Issue #521: merge branch 'develop' at 97ebc4d into feature/ufsda-roco…

…to-jobs

.github/ISSUE_TEMPLATE/NCO_bug_report.md

@@ -0,0 +1,55 @@
+---
+name: NCO Bug report
+about: Create a report from NCO
+title:
+labels: nco-bug
+assignees: aerorahul, KateFriedman-NOAA
+
+---
+
+<!--
+This bug report template is to be used by NCO ONLY to report issues
+encountered within current operations and T2O activities.
+For reporting developer/development bugs, please use the [Bug Report](./bug_report.md) template.
+-->
+
+<!--
+Please remove unwanted/unrelated/irrelevant information such as comments.
+Use proper formatting to separate code snippets from text description.
+Please copy any output files into a Github gist (for e.g.) and link to the gist, rather than relying on paths that might change.
+-->
+
+Your bug may already be reported!
+Please search on the [Issue tracker](https://github.com/NOAA-EMC/global-workflow/issues) before creating one.
+<!--
+Please look through the existing issues to see if this bug has been reported and an Issue has been created.
+If so, please consider using that Issue to add any additional information.
+-->
+
+**Expected behavior**
+<!-- Tell us what should happen. -->
+
+**Current behavior**
+<!-- Tell us what happens instead of the expected behavior. -->
+
+**Machines affected**
+<!-- Tell us which HPC environments have this bug been detected. -->
+
+**To Reproduce**
+<!--- Provide a link to a live example, and/or an unambiguous set of steps to -->
+<!--- reproduce this bug. Include code to reproduce, if relevant -->
+<!--1. -->
+<!--2. -->
+<!--3. -->
+
+**Context**
+<!--- Providing context helps us come up with a solution that is most useful in the real world. -->
+
+**Detailed Description**
+<!--- Provide a detailed description of the change or addition you are proposing. -->
+
+**Additional Information**
+<!-- Any other relevant information that we should know to correctly understand and reproduce the issue. Please describe in as much detail as possible. -->
+
+**Possible Implementation**
+<!--- Not obligatory, but suggest an idea for implementing addition or change. -->

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,55 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title:
+labels: bug
+assignees:
+
+---
+
+<!--
+This bug report template is to be used by developers to report issues
+encountered within the development branches and releases.
+For reporting operational or NCO affected bugs, please use the [NCO Bug Report](./NCO_bug_report.md) template.
+-->
+
+<!--
+Please remove unwanted/unrelated/irrelevant information such as comments.
+Use proper formatting to separate code snippets from text description.
+Please copy any output files into a Github gist (for e.g.) and link to the gist, rather than relying on paths that might change.
+-->
+
+Your bug may already be reported!
+Please search on the [Issue tracker](https://github.com/NOAA-EMC/global-workflow/issues) before creating one.
+<!--
+Please look through the existing issues to see if this bug has been reported and an Issue has been created.
+If so, please consider using that Issue to add any additional information.
+-->
+
+**Expected behavior**
+<!-- Tell us what should happen. -->
+
+**Current behavior**
+<!-- Tell us what happens instead of the expected behavior. -->
+
+**Machines affected**
+<!-- Tell us which HPC environments have this bug been detected. -->
+
+**To Reproduce**
+<!--- Provide a link to a live example, and/or an unambiguous set of steps to -->
+<!--- reproduce this bug. Include code to reproduce, if relevant -->
+<!--1. -->
+<!--2. -->
+<!--3. -->
+
+**Context**
+<!--- Providing context helps us come up with a solution that is most useful in the real world. -->
+
+**Detailed Description**
+<!--- Provide a detailed description of the change or addition you are proposing. -->
+
+**Additional Information**
+<!-- Any other relevant information that we should know to correctly understand and reproduce the issue. Please describe in as much detail as possible. -->
+
+**Possible Implementation**
+<!--- Not obligatory, but suggest an idea for implementing addition or change. -->

