COMP: Make the 'Build and Test' analysis workflow run

[gdevenyi]

The first commit fixes the workflow's trigger: it fires on branch
main, but this repository's default branch is master, so not one
of its jobs -- coverage, valgrind memcheck, scan-build, ASan+UBSan --
has ever executed. It also replaces the retired macos-11 runner and
the deprecated actions/checkout@v3.

The trigger alone is not enough to make 'Build and Test' work. Every job invokes cmake/travis_dashboard.cmake, which begins

set_from_env(CTEST_SITE "TRAVIS_APP_HOST" REQUIRED)

and aborts with a FATAL_ERROR because GitHub Actions does not set that
variable. The script is a half-migrated hybrid: it wants
TRAVIS_APP_HOST from Travis and AGENT_BUILDDIRECTORY from Azure
Pipelines, and the workflow supplies only the latter. All five jobs
fail in about twenty seconds having compiled nothing.

Each job now configures, builds and tests directly:

coverage --coverage build, tests, an lcov summary
valgrind ctest -T memcheck, then a step that fails on any non-zero
ERROR SUMMARY or any definite or indirect leak
use_prefix builds with NIFTI_PACKAGE_PREFIX set
sanitize ASan and UBSan with -fno-sanitize-recover, then
scan-build --status-bugs
macos Release on macos-14

Three details are recorded in comments so they do not have to be
rediscovered:

• valgrind will not start without libc6-dbg -- it reports that it
  cannot redirect memcmp and exits;

• its memcheck needs --trace-children=yes, because most of these tests
  are shell scripts that exec nifti_tool. Without it valgrind
  inspects the shell, finds nothing and reports a clean run;

• ctest -T memcheck exits 0 even when valgrind reports defects, so the
  following step greps the logs. That grep matches the error count
  itself rather than the absence of a clean summary: with
  --trace-children the concurrent processes share one log and their
  lines interleave, and a real run produced

  ==3336== ERROR SUMMARY: ==3300==
  

  which an absence test would have accepted.

This also drops the submission to my.cdash.org. Posting results to the
project's public dashboard from every pull request, including ones from
forks, is not obviously wanted, and nothing else in the workflow needs
it. cmake/travis_dashboard.cmake is left in place; nothing else refers
to it.

Stated plainly: the workflow itself cannot be run locally. The YAML
parses, and every cmake, ctest, valgrind and scan-build invocation in it
was run by hand against this tree, but the jobs are unverified until
they run on a runner.

---

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 pushed as c8d48e7, now a single commit. Partially superseded — this needs a maintainer decision before it is worth reviewing in detail.

What master has already fixed, and this PR therefore no longer contributes:

• The main vs master trigger. master's build.yml already triggers on master, so the first commit of this PR (8dcb6e5, "Trigger the analysis workflow on the branch that exists") is fully redundant and was dropped by the rebase.
• The Travis script. cmake/travis_dashboard.cmake is gone; master uses cmake/github_dashboard.cmake, which takes CTEST_SITE from RUNNER_OS with a default rather than requiring TRAVIS_APP_HOST. The original "all five jobs fail in twenty seconds having compiled nothing" premise no longer holds — the jobs run.
• macos-11 is gone; master uses macos-latest.

What is still genuinely new here, and is the only reason to keep the PR open:

• ctest -T memcheck exits 0 even when valgrind reports defects. master's valgrind job therefore cannot fail on a memory error. This PR adds a log-scanning step that does.
• --trace-children=yes, without which valgrind inspects the shell wrapper and reports a clean run having never looked at the library, and libc6-dbg, without which valgrind will not start at all.
• A use_prefix job exercising NIFTI_PACKAGE_PREFIX, and -fno-sanitize-recover=all on the sanitizer job.
• actions/checkout@v3 -> @v4.
• Failures land in the Actions log instead of only on CDash, and pull requests from forks stop posting to my.cdash.org.

No overlap with cmake-multi-platform.yml, which covers the plain build matrix, the minimal configuration, the oldest supported CMake, the exported-symbol baseline, and the missing-declarations check — none of coverage, valgrind, sanitizers, scan-build, or the package prefix.

The decision is whether to keep the CDash dashboard path or move these five jobs to direct cmake/ctest invocations. If you want to keep CDash, the valgrind gating and the two valgrind flags should be extracted from this PR and applied to the dashboard script instead; the rest can be dropped. I have not closed or retitled anything.

What changed in this update

• Rebased onto master. The trigger commit dropped as redundant. The rewrite commit conflicted with master's Travis-to-GitHub migration in build.yml; resolved by taking this PR's version of the jobs: block, since the commit's whole purpose is to replace it, after confirming that master's version of that block contributes nothing the new one lacks (the trigger and the dashboard-script name are the only differences, and the new jobs use neither).
• Commit message: dropped the Co-Authored-By: naming an AI tool and the Claude-Session: URL; removed the reference to "the previous commit", which no longer exists; and rewrote the rationale, which described travis_dashboard.cmake and a FATAL_ERROR that master has since removed. The message now describes the situation as it is.
• No change to the workflow content itself beyond the rebase.

Why no test

BUILD class. A GitHub Actions workflow has no runtime seam a ctest can observe; it is only exercised by a runner. Per the commit message, the individual cmake, ctest, valgrind and scan-build invocations were run by hand, but the jobs themselves remain unverified until CI runs them.