kentutils: add v455, v460, v464, v465 + package updates (#44413)

This addresses a few issues in the kentutils package:
 - Issue #44372
 - Cleaning up formattting and styles
 - Removing old versions that are not avaialble anymore
 - Removing newer versions that are also not available anymore
 - The installer does not install the static libs
   that are expected by packages that depend on kentutils
 - There are conflicts and less-than-desirable dependencies
   that can be addressed via variants

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>

var/spack/repos/builtin/packages/kentutils/fix-mysql-options-gcc13.patch

@@ -0,0 +1,13 @@
+diff --git a/jksql.c.orig b/jksql.c
+index bf38b3b..69b2c42 100644
+--- a/kent/src/hg/lib/jksql.c
++++ b/kent/src/hg/lib/jksql.c
+@@ -1129,7 +1129,7 @@ mysql_options(conn, MYSQL_OPT_LOCAL_INFILE, NULL);
+ if (sp->verifyServerCert && !sameString(sp->verifyServerCert,"0"))
+     {
+     #if !defined(MARIADB_VERSION_ID) && MYSQL_VERSION_ID >= 80000
+-    mysql_options(conn, MYSQL_OPT_SSL_MODE, SSL_MODE_REQUIRED);
++    mysql_options(conn, MYSQL_OPT_SSL_MODE, (void*) SSL_MODE_REQUIRED);
+     #else
+     my_bool flag = TRUE;
+     mysql_options(conn, MYSQL_OPT_SSL_VERIFY_SERVER_CERT, &flag);

var/spack/repos/builtin/packages/kentutils/mysql-zlib-workaround.patch

@@ -0,0 +1,13 @@
+diff --git a/kent/src/inc/common.mk.orig b/kent/src/inc/common.mk
+index 83803ad..8c90e3a 100644
+--- a/kent/src/inc/common.mk
++++ b/kent/src/inc/common.mk
+@@ -226,6 +226,8 @@ ifeq (${ZLIB},)
+   ZLIB=-lz
+ endif
+ 
++MYSQLLIBS := $(subst -lzlib,, ${MYSQLLIBS})
++
+ # on hgwdev, use the static libraries
+ ifeq (${IS_HGWDEV},yes)
+    FULLWARN = yes

var/spack/repos/builtin/packages/kentutils/package.py

@@ -3,39 +3,154 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
+
 from spack.package import *
 
 
 class Kentutils(MakefilePackage):
-    """Jim Kent command line bioinformatic utilities"""
+    """
+    Jim Kent command line bioinformatic utilities and libraries
+
+    This bundles a custom version of htslib, but can be overridden with ~htslib.
+    Consider adding the ^mysql+client_only dependency to avoid building all mysql/mariadb.
+    """
 
     homepage = "https://genome.cse.ucsc.edu/"
     url = "https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v453.src.tgz"
 
-    version("459", sha256="0b6e89a183e6385c713cf010a7aeead9da6626d8d2f78c363a4f1bc56ccccebb")
+    maintainers("teaguesterling")
-    # The above archive only goes back to v305. v302 is left for now but deprecated. Suggest
+
-    # this is dropped on next update (v302 is from 2014!) and the `requires()` removed.
+    version("465", sha256="eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0")
+    version("464", sha256="24e20fe68e2a2894d802c87662f69a62f71b3c15fafb2e4d6c3c425c63638bb2")
+    version("460", sha256="b955e56ee880074521ef1ab1371491f47e66dc6fdd93b05328386dd675a635fa")
+    version("455", sha256="e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db")
+    # This version isn't present in the archive any more
+    # Might be worth changing url to: https://github.com/ucscGenomeBrowser/kent-core/tags/...
     version(
-        "302.1",
+        "459",
-        commit="d8376c5d52a161f2267346ed3dc94b5dce74c2f9",
+        sha256="0b6e89a183e6385c713cf010a7aeead9da6626d8d2f78c363a4f1bc56ccccebb",
-        git="https://github.com/ENCODE-DCC/kentUtils.git",
         deprecated=True,
     )
 
-    depends_on("libpng")
+    # The bundled version of kentlib has some custom changes that are used by parts of
-    depends_on("openssl")
+    # kentlib. See https://github.com/spack/spack/pull/44501#issuecomment-2162789410
-    depends_on("uuid")
+    # for some additional details. A built-in version SHOULD work for most things though.
-    depends_on("mariadb")
+    variant(
-    depends_on("zlib-api")
+        "builtin_htslib",
-    depends_on("freetype")
+        default=False,
-    depends_on("libiconv")
+        description="Build with bundled htslib (using an external htslib may lead to errors)",
+        sticky=True,
+    )
 
