ci issues fix

catalogbuilder/scripts/configs/config-example.yml

@@ -38,4 +38,5 @@ output_file_template: ['realm','time_range','variable_id']
 #######################################################
 
 input_path:  "archive/am5/am5/am5f3b1r0/c96L65_am5f3b1r0_pdclim1850F/gfdl.ncrc5-deploy-prod-openmp/pp"
-output_path: "/home/runner/work/forkCatalogBuilder-/sample-mdtf-catalog" # ENTER NAME OF THE CSV AND JSON, THE SUFFIX ALONE. e.g catalog (the builder then generates catalog.csv and catalog.json. This can also be an absolute path)
+output_path: "sample-mdtf-catalog"
+#output_path: "/home/runner/work/forkCatalogBuilder-/sample-mdtf-catalog" # ENTER NAME OF THE CSV AND JSON, THE SUFFIX ALONE. e.g catalog (the builder then generates catalog.csv and catalog.json. This can also be an absolute path)

catalogbuilder/scripts/gen_intake_gfdl.py

@@ -101,7 +101,6 @@ def create_catalog(input_path=None, output_path=None, config=None, filter_realm=
                          #if(df['variable_id'].eq(k)).any():
                          df['standard_name'].loc[(df['variable_id'] == k)] = v
                              #df['standard_name'] = v 
-
     if(slow == False) & ('standard_name' in headers):
        if ((df is not None) & (len(df) != 0) ):
            with open(csv_path, 'w') as csvfile:
@@ -110,7 +109,7 @@ def create_catalog(input_path=None, output_path=None, config=None, filter_realm=
     print("JSON generated at:", os.path.abspath(json_path))
     print("CSV generated at:", os.path.abspath(csv_path))
     logger.info("CSV generated at" + os.path.abspath(csv_path))
-    return(os.path.abspath(csv_path),os.path.abspath(json_path))
+    return(csv_path,json_path)
 
 #Setting up argument parsing/flags
 @click.command()

catalogbuilder/scripts/gen_intake_gfdl_runner_config.py

@@ -5,8 +5,9 @@
 
 #This is an example call to run catalog builder using a yaml config file.
 package_dir = os.path.dirname(os.path.abspath(__file__))
-configyaml = os.path.join(package_dir, '../configs/config-example.yml')
+configyaml = os.path.join(package_dir, 'configs/config-example.yml')
 
 def create_catalog_from_config(config=configyaml):
     csv, json = gen_intake_gfdl.create_catalog(config=configyaml)
+    return(csv,json)
 

catalogbuilder/tests/make_sample_data.py

@@ -14,19 +14,22 @@
 import os
 from pathlib import Path
 
-realm_mapping = [realm]
 root_dir = 'archive/am5/am5/am5f3b1r0/c96L65_am5f3b1r0_pdclim1850F/gfdl.ncrc5-deploy-prod-openmp/pp'
-freq_mapping = [freq]
 chunk_freq = '1yr'
 
 def make_sample_data():
     # Create directory
     try: 
         import subdirs
     except:
-        sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+        import sys
+        print((os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),"tests")))
+        sys.path.append(os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),"tests"))
         import subdirs
-    from subdirs import *
+    from subdirs import realm, freq, time,vars 
+    realm_mapping = [realm]
+    freq_mapping = [freq]
+
     realm_ctr = (len(subdirs.realm))
     i = 0
     for j in range(0, realm_ctr):

catalogbuilder/tests/test_create_catalog.py

@@ -1,12 +1,14 @@
 def test_create_catalog():
+      from pathlib import Path
       import catalogbuilder
       from catalogbuilder.scripts import gen_intake_gfdl_runner_config
       from catalogbuilder.tests import make_sample_data
       make_sample_data.make_sample_data()
       json, csv = gen_intake_gfdl_runner_config.create_catalog_from_config()
       #to output success/failure in pytest run with conda pkg local install in extra-tests CI workflow#
-      csv = "/home/runner/work/forkCatalogBuilder-/sample-mdtf-catalog.csv"
-      json = "/home/runner/work/forkCatalogBuilder-/sample-mdtf-catalog.json"
+      csv = "/home/a1r/git/forkCatalogBuilder-/catalogbuilder/sample-mdtf-catalog.csv" # "/home/runner/work/forkCatalogBuilder-/sample-mdtf-catalog.csv"
+      json = "/home/a1r/git/forkCatalogBuilder-/catalogbuilder/sample-mdtf-catalog.json" #"/home/runner/work/forkCatalogBuilder-/sample-mdtf-catalog.json"
+      print(csv)
       csvpath = Path(csv)
       jsonpath = Path(json)
       assert csvpath.is_file()