hdf-eos2: support version @3.0, plus assorted fixes (#41782)

1) support for version @3.0
Unfortunately, download seems to require registration now
so using manual_download mechanism for @3:

2) copying from hdf-eos5 patch from @vanderwb to enable
use of Spack compiler wrappers instead of h4cc

3) Patching an issue in hdf-eos2 configure script.  The
script will test for jpeg, libz libraries, succeed and
append HAVE_LIBJPEG=1, etc to confdefs.h, and then abort
because HAVE_LIBJPEG not set in running environment.

4) Add some LDFLAGS to build environment.  Otherwise
seems to fail to build test script due to rpc dependence
in HDF4.

var/spack/repos/builtin/packages/hdf-eos2/hdf-eos2.configure.patch

@@ -0,0 +1,25 @@
+# Fix some issues with hdf-eos2 configure script
+# configure (according to config.log) would find the jpeg
+# and libz libs, but then abort complaining they were not
+# found because HAVE_LIBJPEG, etc not set (the script just
+# appended the lines to confdefs.h but not set in the environment
+# of the running script and script tests the env variable)
+diff -Naur spack-src/configure spack-src.patched/configure
+--- spack-src/configure	2023-12-18 14:56:50.796875000 -0500
++++ spack-src.patched/configure	2023-12-18 15:01:50.780038643 -0500
+@@ -12488,6 +12488,7 @@
+ _ACEOF
+ 
+   LIBS="-ljpeg $LIBS"
++  HAVE_LIBJPEG=1
+ 
+ else
+ 
+@@ -12863,6 +12864,7 @@
+ _ACEOF
+ 
+   LIBS="-lz $LIBS"
++  HAVE_LIBZ=1
+ 
+ else
+ 

var/spack/repos/builtin/packages/hdf-eos2/package.py

@@ -3,8 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
 import sys
-from os import chmod
 
 from spack.package import *
 
@@ -16,10 +16,15 @@ class HdfEos2(AutotoolsPackage):
     """
 
     homepage = "https://hdfeos.org"
-    # The download URLs are messing, and include sha256 checksum.
+    # Starting with @3, download requires authentication.  So reverting
+    # to a manual download
+    url = "file://{0}/hdf-eos2-3.0-src.tar.gz".format(os.getcwd())
+    manual_download = True
+
+    # The download URLs for @2 versions are messing, and include sha256 checksum.
+    # Templates for url_for_version. 0 is sha256 checksum, 1 is filename
     # This is just a template.  See version_list and url_for_version below
-    # Template for url_for_version. 0 is sha256 checksum, 1 is filename
+    v2url = "https://git.earthdata.nasa.gov/rest/git-lfs/storage/DAS/hdfeos/{0}?response-content-disposition=attachment%3B%20filename%3D%22{1}%22%3B%20filename*%3Dutf-8%27%27{1}"
-    url = "https://git.earthdata.nasa.gov/rest/git-lfs/storage/DAS/hdfeos/{0}?response-content-disposition=attachment%3B%20filename%3D%22{1}%22%3B%20filename*%3Dutf-8%27%27{1}"
 
     maintainers("climbfuji")
 
@@ -29,15 +34,23 @@ class HdfEos2(AutotoolsPackage):
     # In basename expansions, 0 is raw version,
     # 1 is for version with dots => underscores
     version_list = [
+        {
+            "version": "3.0",
+            "basename": "hdf-eos2-{0}-src.tar.gz",
+            "sha256": "3a5564b4d69b541139ff7dfdad948696cf31d9d1a6ea8af290c91a4c0ee37188",
+            "can_auto_download": False,
+        },
         {
             "version": "2.20v1.00",
             "sha256": "cb0f900d2732ab01e51284d6c9e90d0e852d61bba9bce3b43af0430ab5414903",
             "basename": "HDF-EOS{0}.tar.Z",
+            "can_auto_download": True,
         },
         {
             "version": "2.19b",
             "sha256": "a69993508dbf5fa6120bac3c906ab26f1ad277348dfc2c891305023cfdf5dc9d",
             "basename": "hdfeos{1}.zip",
+            "can_auto_download": True,
         },
     ]
 
