-      "      \"cor\": \"0.788\",\n",
-      "      \"rmsn\": \"0.656\",\n",
+      "      \"cor\": \"0.791\",\n",
+      "      \"rmsn\": \"0.650\",\n",
       "      \"threat_score\": \"0.474\"\n",
       "    },\n",
       "    \"SAMM\": {\n",
       "      \"cor\": \"0.770\",\n",
-      "      \"rmsn\": \"0.698\",\n",
-      "      \"threat_score\": \"0.459\"\n",
+      "      \"rmsn\": \"0.695\",\n",
+      "      \"threat_score\": \"0.456\"\n",
       "    },\n",
       "    \"NAFM\": {\n",
-      "      \"cor\": \"0.775\",\n",
-      "      \"rmsn\": \"0.649\",\n",
-      "      \"threat_score\": \"0.409\"\n",
+      "      \"cor\": \"0.776\",\n",
+      "      \"rmsn\": \"0.646\",\n",
+      "      \"threat_score\": \"0.411\"\n",
       "    },\n",
       "    \"SAFM\": {\n",
-      "      \"cor\": \"0.782\",\n",
-      "      \"rmsn\": \"0.673\",\n",
+      "      \"cor\": \"0.780\",\n",
+      "      \"rmsn\": \"0.674\",\n",
       "      \"threat_score\": \"0.645\"\n",
       "    },\n",
       "    \"ASM\": {\n",
-      "      \"cor\": \"0.724\",\n",
-      "      \"rmsn\": \"0.715\",\n",
-      "      \"threat_score\": \"0.403\"\n",
+      "      \"cor\": \"0.726\",\n",
+      "      \"rmsn\": \"0.713\",\n",
+      "      \"threat_score\": \"0.405\"\n",
       "    },\n",
       "    \"AUSM\": {\n",
       "      \"cor\": \"0.835\",\n",
-      "      \"rmsn\": \"0.580\",\n",
+      "      \"rmsn\": \"0.578\",\n",
       "      \"threat_score\": \"0.523\"\n",
       "    }\n",
       "  }\n",
@@ -222,7 +229,6 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Deprecation warning: please use 'import pcmdi_metrics.driver.pmp_parser.PMPParser'\n",
       "******************************************************************************************\n",
       "demo_data/CMIP5_demo_clims/cmip5.historical.CanCM4.r1i1p1.mon.pr.198101-200512.AC.v20200426.nc\n"
      ]
@@ -231,7 +237,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO::2021-11-15 14:52::pcmdi_metrics:: Results saved to a json file: /Users/ordonez4/Documents/git/pcmdi_metrics/doc/jupyter/Demo/demo_output/monsoon_wang/monsoon_wang_ex2.json\n"
+      "/Users/lee1043/mambaforge/envs/pmp_devel_20230223/lib/python3.9/site-packages/cdms2/avariable.py:1289: Warning: \n",
+      "avariable.regrid: regridTool = 'esmf' but your version does not\n",
+      "seems to be built with esmf, will switch to regridTool = 'libcf'\n",
+      "                  \n",
+      "  warnings.warn(message, Warning)\n",
+      "INFO::2023-12-18 12:40::pcmdi_metrics:: Results saved to a json file: /Users/lee1043/Documents/Research/git/pcmdi_metrics_20230620_pcmdi/pcmdi_metrics/doc/jupyter/Demo/demo_output/monsoon_wang/monsoon_wang_ex2.json\n",
+      "2023-12-18 12:40:38,357 [INFO]: base.py(write:250) >> Results saved to a json file: /Users/lee1043/Documents/Research/git/pcmdi_metrics_20230620_pcmdi/pcmdi_metrics/doc/jupyter/Demo/demo_output/monsoon_wang/monsoon_wang_ex2.json\n",
+      "2023-12-18 12:40:38,357 [INFO]: base.py(write:250) >> Results saved to a json file: /Users/lee1043/Documents/Research/git/pcmdi_metrics_20230620_pcmdi/pcmdi_metrics/doc/jupyter/Demo/demo_output/monsoon_wang/monsoon_wang_ex2.json\n"
      ]
     }
    ],
@@ -265,43 +278,43 @@
       "  \"CanCM4\": {\n",
       "    \"AllMW\": {\n",
       "      \"cor\": \"0.754\",\n",
-      "      \"rmsn\": \"0.692\",\n",
+      "      \"rmsn\": \"0.691\",\n",
       "      \"threat_score\": \"0.457\"\n",
       "    },\n",
       "    \"AllM\": {\n",
       "      \"cor\": \"0.757\",\n",
-      "      \"rmsn\": \"0.691\",\n",
+      "      \"rmsn\": \"0.689\",\n",
       "      \"threat_score\": \"0.457\"\n",
       "    },\n",
       "    \"NAMM\": {\n",
-      "      \"cor\": \"0.788\",\n",
-      "      \"rmsn\": \"0.656\",\n",
-      "      \"threat_score\": \"0.476\"\n",
+      "      \"cor\": \"0.791\",\n",
+      "      \"rmsn\": \"0.650\",\n",
+      "      \"threat_score\": \"0.473\"\n",
       "    },\n",
       "    \"SAMM\": {\n",
       "      \"cor\": \"0.770\",\n",
-      "      \"rmsn\": \"0.698\",\n",
-      "      \"threat_score\": \"0.466\"\n",
+      "      \"rmsn\": \"0.695\",\n",
+      "      \"threat_score\": \"0.458\"\n",
       "    },\n",
       "    \"NAFM\": {\n",
-      "      \"cor\": \"0.775\",\n",
-      "      \"rmsn\": \"0.649\",\n",
-      "      \"threat_score\": \"0.385\"\n",
+      "      \"cor\": \"0.776\",\n",
+      "      \"rmsn\": \"0.646\",\n",
+      "      \"threat_score\": \"0.387\"\n",
       "    },\n",
       "    \"SAFM\": {\n",
-      "      \"cor\": \"0.782\",\n",
-      "      \"rmsn\": \"0.673\",\n",
-      "      \"threat_score\": \"0.660\"\n",
+      "      \"cor\": \"0.780\",\n",
+      "      \"rmsn\": \"0.674\",\n",
+      "      \"threat_score\": \"0.667\"\n",
       "    },\n",
       "    \"ASM\": {\n",
-      "      \"cor\": \"0.724\",\n",
-      "      \"rmsn\": \"0.715\",\n",
-      "      \"threat_score\": \"0.365\"\n",
+      "      \"cor\": \"0.726\",\n",
+      "      \"rmsn\": \"0.713\",\n",
+      "      \"threat_score\": \"0.368\"\n",
       "    },\n",
       "    \"AUSM\": {\n",
       "      \"cor\": \"0.835\",\n",
-      "      \"rmsn\": \"0.580\",\n",
-      "      \"threat_score\": \"0.429\"\n",
+      "      \"rmsn\": \"0.578\",\n",
+      "      \"threat_score\": \"0.435\"\n",
       "    }\n",
       "  }\n",
       "}\n"
@@ -324,7 +337,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -338,7 +351,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.9.7"
   },
   "selected_variables": [],
   "vcdat_file_path": "",

