From cebcb49b4008485bff0456ec346692bc9cea6367 Mon Sep 17 00:00:00 2001
From: Akira Sewnath <asewnath@users.noreply.github.com>
Date: Wed, 17 Apr 2024 14:23:10 -0400
Subject: [PATCH] Resolve pandas warnings (#322)

* pandas warning fix

* define hofx layout explicitly

---------

Co-authored-by: dooruk <dorukhan.ardag@nasa.gov>
---
 src/swell/deployment/create_experiment.py       |  2 +-
 src/swell/test/suite_tests/hofx-tier1.yaml      |  2 ++
 src/swell/utilities/gsi_record_parser.py        |  7 +++++--
 src/swell/utilities/observing_system_records.py | 17 +++++++++--------
 4 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/src/swell/deployment/create_experiment.py b/src/swell/deployment/create_experiment.py
index 83760c2d..42a8f481 100644
--- a/src/swell/deployment/create_experiment.py
+++ b/src/swell/deployment/create_experiment.py
@@ -446,7 +446,7 @@ def prepare_cylc_suite_jinja2(logger, swell_suite_path, exp_suite_path, experime
     account = 'g0613'
     qos = 'allnccs'
     partition = None
-    constraint = 'cas'
+    constraint = 'cas|sky'
 
     # Extract from slurm global file
     if 'qos' in slurm_global:
diff --git a/src/swell/test/suite_tests/hofx-tier1.yaml b/src/swell/test/suite_tests/hofx-tier1.yaml
index 6150e89c..9f0e5fff 100644
--- a/src/swell/test/suite_tests/hofx-tier1.yaml
+++ b/src/swell/test/suite_tests/hofx-tier1.yaml
@@ -3,6 +3,8 @@ save_geovals: true
 models:
   geos_atmosphere:
     horizontal_resolution: '91'
+    npx_proc: 2
+    npy_proc: 2
     observations:
     - aircraft
     - airs_aqua
diff --git a/src/swell/utilities/gsi_record_parser.py b/src/swell/utilities/gsi_record_parser.py
index c0b8a9aa..50862b43 100644
--- a/src/swell/utilities/gsi_record_parser.py
+++ b/src/swell/utilities/gsi_record_parser.py
@@ -26,7 +26,10 @@ def __init__(self):
     def get_channel_list(self, start):
         channel_list = []
         rows = self.instr_df.loc[self.instr_df["start"] == start]
-        [channel_list.extend(i) for i in rows["channels"].values]
+        for row_ch_list in rows["channels"].values:
+            ch_list = eval(row_ch_list)
+            channel_list.extend(ch_list)
+
         channel_list = list(set(channel_list))
         channel_list.sort(key=int)
         return channel_list
@@ -62,7 +65,7 @@ def run(self, instr_df):
             start_df = self.instr_df.loc[self.instr_df['start'] == main_start]
             if (len(start_df) == 1):
                 # Only one row to process
-                channel_list = start_df['channels'].values[0]
+                channel_list = eval(start_df['channels'].values[0])
                 comment = start_df['comments'].values[0]
                 self.update_return_df(main_start, main_end, channel_list, comment)
                 done.append(main_start)
diff --git a/src/swell/utilities/observing_system_records.py b/src/swell/utilities/observing_system_records.py
index e840c53d..e0f40e30 100644
--- a/src/swell/utilities/observing_system_records.py
+++ b/src/swell/utilities/observing_system_records.py
@@ -43,15 +43,15 @@ def read_sat_db(path_to_sat_db, column_names):
                     'end': [''],
                     'instr': [''],
                     'channel_num': [0],
-                    'channels': [[]],
+                    'channels': [''],
                     'comments': ['']})
 
                 df = pd.concat([df, new_row], ignore_index=True)
-                df['sat'][idx] = line_parts[0]
-                df['start'][idx] = line_parts[1]+line_parts[2]
-                df['end'][idx] = line_parts[3]+line_parts[4]
-                df['instr'][idx] = line_parts[5]
-                df['channel_num'][idx] = line_parts[6]
+                df.loc[idx, 'sat'] = line_parts[0]
+                df.loc[idx, 'start'] = line_parts[1]+line_parts[2]
+                df.loc[idx, 'end'] = line_parts[3]+line_parts[4]
+                df.loc[idx, 'instr'] = line_parts[5]
+                df.loc[idx, 'channel_num'] = line_parts[6]
 
                 comment_present = next((i for i, x in enumerate(line_parts) if x == '#'), None)
 
@@ -61,11 +61,12 @@ def read_sat_db(path_to_sat_db, column_names):
                     comment_str = ' '.join(comment)
                     # Accounting for no comment
                     if (len(comment_str) != 1):
-                        df['comments'][idx] = comment_str
+                        df.loc[idx, 'comments'] = comment_str
                 else:
                     channel_list = line_parts[7:]
 
-                df['channels'][idx] = channel_list
+                # convert channel list to string
+                df.loc[idx, 'channels'] = str(channel_list)
                 idx += 1
     return df