(towards #3506) stale issue cleanup

[haanahfrost]

WIP draft (follow up to #3506) - some references have been resolved but I have left many for review instead of guessing.
I found that a big portion of the references were closed as 'completed' via a PR only 'towards' it or a duplicate which was also closed, but the specific comment guards were never migrated to use whatever the issue delivered.

Removed via deletion:

#1298, #3143, #2004
#1483/#1392/#298 chain (extract_node.py),
#257 (contradicted by fix in #2707), #1387
#685 (fparser2.py — default loop increment now uses the loop start
node's datatype, approved with Andy)
#730 (examples/gocean/eg5/profile/README.md)
#824, #1991, #2049 (doc/developer_guide/psy_data.rst)
#2125 (inline_trans_test.py)
#813 (lib/read_only/lfric/Makefile)

Removed pointer but kept limitation comment:

SIR backend cluster: #468, #521, #741, #470 - all closed "won't fix"
since SIR is no longer actively developed
#2448 (closed but kept comment)
#1854 (sir_trans_loop.py - reworded to state current fact)

Removed via repointing to an open issue:

• transformations do not recognise typos in option names #613 → Transformation options refactoring #2668 (both loop_tiling_2d_trans.py and profiling.rst)
• Re-implement f2pygen using fparser2 #240 → Extend test compilation support to include Algorithm layer #284 (lfric_alg_test.py)
• Preprocessor directives causing syntax error #3038 → Investigate use of TreeSitter #3083 (4 sites in the treesitter frontend)

Removed and tested behavioural changes:

• #1537 (assignment_trans.py) - removed the array-range SymbolicMaths
  workaround
• #1113 (modify.py example) - specialise() now accepts **kwargs;
  replaced the manual symbol.datatype = ... line with passing it directly.
• #2592 (fortran.py) - swapped to node.symbol, then removed the now-
  redundant container. Backend tests pass
• #229 and #2856 - fixed order and removed the unneeded try/except, updated README to describe current behaviour

#3178 — resolved independently by @LonelyCat124 in #3518 (unrelated work
that happened to touch the same TODO), not by this PR.

Reviewed and requested changes made:

• #1010 - 7 sites (backends_transform.py ×2, lfric_loop_test.py ×2, kern_call_arg_list.py ×2, lfric_loop.py). Each site still exhibits old behaviour

• #3135 - datatypes.py. Closed via #3436

• #1631

• #1806 - lfric_alg.py ×2, tl2ad.py, lfric_adjoint_harness.py. All still use fparser1.

• #1570 - lfric.py. Closed via #3382

• #2623 - 3 test sites. commented-out assert LFRicBuild(tmpdir).code_compiles(psy)

• #1772 / #1453 -examples/psyad/eg2/Makefile. Manual sed rewrite still present.

• #365 - nemo.py, valid_kernel.

• #309 — kernels_trans.py. Traced to #399→#485, but DependencyTools never adopted here.

• #2236 -test_lfric_adjoint.py, lfric_adjoint.py. Successor #2347 also closed; workaround still present.

• #2596 - adjoint_visitor.py. Points at a merged PR; author unsure if related to #1946 or #2729.

• #1556 - test_lfric_adjoint.py

• #753 - ~8 sites across doc/developer_guide/psykal.rst, lfric.py, tests.

• #1272 - goloop_test.py.

• #1504 -fparser2.py. Reverted from an earlier premature deletion flagging rather than removing.

• #1807 - lfric_adjoint.py.

• #2823 - call_test.py. Reverted from an earlier premature deletion flagging rather than removing.

• #3157 - maximal_omp_parallel_region_trans.py

• #3205 - maximal_omp_parallel_region_trans.py.

• #3265 - reference2arrayrange_trans_test.py. Reverted from an earlier premature deletion flagging rather than removing.

• #1351 - kern_call_arg_list.py. Stub generator still uses .remove("dof")/.remove("owned_dof").

• #1930 - kern_call_arg_list.py docstring. String-format migration not done.

• #658 - sir.py, assignment_test.py, type_convert_intrinsic_test.py, intrinsic_call.py. Type-determination capability still missing; one site is a live xfail.

• #1235 - 7 xfail sites in psyad tests.

Todo:

• #753 - 8 references

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (415d670) to head (c9bbc70).

Additional details and impacted files

@@            Coverage Diff            @@
##            master     #3535   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files          397       397           
  Lines        55761     55758    -3     
=========================================
- Hits         55761     55758    -3     

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[sergisiso]

We are almost there now @haanahfrost, see a minor inline comment and you can do the remaining instances by:

#3157 - maximal_omp_parallel_region_trans.py
#3205 - maximal_omp_parallel_region_trans.py.

Remove the paragraph with both issues above.

#3265 - reference2arrayrange_trans_test.py. Reverted from an earlier premature deletion flagging rather than removing.

I can't see the reference in this file, maybe its already gone?

#1351 - kern_call_arg_list.py. Stub generator still uses.remove("dof")/.remove("owned_dof").

I reopened this issue, no modification needed.

#1930 - kern_call_arg_list.py docstring. String-format migration not done.

Use 1883 instead

#658 - sir.py, assignment_test.py, type_convert_intrinsic_test.py, intrinsic_call.py. Type-determination capability still missing; one site is a live xfail.

Replace with 1799

#1235 - 7 xfail sites in psyad tests

I reopened this issue, no modification needed.

[sergisiso]

@haanahfrost Also, you can add "(closes #3506) ..." in the PR title to link the PR with the associate issue. And convert it from a draft PR to a Ready PR.

[sergisiso]

All good now regarding these TODOs/issues @haanahfrost , running the script in utils still finds some other cases, but this PR is big enough, so I decided to approve it but changing "closes" to "towards" and we can look at the remaining in a separate PR.