Merge pull request #147486 from pmiddend/crystfel-init

CrystFEL: init at 0.10.1

4 files changed, 325 insertions, 0 deletions

diff --git a/pkgs/applications/science/physics/crystfel/0002-fix-ftbfs-with-gcc-10.patch b/pkgs/applications/science/physics/crystfel/0002-fix-ftbfs-with-gcc-10.patch
new file mode 100644
index 00000000000..ddd91aec9a6
--- /dev/null
+++ b/pkgs/applications/science/physics/crystfel/0002-fix-ftbfs-with-gcc-10.patch
@@ -0,0 +1,43 @@
+Description: Fixing argument mismatches in Fortran code, addressing #957430.
+Author: Andrius Merkys <merkys@debian.org>
+Forwarded: ccp4-dev@dl.ac.uk
+--- a/fortran/pack_f.f
++++ b/fortran/pack_f.f
+@@ -106,7 +106,7 @@
+          endif
+  10   continue
+       filnarray(len(filn) + 1) = 0
+-      call pack_wordimage_f(data, x, y, filnarray)
++      call pack_longimage_f(data, x, y, filnarray)
+       return
+       end
+ 
+@@ -138,7 +138,7 @@
+          endif
+  10   continue
+       filnarray(len(filn) + 1) = 0
+-      call v2pack_wordimage_f(data, x, y, filnarray)
++      call v2pack_longimage_f(data, x, y, filnarray)
+       return
+       end
+ 
+--- a/fortran/lgglib.f
++++ b/fortran/lgglib.f
+@@ -1236,7 +1236,7 @@
+       B3(2) = XYZ(2) * CELL(2)
+       B3(3) = XYZ(3) * CELL(3)
+ C
+-      CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
++      CALL matmult(3,3,3,1,ORTH,B3,XYZ)
+       END
+ c
+ c
+@@ -1274,7 +1274,7 @@
+       B3(1) = XYZ(1)
+       B3(2) = XYZ(2)
+       B3(3) = XYZ(3)
+-      CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
++      CALL matmult(3,3,3,1,ORTH,B3,XYZ)
+       END
+       character*80 function getnam(filnam)
+       character*(*) filnam
diff --git a/pkgs/applications/science/physics/crystfel/default.nix b/pkgs/applications/science/physics/crystfel/default.nix
new file mode 100644
index 00000000000..85b18eb82fd
--- /dev/null
+++ b/pkgs/applications/science/physics/crystfel/default.nix
@@ -0,0 +1,226 @@
+{ lib
+, stdenv
+, fetchurl
+, fetchFromGitHub
+, cmake
+, lz4
+, bzip2
+, gfortran
+, m4
+, hdf5
+, gsl
+, slurm
+, unzip
+, makeWrapper
+, meson
+, git
+, ninja
+, eigen
+, pkg-config
+, wrapGAppsHook
+, flex
+, bison
+, doxygen
+, opencl-headers
+, ncurses
+, msgpack
+, fftw
+, zeromq
+, ocl-icd
+, gtk3
+, gdk-pixbuf
+, argp-standalone
+, memorymappingHook
+, withGui ? true
+, withBitshuffle ? true
+}:
+
+let
+  libccp4 = stdenv.mkDerivation rec {
+    pname = "libccp4";
+    version = "6.5.1";
+    src = fetchurl {
+      # Original mirror, now times out
+      # url = "ftp://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
+      url = "https://deb.debian.org/debian/pool/main/libc/${pname}/${pname}_${version}.orig.tar.gz";
+      sha256 = "1rfvjliny29vy5bdi6rrjaw9hhhhh72pw536xwvqipqcjlylf2r8";
+    };
+    nativeBuildInputs = [ gfortran m4 ];
+    buildInputs = [ hdf5 gsl ];
+
+    configureFlags = [ "FFLAGS=-fallow-argument-mismatch" ];
+
+    # libccp4 tries to read syminfo.lib by looking at an environment variable, which hinders reproducibility.
