Update readme and add missing file

README.md

@@ -1,5 +1,4 @@
-SPAGeDi
-=======
+# SPAGeDi
 
 SPAGeDi: Spatial Pattern Analysis of Genetic Diversity  
 Copyright &copy; 2002&ndash;2009 Olivier Hardy (<[email protected]>) and Xavier Vekemans
@@ -8,46 +7,39 @@ Portable/Unix source code maintained by Reed A. Cartwright (<[email protected]>
 
 Website: <http://ebe.ulb.ac.be/ebe/SPAGeDi.html>  
 GitHub: <https://github.com/reedacartwright/spagedi>  
-Downloads: <http://scit.us/spagedi/>  
 
-License
--------
+## License
 
 This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 
 This program is distributed in the hope that it will be useful, but **without any warranty**; without even the implied warranty of **merchantability** or **fitness for a particular purpose**.  See the GNU General Public License for more details.
 
 You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-Citation
---------
+## Citation
 
 [Hardy OJ & Vekemans X (2002)](http://iee.ulb.ac.be/sciences/lagev/fichiers/Spagedi_MENotes2002.pdf) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2: 618&ndash;620.
 
-Nota Bene
----------
+## Nota Bene
 
 SPAGeDi has been tested on several data sets and results were checked for consistency with alternative softwares whenever possible. It may nevertheless still contain bugs (corrected bugs are listed at the end of the manual). Some of these bugs are probably easy to detect by causing the program to crash or leading to obvious erroneous results for particular data sets and analyses. But others, more critical, may just cause biased results that appear plausible. Hence, it is advised to take much care checking the consistency of the information from the results file. The authors would appreciate being informed of any detected bug. The authors claim no responsibility if or whenever a bug causes a misinterpretation of the results given by SPAGeDi.
 
-Using SPAGeDi
--------------
+## Using SPAGeDi
 
 See manual.pdf for detailed instructions on using SPAGeDi.
 
-Downloading and Installing
---------------------------
+## Downloading and Installing
 
-Binary packages for SPAGeDi can be downloaded from <http://scit.us/spagedi/>.
+Source code for SPAGeDi can be downloaded from <https://github.com/reedacartwright/spagedi/releases>.
 
-Compiling from Source Code
---------------------------
+### Compiling from Source Code
 
-SPAGeDi requires CMake 2.8 (<http://www.cmake.org/>) to build it from sources.  Many Unix-like operating systems can install CMake through their package systems.
+SPAGeDi requires CMake (<http://www.cmake.org/>) to build it from sources.  Many Unix-like operating systems can install CMake through their package systems.
 
-Download the SPAGeDi source code (<http://scit.us/spagedi/>) and issue the following commands:
+Download the SPAGeDi source code (from <https://github.com/reedacartwright/spagedi/releases>) and issue the following commands:
 
-	tar xvzf SPAGeDi-.*.tar.bz2
-	cd SPAGeDi-.*/build
+	tar xvzf spagedi-*.tar.bz2
+	cd spagedi-*/build
 	cmake ..
 	make
 	make install
@@ -60,9 +52,17 @@ The '-G' option to cmake is used to specify different build systems, e.g. Unix M
 	make
 	make install
 
-This will build an optimized version of SPAGeDi and install it to '/usr/bin'. To specify your own build flags you need to set the environment variables CFLAGS and LDFLAGS as neccessary.  Then specify
+This will build an optimized version of SPAGeDi and install it to '/usr/bin'. To specify your own build flags you need to set the environment variables CFLAGS and LDFLAGS as necessary.  Then specify
 
 	cmake -DCMAKE_BUILD_TYPE= .
 
 See CMake's manual for additional information.
 
+### Compiling from Source Code (alternative)
+
+If you are having trouble getting CMake to work, you can try to compile manually.
+
+	cd spagedi-*/src
+	gcc -O2 -o ./spagedi *.c -lm
+
+You will then have a `spagedi-*/src/spagedi` binary that you can copy wherever is useful to you.

cmake_uninstall.cmake.in

@@ -0,0 +1,21 @@
+if(NOT EXISTS "@CMAKE_BINARY_DIR@/install_manifest.txt")
+  message(FATAL_ERROR "Cannot find install manifest: @CMAKE_BINARY_DIR@/install_manifest.txt")
+endif(NOT EXISTS "@CMAKE_BINARY_DIR@/install_manifest.txt")
+
+file(READ "@CMAKE_BINARY_DIR@/install_manifest.txt" files)
+string(REGEX REPLACE "\n" ";" files "${files}")
+foreach(file ${files})
+  message(STATUS "Uninstalling $ENV{DESTDIR}${file}")
+  if(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}")
+    exec_program(
+      "@CMAKE_COMMAND@" ARGS "-E remove \"$ENV{DESTDIR}${file}\""
+      OUTPUT_VARIABLE rm_out
+      RETURN_VALUE rm_retval
+      )
+    if(NOT "${rm_retval}" STREQUAL 0)
+      message(FATAL_ERROR "Problem when removing $ENV{DESTDIR}${file}")
+    endif(NOT "${rm_retval}" STREQUAL 0)
+  else(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}")
+    message(STATUS "File $ENV{DESTDIR}${file} does not exist.")
+  endif(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}")
+endforeach(file)