Merge pull request #162 from nextstrain/base-import

Import from base with . rather than base.

base/auspice_export.py

@@ -1,7 +1,7 @@
 from __future__ import division, print_function
 import sys, os, time, gzip, glob
-from base.io_util import make_dir, remove_dir, tree_to_json, write_json, myopen
-from base.frequencies import KdeFrequencies
+from .io_util import make_dir, remove_dir, tree_to_json, write_json, myopen
+from .frequencies import KdeFrequencies
 import json
 from pdb import set_trace
 from collections import defaultdict

base/fitness_model.py

@@ -7,8 +7,8 @@
 from scipy.interpolate import interp1d
 from scipy.stats import linregress, spearmanr
 
-from base.io_util import write_json
-from builds.flu.scores import select_nodes_in_season
+from io_util import write_json
+from scores import select_nodes_in_season
 from frequencies import logit_transform, tree_frequencies
 from fitness_predictors import fitness_predictors
 

base/fitness_predictors.py

@@ -6,7 +6,7 @@
 from scipy.stats import linregress
 import sys
 
-from builds.flu.scores import calculate_LBI
+from scores import calculate_LBI
 
 # all fitness predictors should be designed to give a positive sign, ie.
 # number of epitope mutations

base/prediction.py

@@ -2,7 +2,7 @@
 import numpy as np
 import time
 from collections import defaultdict
-from base.io_util import myopen
+from .io_util import myopen
 from itertools import izip
 import pandas as pd
 

base/prepare.py

@@ -3,10 +3,10 @@
 import sys, os
 import numpy as np
 from datetime import datetime
-from base.config import combine_configs
-from base.sequences_prepare import sequence_set
-from base.logger import logger
-from base.utils import generate_cmap, define_latitude_longitude
+from .config import combine_configs
+from .sequences_prepare import sequence_set
+from .logger import logger
+from .utils import generate_cmap, define_latitude_longitude
 # useful for debugging
 from pdb import set_trace
 from pprint import pprint

base/process.py

@@ -2,19 +2,19 @@
 import argparse
 import sys, os, time, gzip, glob
 from collections import defaultdict
-from base.config import combine_configs
-from base.io_util import make_dir, remove_dir, tree_to_json, write_json, myopen
-from base.sequences_process import sequence_set
-from base.utils import num_date, save_as_nexus, parse_date
-from base.tree import tree
-from base.fitness_model import fitness_model
-from base.frequencies import alignment_frequencies, tree_frequencies, make_pivots
-from base.auspice_export import export_metadata_json, export_frequency_json, export_tip_frequency_json
+from .config import combine_configs
+from .io_util import make_dir, remove_dir, tree_to_json, write_json, myopen
+from .sequences_process import sequence_set
+from .utils import num_date, save_as_nexus, parse_date
+from .tree import tree
+from .fitness_model import fitness_model
+from .frequencies import alignment_frequencies, tree_frequencies, make_pivots
+from .auspice_export import export_metadata_json, export_frequency_json, export_tip_frequency_json
 import numpy as np
 from datetime import datetime
 import json
 from pdb import set_trace
-from base.logger import logger
+from .logger import logger
 from Bio import SeqIO
 from Bio import AlignIO
 import cPickle as pickle

base/sequences_prepare.py

@@ -3,7 +3,7 @@
 '''
 from __future__ import division, print_function
 import os, re, time, csv, sys
-from base.titer_model import TiterCollection
+from .titer_model import TiterCollection
 from io_util import myopen
 from collections import defaultdict
 from Bio import SeqIO

base/titer_model.py

@@ -4,7 +4,7 @@
 import numpy as np
 import time
 from collections import defaultdict
-from base.io_util import myopen
+from .io_util import myopen
 from itertools import izip
 import pandas as pd
 from pprint import pprint

base/utils.py

@@ -1,7 +1,7 @@
 import matplotlib as mpl
 #from matplotlib import pyplot as plt
 from datetime import datetime
-from base.io_util import tree_to_json
+from .io_util import tree_to_json
 import numpy as np
 
 def generate_cmap(data, discrete):

builds/flu/flu.process.py

@@ -9,7 +9,7 @@
 from base.io_util import write_json
 from base.frequencies import KdeFrequencies
 from flu_titers import HI_model, HI_export, vaccine_distance
-from scores import calculate_sequence_scores, calculate_metadata_scores, calculate_phylogenetic_scores
+from base.scores import calculate_sequence_scores, calculate_metadata_scores, calculate_phylogenetic_scores
 from flu_info import clade_designations, lineage_to_epitope_mask, lineage_to_glyc_mask, resolution_to_pivot_spacing, vaccine_choices
 import argparse
 import numpy as np