+    # We hard-code this by providing a little patch and then passing the absolute path to syminfo.lib as a
+    # preprocessor flag.
+    preBuild = ''
+      makeFlagsArray+=(CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"$out/share/syminfo.lib\"')
+      export NIX_LDFLAGS="-L${gfortran.cc}/lib64 -L${gfortran.cc}/lib $NIX_LDFLAGS";
+    '';
+    makeFlags = [ "CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/syminfo.lib\"" ];
+
+    patches = [
+      ./libccp4-use-hardcoded-syminfo-lib.patch
+      ./0002-fix-ftbfs-with-gcc-10.patch
+    ];
+  };
+  # This is the statically-linked, pre-built binary of mosflm. Compiling it ourselves turns out to be very difficult
+  # since the build process is very hard-coded for a specific machine, architecture, and libraries.
+  mosflm =
+    let
+      version = "7.4.0";
+      src =
+        if stdenv.isDarwin then
+          fetchurl
+            {
+              url = "https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/ver${builtins.replaceStrings [ "." ] [ "" ] version}/pre-built/mosflm-osx-64-noX11.zip";
+              sha256 = "1da5wimv3kl8bccp49j69vh8gi28cn7axg59lrmb38s68c618h7j";
+            }
+        else
+          fetchurl {
+            url = "https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/ver${builtins.replaceStrings [ "." ] [ "" ] version}/pre-built/mosflm-linux-64-noX11.zip";
+            sha256 = "1rqh3nprxfmnyihllw31nb8i3wfhybmsic6y7z6wn4rafyv3w4fk";
+          };
+      mosflmBinary = if stdenv.isDarwin then "bin/mosflm" else "mosflm-linux-64-noX11";
+    in
+    stdenv.mkDerivation rec {
+      pname = "mosflm";
+
+      inherit version src;
+
+      dontBuild = true;
+
+      nativeBuildInputs = [ unzip makeWrapper ];
+
+      sourceRoot = ".";
+
+      # mosflm statically links against its own libccp4, which as the syminfo.lib environment variable problem.
+      # Here, we circumvent it by creating a little wrapper script that calls mosflm after setting the SYMINFO variable.
+      installPhase = ''
+        mkdir -p $out/bin
+        cp ${mosflmBinary} $out/bin/mosflm-raw
+        makeWrapper $out/bin/mosflm-raw $out/bin/mosflm --set SYMINFO ${libccp4}/share/syminfo.lib --add-flags -n
+      '';
+    };
+
+  xgandalf = stdenv.mkDerivation rec {
+    pname = "xgandalf";
+    version = "c15afa2381d5f87d4aefcc8181a15b4a6fd3a955";
+    src = fetchurl {
+      url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
+      sha256 = "11i1w57a3rpnb4x5y4n8d3iffn5m9w1zydl69syzljdk3aqg2pv8";
+    };
+
+    nativeBuildInputs = [ meson pkg-config ninja ];
+    buildInputs = [ eigen ];
+  };
+
+  pinkIndexer = stdenv.mkDerivation rec {
+    pname = "pinkindexer";
+    version = "8a828788f8272a89d484b00afbd2500c2c1ff974";
+    src = fetchurl {
+      url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
+      sha256 = "1mkgf1xd91ay0z0632kzxm0z3wcxf0cayjvs6a3znds72dkhfsyh";
+    };
+
+    nativeBuildInputs = [ meson pkg-config ninja ];
+    buildInputs = [ eigen ];
+  };
+
+  fdip = stdenv.mkDerivation rec {
+    pname = "fdip";
+    version = "29da626f17f66d5c0780fc59b1eafb7c85b81dd6";
