From 634d51cec2c8b72049c9f8c0e4bb0133b4e24834 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Tue, 19 Apr 2022 07:30:28 -0500
Subject: ctffind: update to version 4.1.14 and add MKL support (#30095)

- patch error in configure for 4.1.8
- use fftw-api
- enable support for MKL FFT
- add needed dependencies for libtiff and jpeg
---
 .../repos/builtin/packages/ctffind/configure.patch | 11 +++++++
 .../repos/builtin/packages/ctffind/package.py      | 37 ++++++++++++++++++++--
 2 files changed, 45 insertions(+), 3 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/ctffind/configure.patch

diff --git a/var/spack/repos/builtin/packages/ctffind/configure.patch b/var/spack/repos/builtin/packages/ctffind/configure.patch
new file mode 100644
index 0000000000..059fa2626c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ctffind/configure.patch
@@ -0,0 +1,11 @@
+--- a/configure	2022-04-10 16:38:34.597174174 -0500
++++ b/configure	2022-04-10 16:39:33.476364063 -0500
+@@ -2981,7 +2981,7 @@
+ fi
+ 
+ 
+-INPUT_CPPFLAGS="$CXXFLAGS"
++INPUT_CPPFLAGS="$CPPFLAGS"
+ INPUT_CXXFLAGS="$CXXFLAGS"
+ 
+ ac_ext=c
diff --git a/var/spack/repos/builtin/packages/ctffind/package.py b/var/spack/repos/builtin/packages/ctffind/package.py
index bc565a351d..36ac2974c1 100644
--- a/var/spack/repos/builtin/packages/ctffind/package.py
+++ b/var/spack/repos/builtin/packages/ctffind/package.py
@@ -9,10 +9,41 @@ from spack import *
 class Ctffind(AutotoolsPackage):
     """Fast and accurate defocus estimation from electron micrographs."""
 
-    homepage = "https://grigoriefflab.umassmed.edu/ctf_estimation_ctffind_ctftilt"
+    homepage = "https://grigoriefflab.umassmed.edu/ctffind4"
     url      = "https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-4.1.8.tar.gz&file=1&type=node&id=26"
 
-    version('4.1.8', sha256='bec43c0b8d32878c740d6284ef6d9d22718c80dc62270be18d1d44e8b84b2729', extension='tar.gz')
+    version('4.1.14',
+            sha256='db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5',
+            extension='tar.gz')
+    version('4.1.8',
+            sha256='bec43c0b8d32878c740d6284ef6d9d22718c80dc62270be18d1d44e8b84b2729',
+            extension='tar.gz')
+
+    def url_for_version(self, version):
+        url = "https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-{0}.tar.gz&file=1&type=node&id=26"
+        return url.format(version)
 
     depends_on('wxwidgets')
-    depends_on('fftw@3:')
+    depends_on('fftw-api')
+    depends_on('libtiff')
+    depends_on('jpeg')
+
+    patch('configure.patch', when='@4.1.8')
+
+    def configure_args(self):
+        config_args = []
+
+        if '^mkl' in self.spec:
+            config_args.extend([
+                '--enable-mkl',
+                'CPPFLAGS=-I{0}'.format(
+                    join_path(
+                        self.spec['fftw-api'].headers.directories[0], 'fftw')),
+            ])
+        else:
+            config_args.extend([
+                '--disable-mkl',
+                'CPPFLAGS={0}'.format(self.spec['fftw-api'].headers.include_flags),
+            ])
+
+        return config_args
-- 
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