From c86d7362818bdeef75074f0ecdeea6866dba1eac Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed, 12 Jul 2023 15:20:05 -0400
Subject: [PATCH] Replace all instances of `pygw` with `wxflow` (#521)

* replace all instances of pygw with wxflow

* import directly from wxflow

* fix CI for wxflow from pygw (#528)

---------

Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
---
 .github/workflows/unittests.yaml                | 10 +++++-----
 .github/workflows/unittests_g-w.yaml            | 17 ++++++++++++-----
 scripts/exgdas_global_marine_analysis_post.py   |  2 +-
 scripts/exgdas_global_marine_analysis_prep.py   |  5 +----
 test/aero/genyaml_3dvar.sh                      |  6 ++----
 test/atm/global-workflow/jjob_ens_final.sh      |  4 ++--
 test/atm/global-workflow/jjob_ens_init.sh       |  4 ++--
 test/atm/global-workflow/jjob_ens_run.sh        |  4 ++--
 test/atm/global-workflow/jjob_var_final.sh      |  4 ++--
 test/atm/global-workflow/jjob_var_init.sh       |  4 ++--
 test/atm/global-workflow/jjob_var_run.sh        |  4 ++--
 .../atm/global-workflow/run_jedi_exe_3denvar.sh |  4 ++--
 test/atm/global-workflow/run_jedi_exe_3dhofx.sh |  4 ++--
 test/atm/global-workflow/run_jedi_exe_3dvar.sh  |  4 ++--
 test/atm/global-workflow/run_jedi_exe_letkf.sh  |  4 ++--
 test/check_valid_yaml.py                        |  2 +-
 test/soca/CMakeLists.txt                        |  2 +-
 test/soca/gw/CMakeLists.txt                     |  2 +-
 ush/ioda/gen_bufr2ioda_yaml.py                  |  3 +--
 ush/run_jedi_exe.py                             |  4 ++--
 ush/soca/run_jjobs.py                           |  2 +-
 ush/socaincr2mom6.py                            |  2 +-
 ush/ufsda/archive.py                            |  2 +-
 ush/ufsda/genYAML.py                            |  3 +--
 ush/ufsda/stage.py                              |  2 +-
 ush/ufsda/yamltools.py                          |  4 ++--
 26 files changed, 54 insertions(+), 54 deletions(-)

diff --git a/.github/workflows/unittests.yaml b/.github/workflows/unittests.yaml
index 2c0ec4d33..2dba08de5 100644
--- a/.github/workflows/unittests.yaml
+++ b/.github/workflows/unittests.yaml
@@ -24,16 +24,16 @@ jobs:
         cd solo && pip install . && cd ..
         cd r2d2 && pip install . && cd ..
 
-    - name: Checkout workflow
+    - name: Checkout wxflow
       uses: actions/checkout@v3
       with:
-        repository: NOAA-EMC/global-workflow
+        repository: NOAA-EMC/wxflow
         ref: develop
-        path: global-workflow
+        path: wxflow
 
-    - name: Install workflow utils
+    - name: Install wxflow
       run: |
-        cd global-workflow/ush/python/pygw
+        cd wxflow
         pip install .
 
     - name: Checkout
diff --git a/.github/workflows/unittests_g-w.yaml b/.github/workflows/unittests_g-w.yaml
index ef65844ad..b187a0de9 100644
--- a/.github/workflows/unittests_g-w.yaml
+++ b/.github/workflows/unittests_g-w.yaml
@@ -25,18 +25,25 @@ jobs:
         cd r2d2 && pip install . && cd ..
         sudo mkdir -p /work/noaa # to trick workflow into thinking this is RDHPCS Orion
 
-    - name: Checkout workflow
+    - name: Checkout wxflow
       uses: actions/checkout@v3
       with:
-        repository: NOAA-EMC/global-workflow
+        repository: NOAA-EMC/wxflow
         ref: develop
-        path: global-workflow
+        path: wxflow
 
-    - name: Install workflow utils
+    - name: Install wxflow
       run: |
-        cd global-workflow/ush/python/pygw
+        cd wxflow
         pip install .
 