@@ -63,19 +76,27 @@ class HdfEos2(AutotoolsPackage):
     depends_on("jpeg")
     depends_on("szip", when="^hdf +szip")
 
+    # Fix some problematic logic in stock configure script
+    # test succeeds, but then script aborts due to env variable not being set
+    patch("hdf-eos2.configure.patch", when="@2:3.0")
+
     # The standard Makefile.am, etc. add a --single_module flag to LDFLAGS
     # to pass to the linker.
     # That appears to be only recognized by the Darwin linker, remove it
     # if we are not running on darwin/
     if sys.platform != "darwin":
-        patch("hdf-eos2.nondarwin-no-single_module.patch")
+        patch("hdf-eos2.nondarwin-no-single_module.patch", when="@2")
 
     def url_for_version(self, version):
         vrec = [x for x in self.version_list if x["version"] == version.dotted.string]
         if vrec:
             fname = vrec[0]["basename"].format(version.dotted, version.underscored)
             sha256 = vrec[0]["sha256"]
-            myurl = self.url.format(sha256, fname)
+            can_auto_download = vrec[0].get("can_auto_download", False)
+            if can_auto_download:
+                myurl = self.v2url.format(sha256, fname)
+            else:
+                myurl = self.url
             return myurl
         else:
             sys.exit(
@@ -83,12 +104,20 @@ def url_for_version(self, version):
                 "version/checksum not found in version_list".format(version)
             )
 
+    @run_before("configure")
+    def fix_configure(self):
         # spack patches the configure file unless autoconf is run,
         # and this fails because configure has the wrong permissions (644)
-    @run_before("configure")
-    def fix_permissions(self):
         if not self.force_autoreconf:
-            chmod(join_path(self.stage.source_path, "configure"), 0o755)
+            os.chmod(join_path(self.stage.source_path, "configure"), 0o755)
+
+        # The configure script as written really wants you to use h4cc.
+        # This causes problems because h4cc differs when HDF is built with
+        # autotools vs cmake, and we lose all the nice flags from the
+        # Spack wrappers.  These filter operations allow us to use the
+        # Spack wrappers again
+        filter_file("\\$CC -show &> /dev/null", "true", "configure")
+        filter_file("CC=./\\$SZIP_CC", "", "configure")
 
     def flag_handler(self, name, flags):
         if self.spec.compiler.name == "apple-clang":
@@ -97,12 +126,19 @@ def flag_handler(self, name, flags):
 
         return flags, None, None
 
+    def setup_build_environment(self, env):
+        # Add flags to LDFLAGS for any dependencies that need it
+        extra_ldflags = []
+        # hdf might have link dependency on rpc, if so need to add flags
+        if "rpc" in self.spec:
+            tmp = self.spec["rpc"].libs.ld_flags
+            extra_ldflags.append(tmp)
+        # Set LDFLAGS
+        env.set("LDFLAGS", " ".join(extra_ldflags))
+
     def configure_args(self):
         extra_args = []
 
-        # Package really wants h4cc to be used
-        extra_args.append("CC={0}/bin/h4cc -Df2cFortran".format(self.spec["hdf"].prefix))
-
         # We always build PIC code
         extra_args.append("--with-pic")
         extra_args.append("--enable-install_include")
@@ -114,7 +150,11 @@ def configure_args(self):
         # Provide config args for dependencies
         extra_args.append("--with-hdf4={0}".format(self.spec["hdf"].prefix))
         if "jpeg" in self.spec:
-            extra_args.append("--with-jpeg={0}".format(self.spec["jpeg"].prefix))
+            # Allow handling whatever provider of jpeg are using
+            tmp = self.spec["jpeg"].libs.directories
+            if tmp:
+                tmp = tmp[0]
+                extra_args.append("--with-jpeg={0}".format(tmp))
         if "szip" in self.spec:
             extra_args.append("--with-szlib={0}".format(self.spec["szip"].prefix))
         if "zlib" in self.spec: