Merge main into deep-heating-dev; simplify heating to efficiency+flux modes only

- Merged origin/main (v1.8.6) into deep-heating-dev
- Simplified DeepHeatingParams: kept only 8 fields (active, P_dep, sigma_P, efficiency, normalization, below_domain, power_mode, F_total)
- Removed ohmic, tidal, and power modes entirely
- Two supported power modes: efficiency (fraction of instellation) and flux (fixed W/m2)
- Updated set_deep_heating, deep_heating, config parsing, and comments

Author: Andrew Cheng-An Hsieh

.github/CODEOWNERS

@@ -0,0 +1,5 @@
+# Tutorial:
+# https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
+
+# Main developer
+* @nichollsh

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,80 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address, without their explicit permission
+* Contacting individual members, contributors, or leaders privately, outside designated community mechanisms, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at opensource@github.com. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 2.0, available at <https://www.contributor-covenant.org/version/2/0/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at <https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.

.github/CONTRIBUTING.md

@@ -0,0 +1,4 @@
+## Contributing to AGNI
+
+Please visit the [contributing page](https://www.h-nicholls.space/AGNI/dev/contributing/) on the online documentation website.
+

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,26 @@
+---
+name: Bug report
+about: For when something is going wrong
+title: ''
+labels: 'Bug'
+assignees: ''
+
+---
+
+## Problem description
+A description of what is happening, and steps outlining what causes it to happen.
+
+## Expected behavior
+A description of what you would have expected to happen.
+
+## Evidence
+Add screenshots and logs to help explain your problem.
+
+## My computer
+Describe the computer used to run the code when the bug was found; e.g Fedora Linux with Python 3.12
+
+## Additional notes
+Add any other context about the problem here; e.g. suggest potential solutions
+
+## Relevant people
+Tag relevant people here.

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: For when something needs to be changed, added, or removed
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+## Feature description
+A short description of what you would like to be done; e.g. a new feature to be added.
+
+## Preferred solution
+Your suggested or preferred solution for implementing this feature or change.
+
+## Additional information
+Any other additional context; e.g. more details, related papers, other solutions.
+
+## Relevant people
+Tag people who should know about this request.

.github/pull_request_template.md

@@ -0,0 +1,26 @@
+## Description
+A short summary of the changes made in this pull-request.
+
+Tag the [related issue](https://github.com/nichollsh/AGNI/issues); e.g. closes #xxx
+
+Include screenshots or log files if appropriate.
+
+## Validation of changes
+Describe what you did to verify that these changes address the tagged issue.
+
+Outline your test configuration; e.g. MacOS with Python 3.13.
+
+
+## Checklist
+
+- [ ] I have followed the [contributing guidelines](https://www.h-nicholls.space/AGNI/dev/contributing/)
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my code
+- [ ] My changes generate no new warnings or errors
+- [ ] I have checked that the tests still pass on my computer
+- [ ] I have updated the docs, as appropriate
+- [ ] I have added tests for these changes, as appropriate
+- [ ] I have checked that all dependencies have been updated, as required
+
+## Relevant people
+Tag people who should know about this PR here

.github/workflows/documentation.yml

@@ -36,7 +36,7 @@ jobs:
 
       - uses: julia-actions/setup-julia@v2
         with:
-          version: '1.10'
+          version: '1.11'
       - uses: julia-actions/cache@v1
 
       - name: Install Documenter
@@ -78,4 +78,6 @@ jobs:
       - name: Build docs and deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
-        run: julia --project="./" docs/make.jl
+        run: |
+          export RAD_DIR="/home/runner/work/AGNI/AGNI/SOCRATES"
+          julia --project="./" docs/make.jl

.github/workflows/install_and_test.yml

@@ -3,6 +3,10 @@
 
 name: Tests
 
+permissions:
+  contents: read
+  pull-requests: write
+
 on:
   pull_request:
     branches: [main]
@@ -14,7 +18,8 @@ jobs:
     runs-on: ubuntu-latest
     name: install_and_test
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout repository
+        uses: actions/checkout@v6
 
       # Setup system
       - name: NetCDF
@@ -33,12 +38,13 @@ jobs:
 
       # Setup SOCRATES
       - name: Get SOCRATES
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: 'nichollsh/SOCRATES'
           path: 'SOCRATES'
 
-      - uses: actions/cache@v4
+      - name: Restore SOCRATES from cache
+        uses: actions/cache@v4
         id: cache-socrates
         with:
           path: |
@@ -47,7 +53,7 @@ jobs:
             SOCRATES/set_rad_env
           key: socrates-${{ hashFiles('SOCRATES/version') }}
 
-      - name: Build SOCRATES
+      - name: Build SOCRATES if required
         if: steps.cache-socrates.outputs.cache-hit != 'true'
         run: |
           export LD_LIBRARY_PATH=""
@@ -64,10 +70,39 @@ jobs:
           export LD_LIBRARY_PATH=""
           julia --project=. -e 'using Pkg; Pkg.build()'
 
-      - name: Test AGNI
+      # Run the tests
+      - name: Run AGNI test suite
         run: |
           export RAD_DIR="/home/runner/work/AGNI/AGNI/SOCRATES"
           export LD_LIBRARY_PATH=""
-          julia --project=. -e 'using Pkg; Pkg.test()'
+          cd test/
+          julia --project=.. --code-coverage runtests.jl
+
+      - name: Get coverage
+        run: |
+          julia --project=. test/get_coverage.jl
+          export total=$(cat coverage.total)
+          echo "total=$total" >> $GITHUB_ENV
 
+      # Upload output dir for inspection by user
+      - name: Upload result as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-artifact
+          path: |
+            out/*
+            coverage.*
+
+      # Make badge
+      - name: Create coverage badge
+        uses: schneegans/dynamic-badges-action@v1.7.0
+        with:
+          auth: ${{ secrets.GIST_TOKEN }}
+          gistID: e20f4fa3c7811c75d34005311fef3696
+          filename: covbadge.svg
+          label: Coverage
+          message: ${{ env.total }}%
+          minColorRange: 50
+          maxColorRange: 90
+          valColorRange: ${{ env.total }}
 

.gitignore

@@ -14,6 +14,7 @@ deps/*.log
 test/out/
 Manifest.toml
 *.cov
+coverage.*
 
 # Docs
 docs/build
@@ -34,18 +35,26 @@ res/thermodynamics/*.nc.chk
 index.html
 
 # Output files
+scratch
+scratch/
 test/out/
 out/*
 runtime.sf
 runtime.sf_k
 socstar.dat
+slurm*.out
+slurm*.log
+sbatch*.out
+sbatch*.log
 
 # Misc files
 .DS_Store
 __pycache__
 debug/
 nogit*
 .osfcli.config
+.venv
+.conda
 
 # RFM
 rfm