Merge pull request #247 from AlexanderRichert-NOAA/ops_update_batch

Ops update batch

.github/workflows/unit_tests.yaml

@@ -151,6 +151,7 @@ jobs:
     - name: Setup repo and non-root user
       run: |
           git --version
+          git config --global --add safe.directory /__w/spack/spack
           git fetch --unshallow
           . .github/workflows/setup_git.sh
           useradd spack-test

var/spack/repos/builtin/packages/apr-util/package.py

@@ -85,6 +85,11 @@ def configure_args(self):
         else:
             args.append("--without-odbc")
 
+        if "+crypto" in spec:
+            if spec["openssl"].satisfies("~shared"):
+                zlibs = self.spec["zlib"].libs
+                args.append("LIBS={0} {1}".format(zlibs.ld_flags, zlibs.link_flags))
+
         return args
 
     def check(self):

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

@@ -39,6 +39,8 @@ class Cairo(AutotoolsPackage):
     variant("fc", default=False, description="Enable cairo's Fontconfig font backend feature")
     variant("png", default=False, description="Enable cairo's PNG functions feature")
     variant("svg", default=False, description="Enable cairo's SVN functions feature")
+    variant("shared", default=True, description="Build shared libraries")
+    variant("pic", default=False, description="Enable position-independent code (PIC)")
 
     depends_on("libx11", when="+X")
     depends_on("libxext", when="+X")
@@ -83,6 +85,13 @@ def configure_args(self):
         args.extend(self.enable_or_disable("gobject"))
         args.extend(self.enable_or_disable("ft"))
         args.extend(self.enable_or_disable("fc"))
+        args.extend(self.enable_or_disable("shared"))
+        args.extend(self.with_or_without("pic"))
+
+        if self.spec.satisfies("+ft"):
+            if self.spec["freetype"].satisfies("~shared"):
+                args.append("LDFLAGS=%s" % self.spec["bzip2"].libs.search_flags)
+                args.append("LIBS=%s" % self.spec["bzip2"].libs.link_flags)
 
         return args
 

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

@@ -186,7 +186,7 @@ class Cdo(AutotoolsPackage):
 
     # Internal compiler error when building with Intel 2022.1.2
     # https://github.com/jcsda/spack-stack/issues/248
-    patch("intel-compare.patch", when="%intel")
+    patch("intel-compare.patch", when="%intel@2022.1.2")
 
     def configure_args(self):
         config_args = []
@@ -204,23 +204,33 @@ def yes_or_prefix(spec_name):
             # Note that the argument of --with-hdf5 is not passed to the
             # configure script of libcdi, therefore we have to provide
             # additional flags regardless of whether hdf5 support is enabled.
-            hdf5_spec = self.spec["hdf5"]
-            if not is_system_path(hdf5_spec.prefix):
-                flags["LDFLAGS"].append(self.spec["hdf5"].libs.search_flags)
+            netcdfc_spec = self.spec["netcdf-c"]
+            if not is_system_path(netcdfc_spec.prefix):
+                if netcdfc_spec.satisfies("+shared"):
+                    flags["LDFLAGS"].append(netcdfc_spec.libs.search_flags)
+                    flags["LIBS"].append(netcdfc_spec.libs.link_flags)
+                else:
+                    ncconfig = which("nc-config")
+                    flags["LDFLAGS"].append(ncconfig("--cflags", output=str).strip())
+                    flags["LIBS"].append(ncconfig("--libs", output=str).strip())
         else:
             config_args.append("--without-netcdf")
 
