Fixes bugs related to paths and adds new fingerprint for Apple Clang + libc++.

.claude/LESSONS.md

@@ -37,6 +37,12 @@ Critical knowledge to avoid repeating mistakes.
 
 ## Python packaging / bindings
 
+- **A wheel repair tool does not protect local source/editable installs.**
+  HiGHS defaults to a shared library on Unix, leaving the installed Python
+  extension with `@rpath/libhighs.1.dylib` but no `LC_RPATH`; cibuildwheel can
+  repair release wheels, while `uv pip install -e .` cannot. Build HiGHS and
+  its extras as scoped PIC static libraries for Python packaging, and assert
+  the resulting CMake target type during configuration.
 - **Never infer Python import provenance from the checkout layout.** The
   2026-07-23 probe found a mixed environment: `dtwcpp` and `_api.py` resolve to
   `python/dtwcpp/` in the repository, while `_dtwcpp_core` resolves to the venv
@@ -435,10 +441,27 @@ Critical knowledge to avoid repeating mistakes.
   `/fp:precise`; Clang without those relaxations matched MSVC. Linux
   libstdc++ produced a third result because the standard does not prescribe
   `uniform_real_distribution`'s engine-to-real mapping; there even the scalar
-  `[-1,1]` bytes differ. A behavior-neutral extraction must compare raw
-  IEEE-754 bytes under each verified compiler-plus-standard-library profile,
-  preserve the distribution type and draw schedule, and never relabel legacy
-  STL-distribution fixtures as `portable-v1`.
+  `[-1,1]` bytes differ. Apple Clang + libc++ is a fourth coherent row:
+  scalar/row `[-1,1]` hashes match libstdc++, but the continuous `[-10,10]`
+  stream differs by a few ULPs while the 3×3 full/band-0 oracles still hash
+  to the libstdc++ matrices. Register that row as `libcxx`; do not skip F15
+  or replace the STL distribution. A behavior-neutral extraction must compare
+  raw IEEE-754 bytes under each verified compiler-plus-standard-library
+  profile, preserve the distribution type and draw schedule, and never
+  relabel legacy STL-distribution fixtures as `portable-v1`.
+- **A last-bit pin is not portable across GCC vs Apple Clang under the
+  Release reassociation set.** Arrhenius `LastTest.log` (2026-09-01) failed
+  three gates that were green on Apple Clang: F13 pinned `nearest[]` bits
+  `0x8000000000000000` (`-0.0`) while GCC flushed them to `+0.0`; F22's
+  canonical probe treated GCC's constructor-NSDMI use of deprecated
+  `maxIter`/`N_repetition` as a canonical diagnostic; F8 Soft-DTW
+  `total_cost` differed by 2 ULP (`CC…` vs `CE…`) after resident≡stream and
+  labels/medoids already matched. Canonicalize signed zeros in the F13
+  oracle the same way as the zero objective; pragma-silence *constructors*
+  (not the fields) in `Problem.hpp`; register a second Soft-DTW cost encoding
+  and keep resident≡stream byte-identity. Do not skip the tests, do not
+  loosen Standard DTW goldens, and do not remove `[[deprecated]]` from the
+  fields. Evidence: `.claude/baselines/2026-09-01-hpc-gcc-fp-and-deprecation.md`.
 - **Catch2 decomposition rejects unparenthesized logical OR.** An expression
   such as `CHECK((a && b) || (c && d))` reaches Catch2's deleted/decomposition
   guard and fails to compile; force the complete predicate to `bool` with one