+    src = fetchurl {
+      url = "https://gitlab.desy.de/philipp.middendorf/fdip/-/archive/${version}/fdip-${version}.tar.gz";
+      sha256 = "184l76r4fgznq54rnhgjk7dg41kqdl0d1da02vr5y4cs2fyqppky";
+    };
+
+    nativeBuildInputs = [ meson ninja pkg-config ];
+    buildInputs = [ eigen ];
+  };
+
+  hdf5-external-filter-plugins = stdenv.mkDerivation rec {
+    pname = "HDF5-External-Filter-Plugins";
+    version = "0.1.0";
+    src = fetchFromGitHub {
+      owner = "nexusformat";
+      repo = pname;
+      rev = "d469f175e5273c1d488e71a6134f84088f57d39c";
+      sha256 = "1jrzzh75i68ad1yrim7s1nx9wy0s49ghkziahs71mm5azprm6gh9";
+    };
+
+    nativeBuildInputs = [ cmake ];
+    buildInputs = [ hdf5 lz4 bzip2 ];
+
+    cmakeFlags = [
+      "-DENABLE_BITSHUFFLE_PLUGIN=yes"
+      "-DENABLE_LZ4_PLUGIN=yes"
+      "-DENABLE_BZIP2_PLUGIN=yes"
+    ];
+  };
+in
+stdenv.mkDerivation rec {
+  pname = "crystfel";
+  version = "0.10.1";
+  src = fetchurl {
+    url = "https://www.desy.de/~twhite/${pname}/${pname}-${version}.tar.gz";
+    sha256 = "0i9d5ggalic7alj97dxjdys7010kxhm2cb4lwakvigl023j8ms79";
+  };
+  nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers ]
+    ++ lib.optionals withGui [ wrapGAppsHook ];
+  buildInputs = [
+    hdf5
+    gsl
+    ncurses
+    msgpack
+    fftw
+    fdip
+    zeromq
+    ocl-icd
+    libccp4
+    mosflm
+    pinkIndexer
+    xgandalf
+  ] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]
+  ++ lib.optionals stdenv.isDarwin [
+    argp-standalone
+    memorymappingHook
+  ]
+  # slurm is not available for Darwin; when it is, remove the condition
+  ++ lib.optionals (!stdenv.isDarwin) [ slurm ]
+  # hdf5-external-filter-plugins doesn't link on Darwin
+  ++ lib.optionals (withBitshuffle && !stdenv.isDarwin) [ hdf5-external-filter-plugins ];
+
+  patches = [ ./link-to-argp-standalone-if-needed.patch ];
+
+  # CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but
+  # we'd have to do that for every CrystFEL executable (indexamajig, crystfel, partialator). Better to just
+  # hard-code mosflm's path once.
+  postPatch = ''
+    sed -i -e 's#execlp("mosflm"#execl("${mosflm}/bin/mosflm"#' libcrystfel/src/indexers/mosflm.c;
+  '';
+
+  postInstall = lib.optionalString (withBitshuffle && !stdenv.isDarwin) ''
+    for file in $out/bin/*; do
+      wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins
+    done
+  '';
+
+  meta = with lib; {
+    description = "Data processing for serial crystallography";
+    longDescription = ''
+      CrystFEL is a suite of programs for processing (and simulating) Bragg diffraction data from "serial crystallography" experiments, often (but not always) performed using an X-ray Free-Electron Laser. Compared to rotation data, some of the particular characteristics of such data which call for a specialised software suite are:
+
+      - The sliced, rather than integrated, measurement of intensity data. Many, if not all reflections are partially integrated.
+      - Many patterns (thousands) are required - high throughput is needed.
+      - The crystal orientations in each pattern are random and uncorrelated.
