Add Reseek (#51882)

* Add Reseek

* Fix move command

* Remove ARM support

* Change compiler

* Add `conda_build_config.yaml`

* Add `{{ stdlib("c") }}`

* Remove `{{ stdlib("c") }}`

* Update `conda_build_config.yaml`

* Update `conda_build_config.yaml`

* Update compiler

* Try to add C compyler

* Skip OSX

recipes/reseek/build.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+set -e
+
+mkdir -p ${PREFIX}/bin
+cd src || exit 1
+echo "0" > gitver.txt
+
+cp ${RECIPE_DIR}/vcxproj_make.py .
+chmod +x vcxproj_make.py
+./vcxproj_make.py --openmp --cppcompiler ${CXX} --ccompiler ${CC}
+
+# Verify binary exists and is executable
+if [ ! -f ../bin/reseek ]; then
+    echo "Error: reseek binary not found"
+    exit 1
+fi
+
+cp ../bin/reseek ${PREFIX}/bin/reseek

recipes/reseek/meta.yaml

@@ -0,0 +1,32 @@
+{% set name = "reseek" %}
+{% set version = "2.0.1" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/rcedgar/reseek/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 79a2aca249547a164ff7a6460abc6875c182a40693ac07068cc859b7cb7a95ec
+
+build:
+  number: 0
+  skip: True  #[osx]
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+
+
+requirements:
+  build:
+    - {{ compiler("cxx") }}
+    - {{ compiler("c") }}
+    - make
+
+test:
+  commands:
+    - reseek -version
+about:
+  home: https://github.com/rcedgar/reseek
+  license: GPL-3.0-only
+  license_file: LICENSE
+  summary: Protein structure alignment and search algorithm

