Merge remote-tracking branch 'origin/develop' into feature/version-files

* origin/develop:
  Add options while setting up Rocoto XML that are useful for CI (NOAA-EMC#1365)
  Revert "Add options while setting up Rocoto XML that are useful for CI (NOAA-EMC#1363)" (NOAA-EMC#1364)
  MOM6 backgrounds in cycled DA mode were hardcoded for IAU  (NOAA-EMC#1355)
  Add options while setting up Rocoto XML that are useful for CI (NOAA-EMC#1363)
  Run executables or scripts from within python. (NOAA-EMC#1341)
  Remove extra 'enkf' from folder/file names in archive scripts (NOAA-EMC#1360)
  Fix bugs to create analysis files for early cycle (NOAA-EMC#1343)
  Make necessary bugfixes to get aerosol cycling going (NOAA-EMC#1349)
  Create production_update.md (NOAA-EMC#1348)
  Update feature_request.md
  Create a template for requesting new features in the global workflow to separate from general issues (NOAA-EMC#1336)
  allow script to access eva yaml generators (NOAA-EMC#1331)
  Add license and status badges for the CI (NOAA-EMC#1332)
  Update ufs_utils hash that supports global_cycle with NoahMP. (NOAA-EMC#1315)
  Save yaml for ocn analysis post and fix bug to save logs (NOAA-EMC#1318)
  Update crtm to v2.4.0 (NOAA-EMC#1319)
  Fix python style errors (NOAA-EMC#1330)
  Fix workflow generation post times for early cycle (NOAA-EMC#1329)
  Change RUN and CDUMP for ensemble jobs (NOAA-EMC#1309)
  Provide default for DEBUG_WORKFLOW in load_ufsda_modules.sh
  Allow increments to be added for ocean and ice cycling. (NOAA-EMC#1308)
  Module base file reorder and reduction (NOAA-EMC#1306)
  Update S4 environment and module files (NOAA-EMC#1303)
  Add in initial 3DVar aerosol DA cycling capability (NOAA-EMC#1106)
  Fix name of MOM6 n restarts for future cycle points (NOAA-EMC#1307)

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,40 @@
+---
+name: Feature Request
+about: Use this template for requesting new features
+title:
+labels: feature
+assignees:
+
+---
+
+
+<!--
+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 consise description of the problem to be addressed by this feature request. -->
+<!-- Please be clear what parts of the problem are considered to be in-scope and out-of-scope -->
+
+**Requirements**
+<!-- What does the new code need to accomplish? -->
+
+**Acceptance Criteria (Definition of Done)**
+<!-- What does it mean for this to be finished? -->
+
+**(Optional): Suggest A Solution**
+<!--
+A concise description of your preferred solution. Things to address include:
+* Details of the technical implementation
+* Tradeoffs made in design decisions
+* Caveats and considerations for the future
+
+If there are multiple solutions, please present each one separately. Save comparisons for the very end.)
+-->

.github/ISSUE_TEMPLATE/production_update.md

@@ -0,0 +1,31 @@
+---
+name: Production Update
+about: Use this template for operational production updates
+title:
+labels: production update
+assignees:
+  - KateFriedman-NOAA
+
+---
+
+**Description**
+<!-- Provide a consise description of the production update. -->
+<!-- Include related issues in component repositories. -->
+<!-- Include expected new version # (e.g. GFS.v#.#.#) -->
+
+**Workflow Changes**
+<!-- What are the anticipated changes coming into the workflow? -->
+<!-- Include version variables, checkout tags, config/parm, etc. -->
+
+**Tasks**
+- [ ] Create release branch
+- [ ] Make workflow changes for upgrade in release branch (add additional checklist items as needed)
+- [ ] Create release notes
+- [ ] Cut hand-off tag for CDF
+- [ ] Submit CDF to NCO
+- [ ] Implementation into operations complete
+- [ ] Merge release branch into operational branch
+- [ ] Cut version tag from operational branch
+- [ ] Release new version tag
+- [ ] Announce to users
+- [ ] Update Read-The-Docs operations status version in develop

.github/workflows/linters.yaml

@@ -1,5 +1,5 @@
 #
-name: linters
+name: shellnorms
 on:
   pull_request:
 

.github/workflows/pynorms.yaml

@@ -1,4 +1,4 @@
-name: Check Norms
+name: pynorms
 on: [push, pull_request]
 
 jobs:

.github/workflows/pytests.yaml

@@ -1,4 +1,4 @@
-name: Run pytests
+name: pytests
 on: [push, pull_request]
 
 jobs:

