Merge dev/3.9.0 into the main HEMCO branch

This merge brings all of the updates for HEMCO 3.9.0 that were
added to the dev/3.9.0 branch into the main branch, in anticipation
of the 3.9.0 release.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -0,0 +1,115 @@
+name: Bug or Issue Report
+description: Report a bug or issue with HEMCO
+title: "Put a one-line description here"
+labels: ["category: Bug"]
+body:
+  - type: input
+    id: name
+    attributes:
+      label: Your name
+    validations:
+      required: true
+  - type: input
+    id: affiliation
+    attributes:
+      label: Your affiliation
+    validations:
+      required: true
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: What happened? What did you expect to happen?
+      placeholder: Describe your issue
+    validations:
+      required: true
+  - type: textarea
+    id: steps-to-reproduce
+    attributes:
+      label: What are the steps to reproduce the bug?
+      placeholder: Explain what you did
+    validations:
+      required: true
+  - type: textarea
+    id: log-files
+    attributes:
+      label: Please attach any relevant configuration and log files.
+      description: Drag and drop files like the HEMCO log file, HEMCO_Config.rc, HEMCO_Diagn.rc, and build_info/summarize_build here. You may need to rename files to end in .txt first.
+    validations:
+      required: false
+  - type: input
+    id: version
+    attributes:
+      label: What HEMCO version were you using?
+      placeholder: e.g. 3.9.0
+    validations:
+      required: true
+  - type: dropdown
+    id: machine
+    attributes:
+      label: What environment were you running HEMCO on?
+      multiple: true
+      options:
+        - Local cluster
+        - AWS
+        - Personal computer
+        - Other (please explain below)
+    validations:
+      required: true
+  - type: input
+    id: compiler-version
+    attributes:
+      label: What compiler and version were you using?
+      placeholder: e.g. gcc 10.2.0, ifort 19.0.5.281
+    validations:
+      required: true
+  - type: dropdown
+    id: implemenation
+    attributes:
+      label: Will you be addressing this bug yourself?
+      description: If Yes, please also assign this issue to yourself (if possible)
+      multiple: false
+      options:
+        - "Yes"
+        - "Yes, but I will need some help"
+        - "No"
+    validations:
+      required: true
+  - type: dropdown
+    id: configuration
+    attributes:
+      label: In what configuration were you running HEMCO?
+      multiple: false
+      options:
+        - Standalone
+        - GCClassic
+        - GCHP
+        - Other (please explain in additional information section below)
+    validations:
+      required: true
+  - type: input
+    id: resolution
+    attributes:
+      label: As what resolution were you running HEMCO?
+      placeholder: "e.g. 4x5, 2x2.5, 0.5x0.625, 0.25x0.3125"
+    validations:
+      required: true
+  - type: dropdown
+    id: meteorology
+    attributes:
+      label: What meterology fields did you use?
+      multiple: false
+      options:
+        - GEOS-FP
+        - GEOS-IT
+        - MERRA-2
+        - GCAP 2.0
+        - Other (please explain in additional information section below)
+    validations:
+      required: true
+  - type: textarea
+    id: additional-info
+    attributes:
+      label: Additional information
+      description: Please provide any additional information here that you think might be relevant.
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/new-feature.yml

@@ -0,0 +1,50 @@
+name: Feature Request
+description: Request a new HEMCO feature
+title: "Put a one-line description here"
+labels: ["category: Feature Request"]
+body:
+  - type: input
+    id: name
+    attributes:
+      label: Your name
+    validations:
+      required: true
+  - type: input
+    id: affiliation
+    attributes:
+      label: Your affiliation
+    validations:
+      required: true
+  - type: textarea
+    id: feature-description
+    attributes:
+      label: Provide a clear and concise overview of the new feature requested.
+    validations:
+      required: true
+  - type: textarea
+    id: reference
+    attributes:
+      label: Reference(s)
+      description: If this is a science update, please provide a literature citation.
+      placeholder: "e.g. Bey et al., Global modeling of tropospheric chemistry with assimilated meteorology: Model description and evaluation, J. Geophys. Res., 106, 23,073-23,096, 2001."
+    validations:
+      required: false
+  - type: dropdown
+    id: implemenation
+    attributes:
+      label: Will you be implementing this feature yourself?
+      description: If Yes, please also assign this issue to yourself (if possible)
+      multiple: false
+      options:
+        - "Yes"
+        - "Yes, but I will need some help"
+        - "No"
+    validations:
+      required: true
+  - type: textarea
+    id: additional-info
+    attributes:
+      label: Additional information
+      description: Please provide any additional information here that you think might be relevant.
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/question-discussion.yml

