Remove all OptionGroup

jcvi/annotation/reformat.py

@@ -19,9 +19,8 @@
 from jcvi.formats.bed import Bed, BedLine, sort
 from jcvi.formats.base import SetFile, must_open, get_number, flexible_cast
 from jcvi.apps.base import (
-    OptionParser,
-    OptionGroup,
     ActionDispatcher,
+    OptionParser,
     cleanup,
     need_update,
     popen,
@@ -608,8 +607,7 @@ def annotate(args):
         help="Specify is locus IDs in `new.bed` file follow ATG nomenclature",
     )
 
-    g1 = OptionGroup(
-        p,
+    g1 = p.add_argument_group(
         "Optional parameters (alignment):\n"
         + "Use if resolving ambiguities based on sequence `alignment`",
     )
@@ -627,10 +625,8 @@ def annotate(args):
         type=float,
         help="Alignment score cutoff",
     )
-    p.add_option_group(g1)
 
-    g2 = OptionGroup(
-        p,
+    g2 = p.add_argument_group(
         "Optional parameters (overlap):\n"
         + "Use if resolving ambiguities based on `overlap` length\n"
         + "Parameters equivalent to `intersectBed`",
@@ -656,7 +652,6 @@ def annotate(args):
         action="store_true",
         help="Require same strandedness",
     )
-    p.add_option_group(g2)
 
     opts, args = p.parse_args(args)
 

jcvi/apps/base.py

@@ -151,7 +151,7 @@ class OptionParser(ArgumentParser):
     features.
     """
 
-    def __init__(self, doc: str):
+    def __init__(self, doc: Optional[str]):
         super(OptionParser, self).__init__(doc, epilog=JCVIHELP)
 
     def add_option(self, *args, **kwargs):
@@ -189,9 +189,6 @@ def add_help_from_choices(self, o):
             help_pf = help_pf.rsplit("[", 1)[0]
         help_pf = help_pf.strip()
 
-        # for k, v in o.__dict__.items():
-        #     print(k, v)
-
         if o.type == "choice":
             if o.default is None:
                 default_tag = "guess"

jcvi/assembly/allmaps.py

@@ -29,9 +29,8 @@
 from ..algorithms.matrix import determine_signs
 from ..apps.base import (
     ActionDispatcher,
-    OptionGroup,
     OptionParser,
-    SUPPRESS_HELP,
+    SUPPRESS,
     cleanup,
     flatten,
     get_today,
@@ -1358,8 +1357,8 @@ def path(args):
     """
     oargs = args
     p = OptionParser(path.__doc__)
-    p.add_option("-b", "--bedfile", help=SUPPRESS_HELP)
-    p.add_option("-s", "--fastafile", help=SUPPRESS_HELP)
+    p.add_option("-b", "--bedfile", help=SUPPRESS)
+    p.add_option("-s", "--fastafile", help=SUPPRESS)
     p.add_option(
         "-w", "--weightsfile", default="weights.txt", help="Use weights from file"
     )
@@ -1411,8 +1410,7 @@ def path(args):
     )
     p.set_cpus(cpus=16)
 
-    q = OptionGroup(p, "Genetic algorithm options")
-    p.add_option_group(q)
+    q = p.add_argument_group("Genetic algorithm options")
     q.add_option(
         "--ngen", default=500, type=int, help="Iterations in GA, higher ~ slower"
     )

jcvi/compara/synfind.py

@@ -35,7 +35,7 @@
 from jcvi.compara.synteny import check_beds, read_blast
 from jcvi.utils.grouper import Grouper
 from jcvi.formats.base import must_open
-from jcvi.apps.base import OptionParser, OptionGroup
+from jcvi.apps.base import OptionParser
 
 
 def transposed(data):
@@ -247,12 +247,12 @@ def main(blastfile, p, opts):
     p.set_stripnames()
     p.set_outfile()
 
-    coge_group = OptionGroup(p, "CoGe-specific options")
+    coge_group = p.add_argument_group("CoGe-specific options")
     coge_group.add_option("--sqlite", help="Write sqlite database")
     coge_group.add_option("--qnote", default="null", help="Query dataset group id")
     coge_group.add_option("--snote", default="null", help="Subject dataset group id")
 
-    params_group = OptionGroup(p, "Synteny parameters")
+    params_group = p.add_argument_group("Synteny parameters")
     params_group.add_option(
         "--window", type=int, default=40, help="Synteny window size"
     )
@@ -270,9 +270,6 @@ def main(blastfile, p, opts):
         help="Scoring scheme",
     )
 
-    p.add_option_group(coge_group)
-    p.add_option_group(params_group)
-
     opts, args = p.parse_args()
 
     if len(args) != 1:

jcvi/formats/agp.py

@@ -27,7 +27,6 @@
 from jcvi.utils.range import range_intersect
 from jcvi.apps.base import (
     OptionParser,
-    OptionGroup,
     ActionDispatcher,
     cleanup,
     flatten,
@@ -1765,8 +1764,7 @@ def bed(args):
         help="Generate bed file for components",
     )
     p.set_outfile()
-    g1 = OptionGroup(
-        p,
+    g1 = p.add_argument_group(
         "GFF specific parameters",
         "Note: If not specified, output will be in `bed` format",
     )
@@ -1782,7 +1780,6 @@ def bed(args):
         default="golden_path_fragment",
         help="Specify a gff3 feature type",
     )
-    p.add_option_group(g1)
     p.set_SO_opts()
 
     opts, args = p.parse_args(args)

