Merge branch 'python3'

.gitignore

@@ -11,6 +11,7 @@ loos.py
 loos/__init__.py
 setup.sh
 setup.csh
+custom.py
 
 # Library files
 *.so

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = LOOS
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v2.3.3-beta
+PROJECT_NUMBER         = v3.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

INSTALL.md

@@ -3,52 +3,52 @@
                    | LOOS    | PyLOOS  |
 Operating System   | Support | Support | Notes
 ----------------   | ------- | ------- | -----
-Fedora 17          | yes     | yes     | Unsupported
 Fedora 18          | yes     | yes     | Deprecated
-Fedora 19          | yes     | yes     |
-Fedora 20          | yes     | yes     |
-Fedora 21          | yes     | yes     |
-Fedora 22          | yes     | yes     |
-Fedora 23          | yes     | yes     |
-Fedora 24          | yes     | yes     |
-Fedora 25          | yes     | yes     |
-Ubuntu 12.04 LTS   | yes     | yes     |
-Ubuntu 14.04 LTS   | yes     | yes     |
-Ubuntu 15.04       | yes     | yes     |
-Ubuntu 15.10       | yes     | yes     |
-Ubuntu 16.04 LTS   | yes     | yes     |
-Debian 7.8         | yes     | yes     |
-Debian 8.1         | yes     | yes     |
-Centos 6.7         | yes     | yes     | See OS notes
-Centos 7           | yes     | yes     | See OS notes
-OpenSUSE 12        | yes     | yes     | See OS notes
-OpenSUSE 13        | yes     | yes     |
-Manjaro 0.8        | yes     | yes     | Unsupported
-Mint 17            | yes     | yes     | Unsupported
-Mint 18            | yes     | yes     |
-Slackware 14.1     | yes     | yes     | Unsupported
-Windows 7 (Cygwin) | yes     | no      | Unsupported
-MacOS 10.11        | yes     | yes     | See OS notes
-
-
-* Deprecated: We used to support thsi configuration, but no longer test it.  It may still work.
+Fedora 19          | yes     | yes     | Deprecated
+Fedora 20          | yes     | yes     | Deprecated
+Fedora 21          | yes     | yes     | Deprecated
+Fedora 22          | yes     | yes     | Deprecated
+Fedora 23          | yes     | yes     | Deprecated
+Fedora 24          | yes     | yes     | Deprecated
+Fedora 25          | yes     | yes     | Deprecated
+Fedora 26          | yes     | yes     | Deprecated
+Fedora 27          | yes     | yes     | Deprecated
+Fedora 28          | yes     | yes     | 
+Fedora 29          | yes     | yes     |
+Ubuntu 12.04 LTS   | yes     | yes     | Deprecated
+Ubuntu 14.04 LTS   | yes     | yes     | Deprecated
+Ubuntu 15.04       | yes     | yes     | Deprecated
+Ubuntu 15.10       | yes     | yes     | Deprecated
+Ubuntu 16.04 LTS   | yes     | yes     | Deprecated
+Ubuntu 18.04       | yes     | yes     |
+Debian 7.8         | yes     | yes     | Deprecated
+Debian 8.1         | yes     | yes     | Deprecated
+Debian 9.8         | yes     | yes     | 
+Centos 7           | yes     | no      | No python 3
+OpenSUSE 12        | yes     | yes     | Deprecated
+OpenSUSE 13        | yes     | yes     | Deprecated
+OpenSUSE 15        | yes     | yes     |
+MacOS X            | yes     | yes     | See OS notes
+
+
+* Deprecated: We used to support this configuration, but no longer test it.  It may still work.
 * Unsupported: We have built LOOS in the past using this configuration, but do not
   regularly test it and provide no direct support for using it.
 
-
+As of LOOS 3.0, we also support building inside a Conda environment.  This is the preferred way to build on MacOS, and on any Linux environment that is not supported.
 
 # Building and Installing LOOS
 
 ## For the Impatient
 
 
-
-
-LOOST requires BOOST 1.36 or higher, SCons, and Atlas/LAPACK.  Please
-refer to the OS-specific instructions below for more details.  For general
-advice about configuring LOOS and building in unusual environments, see
+LOOST requires BOOST 1.36 or higher, SCons, and Atlas/LAPACK or other BLAS.
+Please refer to the OS-specific instructions below for more details.  For
+general advice about configuring LOOS and building in unusual environments, see
 the "General Notes" section at the end of this file.
 
+If you are building on a system where the default python is 2.7, you will need to copy custom.py-proto to custom.py, and uncomment the line setting PYTHON_INC (verifying that it's the correct location for your system).
+
 LOOS can then be built using the following command:
 
     scons
@@ -71,7 +71,6 @@ To use LOOS, your environment must be first setup:
 Target | Description
 ------ | -----------
 core   | LOOS Library and PyLOOS
-docs   | Rebuild only documentation
 tools  | LOOS Library, Tools, and PyLOOS
 all    | LOOS Library, Tools, PyLOOS, and documentation (if necessary), and all Packages (default)
 install| Install library, tools, PyLOOS, documentation, and all Packages
@@ -157,44 +156,61 @@ already multithreaded.
 