recipes/reseek/vcxproj_make.py

@@ -0,0 +1,225 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+import sys
+
+Usage = (
+    "Convert Visual Studio .vcxproj file in current directory to Makefile and run make."
+)
+
+AP = argparse.ArgumentParser(description=Usage)
+
+# Value opts
+AP.add_argument(
+    "--std",
+    required=False,
+    help="C++ standard option for GCC, e.g. c++11 or c++17 (default none)",
+)
+AP.add_argument(
+    "--cppcompiler",
+    required=False,
+    default="g++",
+    help="C++ compiler command name default g++)",
+)
+AP.add_argument(
+    "--ccompiler",
+    required=False,
+    default="gcc",
+    help="C++ compiler command name default gcc)",
+)
+
+# Flag opts
+AP.add_argument("--debug", required=False, action="store_true", help="Debug build")
+AP.add_argument("--openmp", required=False, action="store_true", help="Requires OMP")
+AP.add_argument(
+    "--pthread", required=False, action="store_true", help="Requires pthread"
+)
+AP.add_argument("--lrt", required=False, action="store_true", help="Requires lrt")
+AP.add_argument(
+    "--symbols",
+    required=False,
+    action="store_true",
+    help="Debug symbols (default if --debug)",
+)
+AP.add_argument(
+    "--nostrip",
+    required=False,
+    action="store_true",
+    help="Don't strip symbols (default if --debug or --symbols)",
+)
+
+Args = AP.parse_args()
+debug = Args.debug
+std = Args.std
+cppcompiler = Args.cppcompiler
+ccompiler = Args.ccompiler
+nostrip = debug or Args.symbols
+symbols = debug or Args.symbols
+
+ProjFileName = None
+HdrNames = []
+for FileName in os.listdir("."):
+    if FileName.endswith(".vcxproj"):
+        ProjFileName = FileName
+    elif FileName.endswith(".h"):
+        HdrNames.append(FileName)
+if ProjFileName is None:
+    sys.stderr.write("\nProject file not found in current directory\n")
+    sys.exit(1)
+
+binary = ProjFileName.replace(".vcxproj", "")
+sys.stderr.write("binary=" + binary + "\n")
+
+compiler_opts = " -ffast-math -march=native"
+linker_opts = " -ffast-math -march=native"
+
+if std:
+    compiler_opts += " --std=" + std
+
+if debug:
+    compiler_opts += " -O0 -DDEBUG"
+    linker_opts += " -O0"
+else:
+    compiler_opts += " -O3 -DNDEBUG"
+    linker_opts += " -O3"
+
+if symbols:
+    compiler_opts += " -g3"
+    linker_opts += " -g3"
+
+if Args.openmp:
+    compiler_opts += " -fopenmp"
+    linker_opts += " -fopenmp"
+
+if Args.pthread:
+    compiler_opts += " -pthread"
+    linker_opts += " -lpthread"
+
+rc = os.system(r"rm -rf o/ ../bin/%s*" % binary)
+if rc != 0:
+    sys.stderr.write("\n\nERROR -- failed to clean\n\n")
+    sys.exit(1)
+sys.stderr.write("clean done.\n")
+
+OBJDIR = "o"
+BINDIR = "../bin"
+
+Fields = ProjFileName.split("/")
+n = len(Fields)
+Name = Fields[n - 1]
+Fields = Name.split(".")
+binary = Fields[0]
+
+CXXNames = []
+CNames = []
+with open(ProjFileName) as File:
+    for Line in File:
+        Line = Line.strip()
+        Line = Line.replace('"', "")
+        Line = Line.replace(" ", "")
+        # <ClCompile Include="betadiv.cpp" />
+        if Line.startswith("<ClCompileInclude"):
+            Fields = Line.split("=")
+            if len(Fields) != 2:
+                continue
+            FileName = Fields[1]
+            FileName = FileName.replace("/>", "")
+            if FileName.endswith(".cpp"):
+                FileName = FileName.replace(".cpp", "")
+                CXXNames.append(FileName)
+            elif FileName.endswith(".c"):
+                FileName = FileName.replace(".c", "")
+                CNames.append(FileName)
+
+assert len(CXXNames) > 0 or len(CNames) > 0
+
+with open("Makefile", "w") as f:
+
+    def Out(s):
+        print(s, file=f)
+
+    BINPATH = "$(BINDIR)/%s" % (binary)
+
+    Out("######################################################")
+    Out("# Makefile is generated by " + sys.argv[0])
+    Out("# Don't edit the Makefile -- update the python script")
+    Out("######################################################")
+    Out("")
+    Out("BINDIR := %s" % BINDIR)
+    Out("OBJDIR := %s" % OBJDIR)
+    Out("BINPATH := %s" % BINPATH)
+
+    if CNames:
+        Out("")
+        Out("CC = " + ccompiler)
+        Out("CFLAGS := $(CFLAGS) " + compiler_opts)
+
+    if CXXNames:
+        Out("")
+        Out("CXX = " + cppcompiler)
+        Out("CXXFLAGS := $(CFLAGS) " + compiler_opts)
+
+    Out("")
+    Out("UNAME_S := $(shell uname -s)")
+    Out("LDFLAGS := $(LDFLAGS) " + linker_opts)
+    Out("ifeq ($(UNAME_S),Linux)")
+    Out("    LDFLAGS += -static")
+    Out("endif")
+
+    Out("")
+    Out("HDRS = \\")
+    for Name in sorted(HdrNames):
+        Out("  %s \\" % Name)
+
+    Out("")
+    Out("OBJS = \\")
+    for Name in CXXNames:
+        Out("  $(OBJDIR)/%s.o \\" % (Name))
+
+    for Name in CNames:
+        Out("  $(OBJDIR)/%s.o \\" % (Name))
+
+    Out("")
+    Out(".PHONY: clean")
+
+    Out("")
+    Out("$(BINPATH) : $(BINDIR)/ $(OBJDIR)/ $(OBJS)")
+
+    if len(CXXNames) > 0:
+        Cmd = "\t$(CXX) $(LDFLAGS) $(OBJS) -o $(BINPATH)"
+    else:
+        Cmd = "\t%(CC) $(LDFLAGS) $(OBJS) -o $(BINPATH)"
+
+    if Args.lrt:
+        Cmd += " -lrt"
+    Out(Cmd)
+
+    if not nostrip:
+        Out("	strip $(BINPATH)")
+
+    Out("")
+    Out("$(OBJDIR)/ :")
+    Out("	mkdir -p $(OBJDIR)/")
+
+    Out("")
+    Out("$(BINDIR)/ :")
+    Out("	mkdir -p $(BINDIR)/")
+
+    if CNames:
+        Out("")
+        Out("$(OBJDIR)/%.o : %.c $(HDRS)")
+        Out("	$(CC) $(CPPFLAGS) $(CFLAGS) -c -o $@ $<")
+
+    if CXXNames:
+        Out("")
+        Out("$(OBJDIR)/%.o : %.cpp $(HDRS)")
+        Out("	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<")
+
+sys.stderr.write("Makefile done.\n")
+
+rc = os.system("make")
+if rc != 0:
+    sys.stderr.write("\n\nERROR -- make failed\n\n")
+    sys.exit(1)
+sys.stderr.write("make done.\n")