         if self.spec.variants["grib2"].value == "eccodes":
-            if self.spec.satisfies("@1.9:"):
+            eccodes_spec = self.spec["eccodes"]
+            if self.spec.satisfies("@1.9:") and eccodes_spec.satisfies("+shared"):
                 config_args.append("--with-eccodes=" + yes_or_prefix("eccodes"))
                 config_args.append("--without-grib_api")
             else:
                 config_args.append("--with-grib_api=yes")
-                eccodes_spec = self.spec["eccodes"]
                 eccodes_libs = eccodes_spec.libs
                 flags["LIBS"].append(eccodes_libs.link_flags)
                 if not is_system_path(eccodes_spec.prefix):
                     flags["LDFLAGS"].append(eccodes_libs.search_flags)
+                    if eccodes_spec.satisfies("~shared"):
+                        jpeglib = eccodes_spec.variants["jp2k"].value
+                        flags["LIBS"].append(self.spec[jpeglib].libs.link_flags)
+                        flags["LDFLAGS"].append(self.spec[jpeglib].libs.ld_flags)
         elif self.spec.variants["grib2"].value == "grib-api":
             config_args.append("--with-grib_api=" + yes_or_prefix("grib-api"))
             if self.spec.satisfies("@1.9:"):
@@ -245,6 +255,10 @@ def yes_or_prefix(spec_name):
         config_args += self.with_or_without(
             "udunits2", activation_value=lambda x: yes_or_prefix("udunits")
         )
+        if self.spec.satisfies("+udunits2"):
+            if self.spec["udunits"].satisfies("~shared"):
+                flags["LDFLAGS"].append("-L%s" % self.spec["expat"].prefix.lib)
+                flags["LIBS"].append("-lexpat")
 
         if "+libxml2" in self.spec:
             libxml2_spec = self.spec["libxml2"]
@@ -257,10 +271,34 @@ def yes_or_prefix(spec_name):
                     flags["CPPFLAGS"].append(libxml2_spec.headers.include_flags)
             else:
                 config_args.append("--with-libxml2=" + libxml2_spec.prefix)
+            if self.spec["libxml2"].satisfies("~shared"):
+                for lib in ["libiconv", "xz"]:
+                    flags["LDFLAGS"].append(self.spec[lib].libs.search_flags)
+                    flags["LIBS"].append(self.spec[lib].libs.link_flags)
         else:
             config_args.append("--without-libxml2")
 
         config_args += self.with_or_without("proj", activation_value=yes_or_prefix)
+        if self.spec.satisfies("+proj"):
+            if self.spec["proj"].satisfies("~shared"):
+                if self.spec["proj"].satisfies("^sqlite"):
+                    flags["LDFLAGS"].append("-L%s" % self.spec["sqlite"].prefix.lib)
+                    flags["LIBS"].append("-lsqlite3")
+                if self.spec["proj"].satisfies("+tiff"):
+                    flags["LDFLAGS"].append("-L%s" % self.spec["libtiff"].prefix.lib)
+                    flags["LIBS"].append("-ltiff")
+                    if self.spec["libtiff"].satisfies("+zlib"):
+                        flags["LDFLAGS"].append("-L%s" % self.spec["zlib"].prefix.lib)
+                        flags["LIBS"].append("-lz")
+                    if self.spec["libtiff"].satisfies("+jpeg"):
+                        flags["LDFLAGS"].append("-L%s" % self.spec["jpeg"].prefix.lib)
+                        flags["LIBS"].append(self.spec["jpeg"].libs.link_flags)
+                if self.spec["proj"].satisfies("+curl"):
+                    flags["LDFLAGS"].append("-L%s" % self.spec["curl"].prefix.lib)
+                    flags["LIBS"].append("-lcurl")
+                    if self.spec["curl"].satisfies("tls=openssl"):
+                        flags["LDFLAGS"].append("-L%s" % self.spec["openssl"].prefix.lib)
+                        flags["LIBS"].append("-lssl -lcrypto")
 
         config_args += self.with_or_without("curl", activation_value=yes_or_prefix)
 

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

@@ -390,6 +390,18 @@ def bootstrap_args(self):
             ]
         )
 
+        if self.spec["openssl"].satisfies("~shared"):
+            args.append(
+                "-DOPENSSL_CRYPTO_LIBRARY={0};{1}".format(
+                    find_libraries("libcrypto", self.spec["openssl"].prefix.lib, shared=False),
+                    find_libraries(
+                        "libz",
+                        self.spec["zlib"].prefix.lib,
+                        shared=self.spec["zlib"].satisfies("+shared"),
+                    )
+                )
+            )
+
         return args
 
     def cmake_bootstrap(self):

