add travis yaml. fix docs.

.travis.yml

@@ -0,0 +1,19 @@
+# This file was autogenerated and will overwrite each time you run travis_pypi_setup.py
+deploy:
+  true:
+    python: 2.7
+    repo: jadolfbr/jade
+    tags: true
+  distributions: sdist bdist_wheel
+  password:
+    secure: G/p1USKFALuIkVr3TKGCf81oQKyGMgDQ+x3cpEW0F3XBwYDMAemYRKRg21NOhUp2B7yJF7EQM2noEsDY8Vs6XKzzzYNyGCwwueZ94VhcBEbBd2LjEP6BUkzNnpfWJVElGajR4/nrS8YYPPw7wScHM+Ur+FK/Tp/PVREaroIsl34H3mnLcToqiaeUddw/iOHvyWeCCvN+Zk7k6jEv6WDVOVi1kYlgEZ2lcTxsRnQH/8l3iG3WxgLwG2Lp6V3WeQGMnO4TOenkPoIv0Ly/ydwsSYDsQL/KJc4YQPJR3sHEIfP9eztqzd8WM2Ei4OFLrn3d2eVdUJqHnuhoNIITx/4b+eC8sVKKROAgZXoaJ/SCQLEjZcnLrsiqh7frhr7PLJnte2gj7RkjeBZgcGK4ybNEEZAIVGKUNyRrp+twVeQaO6C9CKAhSdN/3y+DySOYatonkqJjNrBvuNaj+vEUT1Grfeetwp3VNjSTpXpqTM2oQ6E7ANTo7KnWkdDlW8QXnWqgi921qr/AviRYGykJ6dhVDzloyt+qH0BZooVfEm/+Syv+cFHely+fIHRREQNt5mRalQTHW1oJZm2Zw+UQtUqLyT0M8QQRRIDMnGAhfB1BvB0Jlb+1PGmXjj4w4Y8mFeJZo2IaQzcZawIsezRGLnrXScnV91/RyMDESnYRRX+vsz8=
+  provider: pypi
+  user: jadolfbr
+install: pip install -U tox-travis
+language: python
+python:
+- 3.6
+- 3.5
+- 3.4
+- 2.7
+script: tox

apps/pilot/jadolfbr/copy_top_each_strategy.py

@@ -3,8 +3,8 @@
 #Copies the top N of a particular directory to a new directory.  Used in conjunction with RabD BM.  Got sick of doing this by hand.
 
 from argparse import ArgumentParser
-from basic import path
-from basic import general
+from jade.basic import path
+from jade.basic import general
 import glob
 import os
 import sys

apps/public/antibody_benchmark_utils/RunRosettaBenchmarksMPI.py

@@ -1,13 +1,14 @@
 #!/usr/bin/env python
 
 from jade.rosetta_jade.RunRosettaBenchmarks import *
-
+from argparse import ArgumentParser
 
 ##Main to RunRosetta.
 
 def get_parser():
-    run_rosetta = RunRosettaBenchmarks()
-    return run_rosetta.parser
+    parser = ArgumentParser(description="This program runs Rosetta MPI locally or on a cluster using slurm or qsub.  "
+                                        "Relative paths are accepted.")
+    return parser
 
 if __name__ == "__main__":
     run_rosetta = RunRosettaBenchmarks()

apps/public/antibody_benchmark_utils/bm-RAbD_Jade.py

@@ -13,13 +13,12 @@
 import jade.RAbD_BM.tools as tools
 from jade.rosetta_jade.BenchmarkInfo import *
 
-p = os.path.split(os.path.abspath(__file__))[0]
-sys.path.append(p); #Allows all modules to use all other modules, without needing to update pythonpath
+
 
 #Runs all analysis of a particular benchmarking experiment.
 
 def get_parser():
-    parser = ArgumentParser("This program is a GUI used for benchmarking Rosetta Antibody Design."
+    parser = ArgumentParser(description="This program is a GUI used for benchmarking Rosetta Antibody Design."
                             "Before running this application, you will probably want to run 'run_rabd_features_for_benchmarks.py to create the databases required.")
 
     parser.add_argument("--main_dir",
@@ -40,7 +39,6 @@ def get_parser():
 
 def main():
 
-
     parser = get_parser()
     options = parser.parse_args()
 

apps/public/antibody_benchmark_utils/bm-calculate_graft_closure_rabd.py

@@ -14,7 +14,7 @@
 
 
 def get_parser():
-    parser = ArgumentParser("Calculate the frequence of graft closures.")
+    parser = ArgumentParser(description="Calculate the frequence of graft closures.")
 