pcmdi_metrics/enso/enso_driver.py

@@ -15,7 +15,6 @@
     defCollection,
 )
 from EnsoMetrics.EnsoComputeMetricsLib import ComputeCollection
-from genutil import StringConstructor
 
 from pcmdi_metrics import resources
 from pcmdi_metrics.enso.lib import (
@@ -25,8 +24,8 @@
     get_file,
     match_obs_name,
     metrics_to_json,
-    sort_human,
 )
+from pcmdi_metrics.utils import StringConstructor, sort_human
 
 # To avoid below error when using multi cores
 # OpenBLAS blas_thread_init: pthread_create failed for thread XX of 96: Resource temporarily unavailable

pcmdi_metrics/enso/scripts_pcmdi/enso_driver_obsOnly.py

@@ -2,18 +2,16 @@
 # =================================================
 # Dependencies
 # -------------------------------------------------
-from __future__ import print_function
-
 import glob
 import json
 import os
 
 from EnsoMetrics.EnsoCollectionsLib import ReferenceObservations, defCollection
 from EnsoMetrics.EnsoComputeMetricsLib import ComputeCollection_ObsOnly
-from genutil import StringConstructor
 
 from pcmdi_metrics import resources
 from pcmdi_metrics.enso.lib import AddParserArgument, metrics_to_json
+from pcmdi_metrics.utils import StringConstructor
 
 # To avoid below error when using multi cores
 # OpenBLAS blas_thread_init: pthread_create failed for thread XX of 96: Resource temporarily unavailable

pcmdi_metrics/enso/scripts_pcmdi/parallel_driver.py

@@ -13,11 +13,9 @@
 import glob
 import os
 
-from genutil import StringConstructor
-
 from pcmdi_metrics.enso.lib import AddParserArgument, find_realm
 from pcmdi_metrics.misc.scripts import parallel_submitter
-from pcmdi_metrics.variability_mode.lib import sort_human
+from pcmdi_metrics.utils import StringConstructor, sort_human
 
