Merge branch 'master' into rdma_mpi

Author: Malmahrouqi3

.github/copilot-instructions.md

@@ -0,0 +1,75 @@
+# GitHub Copilot Instructions – Pull-Request Reviews for MFC
+
+These instructions guide **GitHub Copilot Code Review** and **Copilot Chat** when they evaluate pull requests in this repository.
+
+---
+
+## 1  Project Context (always include)
+
+* **Project:** MFC (exascale many-physics solver) written in **modern Fortran 2008+**, generated with **Fypp**.
+* **Directory layout:**  
+  * Sources in `src/`, tests in `tests/`, examples in `examples/`.  
+  * Most source files are templated `.fpp`; CMake transpiles them to `.f90`.
+* **Fypp macros** are in `src/<subprogram>/include/`, where `<subprogram>` is `simulation`, `common`, `pre_process`, or `post_process`. Review these first.
+* Only `simulation` (plus its `common` dependencies) is GPU-accelerated with **OpenACC**.
+
+> **Copilot, when reviewing:**  
+> * Treat the codebase as free-form Fortran 2008+ with `implicit none`, explicit `intent`, and standard intrinsics.  
+> * Prefer `module … contains … subroutine foo()` over legacy constructs; flag uses of `COMMON`, file-level `include`, or other global state.
+
+---
+
+## 2  Incremental-Change Workflow
+
+Copilot, when reviewing:
+* Encourage small, buildable commits
+
+---
+
+## 3  Style & Naming Conventions (*.fpp / *.f90)
+
+| Element | Rule |
+|---------|------|
+| Indentation | 2 spaces; continuation lines align beneath &. |
+| Case | Lower-case keywords & intrinsics (do, end subroutine, …). |
+| Modules | m_<feature> (e.g. m_transport). |
+| Public subroutines | s_<verb>_<noun> (s_compute_flux). |
+| Public functions | f_<verb>_<noun>. |
+| Routine size | subroutine ≤ 500 lines, helper ≤ 150, function ≤ 100, file ≤ 1000. |
+| Arguments | ≤ 6; else use a derived-type params struct. |
+| Forbidden | goto (except legacy), COMMON, save globals. |
+| Variables | Every arg has explicit intent; use dimension/allocatable/pointer as appropriate. |
+| Errors | Call s_mpi_abort(<msg>), never stop or error stop. |
+
+Copilot, when reviewing:
+* Flag violations of any cell above.
+* Suggest refactors when size or argument limits are exceeded.
+* Ensure private helpers stay inside their defining module and avoid nested procedures.
+
+---
+
+## 4  OpenACC Guidelines (for GPU kernels)
+
+Wrap tight loops:
+
+```fortran
+!$acc parallel loop gang vector default(present) reduction(...)
+```
+
+* Add collapse(n) when safe.
+* Declare loop-local variables with private(...).
+* Allocate large arrays with managed or move them into a persistent !$acc enter data region at start-up.
+* Avoid stop/error stop inside device code.
+* Code must compile with Cray ftn, NVIDIA nvfortran, GNU gfortran, and Intel ifx/ifort.
+
+---
+
+## 5  Review Checklist (what Copilot should verify)
+
+1.	Buildability: PR includes build instructions or CI passes the staged build.
+2.	Tests: Focused tests are added/updated.
+3.	Style compliance: All rules in §3 are satisfied.
+4.	Module hygiene: No new global state; proper namespacing.
+5.	Performance: GPU code follows §4; no large host/device transfers in hot loops.
+6.	Documentation: Updated in-code comments and, when needed, README or docs site.
+7.	Regressions: No changes to outputs of golden tests without clear justification.

.pr_agent.toml

@@ -1,11 +1,15 @@
 # .pr_agent.toml
 [github_app]
 # Run these tools automatically on every new PR:
-pr_commands = ["/describe", "/review"]
+pr_commands = ["/describe", "/review", "/improve"]
 
 [pr_reviewer]                # (all fields optional)
 num_max_findings        = 5  # how many items to surface
 require_tests_review     = true
 extra_instructions = """
 Focus on duplicate code, the possibility of bugs, and if the PR added appropriate tests if it added a simulation feature.
 """
+
+[pr_code_suggestions]
+commitable_code_suggestions = false   # purely advisory, no write ops
+apply_suggestions_checkbox  = false   # hides the “Apply/Chat” boxes