.claude/baselines/2026-09-01-f15-libcxx-profile.md

@@ -0,0 +1,73 @@
+# F15 libcxx fingerprint row — 2026-09-01
+
+## Scope
+
+Apple Clang + libc++ is a fourth coherent F15 profile. It is not a skip and
+not a generator change. Scalar and per-row `[-1,1]` hashes already matched
+the registered `libstdcxx` schedule; the continuous `[-10,10]` accelerator
+stream differed by a few ULPs, so `profile_for()` returned nullptr.
+
+Registered before the focused rebuild. Dump subject: production
+`accelerator_series_set(3, 4, 42)`, then
+`symmetric_zero_diagonal_matrix` with `dtwFull_L<double>` and
+`dtwBanded<double>(..., 0)`, IEEE SHA-256 of little-endian binary64 bytes
+exactly as `tests/unit/unit_test_deterministic_series.cpp`.
+
+## Environment [confirmed]
+
+```text
+Apple clang version 21.0.0 (clang-2100.1.1.101)
+STL: libc++ (Apple Command Line Tools)
+CMAKE_BUILD_TYPE=Release
+flags include: -O3 -fno-math-errno -fno-trapping-math -freciprocal-math
+  -fassociative-math -fno-signed-zeros -fno-rounding-math -march=native
+host: darwin 25.6.0
+```
+
+## Dumped fingerprints [confirmed]
+
+```text
+scalar_hash=194FB0E76C52FCD84F09960547EEDC6A43788FDCC89F739DF44E3C49AF7B16E0
+rows_hash=1F9E6847BA0FFC7943EBCA024827CD6B5A890B8911BFF4F6C59211F3C28892AB
+accelerator_hash=1D063EF12CB8680807CEEEF9F8C2F35331D0AA91186F824A16D9F3B2954AEF77
+full_hash=7DE312EABCFFB71D857BF97B9CFCE9C08A6F855E7CE25B863342BE46CBC38B73
+band0_hash=E81034CE0654315D254D07FA518DDCE7472A542A4EECBD740935E9DFF891022E
+full_ne_band0=1
+```
+
+Accelerator binary64 masks:
+
+```text
+4017B933480DF696,C01953416B53F15F,40166012566A8F3E,3FFEFDF719BF921C,
+BFF15561688E12F2,C0200041BE89C29E,BFEA14A986DAD398,C00A9B4B96F5696D,
+C01C92166F9FE92A,4008246451B14AA8,C021BE586FDF2D37,4011C288EB7D97C0
+```
+
+Scalar and row hashes match `libstdcxx`. Full and band-0 hashes match
+`libstdcxx`. Band-0 differs from full, so the fixture remains non-degenerate.
+The accelerator stream differs from `libstdcxx` at four ULP positions
+(`…921C` vs `…9220`, `…12F2` vs `…12F0`, `…D398` vs `…D3A0`, `…696D` vs
+`…696C`). Mixing those generator bits with another row's oracle hashes is a
+fail.
+
+Fingerprint-row name: `libcxx` (not a compiler identity).
+
+## Pass band
+
+`unit_test_deterministic_series` must print
+
+```text
+F15_TEST_SUPPORT profile=libcxx scalar=ran row_seeded=ran continuous=ran dense=ran source_audit=ran skips=0
+```
+
+and Catch2 `All tests passed` with the existing assertion/case floor. CTest
+regex accepts `relaxed|precise|libstdcxx|libcxx`.
+
+## Focused execution [confirmed]
+
+```text
+F15_TEST_SUPPORT profile=libcxx scalar=ran row_seeded=ran continuous=ran dense=ran source_audit=ran skips=0
+All tests passed (165 assertions in 6 test cases)
+```
+
+`ctest -R '^unit_test_deterministic_series$'` → Passed.

CHANGELOG.md

@@ -8,6 +8,33 @@ This changelog contains a non-exhaustive list of new features and notable bug-fi
 <br/><br/>
 # Unreleased
 