+      - Merging into lower symmetry point groups may require the resolution of indexing ambiguities.'';
+    homepage = "https://www.desy.de/~twhite/crystfel/";
+    changelog = "https://www.desy.de/~twhite/crystfel/changes.html";
+    downloadPage = "https://www.desy.de/~twhite/crystfel/download.html";
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [ pmiddend ];
+    platforms = [ "x86_64-linux" "x86_64-darwin" ];
+  };
+
+}
diff --git a/pkgs/applications/science/physics/crystfel/libccp4-use-hardcoded-syminfo-lib.patch b/pkgs/applications/science/physics/crystfel/libccp4-use-hardcoded-syminfo-lib.patch
new file mode 100644
index 00000000000..9c5e1365492
--- /dev/null
+++ b/pkgs/applications/science/physics/crystfel/libccp4-use-hardcoded-syminfo-lib.patch
@@ -0,0 +1,30 @@
+diff --git a/ccp4/csymlib.c b/ccp4/csymlib.c
+index 76bc70b..7a0c5dc 100644
+--- a/ccp4/csymlib.c
++++ b/ccp4/csymlib.c
+@@ -137,24 +137,7 @@ CCP4SPG *ccp4spg_load_spacegroup(const int numspg, const int ccp4numspg,
+   }
+ 
+   /* Open the symop file: */
+-  if (!(symopfile = getenv("SYMINFO"))) {
+-    if (debug)
+-      printf("Environment variable SYMINFO not set ... guessing location of symmetry file. \n");
+-    if (!(ccp4dir = getenv("CLIBD"))) {
+-      printf("Environment variable CLIBD not set ... big trouble! \n");
+-      return NULL;
+-    }
+-
+-    symopfile = ccp4_utils_malloc((strlen(ccp4dir)+22)*sizeof(char));
+-    strcpy(symopfile,ccp4_utils_joinfilenames(ccp4dir,"syminfo.lib"));
+-    symopfile[strlen(ccp4dir)+21] = '\0';
+-    ccp4printf(1," SYMINFO file set to %s \n",symopfile);
+-  } else {
+-    if (debug) {
+-      ccp4printf(1,"\n Spacegroup information obtained from library file: \n");
+-      ccp4printf(1," Logical Name: SYMINFO   Filename: %s\n\n",symopfile);
+-    }
+-  }
++  symopfile = NIX_PROVIDED_SYMOP_FILE;
+ 
+   filein = fopen(symopfile,"r");
+   if (!filein) {
diff --git a/pkgs/applications/science/physics/crystfel/link-to-argp-standalone-if-needed.patch b/pkgs/applications/science/physics/crystfel/link-to-argp-standalone-if-needed.patch
new file mode 100644
index 00000000000..707ecafde8b
--- /dev/null
+++ b/pkgs/applications/science/physics/crystfel/link-to-argp-standalone-if-needed.patch
@@ -0,0 +1,26 @@
+diff --git a/meson.build b/meson.build
+index efc9002b..070f37e4 100644
+--- a/meson.build
++++ b/meson.build
+@@ -34,6 +34,12 @@ if slurmdep.found()
+   conf_data.set10('HAVE_SLURM', 1)
+ endif
+ 
++if build_machine.system() == 'darwin' or build_machine.system() == 'freebsd' or not cc.links('#include <argp.h>\nstatic error_t parse_opt (int key, char *arg, struct argp_state *state) { argp_usage(state); return 0; }; void main() {}')
++    argpdep = cc.find_library('argp')
++else
++    argpdep = dependency('', required : false)
++endif
++
+ # Find HDF5 using inbuilt Meson methods.  Requires Meson >= 0.50.0
+ hdf5dep = dependency('hdf5', language: 'c', required: true)
+ 
+@@ -180,7 +186,7 @@ if zmqdep.found()
+ endif
+ 
+ executable('indexamajig', indexamajig_sources,
+-           dependencies: [mdep, libcrystfeldep, gsldep, pthreaddep, zmqdep],
++           dependencies: [mdep, libcrystfeldep, gsldep, pthreaddep, zmqdep, argpdep],
+            install: true,
+            install_rpath: '$ORIGIN/../lib64/:$ORIGIN/../lib')
+