+    - name: Checkout workflow
+      uses: actions/checkout@v3
+      with:
+        repository: NOAA-EMC/global-workflow
+        ref: develop
+        path: global-workflow
+
     - name: Checkout GDASApp
       uses: actions/checkout@v3
       with:
diff --git a/scripts/exgdas_global_marine_analysis_post.py b/scripts/exgdas_global_marine_analysis_post.py
index 8e375d9b2..c1a0b4e11 100755
--- a/scripts/exgdas_global_marine_analysis_post.py
+++ b/scripts/exgdas_global_marine_analysis_post.py
@@ -23,7 +23,7 @@
 import shutil
 import logging
 from datetime import datetime, timedelta
-from pygw.file_utils import FileHandler
+from wxflow import FileHandler
 
 
 # TODO: Move this somewhere else?
diff --git a/scripts/exgdas_global_marine_analysis_prep.py b/scripts/exgdas_global_marine_analysis_prep.py
index e7d7af86a..3147facc6 100755
--- a/scripts/exgdas_global_marine_analysis_prep.py
+++ b/scripts/exgdas_global_marine_analysis_prep.py
@@ -32,10 +32,7 @@
 from netCDF4 import Dataset
 import xarray as xr
 import numpy as np
-from pygw.attrdict import AttrDict
-from pygw.template import Template, TemplateConstants
-from pygw.yaml_file import YAMLFile
-from pygw.file_utils import FileHandler
+from wxflow import (AttrDict, Template, TemplateConstants, YAMLFile, FileHandler)
 
 # set up logger
 logging.basicConfig(format='%(asctime)s:%(levelname)s:%(message)s', level=logging.INFO, datefmt='%Y-%m-%d %H:%M:%S')
diff --git a/test/aero/genyaml_3dvar.sh b/test/aero/genyaml_3dvar.sh
index f522ba6f6..74ae035a1 100755
--- a/test/aero/genyaml_3dvar.sh
+++ b/test/aero/genyaml_3dvar.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # generate YAML from a template
-# using pygw YAML tools
+# using wxflow YAML tools
 bindir=$1
 srcdir=$2
 
@@ -27,9 +27,7 @@ mkdir -p $DATA
 
 # run some python code to generate the YAML
 python3 - <<EOF
-from pygw.attrdict import AttrDict
-from pygw.template import Template, TemplateConstants
-from pygw.yaml_file import YAMLFile
+from wxflow import AttrDict, Template, TemplateConstants, YAMLFile
 import datetime
 
 config = YAMLFile(path='$YAMLin')
diff --git a/test/atm/global-workflow/jjob_ens_final.sh b/test/atm/global-workflow/jjob_ens_final.sh
index 0a94cddf9..8296fb29a 100755
--- a/test/atm/global-workflow/jjob_ens_final.sh
+++ b/test/atm/global-workflow/jjob_ens_final.sh
@@ -25,8 +25,8 @@ export NMEM_ENS=3
 export ACCOUNT=da-cpu
 
 # Set python path for workflow utilities and tasks
-pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
 export PYTHONPATH
 
 # Detemine machine from config.base
diff --git a/test/atm/global-workflow/jjob_ens_init.sh b/test/atm/global-workflow/jjob_ens_init.sh
index d1891be5d..fbeabd5f7 100755
--- a/test/atm/global-workflow/jjob_ens_init.sh
+++ b/test/atm/global-workflow/jjob_ens_init.sh
@@ -30,8 +30,8 @@ source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/parm/config/gfs/config.com"
 
 # Set python path for workflow utilities and tasks
-pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
 export PYTHONPATH
 
 # Detemine machine from config.base
diff --git a/test/atm/global-workflow/jjob_ens_run.sh b/test/atm/global-workflow/jjob_ens_run.sh
index dfb635e3e..56e384f79 100755
--- a/test/atm/global-workflow/jjob_ens_run.sh
+++ b/test/atm/global-workflow/jjob_ens_run.sh
@@ -28,8 +28,8 @@ export NMEM_ENS=3
 export ACCOUNT=da-cpu
 