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

@@ -3,6 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
+
 from spack.package import *
 from spack.pkg.builtin.boost import Boost
 
@@ -33,6 +35,7 @@ class Ecflow(CMakePackage):
         "static_boost", default=False, description="Use also static boost libraries when compiling"
     )
     variant("ui", default=False, description="Enable ecflow_ui")
+    variant("pic", default=False, description="Enable position-independent code (PIC)")
 
     extends("python")
 
@@ -73,23 +76,41 @@ def patch(self):
             "Pyext/CMakeLists.txt",
         )
 
+    @when("+ssl ^openssl~shared")
+    def setup_build_environment(self, env):
+        env.set("LIBS", self.spec["zlib"].libs.search_flags)
+
     def cmake_args(self):
-        boost_lib = self.spec["boost"].prefix.lib
-        return [
+        spec = self.spec
+        boost_lib = spec["boost"].prefix.lib
+        args = [
             self.define("Boost_PYTHON_LIBRARY_RELEASE", boost_lib),
             self.define_from_variant("ENABLE_UI", "ui"),
             self.define_from_variant("ENABLE_GUI", "ui"),
             self.define_from_variant("ENABLE_SSL", "ssl"),
             # https://jira.ecmwf.int/browse/SUP-2641#comment-208943
             self.define_from_variant("ENABLE_STATIC_BOOST_LIBS", "static_boost"),
-            self.define("Python3_EXECUTABLE", self.spec["python"].package.command),
-            self.define("BOOST_ROOT", self.spec["boost"].prefix),
+            self.define("Python3_EXECUTABLE", spec["python"].package.command),
+            self.define("BOOST_ROOT", spec["boost"].prefix),
+            self.define_from_variant("CMAKE_POSITION_INDEPENDENT_CODE", "pic"),
         ]
 
+        if spec.satisfies("+ssl ^openssl ~shared"):
+            ssl_libs = [os.path.join(spec["openssl"].prefix.lib, "libcrypto.a")]
+            ssl_libs.extend(spec["zlib"].libs)
+            args.append(self.define("OPENSSL_CRYPTO_LIBRARY", ";".join(ssl_libs)))
+
+        return args
+
     # A recursive link in the ecflow source code causes the binary cache
     # creation to fail. This file is only in the install tree if the
     # --source option is set when installing the package, but force_remove
     # acts like "rm -f" and won't abort if the file doesn't exist.
     @run_after("install")
     def remove_recursive_symlink_in_source_code(self):
         force_remove(join_path(self.prefix, "share/ecflow/src/cereal/cereal"))
+
+    @when("+ssl ^openssl~shared")
+    def patch(self):
+        for sdir in ["Client", "Server"]:
+            filter_file("(target_link_libraries.*pthread)", r"\1 ssl crypto z", os.path.join(sdir, "CMakeLists.txt"))

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

@@ -25,6 +25,7 @@ class FftwBase(AutotoolsPackage):
     )
     variant("openmp", default=False, description="Enable OpenMP support.")
     variant("mpi", default=True, description="Activate MPI support")
+    variant("shared", default=True, description="Build shared libraries")
 
     depends_on("mpi", when="+mpi")
     depends_on("llvm-openmp", when="%apple-clang +openmp")
@@ -97,7 +98,9 @@ def setup_build_environment(self, env):
 
     def configure(self, spec, prefix):
         # Base options
-        options = ["--prefix={0}".format(prefix), "--enable-shared", "--enable-threads"]
+        options = ["--prefix={0}".format(prefix), "--enable-threads"]
+        options.extend(self.enable_or_disable("shared"))
+
         if not self.compiler.f77 or not self.compiler.fc:
             options.append("--disable-fortran")
         if spec.satisfies("@:2"):