     ############################
     ## Required Options

apps/public/antibody_benchmark_utils/bm-run_rabd_benchmarks.py

@@ -1,10 +1,12 @@
 #!/usr/bin/env python2.7
 
 from jade.RAbD_BM.RunBenchmarksRAbD import RunBenchmarksRAbD
+from argparse import ArgumentParser
 
 def get_parser():
-    bm = RunBenchmarksRAbD()
-    return bm.parser
+    parser = ArgumentParser(description="This program runs Rosetta MPI locally or on a cluster using slurm or qsub.  "
+                                        "Relative paths are accepted.")
+    return parser
 
 if __name__ == "__main__":
     bm = RunBenchmarksRAbD()

apps/public/antibody_utils/RAbD_Jade.py

@@ -11,9 +11,6 @@
 from Tkinter import *
 import tkMessageBox
 
-p = os.path.split(os.path.abspath(__file__))[0]
-sys.path.append(p);  # Allows all modules to use all other modules, without needing to update pythonpath
-
 # PyIgD
 from jade.antibody.cdr_data.CDRDataTypes import *
 from jade.basic.threading.Threader import *
@@ -51,7 +48,7 @@
 #      --pyigclassify_dir /Users/jadolfbr/Documents/projects/PyIgClassify --analysis_name testing
 
 def get_parser():
-    parser = ArgumentParser("GUI application to analyze designs output by RosettaAntibodyDesign.  "
+    parser = ArgumentParser(description="GUI application to analyze designs output by RosettaAntibodyDesign.  "
                             "Designs should first be analyzed by both the AntibodyFeatures and CDRClusterFeatures reporters "
                             "into sqlite3 databases.")
 

apps/public/antibody_utils/convert_IMGT_to_fasta.py

@@ -19,7 +19,7 @@
 #Sequence number	Sequence ID	Functionality	V-GENE and allele	J-GENE and allele	D-GENE and allele	V-D-J-REGION	V-J-REGION	V-REGION	FR1-IMGT	CDR1-IMGT	FR2-IMGT	CDR2-IMGT	FR3-IMGT	CDR3-IMGT	JUNCTION	J-REGION	FR4-IMGT
 
 def get_parser():
-    parser = ArgumentParser("#This script converts an IMGT output file (5_AA-seqs.csv) to a FASTA.  All Framework and CDRs are concatonated.  * is skipped.\n"
+    parser = ArgumentParser(description="This script converts an IMGT output file (5_AA-seqs.csv) to a FASTA.  All Framework and CDRs are concatonated.  * is skipped.\n"
                             "The FASTA file can then be used by PyIgClassify.")
 
     parser.add_argument("--inpath", "-i",

apps/public/antibody_utils/create_features_json.py

@@ -10,7 +10,7 @@
 from argparse import ArgumentParser
 
 def get_parser():
-    parser = ArgumentParser("This script will create either cluster features or antibody features json for use in Features R script.\n"
+    parser = ArgumentParser(description="This script will create either cluster features or antibody features json for use in Features R script.\n"
                             "Example Cmd-line:  python create_features_json.py --database databases/baseline_comparison.txt --scripts cluster")
 
     parser.add_argument("--databases", "-l",

apps/public/antibody_utils/generate_rabd_features_dbs.py

@@ -17,7 +17,18 @@
 from jade.basic.general import *
 from jade.basic import path
 
-def get_run_rosetta():
+
+def get_parser():
+    parser = ArgumentParser(description="Generates RAbD Features DBs using RunRosettaMPI in db mode.")
+    return parser
+
+def main():
+
+    ####################################################################################################################
+    ##                                                  OPTIONS
+    ####################################################################################################################
+
+
     parser = ArgumentParser("Creates Features Databases for antibody design using MPI.  "
                             "This uses RunRosettaMPI, so that it can be run locally or on a cluster.")
 