+- Fixed macOS Python source and editable installs by statically bundling HiGHS
+  into the native extension, eliminating the unresolved
+  `@rpath/libhighs.1.dylib` import dependency.
+- Canonical construction of `Problem` no longer diagnoses the deprecated
+  `maxIter` / `N_repetition` fields under GCC's constructor NSDMI check, so
+  the F22 canonical probe stays silent while caller access of those fields
+  still warns. The F13 assignment oracle now stores exact-zero nearest/second
+  distances as `+0.0`, matching the existing zero-objective rule, because
+  `-fno-signed-zeros` lets GCC flush `-0.0`. F8 Soft-DTW resident/stream
+  parity still requires byte-identical checkpoints and exact labels/medoids,
+  and now accepts a registered 2-ULP GCC encoding of `total_cost` alongside
+  the original MSVC/Apple Clang bytes.
+- Registered the F15 `libcxx` deterministic-series fingerprint row for Apple
+  Clang + libc++. Scalar/row hashes match the existing libstdc++ schedule;
+  the continuous accelerator stream differs by a few ULPs and is now an
+  accepted coherent profile rather than a `profile == nullptr` failure.
+- Fixed the F22 C++ deprecation probe so Apple Clang's paired
+  `-Xpreprocessor -fopenmp` (and `-Xclang -fopenmp`) is copied from
+  `compile_commands.json` instead of a bare `-fopenmp`, which Apple Clang
+  rejects as an unsupported option. Unix absolute paths such as `/Users/...`
+  are no longer treated as MSVC `/U` flags. LLFIO's libc++
+  `char_traits<std::byte>` deprecation is ignored only inside
+  `llfio_include.hpp`, so `-Werror=deprecated-declarations` still diagnoses
+  DTWC++ aliases.
+- Fixed the F14 distance-matrix CSV contract so path markers use a single
+  separator (`matrix_path` / `cache_path`) instead of a doubled slash, which
+  made the real CLI's POSIX output miss the registered exact-path check.
 - Enforced the frozen C++ deprecation policy for all 33 retained 1.x
   compatibility entities. `Problem::maxIter`/`N_repetition` and the seven
   legacy Problem I/O overloads now emit their registered replacement

PLAN.md

@@ -1164,3 +1164,12 @@ colour system transfer verbatim**.
   clustering (a)–(f). AGENTS.md floors updated to the current 122/122/122/124
   CTest and 1009/12/1-expected-F39-red Python inventories. Cursor unchanged:
   F22 final serial full-gate adjudication, then F23 per the cadence.
+- 2026-09-01 (HPC GCC vs Apple Clang gate repairs): Arrhenius
+  `LastTest.log` failed F13 signed-zero nearest bits, F22 canonical
+  `Problem` construction, and F8 Soft-DTW `total_cost` last bits (2 ULP)
+  after F14/F15 from `95bd137` already passed. Binding repairs: F13 oracle
+  stores exact-zero nearest/second as `+0.0`; F22 silences GCC constructor
+  NSDMI diagnostics around `Problem` constructors only; F8 accepts
+  `CE31540B20B024C0` as a second Soft-DTW cost encoding while resident≡stream
+  and labels/medoids stay exact. Do not skip these tests. Evidence:
+  `.claude/baselines/2026-09-01-hpc-gcc-fp-and-deprecation.md`.