.github/ISSUE_TEMPLATE/general_issue.md

@@ -0,0 +1,41 @@
+---
+name: General Issue
+about: Use this template for general issues
+title:
+labels: 
+assignees:
+
+---
+
+
+If this is a bug, please consider using the [Bug Report](./bug_report.md) template.
+Your issue may already have been created!
+Please search on the [Issue tracker](https://github.com/NOAA-EMC/global-workflow/issues) before creating one.
+<!--
+Please look through the existing issues to see if this issue has been created.
+If so, please consider using that Issue to add any additional information.
+-->
+
+<!--
+Please remove unwanted/unrelated/irrelevant information such as comments.
+Use proper formatting to separate code snippets from text description.
+Please copy any output files into a Github gist (for e.g.) and link to the gist, rather than relying on paths that might change.
+-->
+
+**Description**
+<!-- Provide a detailed description of this issue. -->
+<!-- What problem needs to be fixed? -->
+<!-- What new capability needs to be added? -->
+
+**Requirements**
+<!-- If this is a new feature:  -->
+<!-- What does the new code need to accomplish? -->
+<!-- Does it require an update to version of software (e.g. modules of NCEPLibs, NetCDF, etc., or GFS components e.g. UFS-Weather-Model, GSI, etc., or updates to system tools e.g. python3) -->
+<!-- If this is a bugfix: What is the expected behavior? -->
+
+**Acceptance Criteria (Definition of Done)**
+<!-- What does it mean for this to be finished? -->
+
+**Dependencies**
+<!-- What must be done before this can be done?  Add issue dependencies as appropriate e.g. depends on #IssueNumber -->
+<!-- Does this block progress on other issues? Add this issue as a dependency to other issues as appropriate e.g. #IssueNumber has a dependency on this issue -->

.github/pull_request_template.md

@@ -0,0 +1,50 @@
+<!-- PLEASE READ -->
+<!--
+Before opening a PR, please note these guidelines:
+
+- Each PR should only address ONE topic and have an associated issue
+- No hardcoded or paths to personal directories should be present
+- No temporary or backup files should be committed
+- Any code that was disabled by being commented out should be removed
+-->
+
+**Description**
+
+<!-- Please include relevant motivation and context. -->
+<!-- Please include a summary of the change and which issue is fixed. -->
+<!-- List any dependencies that are required for this change. -->
+
+<!-- Please provide reference to the issue this pull request is addressing. -->
+<!-- For e.g. Fixes #IssueNumber -->
+
+**Type of change**
+
+Please delete options that are not relevant.
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] This change requires a documentation update
+
+**How Has This Been Tested?**
+
+<!-- Please describe the tests that you ran to verify your changes and on the platforms these tests were conducted. -->
+<!-- Provide instructions so we can reproduce. -->
+<!-- Please also list any relevant details for your test configuration -->
+
+<!-- Use the following as a guide to list your tests and delete options that are not relevant. Expand as necessary. -->
+<!--
+- [ ] Clone and Build tests on WCOSS Dell P3
+- [ ] Cycled test on Orion
+- [ ] Forecast-only test on Hera
+-->
+
+**Checklist**
+
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my own code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] My changes need updates to the documentation. I have made corresponding changes to the documentation
+- [ ] My changes generate no new warnings
+- [ ] New and existing tests pass with my changes
+- [ ] Any dependent changes have been merged and published

.gitignore

@@ -4,6 +4,7 @@ __pycache__
 *.pyc
 *.[aox]
 *.mod
+*.sw[a-p]
 
 # Ignore folders
 #-------------------

docs/doxygen/compile

@@ -14,7 +14,7 @@ elif [ $machine = "JET" ]; then
 else
     echo "machine $machine is unrecognized, ABORT!"
     echo "try system doxygen"
-    doxygen=`which doxygen`
+    doxygen=$(which doxygen)
 fi
 
 $doxygen

driver/gdas/run_JGDAS_NCEPPOST.sh

@@ -43,7 +43,7 @@ export envir=prod
 
 # set up running dir
 
-export user=`whoami`
+export user=$(whoami)
 export DATA=/gpfs/hps/ptmp/${user}/gdas.${PDY}${cyc}_nemsio_mpiio
 mkdir -p $DATA
 cd $DATA

driver/gdas/test_gdas_analysis_high.sh

@@ -25,8 +25,8 @@ export CDATE=2017030806
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_analysis_high_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

driver/gdas/test_gdas_enkf_fcst.sh

@@ -34,8 +34,8 @@ fi
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_fcst_grp${grp}_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

driver/gdas/test_gdas_enkf_inflate_recenter.sh

@@ -27,8 +27,8 @@ export CDATE=2017011900
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_inflate_recenter_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

