deps: bump lief to 0.16.6

Some of the primary changes are:
- lief.EXE_FORMATS became lief.Binary.FORMATS IN 0.14.0
        - https://github.com/lief-project/LIEF/blob/494f116c6b8c9163fc4b5f6497233f18424981ee/doc/sphinx/changelog.rst?plain=1#L702
- lief.ARCHITECTURES became lief.Header.ARCHITECTURES in 0.16.0
        - https://github.com/lief-project/LIEF/blob/494f116c6b8c9163fc4b5f6497233f18424981ee/doc/sphinx/changelog.rst?plain=1#L226C18-L227C18
- lief.ELF.ARCH.x86_64 became lief.ELF.ARCH.X86_64

This commit includes a workaround for the bug fixed in
https://github.com/lief-project/LIEF/pull/1218, but the workaround can
be kept, since it makes `has_nx` checks stricter by enforcing both heap
and stack are non-executable.

This change also requires a patch to partially revert a commit to LIEF
(https://github.com/lief-project/LIEF/commit/f23ced2f4ffc170d0a6f40ff4a1bee575e3447cf)
which broke compatibility with versions of scikit-build-core <= 0.10.x.

This patch can be dropped once the guix time machine advances to or
beyond https://codeberg.org/guix/guix/commit/35c5f07e967155d2276c7ec58e5108e4da02c974,
which bumps the scikit-build-core version in guix from 0.9.3 to 0.10.7.

Co-authored-by: willcl-ark <will8clark@gmail.com>
Co-authored-by: fanquake <fanquake@gmail.com>
Co-authored-by: Hennadii Stepanov <32963518+hebasto@users.noreply.github.com>

contrib/guix/manifest.scm

@@ -15,8 +15,10 @@
              (gnu packages ninja)
              (gnu packages pkg-config)
              ((gnu packages python) #:select (python-minimal))
-             ((gnu packages python-build) #:select (python-tomli python-poetry-core))
+             ((gnu packages python-build) #:select (python-poetry-core))
              ((gnu packages python-crypto) #:select (python-asn1crypto))
+             ((gnu packages python-science) #:select (python-scikit-build-core))
+             ((gnu packages python-xyz) #:select (python-pydantic-2 python-pydantic-core))
              ((gnu packages tls) #:select (openssl))
              ((gnu packages version-control) #:select (git-minimal))
              (guix build-system cmake)
@@ -158,37 +160,35 @@ chain for " target " development."))
 (define-public python-lief
   (package
     (name "python-lief")
-    (version "0.13.2")
+    (version "0.16.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/lief-project/LIEF")
                     (commit version)))
               (file-name (git-file-name name version))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; Configure build for Python bindings.
-                  (substitute* "api/python/config-default.toml"
-                    (("(ninja         = )true" all m)
-                     (string-append m "false"))
-                    (("(parallel-jobs = )0" all m)
-                     (string-append m (number->string (parallel-job-count)))))))
               (sha256
                (base32
-                "0y48x358ppig5xp97ahcphfipx7cg9chldj2q5zrmn610fmi4zll"))))
-    (build-system python-build-system)
-    (native-inputs (list cmake-minimal python-tomli))
+                "1pq9nagrnkl1x943bqnpiyxmkd9vk99znfxiwqp6vf012b50bz2a"))
+              (patches (search-our-patches "lief-scikit-0-9.patch"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list cmake-minimal
+                         ninja
+                         python-scikit-build-core
+                         python-pydantic-core
+                         python-pydantic-2))
     (arguments
      (list
       #:tests? #f                  ;needs network
       #:phases #~(modify-phases %standard-phases
-                   (add-before 'build 'change-directory
+                   (add-before 'build 'set-pythonpath
                      (lambda _
-                       (chdir "api/python")))
-                   (replace 'build
+                       (setenv "PYTHONPATH"
+                         (string-append (string-append (getcwd) "/api/python/backend")
+                                      ":" (or (getenv "PYTHONPATH") "")))))
+                  (add-after 'set-pythonpath 'change-directory
                      (lambda _
-                       (invoke "python" "setup.py" "build"))))))
+                       (chdir "api/python"))))))
     (home-page "https://github.com/lief-project/LIEF")
     (synopsis "Library to instrument executable formats")
     (description