 # Set python path for workflow utilities and tasks
-pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
 export PYTHONPATH
 
 # Detemine machine from config.base
diff --git a/test/atm/global-workflow/jjob_var_final.sh b/test/atm/global-workflow/jjob_var_final.sh
index 33288f854..fa03cc927 100755
--- a/test/atm/global-workflow/jjob_var_final.sh
+++ b/test/atm/global-workflow/jjob_var_final.sh
@@ -25,8 +25,8 @@ export NMEM_ENS=0
 export ACCOUNT=da-cpu
 
 # Set python path for workflow utilities and tasks
-pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
 export PYTHONPATH
 
 # Detemine machine from config.base
diff --git a/test/atm/global-workflow/jjob_var_init.sh b/test/atm/global-workflow/jjob_var_init.sh
index 4b93df4b7..2bd4ce637 100755
--- a/test/atm/global-workflow/jjob_var_init.sh
+++ b/test/atm/global-workflow/jjob_var_init.sh
@@ -30,8 +30,8 @@ source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/parm/config/gfs/config.com"
 
 # Set python path for workflow utilities and tasks
-pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
 export PYTHONPATH
 
 # Detemine machine from config.base
diff --git a/test/atm/global-workflow/jjob_var_run.sh b/test/atm/global-workflow/jjob_var_run.sh
index ff9086b0e..200fdd1b2 100755
--- a/test/atm/global-workflow/jjob_var_run.sh
+++ b/test/atm/global-workflow/jjob_var_run.sh
@@ -28,8 +28,8 @@ export NMEM_ENS=0
 export ACCOUNT=da-cpu
 
 # Set python path for workflow utilities and tasks
-pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
 export PYTHONPATH
 
 # Detemine machine from config.base
diff --git a/test/atm/global-workflow/run_jedi_exe_3denvar.sh b/test/atm/global-workflow/run_jedi_exe_3denvar.sh
index 4e7b9b24c..3e94394de 100755
--- a/test/atm/global-workflow/run_jedi_exe_3denvar.sh
+++ b/test/atm/global-workflow/run_jedi_exe_3denvar.sh
@@ -33,8 +33,8 @@ fi
 # Setup python path for workflow utilities and tasks
 export HOMEgfs=$srcdir/../../ # TODO: HOMEgfs had to be hard-coded in config
 echo $HOMEgfs
-pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
 export PYTHONPATH
 
 # Create test run directory
diff --git a/test/atm/global-workflow/run_jedi_exe_3dhofx.sh b/test/atm/global-workflow/run_jedi_exe_3dhofx.sh
index d7c3b3d86..fb1a6a99e 100755
--- a/test/atm/global-workflow/run_jedi_exe_3dhofx.sh
+++ b/test/atm/global-workflow/run_jedi_exe_3dhofx.sh
@@ -33,8 +33,8 @@ fi
 # Setup python path for workflow utilities and tasks
 export HOMEgfs=$srcdir/../../ # TODO: HOMEgfs had to be hard-coded in config
 echo $HOMEgfs
-pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
 export PYTHONPATH
 
 # Create test run directory
diff --git a/test/atm/global-workflow/run_jedi_exe_3dvar.sh b/test/atm/global-workflow/run_jedi_exe_3dvar.sh
index ca530f280..459f52121 100755
--- a/test/atm/global-workflow/run_jedi_exe_3dvar.sh
+++ b/test/atm/global-workflow/run_jedi_exe_3dvar.sh
@@ -33,8 +33,8 @@ fi
 # Setup python path for workflow utilities and tasks
 export HOMEgfs=$srcdir/../../ # TODO: HOMEgfs had to be hard-coded in config
 echo $HOMEgfs
-pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
 export PYTHONPATH
 