@@ -53,21 +64,6 @@ def get_run_rosetta():
                       default = False,
                       action = "store_true")
 
-    run_mpi_rosetta = RunRosetta(program="rosetta_scripts", parser=parser, db_mode=True)
-
-    return run_mpi_rosetta
-
-def get_parser():
-    return get_run_rosetta().parser
-
-def main():
-
-    ####################################################################################################################
-    ##                                                  OPTIONS
-    ####################################################################################################################
-
-
-    run_mpi_rosetta = get_run_rosetta()
 
     run_mpi_rosetta = RunRosetta(program = "rosetta_scripts", parser = parser, db_mode=True)
 

apps/public/antibody_utils/match_antibody_structures.py

@@ -11,7 +11,7 @@
 from jade.pymol_jade.PyMolScriptWriter import PyMolScriptWriter
 
 def get_parser():
-    parser = ArgumentParser("This App aims to make pymol alignments using the PyIgClassify database and structures, matching specific criterion.")
+    parser = ArgumentParser(description="This App aims to make pymol alignments using the PyIgClassify database and structures, matching specific criterion.")
 
     required = parser.add_argument_group("Required Arguments")
 

apps/public/antibody_utils/order_ab_chains.py

@@ -24,7 +24,7 @@ def reorder_and_save_chains(in_path, out_path, remove_het = False):
     blank_pdb.save_PDB(out_path)
 
 def get_parser():
-    parser = ArgumentParser("Reorders PDBFiles in a dirctory according to A_LH in order for Rosetta Antibody Design benchmarking. Removes HetAtm")
+    parser = ArgumentParser(description="Reorders PDBFiles in a dirctory according to A_LH in order for Rosetta Antibody Design benchmarking. Removes HetAtm")
 
     parser.add_argument("--in_dir", "-i",
                         default = os.getcwd(),

apps/public/antibody_utils/split_antibody_components.py

@@ -1,11 +1,13 @@
+#!/usr/bin/env python
+
 # Author: Jared Adolf-Bryfogle
 # Description: Script for splitting AHO renumbered antibodies into FAB, Fv, Fc, and linker regions
 
 from jade.antibody.split_structure import *
 from argparse import ArgumentParser
 
 def get_parser():
-    parser = ArgumentParser("Script for splitting AHO renumbered antibodies into Fv, Fc, and linker regions")
+    parser = ArgumentParser(description="Script for splitting AHO renumbered antibodies into Fv, Fc, and linker regions")
 
     parser.add_argument("--any_structure",
                         default=False,

apps/public/general/canceljobs.py

@@ -5,7 +5,7 @@
 from argparse import ArgumentParser
 
 def get_parser():
-    parser = ArgumentParser("Call scancel to cancel a consecutive set of cluster job numbers")
+    parser = ArgumentParser(description="Call scancel to cancel a consecutive set of cluster job numbers")
     return parser
 
 

apps/public/general/convert_fig.py

@@ -6,7 +6,7 @@
 from argparse import ArgumentParser
 
 def get_parser():
-    parser = ArgumentParser("Converts images to TIFF figures at 300 DPI for publication using sips. "
+    parser = ArgumentParser(description="Converts images to TIFF figures at 300 DPI for publication using sips. "
                             "Arguments: INFILE OUTFILE")
 
     return parser

apps/public/general/genscript_to_fasta.py

@@ -43,7 +43,7 @@ def write_fasta(sequence, label, HANDLE):
     HANDLE.write(sequence + "\n")
 
 def get_parser():
-    parser = ArgumentParser("This script outputs fasta files from a genscript format.  Pass the --format option to control which genscript format as input"
+    parser = ArgumentParser(description="This script outputs fasta files from a genscript format.  Pass the --format option to control which genscript format as input"
                             "  ~~~ Ex: python genscript_mut_to_fasta.py --format mutagenesis MutagenesisFormatU68  ~~~")
 
     parser.add_argument("infile", help = "The mutagenesis format file.")

apps/public/general/rename_designs.py

@@ -10,7 +10,7 @@
 from jade.basic import path
 
 def get_parser():
-    parser = ArgumentParser("Renames original files to new names for design ordering.  Copy all models going to be ordered into a single directory first. Run from directory with pdb files already copied in!")
+    parser = ArgumentParser(description="Renames original files to new names for design ordering.  Copy all models going to be ordered into a single directory first. Run from directory with pdb files already copied in!")
     parser.add_argument("-i", "--new_names",
                         help = "File with new to old names.  Example line: new_name  *  filename.  Can have lines that don't have all three.  Will only rename if it has a star in the second column.",
                         required = True)