Externals.cfg

@@ -1,7 +1,7 @@
 # External sub-modules of global-workflow
 
 [UFS]
-tag = 6b73f5d
+tag = c22aaad
 local_path = sorc/ufs_model.fd
 repo_url = https://github.com/ufs-community/ufs-weather-model.git
 protocol = git
@@ -15,9 +15,9 @@ protocol = git
 required = True
 
 [UFS-Utils]
-hash = 8b990c0
+hash = 5b67e4d
 local_path = sorc/ufs_utils.fd
-repo_url = https://github.com/NOAA-EMC/UFS_UTILS.git
+repo_url = https://github.com/ufs-community/UFS_UTILS.git
 protocol = git
 required = True
 
@@ -50,7 +50,7 @@ protocol = git
 required = False
 
 [GDASApp]
-hash = f7c23af
+hash = a00b5da
 local_path = sorc/gdas.cd
 repo_url = https://github.com/NOAA-EMC/GDASApp.git
 protocol = git

LICENSE.md

@@ -0,0 +1,157 @@
+### GNU LESSER GENERAL PUBLIC LICENSE
+
+Version 3, 29 June 2007
+
+Copyright (C) 2007 Free Software Foundation, Inc.
+<https://fsf.org/>
+
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+
+This version of the GNU Lesser General Public License incorporates the
+terms and conditions of version 3 of the GNU General Public License,
+supplemented by the additional permissions listed below.
+
+#### 0. Additional Definitions.
+
+As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the
+GNU General Public License.
+
+"The Library" refers to a covered work governed by this License, other
+than an Application or a Combined Work as defined below.
+
+An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+A "Combined Work" is a work produced by combining or linking an
+Application with the Library. The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+#### 1. Exception to Section 3 of the GNU GPL.
+
+You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+#### 2. Conveying Modified Versions.
+
+If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+-   a) under this License, provided that you make a good faith effort
+    to ensure that, in the event an Application does not supply the
+    function or data, the facility still operates, and performs
+    whatever part of its purpose remains meaningful, or
+-   b) under the GNU GPL, with none of the additional permissions of
+    this License applicable to that copy.
+
+#### 3. Object Code Incorporating Material from Library Header Files.
+
+The object code form of an Application may incorporate material from a
+header file that is part of the Library. You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+-   a) Give prominent notice with each copy of the object code that
+    the Library is used in it and that the Library and its use are
+    covered by this License.
+-   b) Accompany the object code with a copy of the GNU GPL and this
+    license document.
+
+#### 4. Combined Works.
+
+You may convey a Combined Work under terms of your choice that, taken
+together, effectively do not restrict modification of the portions of
+the Library contained in the Combined Work and reverse engineering for
+debugging such modifications, if you also do each of the following:
+
+-   a) Give prominent notice with each copy of the Combined Work that
+    the Library is used in it and that the Library and its use are
+    covered by this License.
+-   b) Accompany the Combined Work with a copy of the GNU GPL and this
+    license document.
+-   c) For a Combined Work that displays copyright notices during
+    execution, include the copyright notice for the Library among
+    these notices, as well as a reference directing the user to the
+    copies of the GNU GPL and this license document.
+-   d) Do one of the following:
+    -   0) Convey the Minimal Corresponding Source under the terms of
+        this License, and the Corresponding Application Code in a form
+        suitable for, and under terms that permit, the user to
+        recombine or relink the Application with a modified version of
+        the Linked Version to produce a modified Combined Work, in the
+        manner specified by section 6 of the GNU GPL for conveying
+        Corresponding Source.
+    -   1) Use a suitable shared library mechanism for linking with
+        the Library. A suitable mechanism is one that (a) uses at run
+        time a copy of the Library already present on the user's
+        computer system, and (b) will operate properly with a modified
+        version of the Library that is interface-compatible with the
+        Linked Version.
+-   e) Provide Installation Information, but only if you would
+    otherwise be required to provide such information under section 6
+    of the GNU GPL, and only to the extent that such information is
+    necessary to install and execute a modified version of the
+    Combined Work produced by recombining or relinking the Application
+    with a modified version of the Linked Version. (If you use option
+    4d0, the Installation Information must accompany the Minimal
+    Corresponding Source and Corresponding Application Code. If you
+    use option 4d1, you must provide the Installation Information in
+    the manner specified by section 6 of the GNU GPL for conveying
+    Corresponding Source.)
+
+#### 5. Combined Libraries.
+
+You may place library facilities that are a work based on the Library
+side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+-   a) Accompany the combined library with a copy of the same work
+    based on the Library, uncombined with any other library
+    facilities, conveyed under the terms of this License.
+-   b) Give prominent notice with the combined library that part of it
+    is a work based on the Library, and explaining where to find the
+    accompanying uncombined form of the same work.
+
+#### 6. Revised Versions of the GNU Lesser General Public License.
+
+The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Library
+as you received it specifies that a certain numbered version of the
+GNU Lesser General Public License "or any later version" applies to
+it, you have the option of following the terms and conditions either
+of that published version or of any later version published by the
+Free Software Foundation. If the Library as you received it does not
+specify a version number of the GNU Lesser General Public License, you
+may choose any version of the GNU Lesser General Public License ever
+published by the Free Software Foundation.
+
+If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

