Restore .travis.yml; fix scons conda install and update rna_suites fu…

…llhelp

.travis.yml

@@ -0,0 +1,50 @@
+language: cpp
+
+branches:
+  only:
+    - master
+
+matrix:
+  include:
+    - os: linux
+    - os: osx
+      osx_image: xcode10.1
+
+
+#addons:
+#  apt:
+#     packages:
+#      - scons
+#      - libboost-all-dev
+#      - libboost-regex-dev
+#      - libatlas-base-dev
+#      - libnetcdf-dev
+#      - swig
+#      - python3-dev
+#      - python3-numpy
+#      - python3-scipy
+#      - libeigen3-dev
+#
+#before_install:
+#  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update          ; fi
+##  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install boost; fi
+##  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install netcdf; fi
+#  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install swig; fi
+#  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install doxygen; fi
+#  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install graphviz; fi
+#  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install scons; fi
+#  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install eigen; fi
+
+install:
+    - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+          wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+      elif [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+          wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
+      fi
+    - bash miniconda.sh -b -p $HOME/miniconda
+    - source "$HOME/miniconda/etc/profile.d/conda.sh"
+    - hash -r
+    - conda config --set always_yes yes --set changeps1 no
+
+script:
+    - ./conda_build.sh loos 1

Tools/rna_suites.cpp

@@ -91,11 +91,12 @@ string fullHelpMessage(void) {
 "    reference suites on the command-line. The format is explained in the next\n"
 "    section. An example of the format that implements the suites as defined in\n"
 "    the software suitename (Richardson et al. (2008) RNA 14, 465-481) is\n"
-"    included as $PREFIX/share/suitename_definitions.dat, where $PREFIX is the\n"
-"    PREFIX argument given to \"scons install\". The default scons prefix is\n"
-"    PREFIX=/opt/LOOS. This suitename_defintions.dat file should be sufficient\n"
-"    for typical users, but you must specify the path to it as the first\n"
-"    positional argument.\n"
+"    included as share/suitename_definitions.dat in the top-level directory of\n"
+"    the LOOS source tree. If installing within a conda environment, this file\n"
+"    can also be found in $CONDA_PREFIX/share/loos/suitename_definitions.dat;\n"
+"    otherwise, it can be found in $LOOS/share/suitename_definitions.dat. The\n"
+"    suitename_defintions.dat file should be sufficient for typical users, but\n"
+"    you must specify the path to it as the first positional argument.\n"
 "\n"
 "SUITE DEFINITON FILE FORMAT\n"
 "    Each line in the file is parsed as a record containing fields with a width\n"
@@ -126,14 +127,14 @@ string fullHelpMessage(void) {
 "        is given in field 2 and maximum value in field 3.\n"
 "\n"
 "EXAMPLES\n"
-"    rna_suites $CONDA_PREFIX/share/suitename_defintions.dat foo.pdb foo.dcd\n"
+"    rna_suites $CONDA_PREFIX/share/loos/suitename_defintions.dat foo.pdb foo.dcd\n"
 "        Assign backbone suites using the install prefix from a conda install.\n"
 "\n"
-"    rna_suites -s 'resid <= 10' $CONDA_PREFIX/share/suitename_defintions.dat \\\n"
+"    rna_suites -s 'resid <= 10' $CONDA_PREFIX/share/loos/suitename_defintions.dat \\\n"
 "        foo.pdb foo.dcd\n"
 "        Assign backbone suites only for the first 10 residues.\n"
 "\n"
-"    rna_suites -c 0.001 $CONDA_PREFIX/share/suitename_defintions.dat \\\n"
+"    rna_suites -c 0.001 $CONDA_PREFIX/share/loos/suitename_defintions.dat \\\n"
 "        foo.pdb foo.dcd\n"
 "        Assign backbone suites using a minimum suiteness of 0.001 for\n"
 "        non-outliers.\n";

share/SConscript

@@ -29,7 +29,12 @@ clone.Prepend(LIBS = [loos])
 
 files = 'suitename_definitions.dat'
 PREFIX = env['PREFIX']
-share_path = os.path.join(PREFIX, "share")
+
+if env.USING_CONDA:
+    share_path = os.path.join(PREFIX, "share", "loos")
+else:
+    share_path = os.path.join(PREFIX, "share")
+
 shared_files = env.Install(share_path, Split(files))
 
 shared_list = Split(files)