 ### Documentation
 
-If you download a LOOS release from SourceForge, then you will already
-have pre-built documentation.  If you download a release from GitHub,
-then you can also download the prebuilt documentation that corresponds
-to the release (e.g. loos-2.3.2-docs.tar.gz).  Simply place the
-compressed tar-file in your LOOS source directory and scons will
-unpack it for you and move it into place.
-
 However, if you clone LOOS from GitHub, you will need to either:
 
 1. consult the online documentation at http://grossfieldlab.github.io/loos/
 
 2. build a new copy of the documentation.  To do so, you will need to
    install doxygen and graphviz (available in most package managers).
-   SCons will now generate new documentation in the docs/ directory
-   for the docs, all, and install targets.
+
+   doxygen
+
 
 ======
 
 # OS Specific Notes
 
+## Conda
+
+Assuming you already have a working install of Anaconda or miniconda, you'll
+need to say
+
+    conda create loos
+    conda activate loos
+    conda install swig scons numpy scipy boost blas libnetcdf
+
+Then, run the newly installed scons to build LOOS
+
+    $CONDA_PREFIX/bin/scons
+
+### Documentation
+
+To build the documentation, you will also require doxygen and graphviz,
+
+    conda install doxygen graphviz
+    doxygen
+
+
 ## Fedora
 
 LOOS has been tested on Fedora (64-bit).  We assume you already have
 the basic compiler tools installed (i.e. g++).  You will need to
 install scons, boost, and atlas:
 
-    sudo dnf install gcc-c++ scons boost-devel atlas-devel netcdf-devel python-devel swig python2-numpy python2-scipy
-
-LOOS/PyLOOS only supports Python 2, so you must specify which version of numpy and scipy to use for
-Fedora 24.  For Fedora 23 and older, use the following:
+    sudo dnf install gcc-c++ scons boost-devel atlas-devel netcdf-devel python3-devel swig python3-numpy python3-scipy
 
-    sudo dnf install gcc-c++ scons boost-devel atlas-devel netcdf-devel python-devel swig numpy scipy
+Copy custom.py-proto to custom.py, and uncomment the line setting PYTHON_INC (verifying that it's the correct location for your system).
 
+LOOS/PyLOOS only supports Python 3, so you must specify which version of numpy
+and scipy to use for Fedora 24 and later.  For earlier Fedoras, which don't have
+python3 packages for numpy and scipy, you can either install them manually or
+use conda.
 ### Documentation
 
 To build the documentation, you will also require doxygen and graphviz,
 
-   sudo dnf install doxygen graphviz
+    sudo dnf install doxygen graphviz
+    doxygen
 
 ---
 
@@ -213,6 +229,7 @@ Then install the packages,
 
 To build the documentation, also install:
    sudo yum install doxygen graphviz
+   doxygen
 
 
 ### PyLOOS
@@ -226,12 +243,15 @@ CentOS 6: Yum install python-devel and pcre-devel, then download
 
 ## Ubuntu, Debian, Mint
 
-    sudo apt-get install g++ scons libboost-all-dev libatlas-base-dev libatlas-dev libnetcdf-dev swig python-dev python-numpy python-scipy
+    sudo apt-get install g++ scons libboost-all-dev libatlas-base-dev libnetcdf-dev swig python3-dev python3-numpy python3-scipy
+
+Copy custom.py-proto to custom.py, and uncomment the line setting PYTHON_INC (verifying that it's the correct location for your system).
 
 ### Documentation
 
 To build the documentation:
    sudo apt-get install doxygen graphviz
+   doxygen
 
 ---
 
@@ -244,7 +264,8 @@ be ignored by the LOOS build.
 
 Using zypper (or your favorite package manager), install the following:
 
-    sudo zypper install gcc-c++ scons boost-devel lapack-devel blas-devel swig netcdf-devel python-numpy python-numpy-devel python-scipy
+    sudo zypper install gcc-c++ scons boost-devel lapack-devel blas-devel swig netcdf-devel python-numpy python3-numpy-devel python3-scipy libboost_filesystem1_66_0-devel libboost_program_options1_66_0 libboost_program_options1_66_0-devel libboost_regex1_66_0 libboost_regex1_66_0-dev libboost_system1_66_0-devel libboost_thread1_66_0-devel
+
 
 You should get the blas as a dependency for lapack.  You may also have lapack3
 installed by default, however we've found that lapack must also be installed
@@ -254,6 +275,7 @@ in order to build LOOS.
 