apps/public/pdb_utils/place_TERs.py

@@ -5,7 +5,7 @@
 from argparse import ArgumentParser
 
 def get_parser():
-    parser = ArgumentParser("This script places ters between ATOM/HETATM columns.  This is currently needed to reload symmetrized glycan poses"
+    parser = ArgumentParser(description= "This script places ters between ATOM/HETATM columns.  This is currently needed to reload symmetrized glycan poses"
                             "created by the god aweful make_symm_file.pl Rosetta script. USE: place_TERs.py my_pdb - Does it in place. ")
 
     parser.add_argument("pdb_files", help="Path to PDB files we will be stripping.", nargs="*")

apps/public/pdb_utils/strip_ANISOU.py

@@ -5,7 +5,7 @@
 import re
 
 def get_parser():
-    parser = ArgumentParser(" Strips ANISOU lines out of PDBs.")
+    parser = ArgumentParser(description=" Strips ANISOU lines out of PDBs.")
 
     parser.add_argument("pdb_files", help = "Path to PDB file we will be stripping.", nargs="*")
 

apps/public/pdb_utils/strip_ter.py

@@ -3,7 +3,7 @@
 from argparse import ArgumentParser
 
 def get_parser():
-    parser = ArgumentParser(" This simple script strips ters out of a PDB file and overwrites the input.  PyMol places ters "
+    parser = ArgumentParser(description=" This simple script strips ters out of a PDB file and overwrites the input.  PyMol places ters "
                             "when th numbering is not 1-1.  And then Rosetta will F your Shit up.")
 
     parser.add_argument("pdb_files", help = "Path to PDB file we will be stripping.", nargs="*")

apps/public/pyrosetta/build_loop_pyrosetta.py

@@ -14,7 +14,7 @@
 
 
 def get_parser():
-    parser = ArgumentParser( "This script builds a loop between two places in a structure with the given sequence, and closes the loop."
+    parser = ArgumentParser( description="This script builds a loop between two places in a structure with the given sequence, and closes the loop."
                     "It is not meant to be the last modeling step, just to create missing density or to prepare for loop modeling.")
 
 

apps/public/pyrosetta/find_my_glycans.py

@@ -12,7 +12,7 @@
 #Useful while we figure out this PDBInfo problem...
 
 def get_parser():
-    parser = ArgumentParser("This app is the PyRosetta equivalent of GlycanInfo.  "
+    parser = ArgumentParser(description="This app is the PyRosetta equivalent of GlycanInfo.  "
                             "Print carbohydrate info about the pose. Pass the pose in as an argument")
 
     return parser

apps/public/pyrosetta/find_my_residues.py

@@ -13,7 +13,7 @@ def get_parser():
 
 
 
-    parser = ArgumentParser("Simple app to scan a PDB file and print PDB info and Rosetta understood chains and resnums.")
+    parser = ArgumentParser(description="Simple app to scan a PDB file and print PDB info and Rosetta understood chains and resnums.")
 
     parser.add_argument("pdb_file", help = "The PDB file to scan.")
 

apps/public/pyrosetta/get_mutation_energy.py

@@ -26,7 +26,7 @@
 
 ##Setup Options and Script Inputs:
 def get_parser():
-    parser = ArgumentParser()
+    parser = ArgumentParser(description= "Basic app to get mutation energy of each residue in a particular region using PyRosetta")
 
     parser.add_argument("--pdb", "-s",
 

apps/public/rosetta/RunRosettaDBMode.py

@@ -1,10 +1,12 @@
 #!/usr/bin/env python
 
 from jade.rosetta_jade.RunRosetta import *
+from argparse import ArgumentParser
 
 def get_parser():
-    run_rosetta = RunRosetta(db_mode=True)
-    return run_rosetta.parser
+    parser = ArgumentParser("This program runs Rosetta MPI locally or on a cluster using slurm or qsub.  "
+                                        "Relative paths are accepted.")
+    return parser
 
 ##Main to RunRosetta.
 

apps/public/rosetta/RunRosettaMPI.py

@@ -1,10 +1,12 @@
 #!/usr/bin/env python
 
 from jade.rosetta_jade.RunRosetta import *
+from argparse import ArgumentParser
 
 def get_parser():
-    run_rosetta = RunRosetta()
-    return run_rosetta.parser
+    parser = ArgumentParser("This program runs Rosetta MPI locally or on a cluster using slurm or qsub.  "
+                                        "Relative paths are accepted.")
+    return parser
 
 ##Main to RunRosetta.