-    requires("%gcc", when="@302.1")
+    with default_args(type=("build", "link", "run")):
+        depends_on("libpng")
+        depends_on("openssl")
+        depends_on("uuid")
+        depends_on("mysql-client")
+        depends_on("zlib-api")
+        depends_on("freetype")
+        depends_on("libiconv")
+        depends_on("htslib+pic", when="~builtin_htslib")
+
+    # The bgzip.c bug present in other packages is present in kent/src/htslib/bgzf.c
+    # Conflicting line: assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+    # We can patch this by removing the assertion, but there are still performance issues
+    # See: https://github.com/samtools/htslib/issues/1257
+    conflicts("zlib-ng")
+
+    # Does not add a link to mysql_config, which is required for compilation
+    conflicts("mariadb-c-client")
+
+    # MySQL pointer/integer conversion issue (https://github.com/ucscGenomeBrowser/kent/pull/87)
+    patch("fix-mysql-options-gcc13.patch", when="%gcc@13: ^mysql")
+    # MySQL build flags from `mysql_config` are not compatible with Spack's method of building
+    # and includes zlib when it's not needed/available, leading to a linking failure.
+    patch("mysql-zlib-workaround.patch", when="%gcc ^mysql")
 
     def flag_handler(self, name, flags):
-        if name == "ldflags":
+        if name == "cflags":
+            flags.append(self.compiler.cc_pic_flag)
+        elif name == "ldflags":
             flags.append(f'{self.spec["libiconv"].libs.ld_flags}')
         return (flags, None, None)
 
+    @property
+    def machtype(self):
+        # This is hard-coded in the Makefile and included here for reference
+        # and to make it adjustable if we need to adjust this in the future
+        return "local"
+
+    @property
+    def headers(self):
+        headers = []
+        headers.extend(find_headers("*", self.prefix.inc, recursive=True))
+        if self.spec.satisfies("+builtin_htslib"):
+            headers.extend(find_headers("*", self.prefix.htslib, recursive=True))
+        return HeaderList(headers)
+
+    @property
+    def libs(self):
+        return LibraryList([join_path(self.prefix, lib) for lib in self.local_libs])
+
+    @property
+    def local_libs(self):
+        libs = [
+            f"lib/{self.machtype}/jkweb.a",
+            f"lib/{self.machtype}/jkOwnLib.a",
+            f"lib/{self.machtype}/jkhgap.a",
+            f"lib/{self.machtype}/jkhgapcgi.a",
+            f"hg/altSplice/lib/{self.machtype}/libSpliceGraph.a",
+        ]
+        if self.spec.satisfies("+builtin_htslib"):
+            libs.append("htslib/libhts.a")
+        return LibraryList(libs)
+
+    @property
+    def lib_dir(self):
+        return join_path(self.prefix.lib, self.machtype)
+
+    @property
+    def htslib_include_dir(self):
+        if self.spec.satisfies("~builtin_htslib"):
+            # If we're not using the bundled version, just defer to htslib
+            return self.spec["htslib"].prefix.include
+        else:
+            # In the event we're using the bundled htslib, the htslib
+            # headers live in a different part of the installed tree
+            return self.prefix.htslib
+
+    # Packages that link to kentlib (and potential, htslib) often have
+    # idiosyncratic ways of setting up their includes and linker paths.
+    # Having these paths available will make things cleaner downstream.
+    def setup_dependent_package(self, module, dep_spec):
+        setattr(module, "kentutils_include_dir", self.prefix.inc)
+        setattr(module, "kentutils_lib_dir", self.lib_dir)
+        setattr(module, "kentutils_htslib_include_dir", self.htslib_include_dir)
+
+    def install_libs_from_stage(self, spec, prefix):
+        # Dependent packages expect things in the source tree, but we don't
+        # want to copy all of the compilation artifacts in so we'll do them
+        # manually instead of leaving the build directory around
+
+        src_prefix = "kent/src"
+
+        def install_kent(path, tree):
+            src = join_path(src_prefix, path)
+            dest = join_path(prefix, path)
+            mkdirp(os.path.dirname(dest))
+            if tree:
+                install_tree(src, dest)
+            else:
+                install(src, dest)
+
+        install_kent("inc", tree=True)
+        if spec.satisfies("+builtin_htslib"):
+            install_kent("htslib/htslib", tree=True)
+
+        for lib in self.local_libs:
+            install_kent(lib, tree=False)
+
     def install(self, spec, prefix):
         install_tree("bin", prefix.bin)
+        self.install_libs_from_stage(spec, prefix)