cmake/Dependencies.cmake

@@ -39,22 +39,48 @@ function(dtwc_setup_dependencies)
   else()
     set(CUPDLP_GPU OFF CACHE BOOL "Enable HiGHS cuPDLP GPU support" FORCE)
   endif()
-  CPMAddPackage(
-    NAME highs
-    URL "https://github.com/ERGO-Code/HiGHS/archive/refs/tags/v1.15.1.tar.gz"
-    # SHA256 pinned (Task 0.12). Computed 2026-07-08 from the GitHub release
-    # tarball for the immutable tag v1.15.1 (`curl -sL … | sha256sum`).
-    URL_HASH SHA256=a840d269dff2fafb371dd247df13ad5e026d7ce3b35ad3dc1eedd59bf0c2fb16
-    SYSTEM
-    EXCLUDE_FROM_ALL
-    OPTIONS
-      "CI OFF"
-      "ZLIB OFF"
-      "BUILD_CXX_EXE OFF"
-      "BUILD_EXAMPLES OFF"
-      "BUILD_TESTING OFF"
-      "FAST_BUILD ON"
-    )
+  # A Python extension cannot rely on HiGHS' Unix default of BUILD_SHARED_LIBS=ON:
+  # the resulting @rpath/libhighs dependency is outside site-packages in local
+  # source/editable installs.  Keep these normal variables scoped to the HiGHS
+  # subproject so native DTWC++ builds retain their requested shared-library
+  # policy.  HiGHS sets PIC on its static target, making it safe to fold into the
+  # extension.  GPU HiGHS is exempt because its Windows CUDA build requires DLLs.
+  block(SCOPE_FOR VARIABLES)
+    if(DTWC_BUILD_PYTHON AND NOT DTWC_HIGHS_GPU)
+      set(BUILD_SHARED_LIBS OFF)
+      set(BUILD_SHARED_EXTRAS_LIB OFF)
+    endif()
+
+    CPMAddPackage(
+      NAME highs
+      URL "https://github.com/ERGO-Code/HiGHS/archive/refs/tags/v1.15.1.tar.gz"
+      # SHA256 pinned (Task 0.12). Computed 2026-07-08 from the GitHub release
+      # tarball for the immutable tag v1.15.1 (`curl -sL … | sha256sum`).
+      URL_HASH SHA256=a840d269dff2fafb371dd247df13ad5e026d7ce3b35ad3dc1eedd59bf0c2fb16
+      SYSTEM
+      EXCLUDE_FROM_ALL
+      OPTIONS
+        "CI OFF"
+        "ZLIB OFF"
+        "BUILD_CXX_EXE OFF"
+        "BUILD_EXAMPLES OFF"
+        "BUILD_TESTING OFF"
+        "FAST_BUILD ON"
+      )
+  endblock()
+
+    # Fail during configuration, rather than shipping another extension with an
+    # unresolved libhighs dependency, if HiGHS changes how it honours
+    # BUILD_SHARED_LIBS.
+    if(DTWC_BUILD_PYTHON AND NOT DTWC_HIGHS_GPU AND TARGET highs)
+      get_target_property(_dtwc_highs_library_type highs TYPE)
+      if(NOT _dtwc_highs_library_type STREQUAL "STATIC_LIBRARY")
+        message(FATAL_ERROR
+          "Python packages require statically bundled HiGHS; got "
+          "${_dtwc_highs_library_type}")
+      endif()
+    endif()
+
     # Historically HiGHS <=1.14.0 had a debug assertion (ub_consistent) that
     # fired on valid warm-start MIP solves (primal-dual integral bookkeeping
     # tolerance 1e-12 too tight after a presolve reset). Retained defensively:

dtwc/Problem.hpp

@@ -276,6 +276,20 @@ class Problem
   std::vector<int> centroids_ind; //!< indices of cluster centroids. [0, Np)
 
   // Constructors:
+  // GCC emits -Wdeprecated-declarations for in-class initializers of the
+  // deprecated maxIter / N_repetition fields at every constructor definition.
+  // Canonical construction must stay silent (F22); caller access of those
+  // fields must still diagnose. Same push/pop as Problem.cpp accessors.
+#if defined(__clang__)
+#  pragma clang diagnostic push
+#  pragma clang diagnostic ignored "-Wdeprecated-declarations"
+#elif defined(__GNUC__)
+#  pragma GCC diagnostic push
+#  pragma GCC diagnostic ignored "-Wdeprecated-declarations"
+#elif defined(_MSC_VER)
+#  pragma warning(push)
+#  pragma warning(disable : 4996)
+#endif
   Problem() { rebind_dtw_fn(); }
   Problem(std::string_view problem_name) : name_{ problem_name }
   {
@@ -287,6 +301,13 @@ class Problem
     adopt_loaded_data(loader.load_stored());
     refresh_distance_matrix(); // also calls rebind_dtw_fn()
   }
+#if defined(__clang__)
+#  pragma clang diagnostic pop
+#elif defined(__GNUC__)
+#  pragma GCC diagnostic pop
+#elif defined(_MSC_VER)
+#  pragma warning(pop)
+#endif
   Problem(const Problem &) = delete;
   Problem &operator=(const Problem &) = delete;
   Problem(Problem &&);

dtwc/core/llfio_include.hpp

@@ -7,9 +7,13 @@
 
 // quickcpplib/ringbuffer_log.hpp installs an unbalanced Clang ignore for
 // -Wdeprecated-declarations on Windows. Preserve the caller's diagnostic state
-// across the complete third-party include.
+// across the complete third-party include. Apple libc++ also deprecates
+// std::char_traits<std::byte> inside LLFIO headers; ignore that only while
+// the dependency is parsed so a later -Werror=deprecated-declarations still
+// diagnoses DTWC++ [[deprecated]] names (F22 / F45).
 #if defined(__clang__)
 #  pragma clang diagnostic push
+#  pragma clang diagnostic ignored "-Wdeprecated-declarations"
 #endif
 
