Address Sphinx build warnings about docstring formatting

Corrects docstring indentation and converts tabular data in docstrings to rST
tables. Also, updates descriptions of method parameters to NumPy format in the
associated methods.

With this commit there are no more Sphinx warnings except for one about the
RTD's theme.

augur/export.py

@@ -15,6 +15,7 @@ def convert_tree_to_json_structure(node, metadata, div=0, nextflu_schema=False,
     converts the Biopython tree structure to a dictionary that can
     be written to file as a json. This is called recursively.
     Creates the strain property & divergence on each node
+
     input
         node -- node for which top level dict is produced.
         div  -- cumulative divergence (root = 0)

augur/sequence_traits.py

@@ -98,40 +98,52 @@ def mutation_struct():
 def read_in_features(drm_file):
     '''
     Reads in and stores position, alt base/AA, feature, gene,
-    and 'display name' (optional) of mutations such 
+    and 'display name' (optional) of mutations such
     as drug-resistance mutations
 
     Format to map by both nucleotide and AA sites:
-    ----------------------------------------------
-    GENE	SITE	ALT	DISPLAY_NAME	FEATURE
-    gyrB	461	N		Fluoroquinolones
-    nuc	1472358	T	rrs: C513T	Streptomycin
-    nuc	1673425	T	fabG1: C-15T	Isoniazid Ethionamide
-    ethA	175	T		Ethionamide
+
+    ====  =======  ===  ============  =====================
+    GENE  SITE     ALT  DISPLAY_NAME  FEATURE
+    ====  =======  ===  ============  =====================
+    gyrB  461      N                  Fluoroquinolones
+    nuc   1472358  T    rrs: C513T    Streptomycin
+    nuc   1673425  T    fabG1: C-15T  Isoniazid Ethionamide
+    ethA  175      T                  Ethionamide
+    ====  =======  ===  ============  =====================
 
     Format to map by AA site:
-    -------------------------
-    GENE	SITE	ALT	FEATURE
-    gyrB	461	N	Fluoroquinolones
-    gyrB	499	D	Fluoroquinolones
-    rpoB	170	F	Rifampicin
-    rpoB	359	A	Rifampicin
+
+    ====  ====  ===  ================
+    GENE  SITE  ALT  FEATURE
+    ====  ====  ===  ================
+    gyrB  461   N    Fluoroquinolones
+    gyrB  499   D    Fluoroquinolones
+    rpoB  170   F    Rifampicin
+    rpoB  359   A    Rifampicin
+    ====  ====  ===  ================
 
     Format to map by nucleotide site:
-    -----------------------------------
-    SITE    ALT    DISPLAY_NAME    FEATURE
-    6505    T    D461N    Fluoroquinolones
-    6505    C    D461N    Fluoroquinolones
-    760314    T    V170F    Rifampicin
-    760882    C    V359A    Rifampicin
-
-    or to map by nucleotide site and display mutations:
-    ---------------------------------------------------
-    SITE    ALT    FEATURE
+
+    ======  ===  ============  ================
+    SITE    ALT  DISPLAY_NAME  FEATURE
+    ======  ===  ============  ================
+    6505    T    D461N         Fluoroquinolones
+    6505    C    D461N         Fluoroquinolones
+    760314  T    V170F         Rifampicin
+    760882  C    V359A         Rifampicin
+    ======  ===  ============  ================
+
+    Or to map by nucleotide site and display mutations:
+
+    ======  ===  ================
+    SITE    ALT  FEATURE
+    ======  ===  ================
     6505    T    Fluoroquinolones
     6505    C    Fluoroquinolones
-    760314    T    Rifampicin
-    760882    C    Rifampicin
+    760314  T    Rifampicin
+    760882  C    Rifampicin
+    ======  ===  ================
 
     Parameters
     ----------
@@ -235,8 +247,8 @@ def annotate_strains(all_features, all_sequences):
 def attach_features(annotations, label, count):
     '''
     'Attaches' features to nodes and lists the corresponding mutations
-    as values, that is
-    >>>
+    as values, that is:
+
         {nodename:{"Resistance 1":"mut1,mut2", "Resistance 2":"mut1"}}
 
     Parameters

augur/translate.py

@@ -80,12 +80,21 @@ def safe_translate(sequence, report_exceptions=False):
 
 def translate_feature(aln, feature):
     '''
-    translates a subsequence of input nucleotide sequences
-    input:
-        aln -- dictionary of sequences indexed by node name
-        feature -- Biopython sequence feature
-    returns:
-        dictionary of translated sequences indexed by node name
+    Translates a subsequence of input nucleotide sequences.
+
+    Parameters
+    ----------
+    aln : dict
+        sequences indexed by node name
+
+    feature : Bio.Seq.Seq
+        BioPython sequence feature
+
+    Returns
+    -------
+    dict :
+        translated sequences indexed by node name
+
     '''
     translations = {}
     for sname, seq in aln.items():
@@ -96,16 +105,25 @@ def translate_feature(aln, feature):
 
 
 def translate_vcf_feature(sequences, ref, feature):
-    '''
-    translates a subsequence of input nucleotide sequences
-    input:
-        sequences -- TreeTime format dictionary from VCF-input of sequences
-                        indexed by node name
-        ref -- reference alignment the VCF was mapped to
-        feature -- Biopython sequence feature
-    returns:
-        dictionary giving the translated reference gene, positions of AA differences,
-        and AA differences indexed by node name
+    '''Translates a subsequence of input nucleotide sequences.
+
+    Parameters
+    ----------
+    sequences : dict
+        TreeTime format dictionary from VCF-input of sequences indexed by node name
+
+    ref :
+        reference alignment the VCF was mapped to
+
+    feature : Bio.Seq.Seq
+        BioPython sequence feature
+
+    Returns
+    -------
+    dict :
+        translated reference gene, positions of AA differences, and AA
+        differences indexed by node name
+
     '''
     def str_reverse_comp(str_seq):
         #gets reverse-compliment of a string and returns it as a string