From d7a1a61702e3487f19db8035152e9b6c65815ff1 Mon Sep 17 00:00:00 2001
From: Rocco Meli <r.meli@bluemail.ch>
Date: Wed, 19 Jul 2023 02:57:55 +0200
Subject: [PATCH] Improve RDKit package (#36566)

---
 .../builtin/packages/freesasa/libcpp.patch    | 21 +++++++
 .../builtin/packages/freesasa/package.py      |  4 ++
 .../repos/builtin/packages/rdkit/package.py   | 56 ++++++++++++++++---
 3 files changed, 73 insertions(+), 8 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/freesasa/libcpp.patch

diff --git a/var/spack/repos/builtin/packages/freesasa/libcpp.patch b/var/spack/repos/builtin/packages/freesasa/libcpp.patch
new file mode 100644
index 0000000000..e62fbdc103
--- /dev/null
+++ b/var/spack/repos/builtin/packages/freesasa/libcpp.patch
@@ -0,0 +1,21 @@
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 140259f..4e2ed3f 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -1,6 +1,5 @@
+ AM_LDFLAGS =
+ AM_CFLAGS =
+-freesasa_LDADD = -lc++
+ AM_CPPFLAGS = -I$(top_srcdir)/third-party/gemmi/include/
+ 
+ if COND_GCOV
+@@ -29,7 +28,7 @@ libfreesasa_a_SOURCES = classifier.c classifier.h \
+        selection.h selection.c $(lp_output)
+ freesasa_SOURCES = main.cc cif.cc cif.hh
+ example_SOURCES = example.c
+-freesasa_LDADD += libfreesasa.a
++freesasa_LDADD = libfreesasa.a
+ example_LDADD = libfreesasa.a
+ 
+ lp_output = lexer.c lexer.h parser.c parser.h
+
diff --git a/var/spack/repos/builtin/packages/freesasa/package.py b/var/spack/repos/builtin/packages/freesasa/package.py
index 135b65363d..387c44cc43 100644
--- a/var/spack/repos/builtin/packages/freesasa/package.py
+++ b/var/spack/repos/builtin/packages/freesasa/package.py
@@ -30,6 +30,10 @@ class Freesasa(AutotoolsPackage):
     depends_on("json-c", when="+json")
     depends_on("libxml2", when="+xml")
 
+    # Remove hard-coded -lc++ flag from Makefile, preventing successful
+    # compilation with GCC 11 (see #36566 for details)
+    patch("libcpp.patch", when="@2.1.2")
+
     def autoreconf(self, spec, prefix):
         autoreconf("--install", "--verbose", "--force")
 
diff --git a/var/spack/repos/builtin/packages/rdkit/package.py b/var/spack/repos/builtin/packages/rdkit/package.py
index eed3b8d8ae..15a68ab8b1 100644
--- a/var/spack/repos/builtin/packages/rdkit/package.py
+++ b/var/spack/repos/builtin/packages/rdkit/package.py
@@ -14,7 +14,7 @@ class Rdkit(CMakePackage):
     homepage = "https://www.rdkit.org"
     url = "https://github.com/rdkit/rdkit/archive/refs/tags/Release_2021_03_2.tar.gz"
 
-    maintainers("bvanessen")
+    maintainers("bvanessen", "RMeli")
 
     version("2023_03_1", sha256="db346afbd0ba52c843926a2a62f8a38c7b774ffab37eaf382d789a824f21996c")
     version("2022_09_5", sha256="2efe7ce3b527df529ed3e355e2aaaf14623e51876be460fa4ad2b7f7ad54c9b1")
@@ -46,17 +46,57 @@ class Rdkit(CMakePackage):
 
     variant("freetype", default=True, description="Build freetype support")
 
-    depends_on("python@3:")
+    with when("@2022_09_5:"):
+        variant(
+            "python",
+            default=True,
+            when="@2022_09_5:",
+            description="Build standard Python wrappers",
+        )
+        variant("contrib", default=False, description="Build Contrib directory")
+        variant("freesasa", default=False, description="Build freesasa wrapper")
+        variant("coordgen", default=True, description="Build coordgen wrapper")
+        variant("maeparser", default=True, description="Build MAE parser wrapper")
+        variant("yaehmop", default=True, description="Build YAeHMOP wrapper")
+        variant("xyz2mol", default=False, description="Build support for RDKit xyz2mol")
+        variant("descriptors3d", default=True, description="Build 3D descriptors calculators")
+
+        depends_on("freesasa", when="+freesasa")
+        depends_on("coordgen", when="+coordgen")
+        depends_on("maeparser", when="+maeparser")
+        depends_on("eigen@3:", when="+descriptors3d")
+        depends_on("python@3:", when="+python")
+        depends_on("py-numpy", when="+python")
+
+        extends("python", when="+python")
+
+        conflicts("+xyz2mol", when="~yaehmop", msg="XY2MOL requires YAeHMOP")
+
     depends_on("boost@1.53.0: +python +serialization +iostreams +system")
-
-    depends_on("py-numpy")
     depends_on("sqlite")
-
     depends_on("freetype", when="@2020_09_1: +freetype")
 
-    extends("python")
+    with when("@:2021_09_5"):
+        depends_on("python@3:")
+        depends_on("py-numpy")
+        extends("python")
 
     def cmake_args(self):
-        args = ["-DCMAKE_CXX_STANDARD=14", "-DRDK_INSTALL_INTREE=OFF"]
-        args.append(self.define_from_variant("RDK_BUILD_FREETYPE_SUPPORT", "freetype"))
+        args = [
+            "-DRDK_INSTALL_INTREE=OFF",
+            self.define_from_variant("RDK_BUILD_FREETYPE_SUPPORT", "freetype"),
+        ]
+        if "@2022_09_5:" in self.spec:
+            args.extend(
+                [
+                    self.define_from_variant("RDK_BUILD_PYTHON_WRAPPERS", "python"),
+                    self.define_from_variant("RDK_BUILD_CONTRIB", "contrib"),
+                    self.define_from_variant("RDK_BUILD_FREESASA_SUPPORT", "freesasa"),
+                    self.define_from_variant("RDK_BUILD_COORDGEN_SUPPORT", "coordgen"),
+                    self.define_from_variant("RDK_BUILD_MAEPARSER_SUPPORT", "maeparser"),
+                    self.define_from_variant("RDK_BUILD_XYZ2MOL_SUPPORT", "xyz2mol"),
+                    self.define_from_variant("RDK_BUILD_DESCRIPTORS3D", "descriptors3d"),
+                ]
+            )
+
         return args