 # Create test run directory
diff --git a/test/atm/global-workflow/run_jedi_exe_letkf.sh b/test/atm/global-workflow/run_jedi_exe_letkf.sh
index 0574184b1..d507af5b6 100755
--- a/test/atm/global-workflow/run_jedi_exe_letkf.sh
+++ b/test/atm/global-workflow/run_jedi_exe_letkf.sh
@@ -33,8 +33,8 @@ fi
 # Setup python path for workflow utilities and tasks
 export HOMEgfs=$srcdir/../../ # TODO: HOMEgfs had to be hard-coded in config
 echo $HOMEgfs
-pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
 export PYTHONPATH
 
 # Create test run directory
diff --git a/test/check_valid_yaml.py b/test/check_valid_yaml.py
index 19dc5b8c9..cbc6ad46a 100644
--- a/test/check_valid_yaml.py
+++ b/test/check_valid_yaml.py
@@ -4,7 +4,7 @@
 import os
 import pathlib
 import sys
-from pygw.yaml_file import YAMLFile
+from wxflow import YAMLFile
 
 
 def check_valid_yaml(repodir):
diff --git a/test/soca/CMakeLists.txt b/test/soca/CMakeLists.txt
index a0383f260..dae969769 100644
--- a/test/soca/CMakeLists.txt
+++ b/test/soca/CMakeLists.txt
@@ -69,7 +69,7 @@ add_test(NAME test_gdasapp_soca_obsdb
          WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/obs/)
 set_tests_properties(test_gdasapp_soca_obsdb
     PROPERTIES
-    ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/ush:${PROJECT_SOURCE_DIR}/../../ush/python/pygw/src:$ENV{PYTHONPATH};SOCA_TEST_OBS=${PROJECT_SOURCE_DIR}/test/soca/testdata")
+    ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/ush:${PROJECT_SOURCE_DIR}/../../ush/python/wxflow/src:$ENV{PYTHONPATH};SOCA_TEST_OBS=${PROJECT_SOURCE_DIR}/test/soca/testdata")
 
 # Test exgdas scripts from the global-worflow
 if (WORKFLOW_TESTS)
diff --git a/test/soca/gw/CMakeLists.txt b/test/soca/gw/CMakeLists.txt
index 1ba787f8b..2e1117909 100644
--- a/test/soca/gw/CMakeLists.txt
+++ b/test/soca/gw/CMakeLists.txt
@@ -8,7 +8,7 @@ add_test(NAME test_gdasapp_soca_prep
          WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/gw)
        set_tests_properties(test_gdasapp_soca_prep
       PROPERTIES
-      ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/ush:${PROJECT_SOURCE_DIR}/../../ush/python/pygw/src:$ENV{PYTHONPATH}")
+      ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/ush:${PROJECT_SOURCE_DIR}/../../ush/python/wxflow/src:$ENV{PYTHONPATH}")
 
 # Identify machine
 set(MACHINE "container")
diff --git a/ush/ioda/gen_bufr2ioda_yaml.py b/ush/ioda/gen_bufr2ioda_yaml.py
index 1ea2e122d..cd0dd1ce6 100755
--- a/ush/ioda/gen_bufr2ioda_yaml.py
+++ b/ush/ioda/gen_bufr2ioda_yaml.py
@@ -5,8 +5,7 @@
 # and certain configuration parameters
 import argparse
 import os
-from pygw.template import Template, TemplateConstants
-from pygw.yaml_file import YAMLFile
+from wxflow import Template, TemplateConstants, YAMLFile
 
 
 # list of satellite radiance BUFR files that need split by SatId
diff --git a/ush/run_jedi_exe.py b/ush/run_jedi_exe.py
index 62c0d4a76..442339281 100755
--- a/ush/run_jedi_exe.py
+++ b/ush/run_jedi_exe.py
@@ -7,8 +7,8 @@
 import subprocess
 import sys
 import yaml
-import pygw
-from pygw.yaml_file import parse_j2yaml, save_as_yaml
+import wxflow
+from wxflow import parse_j2yaml, save_as_yaml
 
 
 def export_envar(yamlfile, bashout):
diff --git a/ush/soca/run_jjobs.py b/ush/soca/run_jjobs.py
index 30700ef99..1cbb5bd5c 100755
--- a/ush/soca/run_jjobs.py
+++ b/ush/soca/run_jjobs.py
@@ -81,7 +81,7 @@ def export_env_vars_script(self):
         self.f.write(f"export CDATE='{CDATE}'\n")
 
         # Add to python environement
-        self.f.write("PYTHONPATH=${HOMEgfs}/ush/python/pygw/src:${PYTHONPATH}\n")
+        self.f.write("PYTHONPATH=${HOMEgfs}/ush/python/wxflow/src:${PYTHONPATH}\n")
 
     def setupexpt(self):
         """
diff --git a/ush/socaincr2mom6.py b/ush/socaincr2mom6.py
index fd23a1493..f1c8add03 100755
--- a/ush/socaincr2mom6.py
+++ b/ush/socaincr2mom6.py
@@ -6,7 +6,7 @@
 from netCDF4 import Dataset
 from scipy.interpolate import griddata
 import ufsda
-from pygw.yaml_file import YAMLFile
+from wxflow import YAMLFile
 
 
 def socaincr2mom6(incr, bkg, grid, incr_out, nsst_yaml=None):
diff --git a/ush/ufsda/archive.py b/ush/ufsda/archive.py
index de7e705c6..07bfc65ae 100644
--- a/ush/ufsda/archive.py
+++ b/ush/ufsda/archive.py
@@ -5,7 +5,7 @@
 import shutil
 import datetime as dt
 import ufsda
-from pygw.yaml_file import YAMLFile
+from wxflow import YAMLFile
 
 __all__ = ['atm_diags']
 
diff --git a/ush/ufsda/genYAML.py b/ush/ufsda/genYAML.py
index 485ce3f0f..accc8d5c5 100644
--- a/ush/ufsda/genYAML.py
+++ b/ush/ufsda/genYAML.py
@@ -8,8 +8,7 @@
 import os
 import re
 import yaml
-from pygw.template import Template, TemplateConstants
-from pygw.yaml_file import YAMLFile
+from wxflow import Template, TemplateConstants, YAMLFile
 
 
 def genYAML(yamlconfig, output=None):
diff --git a/ush/ufsda/stage.py b/ush/ufsda/stage.py
index e9be7dfff..989589a53 100644
--- a/ush/ufsda/stage.py
+++ b/ush/ufsda/stage.py
@@ -12,7 +12,7 @@
 import logging
 import glob
 import numpy as np
-from pygw.yaml_file import YAMLFile, parse_yaml, parse_j2yaml
+from wxflow import YAMLFile, parse_yaml, parse_j2yaml
 import ufsda.soca_utils
 
 __all__ = ['atm_background', 'atm_obs', 'bias_obs', 'background', 'background_ens', 'fv3jedi', 'obs', 'berror', 'gdas_fix', 'gdas_single_cycle']
diff --git a/ush/ufsda/yamltools.py b/ush/ufsda/yamltools.py
index 03c0d5ab8..4207afcd6 100644
--- a/ush/ufsda/yamltools.py
+++ b/ush/ufsda/yamltools.py
@@ -5,7 +5,7 @@
 from solo.yaml_file import YAMLFile
 from solo.template import TemplateConstants, Template
 from ufsda.misc_utils import isTrue
-import pygw
+import wxflow
 
 logging.basicConfig(format='%(asctime)s:%(levelname)s:%(message)s',
                     level=logging.INFO, datefmt='%Y-%m-%d %H:%M:%S')
@@ -36,7 +36,7 @@ def save_check(config, target, app='var'):
     config['cost function']['observations']['observers'] = cleaned_obs_spaces
 
     # save cleaned yaml
-    pygw.yaml_file.save_as_yaml(config, target)
+    wxflow.save_as_yaml(config, target)
 
 
 def parse_config(input_config_dict, template=None, clean=True):