driver/gdas/test_gdas_enkf_innovate_obs.sh

@@ -31,8 +31,8 @@ fi
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_innovate_obs_grp${grp}_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

driver/gdas/test_gdas_enkf_post.sh

@@ -24,8 +24,8 @@ export CDATE=2017011900
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_post_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

driver/gdas/test_gdas_enkf_select_obs.sh

@@ -24,8 +24,8 @@ export CDATE=2017030806
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_select_obs_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

driver/gdas/test_gdas_enkf_update.sh

@@ -25,8 +25,8 @@ export CDATE=2017030806
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_update_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

driver/gdas/test_gdas_forecast_high.sh

@@ -27,8 +27,8 @@ export CDATE=2017012506
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_forecast_high_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

driver/gdas/test_gdas_gldas.sh

@@ -32,12 +32,12 @@ export CDATE=${CDATE:-2019110700}
 #############################################################
 export KMP_AFFINITY=disabled
 
-export PDY=`date -u +%Y%m%d`
-export PDY=`echo $CDATE | cut -c1-8`
+export PDY=$(date -u +%Y%m%d)
+export PDY=$(echo $CDATE | cut -c1-8)
 
-export PDY1=`expr $PDY - 1`
+export PDY1=$(expr $PDY - 1)
 
-export cyc=`echo $CDATE | cut -c9-10`
+export cyc=$(echo $CDATE | cut -c9-10)
 export cycle=t${cyc}z
 
 set -xa

driver/gdas/test_jgdas_verfozn.sh

@@ -23,14 +23,14 @@ export NET=${NET:-gfs}
 export RUN=${RUN:-gdas}
 
 
-export PDY=`echo $PDATE | cut -c1-8`
-export cyc=`echo $PDATE | cut -c9-10`
+export PDY=$(echo $PDATE | cut -c1-8)
+export cyc=$(echo $PDATE | cut -c9-10)
 export job=gdas_verfozn.${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}
 export envir=${envir:-test}
 
-me=`hostname | cut -c1`
+me=$(hostname | cut -c1)
 export DATAROOT=${DATAROOT:-/gpfs/${me}d2/emc/da/noscrub/${LOGNAME}/test_data}
 export COMROOT=${COMROOT:-/ptmpp1/${LOGNAME}/com}
 export OZN_WORK_DIR=${OZN_WORK_DIR:-/stmpp1/${LOGNAME}/oznmon.${pid}}

driver/gdas/test_jgdas_verfozn_cray.sh

@@ -21,14 +21,14 @@ export NET=${NET:-gfs}
 export RUN=${RUN:-gdas}
 
 
-export PDY=`echo $PDATE | cut -c1-8`
-export cyc=`echo $PDATE | cut -c9-10`
+export PDY=$(echo $PDATE | cut -c1-8)
+export cyc=$(echo $PDATE | cut -c9-10)
 export job=gdas_verfozn.${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}
 export envir=${envir:-test}
 
-me=`hostname | cut -c1`
+me=$(hostname | cut -c1)
 export DATAROOT=${DATAROOT:-/gpfs/hps3/emc/da/noscrub/${LOGNAME}/test_data}
 export COMROOT=${COMROOT:-/gpfs/hps2/ptmp/${LOGNAME}/com}
 export OZN_WORK_DIR=${OZN_WORK_DIR:-/gpfs/hps2/stmp/${LOGNAME}/oznmon.${pid}}

driver/gdas/test_jgdas_verfrad.sh

@@ -18,13 +18,13 @@ export PDATE=${PDATE:-2018022112}
 #############################################################
 # Specify whether the run is production or development
 #############################################################
-export PDY=`echo $PDATE | cut -c1-8`
-export cyc=`echo $PDATE | cut -c9-10`
+export PDY=$(echo $PDATE | cut -c1-8)
+export cyc=$(echo $PDATE | cut -c9-10)
 export job=gdas_verfrad.${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}
 export envir=para
-me=`hostname | cut -c1`
+me=$(hostname | cut -c1)
 export DATAROOT=${DATAROOT:-/gpfs/${me}d2/emc/da/noscrub/${LOGNAME}/test_data}
 export COMROOT=${COMROOT:-/ptmpp1/$LOGNAME/com}