 #include <llfio/v2.0/llfio.hpp>

scripts/test_f22_cpp_deprecations.py

@@ -379,6 +379,8 @@ def compile_context(arguments: list[str]) -> tuple[str, list[str]]:
     if not arguments:
         raise RuntimeError("empty compile command")
     compiler = arguments[0].strip('"')
+    compiler_name = Path(compiler).name.lower()
+    msvc_slash_flags = compiler_name in ("cl", "cl.exe") or "clang-cl" in compiler_name
     context: list[str] = []
     index = 1
     paired_options = {
@@ -388,7 +390,14 @@ def compile_context(arguments: list[str]) -> tuple[str, list[str]]:
         "--sysroot",
         "-target",
         "--target",
+        # Apple Clang rejects a bare -fopenmp; CMake records
+        # -Xpreprocessor -fopenmp (and sometimes -Xclang -fopenmp).
+        "-Xpreprocessor",
+        "-Xclang",
     }
+    define_include_prefixes = ("-I", "-D", "-U")
+    if msvc_slash_flags:
+        define_include_prefixes += ("/I", "/D", "/U")
     while index < len(arguments):
         argument = arguments[index]
         if argument in paired_options:
@@ -398,7 +407,7 @@ def compile_context(arguments: list[str]) -> tuple[str, list[str]]:
             index += 2
             continue
         if (
-            argument.startswith(("-I", "/I", "-D", "/D", "-U", "/U"))
+            argument.startswith(define_include_prefixes)
             and '\\"' not in argument
         ):
             context.append(argument.strip('"'))

tests/CMakeLists.txt

@@ -284,7 +284,7 @@ if(TARGET unit_test_deterministic_series)
         TEST unit_test_deterministic_series
         PROPERTY SKIP_RETURN_CODE)
     set(_f15_focused_regex
-        "F15_TEST_SUPPORT profile=(relaxed|precise|libstdcxx) scalar=ran row_seeded=ran continuous=ran dense=ran source_audit=ran skips=0(.|[\r\n])*All tests passed \\((3[5-9]|[4-9][0-9]|[1-9][0-9][0-9]+) assertions in ([5-9]|[1-9][0-9]+) test cases\\)")
+        "F15_TEST_SUPPORT profile=(relaxed|precise|libstdcxx|libcxx) scalar=ran row_seeded=ran continuous=ran dense=ran source_audit=ran skips=0(.|[\r\n])*All tests passed \\((3[5-9]|[4-9][0-9]|[1-9][0-9][0-9]+) assertions in ([5-9]|[1-9][0-9]+) test cases\\)")
     set_tests_properties(
         unit_test_deterministic_series
         PROPERTIES

tests/integration/test_distance_matrix_csv_contract.cmake

@@ -166,7 +166,7 @@ function(run_cli_route route output_dir threshold expect_mmap)
         "${route} distance-matrix output")
     require_occurrences(
         "${normalized_stdout}"
-        "\"${output_dir}//conformance_distance_matrix.csv\"" 1
+        "\"${matrix_path}\"" 1
         "${route} exact distance-matrix path")
     foreach(execution_marker IN ITEMS
             "DTWC++ Clustering"
@@ -185,7 +185,7 @@ function(run_cli_route route output_dir threshold expect_mmap)
             "${route} mmap route")
         require_occurrences(
             "${normalized_stdout}"
-            "\"${output_dir}//conformance_distmat.cache\"" 1
+            "\"${cache_path}\"" 1
             "${route} exact mmap cache")
         if(NOT EXISTS "${cache_path}")
             message(FATAL_ERROR