COMP: Add CI jobs for clang-tidy and for building with -Werror

[gdevenyi]

A new workflow with two jobs, so that the configuration added in #32 and
#33 is exercised rather than merely present.

clang-tidy configures with CMAKE_EXPORT_COMPILE_COMMANDS and
runs run-clang-tidy. It reports findings without
failing: 331 on master with #32's configuration,
falling to 198 once the rest of this set of PRs is
applied, across 16 checks. They are all real
defect classes rather than style noise, and want
fixing one class at a time. Removing the
'|| true' is the last step of that work.
warnings-as-errors a gcc and a clang job, each configuring with
NIFTI_WARNINGS_AS_ERRORS=ON, building and testing.

Stated plainly, because it decides when this can be merged: the
warnings-as-errors job cannot pass today. With every PR in this set
applied, 17 warning sites remain, and every one of them is on a line an
open PR already rewrites, so they were deliberately left alone:

 9  -Wsign-conversion         5 in fsliolib/fslio.c (#22),
                              2 in nifti2/nifti2_io.c (#24),
                              2 in nifti_tester001.c (#24)
 8  -Wcalloc-transposed-args  nifti_findhdrname() and
                              nifti_findimgname() in both libraries,
                              which #11 rewrites

clang sees 9 of the 17; it has no -Wcalloc-transposed-args.

This PR is therefore blocked on #11, #22 and #24. Once those merge the
count is zero and the job goes green; if they are not going to merge, say
so and I will take those lines in a follow-up instead.

Depends on #32 for .clang-tidy and #33 for NIFTI_WARNINGS_AS_ERRORS.
Neither is included here, because neither shares a file with this one.

Interface impact: none. On the union of all these changes, configured with USE_FSL_CODE=ON and USE_CIFTI_CODE=ON: all 448 exported symbols across libniftiio, libnifti2, libznz, libfslio, libnifticdf and libcifti are identical to master under nm -D --defined-only, and all ten installed headers are identical under gcc -E -P. Under gcc -dM -E one macro definition differs, intentionally and only in text: #61 makes FSL_RADIOLOGICAL read (-1) so it is safe inside an expression. Its value is still -1, checked by compiling against each installed fslio.h and printing it.

Verification. This branch: builds with gcc 16.1.1, ctest unchanged from master (2 of 345 fail on master itself in this environment; #31 and #29 each fix one). The union of all the PRs: 0 errors under both gcc 16.1.1 and clang 22.1.8, ctest 345/345 under each, and the whole suite under valgrind memcheck with --trace-children=yes gives 484 traced processes with no invalid access, no uninitialised value and no leak in any nifti binary.

Coordination. Every line of every branch was compared, whitespace-normalised, against the diffs of the open PRs (#11, #21, #22, #23, #24). Where one of those already changes a line, the line was left alone, and the few deliberate overlaps are named in the text above. What survives is 17 compiler warnings, all of them on those lines: 9 -Wsign-conversion (5 in fslio.c for #22, 2 in nifti2_io.c and 2 in nifti_tester001.c for #24) and 8 -Wcalloc-transposed-args in nifti_findhdrname and nifti_findimgname, which #11 rewrites. No formatting changes appear anywhere, to stay clear of #10 and #12.

One of a set of independent, single-purpose PRs. Each bases on master and can be merged on its own, in any order.

The full set of PRs (35)

The union of all of them is on the fork as all-changes, if you want to build and test the lot at once.

CI and build

• COMP: Show test output when the starter workflow fails #28 — COMP: Show test output when the starter workflow fails
• COMP: Give install_linking the source directory instead of guessing it #29 — COMP: Give install_linking the source directory instead of guessing it
• COMP: Guard the CMP0169 policy setting so older CMake still configures #30 — COMP: Guard the CMP0169 policy setting so older CMake still configures
• BUG: Compare NIfTI test output by content, not by compressed bytes #31 — BUG: Compare NIfTI test output by content, not by compressed bytes
• COMP: Make the 'Build and Test' analysis workflow run #57 — COMP: Make the 'Build and Test' analysis workflow run

Configuration and documentation

• ENH: Rework the clang-tidy configuration for C11 #32 — ENH: Rework the clang-tidy configuration for C11
• COMP: Add a shared compiler warning set #33 — COMP: Add a shared compiler warning set
• COMP: Enable _FORTIFY_SOURCE in optimized builds #34 — COMP: Enable _FORTIFY_SOURCE in optimised builds
• COMP: Build as ISO C11 with no compiler extensions #38 — COMP: Build as ISO C11 with no compiler extensions
• DOC: Describe the CMake build and how to run the memory checks #58 — DOC: Describe the CMake build and how to run the memory checks
• COMP: Add CI jobs for clang-tidy and for building with -Werror #59 — COMP: Add CI jobs for clang-tidy and for building with -Werror