 To build the documentation:
     sudo zypper install doxygen graphviz
+    doxygen
 
 ### OpenSUSE 12
 
@@ -269,11 +291,14 @@ The package-manager installed scons is too old.  Download and install SCons
 There is a problem with using PyLOOS with the new System Integrity
 Protection (SIP) enabled (see https://support.apple.com/en-us/HT204899
 for more information about SIP).  We are aware of this and working on
-a decent solution.  Until then, there are three options for building and
+a decent solution.  Until then, there are four options for building and
 using PyLOOS under El Capitan.
 
+#### Use conda (recommended)
+
+See the conda install instructions above.
 
-#### Build your own Python (Recommended)
+#### Build your own Python
 
 The first way is to download and install your own local Python and use
 this to run SCons and PyLOOS.  Here again, you have two options: build

Packages/Convergence/SConscript

@@ -72,7 +72,7 @@ for file in Split(scripts):
     Command(PREFIX_BIN + file, file,
             [
             Copy("$TARGET", "$SOURCE"),
-            Chmod("$TARGET", 0755)
+            Chmod("$TARGET", 0o755)
             ])
 
 env.Alias('convergence_package', conv_tools)

Packages/HydrogenBonds/SConscript

@@ -55,7 +55,7 @@ for file in Split(scripts):
     Command(PREFIX_BIN + file, file,
             [
             Copy("$TARGET", "$SOURCE"),
-            Chmod("$TARGET", 0755)
+            Chmod("$TARGET", 0o755)
             ])
 
 

Packages/OptimalMembraneGenerator/LipidLibrary.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import os
 import glob
@@ -16,7 +16,7 @@ class LipidLibrary:
     def __init__(self, path):
        self.path = path
        if not os.path.exists(path):
-           print self.error_message()
+           print(self.error_message())
            sys.exit()
 
        all_files = os.listdir(self.path)
@@ -28,14 +28,14 @@ def __init__(self, path):
                 self.structures.append(file)
 
        if self.size() == 0:
-           print self.error_message()
+           print(self.error_message())
            sys.exit()
 
     def size(self):
         return len(self.structures)
 
     def pick_structure(self):
-        # pick a structure file at random, and build up the filename 
+        # pick a structure file at random, and build up the filename
         filename = os.path.join(self.path, random.choice(self.structures))
 
         # read the file

Packages/OptimalMembraneGenerator/NAMD.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import subprocess
 import sys
@@ -7,7 +7,7 @@
 
 # @cond TOOLS_INTERNAL
 class NAMD:
-    
+
     def __init__(self, psf_file, start_pdb, end_pdb, param_file, box,
                  command):
         self.psf_file = psf_file
@@ -21,7 +21,7 @@ def __init__(self, psf_file, start_pdb, end_pdb, param_file, box,
             self.command = command
 
         # in case we're going to do constraints, construct this filename
-        self.cons_k_filename = self.start_pdb[:-4] + ".cons.pdb" 
+        self.cons_k_filename = self.start_pdb[:-4] + ".cons.pdb"
 
         self.x_box = box.x()
         self.y_box = box.y()
@@ -87,7 +87,7 @@ def write_restraintfile(self, directory, atomicgroup, spring=10.0):
         pdb_file = open(os.path.join(directory,self.cons_k_filename), "w")
         pdb_file.write(str(pdb))
         pdb_file.close()
-        
+
 
     def construct_constraints(self):
         lines = [ "constraints on",
@@ -111,10 +111,10 @@ def run_namd(self, inputfilename, outfilename):
         """
         outfile = open(outfilename, "w")
         try:
-            subprocess.check_call([self.command, "+p4", inputfilename], 
+            subprocess.check_call([self.command, "+p4", inputfilename],
                                   stdout=outfile)
         except subprocess.CalledProcessError:
-            sys.stderr.write("NAMD call failed, inp = %s, out = %s\n" % 
+            sys.stderr.write("NAMD call failed, inp = %s, out = %s\n" %
                              (inputfilename, outfilename))
             sys.exit(-1)
 
@@ -155,20 +155,20 @@ def template(self):
 
     box = loos.GCoord(377, 377, 1000)
     n = NAMD("generated.psf", "t.pdb", "end", "toppar/par_build.inp", box)
-    print n.construct_header()
+    print(n.construct_header())
 
-    print n.construct_box()
+    print(n.construct_box())
 
     box[0] = 60
     n.update_box(box)
-    print n.construct_box()
+    print(n.construct_box())
     box[0] = 377
     n.update_box(box)
 
-    print n.construct_mini()
+    print(n.construct_mini())
     #print n.construct_mini(1000)
 
     n.write_inputfile("n.inp", 50)
-    print "launching NAMD"
+    print("launching NAMD")
     n.run_namd("n.inp", "n.out")
-    print "finished NAMD"
+    print("finished NAMD")