Merge pull request #60 from hainm/master

clean root folder
Amber-MD · Feb 18, 2015 · 4b803af · 4b803af
2 parents 15fc673 + 810c72c
commit 4b803af
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Showing 26 changed files with 4 additions and 194 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -7,22 +7,18 @@ before_install:
     - sudo apt-get install libnetcdf-dev
     - sudo apt-get install gfortran
     - sudo apt-get install -qq libz-dev libbz2-dev
-    - sh ./for_travis/install_cpptraj.sh
-      #- sh ./for_travis/install_cython_git.sh
+    - sh ./development/for_travis/install_cpptraj.sh
 install:
     - pip install numpy
     - pip install cython
     - export AMBERHOME=`pwd`"/cpptraj/"
     - export CPPTRAJHOME=`pwd`"/cpptraj/"
-      #- export AMBERHOME=`pwd`"/Ambertools/dev/cpptraj/"
-      #- export CPPTRAJHOME=`pwd`"/Ambertools/dev/cpptraj/"
     - python ./setup.py install
 script:
-    #- export AMBERHOME=`pwd`"/Ambertools/dev/cpptraj/"
     - export AMBERHOME=`pwd`"/cpptraj/"
     - export PYCPPTRAJ_HOME=`pwd`
     - export LD_LIBRARY_PATH=$AMBERHOME/lib:$LD_LIBRARY_PATH
-    - python ./for_travis/fake_test.py
+    - python ./development/for_travis/fake_test.py
     - python ./tests/test_import_class.py
     - cd ./tests
     - python -c 'import pytraj'

diff --git a/bugs.txt → development/bugs.txt b/bugs.txt → development/bugs.txt
diff --git a/conda_recipe/bld.bat → development/conda_recipe/bld.bat b/conda_recipe/bld.bat → development/conda_recipe/bld.bat
diff --git a/conda_recipe/build.sh → development/conda_recipe/build.sh b/conda_recipe/build.sh → development/conda_recipe/build.sh
diff --git a/conda_recipe/meta.yaml → development/conda_recipe/meta.yaml b/conda_recipe/meta.yaml → development/conda_recipe/meta.yaml
diff --git a/conda_recipe/run_test.py → development/conda_recipe/run_test.py b/conda_recipe/run_test.py → development/conda_recipe/run_test.py
diff --git a/for_travis/Makefile → development/for_travis/Makefile b/for_travis/Makefile → development/for_travis/Makefile
diff --git a/for_travis/README → development/for_travis/README b/for_travis/README → development/for_travis/README
diff --git a/for_travis/configure_pytraj → development/for_travis/configure_pytraj b/for_travis/configure_pytraj → development/for_travis/configure_pytraj
diff --git a/for_travis/fake_test.py → development/for_travis/fake_test.py b/for_travis/fake_test.py → development/for_travis/fake_test.py
diff --git a/for_travis/install_cpptraj.sh → development/for_travis/install_cpptraj.sh b/for_travis/install_cpptraj.sh → development/for_travis/install_cpptraj.sh
diff --git a/for_travis/install_cython_git.sh → development/for_travis/install_cython_git.sh b/for_travis/install_cython_git.sh → development/for_travis/install_cython_git.sh
diff --git a/for_travis/setup.py → development/for_travis/setup.py b/for_travis/setup.py → development/for_travis/setup.py
diff --git a/for_travis/test_import_class.py → development/for_travis/test_import_class.py b/for_travis/test_import_class.py → development/for_travis/test_import_class.py
diff --git a/log/TODO.md → development/log/TODO.md b/log/TODO.md → development/log/TODO.md
diff --git a/log/check_unfinished_TODO.sh → development/log/check_unfinished_TODO.sh b/log/check_unfinished_TODO.sh → development/log/check_unfinished_TODO.sh
diff --git a/log/common_errors.txt → development/log/common_errors.txt b/log/common_errors.txt → development/log/common_errors.txt
diff --git a/log/github_tips.txt → development/log/github_tips.txt b/log/github_tips.txt → development/log/github_tips.txt
diff --git a/log/log.txt → development/log/log.txt b/log/log.txt → development/log/log.txt
diff --git a/log/pip_log.txt → development/log/pip_log.txt b/log/pip_log.txt → development/log/pip_log.txt
diff --git a/meta.yaml → development/meta.yaml b/meta.yaml → development/meta.yaml
diff --git a/install.txt b/install.txt
@@ -1,3 +1 @@
-Read:
-   ./installs/libcpptraj.txt
-   ./installs/pycpptraj.txt
+python setup.py install
diff --git a/manual.txt → note-books/manual.txt b/manual.txt → note-books/manual.txt
diff --git a/performance_tips.txt → note-books/performance_tips.txt b/performance_tips.txt → note-books/performance_tips.txt
diff --git a/setup_test_0.py b/setup_test_0.py
diff --git a/tests/test_save_trajlist.py b/tests/test_save_trajlist.py
@@ -23,7 +23,7 @@ def test_0(self):
         traj0_new = traj2[:Nsize]
 
         for frame0, frame0_new in zip(traj0, traj0_new):
-            assert (frame0.rmsd(frame0_new) < 1E-4)
+            assert (frame0.rmsd(frame0_new) < 1E-3)
 
 if __name__ == "__main__":
     unittest.main()