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

@@ -82,7 +82,7 @@ class Fms(CMakePackage):
         when="@2022.02:",
     )
     variant(
-        "fpic", default=False, description="Build with position independent code", when="@2022.02:"
+        "pic", default=False, description="Build with position independent code", when="@2022.02:"
     )
 
     depends_on("netcdf-c")
@@ -103,7 +103,7 @@ def cmake_args(self):
             self.define_from_variant("ENABLE_QUAD_PRECISION", "quad_precision"),
             self.define_from_variant("WITH_YAML", "yaml"),
             self.define_from_variant("CONSTANTS"),
-            self.define_from_variant("FPIC"),
+            self.define_from_variant("FPIC", "pic"),
             self.define("32BIT", "precision=32" in self.spec),
             self.define("64BIT", "precision=64" in self.spec),
         ]

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

@@ -28,6 +28,8 @@ class Fontconfig(AutotoolsPackage):
     depends_on("uuid", when="@2.13.1:")
     depends_on("python@3:", type="build", when="@2.13.93:")
 
+    variant("pic", default=False, description="Enable position-independent code (PIC)")
+
     def patch(self):
         """Make test/run-test.sh compatible with dash"""
         filter_file("SIGINT SIGTERM SIGABRT EXIT", "2 15 6 0", "test/run-test.sh")
@@ -40,8 +42,27 @@ def _rm_offending_header(self):
 
     def configure_args(self):
         font_path = join_path(self.spec["font-util"].prefix, "share", "fonts")
+        args = ["--enable-libxml2", "--disable-docs", "--with-default-fonts={0}".format(font_path)]
+        ldflags = []
+        libs = []
+        deps = []
+        if self.spec["bzip2"].satisfies("~shared"):
+            deps.append("bzip2")
+        if not self.spec["libpng"].satisfies("libs=shared"):
+            deps.append("libpng")
+        if self.spec["libxml2"].satisfies("~shared"):
+            deps.extend(["zlib", "xz", "iconv"])
+        if deps:
+            for lib in deps:
+                ldflags.append(self.spec[lib].libs.ld_flags)
+                libs.append(self.spec[lib].libs.link_flags)
+            args.append("LDFLAGS=%s" % " ".join(ldflags))
+            args.append("LIBS=%s" % " ".join(libs))
+
+        args.extend(self.with_or_without("pic"))
 
-        return ["--enable-libxml2", "--disable-docs", "--with-default-fonts={0}".format(font_path)]
+        return args
+
 
     @run_after("install")
     def system_fonts(self):

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

@@ -44,6 +44,14 @@ class Freetype(AutotoolsPackage, CMakePackage):
         "support __builtin_shuffle)",
     )
 
+    variant("shared", default=True, description="Build shared libraries")
+    variant(
+        "pic",
+        default=False,
+        description="Enable position-independent code (PIC)",
+        when="build_system=cmake",
+    )
+
     patch("windows.patch", when="@2.9.1")
 
     @property
@@ -52,7 +60,6 @@ def headers(self):
         headers.directories = [self.prefix.include.freetype2]
         return headers
 
-
 class AutotoolsBuilder(AutotoolsBuilder):
     def configure_args(self):
         args = [
@@ -64,8 +71,12 @@ def configure_args(self):
         ]
         if self.spec.satisfies("@2.9.1:"):
             args.append("--enable-freetype-config")
+        args.extend(self.enable_or_disable("shared"))
         return args
 
+    def setup_build_environment(self, env):
+        if self.spec.satisfies("+pic"):
+            env.set("CFLAGS", "-fPIC")
 
 class CMakeBuilder(CMakeBuilder):
     def cmake_args(self):
@@ -75,4 +86,6 @@ def cmake_args(self):
             self.define("FT_DISABLE_HARFBUZZ", True),
             self.define("FT_REQUIRE_PNG", True),
             self.define("FT_REQUIRE_BZIP2", True),
+            self.define_from_variant("BUILD_SHARED_LIBS", "shared"),
+            self.define_from_variant("CMAKE_POSITION_INDEPENDENT_CODE", "pic"),
         ]