Defects

• BUG: Fix cdfbin's argument range check, which could never fire #39 — BUG: Fix cdfbin's argument range check, which could never fire
• BUG: Fix an out-of-bounds indirect call in axio_show_mim_summary #40 — BUG: Fix an out-of-bounds indirect call in axio_show_mim_summary
• BUG: Bound the formatted write in znzprintf, and end the va_list on failure #41 — BUG: Bound the formatted write in znzprintf, and end the va_list on failure
• BUG: Report XML read errors instead of treating them as end of input #42 — BUG: Report XML read errors instead of treating them as end of input
• BUG: Stop returning -1 from functions that return size_t #43 — BUG: Stop returning -1 from functions that return size_t
• BUG: Fix the ambiguous-filename path in nifti_findhdrname #54 — BUG: Stop the library calling exit(), and fix the defects beside it
• BUG: Check the allocations whose result is used immediately #55 — BUG: Check the allocations whose result is used immediately
• BUG: Fix cifti_tool's CIFTI extension search, which never advanced #56 — BUG: Fix cifti_tool's CIFTI extension search, which never advanced
• BUG: Free the extension data when nifti_add_extension fails #62 — BUG: Free the extension data when nifti_add_extension fails
• BUG: Free the header on nifti_tool's duplicate-file failure paths #60 — BUG: Free the header on nifti_tool's duplicate-file failure paths
• BUG: Use memcpy instead of casting to over-aligned pointer types #44 — BUG: Use memcpy instead of casting to over-aligned pointer types
• BUG: Stop casting away const in fslio and cifti #45 — BUG: Stop casting away const in fslio and cifti
• BUG: Bound the aux_file copy by sizeof rather than a repeated 24 #46 — BUG: Bound the aux_file copy by sizeof rather than a repeated 24
• ENH: Make the 64-to-32 bit truncations explicit #52 — BUG: Fix 64-to-32 bit truncations, including a real overflow in fslio
• BUG: Fix signed/unsigned comparisons in the nifti tools #51 — BUG: Fix signed/unsigned comparisons in the nifti tools

Warning and check classes

• STYLE: Add the missing newline at end of nifti1_tool.h #35 — STYLE: Add the missing newline at end of nifti1_tool.h
• ENH: Give the cifti tools' gopt internal linkage #36 — ENH: Give the cifti tools' gopt internal linkage
• COMP: Declare the exported functions that no header declares #37 — COMP: Declare the exported functions that no header declares
• BUG: Give i and j a defined value in nifti_mat44_to_orientation #47 — BUG: Give i and j a defined value in nifti_mat44_to_orientation
• ENH: Zero-initialize the matrix locals clang cannot prove are filled #48 — ENH: Zero-initialise the matrix locals clang cannot prove are filled
• BUG: Give the statement macros a do/while(0) body and drop the stray semicolons #49 — BUG: Give the statement macros a do/while(0) body
• ENH: Pass calloc its arguments in the documented order #50 — ENH: Pass calloc its arguments in the documented order
• BUG: Parenthesize macro arguments and replacement lists #61 — BUG: Parenthesise macro arguments and replacement lists
• ENH: Make the implicit sign conversions explicit #53 — ENH: Make the implicit sign conversions explicit

[hjmjohnson]

Rebased onto current master (b4876bf) and the commit message rewritten. The blocker described in the original message is gone: the warnings-as-errors job passes today.

The message said the job "cannot pass today" and listed 17 remaining warning sites blocked on three other PRs. Those have since landed, so I measured rather than repeating the claim:

Compiler	NIFTI_WARNINGS_AS_ERRORS=ON on b4876bf
GCC 13.3 (Ubuntu 24.04, same major as ubuntu-latest)	build rc=0
AppleClang	build rc=0, 363/363 tests

What changed in the commit message, and why

master's last 44 commits were rewritten on 2026-09-22 to drop trailers that do not belong in permanent history, and this PR is held to the same standard:

• removed Co-Authored-By: naming an AI tool, and the Claude-Session: URL
• removed eight bare #NNN cross-references. This is a fork, so a number means one PR here and a different one upstream; when a commit travels to NIFTI-Imaging/nifti_clib or into a vendored copy in ITK, AFNI, FSL, dcm2niix or Slicer, the number points at the wrong thing.
• rewrote the blocked-on paragraph, which was no longer true

Author, committer, and dates are unchanged.

Two things worth a maintainer decision

The clang-tidy job cannot fail. It ends in || true, so it reports findings and always exits 0. That is a deliberate choice stated in the message, and reasonable while the tree is not clean — but it means the job guards nothing today. A separate, cheap guard that can fail is clang-tidy --verify-config, which catches exactly the configuration rot that motivated reworking .clang-tidy. Note it exits 0 whether or not the config is valid, so the step has to assert on its output text rather than on $?.

The warnings-as-errors job is green by virtue of the runner's compiler. It passes on GCC 13.x and AppleClang. Under GCC 16 there is still one site, fsliolib/fslio.c:936: 'nx' may be used uninitialized. So the job will go red the day ubuntu-latest moves to a newer GCC. Either fix that site first, or pin the compiler, or accept that the job tracks the runner.