 # =================================================
 # Collect user defined options

pcmdi_metrics/enso/scripts_pcmdi/post_process_merge_jsons.py

@@ -7,8 +7,7 @@
 import json
 import os
 
-from genutil import StringConstructor
-
+from pcmdi_metrics.utils import StringConstructor
 from pcmdi_metrics.variability_mode.lib import dict_merge
 
 

pcmdi_metrics/graphics/deprecated/portraits.py

@@ -13,7 +13,8 @@
 import numpy
 import pkg_resources
 import vcs
-from genutil import StringConstructor
+
+from pcmdi_metrics.utils import StringConstructor
 
 pmp_egg_path = pkg_resources.resource_filename(
     pkg_resources.Requirement.parse("pcmdi_metrics"), "share"

pcmdi_metrics/io/base.py

@@ -19,6 +19,7 @@
 
 import pcmdi_metrics
 from pcmdi_metrics import LOG_LEVEL
+from pcmdi_metrics.utils import StringConstructor
 
 value = 0
 cdms2.setNetcdfShuffleFlag(value)  # where value is either 0 or 1
@@ -143,9 +144,9 @@ def default(self, o):
         return {o.id: "cdutil.region.domain(%s)" % args}
 
 
-class Base(cdp.cdp_io.CDPIO, genutil.StringConstructor):
+class Base(cdp.cdp_io.CDPIO, StringConstructor):
     def __init__(self, root, file_template, file_mask_template=None):
-        genutil.StringConstructor.__init__(self, root + "/" + file_template)
+        StringConstructor.__init__(self, root + "/" + file_template)
         self.target_grid = None
         self.mask = None
         self.target_mask = None
@@ -156,7 +157,7 @@ def __init__(self, root, file_template, file_mask_template=None):
         self.setup_cdms2()
 
     def __call__(self):
-        path = os.path.abspath(genutil.StringConstructor.__call__(self))
+        path = os.path.abspath(StringConstructor.__call__(self))
         if self.type in path:
             return path
         else:

pcmdi_metrics/mean_climate/lib/pmp_parameter.py

@@ -2,9 +2,9 @@
 import os
 
 import cdp.cdp_parameter
-import genutil
 
 from pcmdi_metrics import LOG_LEVEL
+from pcmdi_metrics.utils import StringConstructor
 
 try:
     basestring  # noqa
@@ -17,12 +17,12 @@ def __init__(self):
         logging.getLogger("pmp").setLevel(LOG_LEVEL)
 
     def process_templated_argument(self, name, default_value="*", extras=None):
-        """Applies arg parse values to a genutil.StringConstructor template type argument
+        """Applies arg parse values to a StringConstructor template type argument
         Input:
            name: name of the argument to process
            extra: other object(s) to get keys from, superseeds argparse object
         Output:
-           formatted argument as a genutil.StringConstructor
+           formatted argument as a StringConstructor
         """
 
         process = getattr(self, name, None)
@@ -31,7 +31,7 @@ def process_templated_argument(self, name, default_value="*", extras=None):
         ):  # Ok not an argument from arg_parse maybe a template or string constructor itself
             if isinstance(name, basestring):
                 process = name
-            elif isinstance(name, genutil.StringConstructor):
+            elif isinstance(name, StringConstructor):
                 process = name.template
             else:
                 raise RuntimeError(
@@ -49,7 +49,7 @@ def process_templated_argument(self, name, default_value="*", extras=None):
             sources = [extras]
 
         sources.insert(0, self)  # will use itself as default source
-        process = genutil.StringConstructor(process)
+        process = StringConstructor(process)
         for key in process.keys():
             for source in sources:
                 setattr(process, key, getattr(source, key, default_value))

pcmdi_metrics/mean_climate/pcmdi_compute_climatologies.py

@@ -2,10 +2,9 @@
 
 import datetime
 
-from genutil import StringConstructor
-
 from pcmdi_metrics.mean_climate.lib import calculate_climatology
 from pcmdi_metrics.mean_climate.lib.pmp_parser import PMPMetricsParser
+from pcmdi_metrics.utils import StringConstructor
 
 ver = datetime.datetime.now().strftime("v%Y%m%d")