@@ -0,0 +1,23 @@
+name: Question or Discussion
+description: Ask a question about HEMCO or start a discussion
+title: "Put a one-line description here"
+labels: ["category: Question"]
+body:
+  - type: input
+    id: name
+    attributes:
+      label: Your name
+    validations:
+      required: true
+  - type: input
+    id: affiliation
+    attributes:
+      label: Your affiliation
+    validations:
+      required: true
+  - type: textarea
+    id: description
+    attributes:
+      label: Please provide a clear and concise description of your question or discussion topic.
+    validations:
+      required: true

.github/PULL_REQUEST_TEMPLATE.md

@@ -3,10 +3,6 @@
 Name:
 Institution:
 
-### Confirm you have reviewed the following documentation
-
-- [ ] [Contributing guidelines](https://hemco.readthedocs.io/en/stable/reference/CONTRIBUTING.html)
-
 ### Describe the update
 
 Please provide a clear and concise overview of the update.
@@ -19,6 +15,6 @@ Please provide details on how this update will impact model output and include p
 
 If this is a science update, please provide a literature citation.
 
-### Related Github Issue(s)
+### Related Github Issue
 
-Please link to the corresponding Github issue here. If fixing a bug, there should be an issue describing it with steps to reproduce.
+Please link to the corresponding Github issue(s) here. If fixing a bug, there should be an issue describing it with steps to reproduce.

.github/workflows/stale.yml

@@ -0,0 +1,38 @@
+# This workflow warns and then closes issues that have had no activity for a specified amount of time.
+#
+# You can adjust the behavior by modifying this file.
+# For more information, see:
+# https://github.com/actions/stale
+name: Mark stale issues
+
+on:
+  schedule:
+  - cron: '0 0 * * *' # Run every night at midnight
+
+jobs:
+  stale:
+
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+
+    steps:
+    - uses: actions/stale@v5
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        stale-issue-label: 'stale'
+        exempt-issue-labels:
+          - 'category: Discussion'
+          - 'category: Feature Request'
+          - 'deferred'
+          - 'help needed: Open Research Problem'
+          - 'help needed: Request Input from Community'
+          - 'never stale'
+          - 'TODO: Documentation'
+        days-before-issue-stale: 30
+        days-before-issue-close: 7
+        stale-issue-message: 'This issue has been automatically marked as stale because it has not had recent activity. If there are no updates within 7 days it will be closed. You can add the "never stale" tag to prevent the issue from closing this issue.'
+        close-issue-message: 'Closing due to inactivity'
+        days-before-pr-stale: -1
+        days-before-pr-close: -1

.readthedocs.yaml

@@ -14,7 +14,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.7"
+    python: "3.12"
     nodejs: "14"
     rust:   "1.55"
     golang: "1.17"

AUTHORS.txt

@@ -1,5 +1,5 @@
 List of Developers for GEOS-Chem, HEMCO, and Related Software
-(11 Jul 2023)
+(23 May 2024)
 ===============================================================================
 
 ADAMS, Peter
@@ -23,6 +23,7 @@ BONILLA, Eimy
 BOVY, Benoit
 BOWMAN, Kevin
 BOYS, Brian
+BRANFORD, Simon
 BRATTICH, Erika
 BREIDER, Tom
 BREWER, Jared
@@ -290,6 +291,7 @@ SUTHERLAND, Bethany
 SUTO, Kimito
 SZELAG, Monika
 TAI, Amos
+TANG, Yidan
 TANIMOTO, Hiroshi
 TANNAHILL, John
 TAO, Shu
@@ -312,6 +314,7 @@ VAN DONKELAAR, Aaron
 VAROTSOS, Kostas
 VINKEN, Geert
 VITT, Francis
+VOHRA, Karn
 WAGSTROM, Kristina
 WALKER, Thomas
 WANG, James
@@ -359,6 +362,7 @@ ZHANG, Li
 ZHANG, Lin
 ZHANG, Qiang
 ZHANG, Yanxu
+ZHU, Haihui
 ZHU, Lei
 ZHU, Liye
 ZHUANG, Jiawei

CHANGELOG.md

@@ -5,6 +5,18 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased] - TBD
+### Added
+- GitHub Action config file `.github/workflows/stale.yml`, which replaces StaleBot
+
+### Removed
+- GitHub config files `.github/stale.yml` and `.github/no-response.yml`
+
+### Changed
+- Converted Github issue templates into issue forms using YAML definition files
+- Updated Python package versions for ReadTheDocs in `docs/requirements.txt`
+- Now request Python 3.12 for ReadTheDocs builds in `.readthedocs.yaml`
+
 ## [3.8.1] - 2024-04-02
 ### Changed
 - Now allow up to 10 nested brackets (`((( )))`) in the `HEMCO_Config.rc` file