README.md

@@ -1,20 +1,40 @@
+[![Read The Docs Status](https://readthedocs.org/projects/global-workflow/badge/?badge=latest)](http://global-workflow.readthedocs.io/)
+[![shellnorms](https://github.com/NOAA-EMC/global-workflow/actions/workflows/linters.yaml/badge.svg)](https://github.com/NOAA-EMC/global-workflow/actions/workflows/linters.yaml)
+[![pynorms](https://github.com/NOAA-EMC/global-workflow/actions/workflows/pynorms.yaml/badge.svg)](https://github.com/NOAA-EMC/global-workflow/actions/workflows/pynorms.yaml)
+[![pytests](https://github.com/NOAA-EMC/global-workflow/actions/workflows/pytests.yaml/badge.svg)](https://github.com/NOAA-EMC/global-workflow/actions/workflows/pytests.yaml)
+
 # global-workflow
-Global Workflow currently supporting the Global Forecast System (GFS) with the UFS-weather-model and GSI-based Data Assimilation System.
+Global Workflow currently supporting the Global Forecast System (GFS) with the [UFS-weather-model](https://github.com/ufs-community/ufs-weather-model) and [GSI](https://github.com/NOAA-EMC/GSI)-based Data Assimilation System.
 
-The global-workflow depends on the following prerequisities to be available on the system:
+The `global-workflow` depends on the following prerequisities to be available on the system:
 
-* workload management platform / scheduler - LSF or SLURM
-* workflow manager - ROCOTO (https://github.com/christopherwharrop/rocoto)
-* modules - NCEPLIBS (various), esmf v8.0.0bs48, hdf5, intel/ips v18, impi v18, wgrib2, netcdf v4.7.0, hpss, gempak (see module files under /modulefiles for additional details)
+* Workflow Engine - [Rocoto](https://github.com/christopherwharrop/rocoto) and [ecFlow](https://github.com/ecmwf/ecflow) (for NWS Operations)
+* Compiler - Intel Compiler Suite
+* Software - NCEPLIBS (various), ESMF, HDF5, NetCDF, and a host of other softwares (see module files under /modulefiles for additional details)
 
-The global-workflow current supports the following tier-1 machines:
+The `global-workflow` current supports the following tier-1 machines:
 
-* Hera
-* Orion
-* WCOSS2 - NOAA's operational HPC
+* NOAA RDHPCS - Hera
+* MSU HPC - Orion
+* NOAA's operational HPC - WCOSS2
 
 Additionally, the following tier-2 machine is supported:
-* S4 (Note that S2S+ experiments are not fully supported)
+* SSEC at Univ. of Wisconsin - S4 (Note that S2S+ experiments are not fully supported)
+
+Documentation (in progress) is available [here](https://global-workflow.readthedocs.io/en/latest/).
+
+# Disclaimer
 
-Documentation (in progress) is available [here](https://global-workflow.readthedocs.io/en/latest/)
+The United States Department of Commerce (DOC) GitHub project code is provided
+on an "as is" basis and the user assumes responsibility for its use. DOC has
+relinquished control of the information and no longer has responsibility to
+protect the integrity, confidentiality, or availability of the information. Any
+claims against the Department of Commerce stemming from the use of its GitHub
+project will be governed by all applicable Federal law. Any reference to
+specific commercial products, processes, or services by service mark,
+trademark, manufacturer, or otherwise, does not constitute or imply their
+endorsement, recommendation or favoring by the Department of Commerce. The
+Department of Commerce seal and logo, or the seal and logo of a DOC bureau,
+shall not be used in any manner to imply endorsement of any commercial product
+or activity by DOC or the United States Government.
 

docs/source/setup.rst

@@ -156,6 +156,8 @@ Example:
 
    ./setup_xml.py /some_safe_disk_area/Joe.Schmo/expdir/test
 
+Additional options for setting up Rocoto are available with `setup_xml.py -h` that allow users to change the number of failed tries, number of concurrent cycles and tasks as well as Rocoto's verbosity levels.
+
 ****************************************
 Step 4: Confirm files from setup scripts
 ****************************************