Update kallisto (with hackery on std_cmake_args) (#15278)

* Filter problematic flag from std_cmake_args

Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args causes
bits of cmake's output to end up in the autoconf-generated configure
script.  See https://github.com/spack/spack/issues/15274 and

* Don't build in parallel (sigh)

* Constrain hackery for newer versions...

... to newer versions.

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

@@ -13,8 +13,37 @@ class Kallisto(CMakePackage):
     homepage = "http://pachterlab.github.io/kallisto"
     url      = "https://github.com/pachterlab/kallisto/archive/v0.43.1.tar.gz"
 
+    version('0.46.2', sha256='c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2')
     version('0.43.1', sha256='7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400')
 
     depends_on('zlib')
     depends_on('hdf5')
     depends_on('mpich')
+
+    # htslib isn't built in time to be used....
+    parallel = False
+
+    # v0.44.0 vendored a copy of htslib and uses auto* to build
+    # its configure script.
+    depends_on('autoconf', type='build', when='@0.44.0:')
+    depends_on('automake', type='build', when='@0.44.0:')
+    depends_on('libtool',  type='build', when='@0.44.0:')
+    depends_on('m4',       type='build', when='@0.44.0:')
+
+    # Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args
+    # causes bits of cmake's output to end up in the autoconf-generated
+    # configure script.
+    # See https://github.com/spack/spack/issues/15274 and
+    # https://github.com/pachterlab/kallisto/issues/253
+    @property
+    def std_cmake_args(self):
+        """Call the original std_cmake_args and then filter the verbose
+        setting.
+        """
+        a = super(Kallisto, self).std_cmake_args
+        if (self.spec.version >= Version('0.44.0')):
+            args = [i for i in a if i != '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON']
+        else:
+            args = a
+
+        return args