Merge pull request #195 from nichollsh/hn/taulevel

Calculate photospheric radius as a function of wavelength

Author: nichollsh

.github/CONTRIBUTING.md

@@ -157,8 +157,7 @@ Unit tests are individual files (`test_consts.jl`, `test_phys.jl`, etc.) include
 
 ### Testing Standards
 
-AGNI is scientific simulation code, so the test suite is held to physics-grade rigor. The rules below are the contract; the deep-dive (anti-happy-path patterns, discriminating-value guards, certification markers, adversarial-review trigger, buffer-flip propagation, hypothesis seed stability, solver intermediate-state assertions) lives in `.github/agni-tests.md`. Read that file before editing any test file or any source file under `src/**`. The two files must be kept in sync; if you change one, mirror the change in the other.
-
+AGNI is scientific simulation code, so the test suite is held to physics-grade rigor. The rules below are the contract.
 
 
 ### Anti-happy-path rules (every new test)
@@ -173,7 +172,7 @@ Every new test function MUST include:
 
 - Single-assert test functions.
 - Standalone weak assertions as the only meaningful check (e.g. assert result is not None).
-- Tests with no function-level docstring.
+- Tests with no function-level comment (comments should be a clear statement of the physical scenario or contract clause being verified, and formatted with a `#` symbol).
 - Tests using `==` adjacent to float literals.
 - Tests asserting on a fixture's implicit default.
 
@@ -183,8 +182,8 @@ NEVER use `==` for floats. Use functions which check for equality within a toler
 
 ### Documentation per test
 
-- File-level docstring: name the source under test, list the invariants and contract clauses the file exercises.
-- Function-level docstring: state the physical scenario or contract clause being verified. Required (lint-enforced).
+- File-level comment: name the source under test, list the invariants and contract clauses the file exercises (formatted with `#` rather than with quotes).
+- Function-level comment: state the physical scenario or contract clause being verified. Required (lint-enforced).
 - Inline comments: explain **why** a specific input range was chosen.
 
 **Remember**: Trust these instructions. Only search if information is incomplete or found to be in error.

.github/copilot-instructions.md

@@ -0,0 +1,19 @@
+# Basic `dependabot.yml` file with
+
+version: 2
+updates:
+  # Enable version updates for Julia packages
+  - package-ecosystem: "julia"
+    # Look for `Project.toml` and `Manifest.toml` files in the `root` directory
+    directory: "/"
+    # Check for updates once a week
+    schedule:
+      interval: "weekly"
+
+  # Enable version updates for GitHub Actions
+  - package-ecosystem: "github-actions"
+    # Workflow files stored in the default location of `.github/workflows`
+    # You don't need to specify `/.github/workflows` for `directory`. You can use `directory: "/"`.
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/dependabot.yml

@@ -21,13 +21,18 @@ on:
 
 jobs:
   build:
+    if: github.event.pull_request.draft == false
+
     permissions:
       contents: write
       pull-requests: read
       statuses: write
+
     runs-on: ubuntu-latest
+    name: documentation
+
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: NetCDF
         run: |
@@ -37,19 +42,19 @@ jobs:
       - uses: julia-actions/setup-julia@v2
         with:
           version: '1.11'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v3
 
       - name: Install Documenter
         run: julia -e 'using Pkg; Pkg.add(["Documenter", "DocumenterPages"]); Pkg.instantiate()'
 
       # Setup SOCRATES
       - name: Get SOCRATES
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: 'FormingWorlds/SOCRATES'
           path: 'SOCRATES'
 
-      - uses: actions/cache@v4
+      - uses: actions/cache@v5
         id: cache-socrates
         with:
           path: |

.github/workflows/documentation.yml

@@ -3,10 +3,6 @@
 
 name: Tests
 
-permissions:
-  contents: read
-  pull-requests: write
-
 on:
   pull_request:
     branches: [main]
@@ -18,9 +14,15 @@ env:
 
 jobs:
   install:
+
     if: github.event.pull_request.draft == false
+    permissions:
+      contents: read
+      pull-requests: write
+
     runs-on: ubuntu-latest
     name: install_and_test
+
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6

.github/workflows/install_and_test.yml

@@ -22,7 +22,7 @@
         }
     ],
     "title": "AGNI: An open-source model for extreme atmospheres on rocky exoplanets",
-    "version": "1.10.3",
+    "version": "1.10.4",
     "access_right": "open",
     "related_identifiers": [
         {

.zenodo.json

@@ -10,7 +10,7 @@ title: "AGNI: An open-source model for extreme atmospheres on rocky exoplanets"
 doi: 10.21105/joss.07726
 date-released: 2025-11-20
 
-version: 1.10.3
+version: 1.10.4
 url: "https://github.com/nichollsh/AGNI"
 type: software
 license: "GPL-3.0"

CITATION.cff

@@ -0,0 +1,57 @@
+# How to contribute to AGNI
+
+## Bug reporting
+
+* **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/nichollsh/AGNI/issues).
+
+* If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/nichollsh/AGNI/issues/new). Be sure to include a **title and clear description**, as much relevant information as possible, and a **code sample** or an **executable test case** demonstrating the expected behavior that is not occurring.
+
+* For more general information on submitting a bug report, visit [this page](https://www.chiark.greenend.org.uk/~sgtatham/bugs.html).
+
+## Bug fixing
+
+* Open a new GitHub pull request (PR) with the patch.
+
+* Ensure the PR description clearly describes the problem and solution. Include the relevant issue number if applicable.
+
+* Before submitting, please ensure your changes are consistent with the existing codebase. These can also be viewed in the [API reference guide](https://www.h-nicholls.space/AGNI/dev/reference/api/).
+
+
+## New features
+
+* Suggest your change on the [issues page](https://github.com/nichollsh/AGNI/issues/new) and start writing code.
+
+## Coding style
+- Indentation uses 4 spaces, no tabs.
+- Function names should be lowercase, with words separated by underscores .
+- Lines should aim to have a length of no more than 92 characters.
+- All functions should have docstrings, ideally with Arguments and Returns listed.
+- More comments are always better, even if they seem redundant.
+- Use type hinting where possible.
+- Print statements should be made through the logger where possible.
+- The core package code should not contain global variables, except in the phys module.
+
+## Testing
+
+When contributing code changes, please:
+- Run the test suite to ensure your changes don't break existing functionality
+- Add tests for new features or bug fixes
+- Aim for >80% line coverage for new utility functions
+- Keep tests fast (avoid expensive setup/teardown when possible)
+
+See the [Testing Documentation](https://www.h-nicholls.space/AGNI/dev/howto/testing/) for detailed information on:
+- Running tests locally
+- Generating coverage reports
+- Adding new tests
+- Test design principles
+
+## Queries and questions
+
+* Ask a question about how to use or contribute to AGNI, please use the [discussions page](https://github.com/nichollsh/AGNI/discussions) or contact [Harrison Nicholls](https://www.h-nicholls.space/) directly.
+
+## Open source
+
+AGNI is free, libre, and open source software. I encourage your contributions and suggestions.
+
+Thanks,
+-Harrison

.github/CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md.github/CODE_OF_CONDUCT.md renamed to CODE_OF_CONDUCT.md

@@ -1,7 +1,7 @@
 name = "AGNI"
 uuid = "ede838c1-9ec3-4ebe-8ae8-da4091b3f21c"
+version = "1.10.4"
 authors = ["Harrison Nicholls <contact@h-nicholls.space>"]
-version = "1.10.3"
 
 [deps]
 Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"