jcvi/formats/gff.py

@@ -11,7 +11,6 @@
 
 from ..apps.base import (
     OptionParser,
-    OptionGroup,
     ActionDispatcher,
     cleanup,
     flatten,
@@ -1170,7 +1169,7 @@ def filter(args):
     p.add_option(
         "--type", default="mRNA", help="The feature to scan for the attributes"
     )
-    g1 = OptionGroup(p, "Filter by identity/coverage attribute values")
+    g1 = p.add_argument_group("Filter by identity/coverage attribute values")
     g1.add_option("--id", default=95, type=float, help="Minimum identity")
     g1.add_option("--coverage", default=90, type=float, help="Minimum coverage")
     g1.add_option(
@@ -1179,8 +1178,7 @@ def filter(args):
         action="store_true",
         help="Case insensitive lookup of attribute names",
     )
-    p.add_option_group(g1)
-    g2 = OptionGroup(p, "Filter by child feature bp length")
+    g2 = p.add_argument_group("Filter by child feature bp length")
     g2.add_option(
         "--child_ftype", default=None, type=str, help="Child featuretype to consider"
     )
@@ -1190,7 +1188,6 @@ def filter(args):
         type=int,
         help="Filter by total bp of children of chosen ftype",
     )
-    p.add_option_group(g2)
     p.set_outfile()
 
     opts, args = p.parse_args(args)
@@ -1549,7 +1546,7 @@ def format(args):
 
     p = OptionParser(format.__doc__)
 
-    g1 = OptionGroup(p, "Parameter(s) used to modify GFF attributes (9th column)")
+    g1 = p.add_argument_group("Parameter(s) used to modify GFF attributes (9th column)")
     g1.add_option("--name", help="Add Name attribute from two-column file")
     g1.add_option("--note", help="Add Note attribute from two-column file")
     g1.add_option(
@@ -1597,9 +1594,8 @@ def format(args):
         action="store_true",
         help="Do not maintain attribute order",
     )
-    p.add_option_group(g1)
 
-    g2 = OptionGroup(p, "Parameter(s) used to modify content within columns 1-8")
+    g2 = p.add_argument_group("Parameter(s) used to modify content within columns 1-8")
     g2.add_option(
         "--seqid",
         help="Switch seqid from two-column file. If not"
@@ -1621,10 +1617,9 @@ def format(args):
         action="store_true",
         help="Change phase 1<->2, 2<->1",
     )
-    p.add_option_group(g2)
 
-    g3 = OptionGroup(
-        p, "Other parameter(s) to perform manipulations to the GFF " + "file content"
+    g3 = p.add_argument_group(
+        "Other parameter(s) to perform manipulations to the GFF file content"
     )
     g3.add_option(
         "--unique", default=False, action="store_true", help="Make IDs unique"
@@ -1678,7 +1673,6 @@ def format(args):
         action="store_true",
         help="Store entire GFF file in memory during first iteration",
     )
-    p.add_option_group(g3)
 
     p.set_outfile()
     p.set_SO_opts()
@@ -3250,7 +3244,7 @@ def load(args):
         help="Specify if full FASTA header (with seqid, coordinates and datestamp) should be generated",
     )
 
-    g1 = OptionGroup(p, "Optional parameters (if generating full header)")
+    g1 = p.add_argument_group("Optional parameters (if generating full header)")
     g1.add_option(
         "--sep",
         dest="sep",
@@ -3269,7 +3263,6 @@ def load(args):
         action="store_true",
         help="Specify if `conf_class` attribute should be parsed and placed in the header",
     )
-    p.add_option_group(g1)
 
     p.set_outfile()
 

jcvi/graphics/grabseeds.py

@@ -40,9 +40,8 @@
 )
 from ..algorithms.formula import get_kmeans, reject_outliers
 from ..apps.base import (
-    OptionParser,
-    OptionGroup,
     ActionDispatcher,
+    OptionParser,
     datadir,
     logger,
     iglob,
@@ -268,7 +267,7 @@ def add_seeds_options(p, args):
     """
     Add options to the OptionParser for seeds() and batchseeds() functions.
     """
-    g1 = OptionGroup(p, "Image manipulation")
+    g1 = p.add_argument_group("Image manipulation")
     g1.add_option("--rotate", default=0, type=int, help="Rotate degrees clockwise")
     g1.add_option(
         "--rows", default=":", help="Crop rows e.g. `:800` from first 800 rows"
@@ -285,9 +284,8 @@ def add_seeds_options(p, args):
         choices=valid_colors,
         help="Changes background color",
     )
-    p.add_option_group(g1)
 
-    g2 = OptionGroup(p, "Object recognition")
+    g2 = p.add_argument_group("Object recognition")
     g2.add_option(
         "--minsize",
         default=0.05,
@@ -304,9 +302,8 @@ def add_seeds_options(p, args):
         action="store_true",
         help="Run watershed to segment touching objects",
     )
-    p.add_option_group(g2)
 
-    g3 = OptionGroup(p, "De-noise")
+    g3 = p.add_argument_group("De-noise")
     valid_filters = ("canny", "roberts", "sobel")
     g3.add_option(
         "--filter",
@@ -329,9 +326,8 @@ def add_seeds_options(p, args):
     g3.add_option(
         "--border", default=5, type=int, help="Remove image border of certain pixels"
     )
-    p.add_option_group(g3)
 
-    g4 = OptionGroup(p, "Output")
+    g4 = p.add_argument_group("Output")
     g4.add_option("--calibrate", help="JSON file to correct distance and color")
     g4.add_option(
         "--edges",
@@ -346,7 +342,6 @@ def add_seeds_options(p, args):
     g4.add_option(
         "--noheader", default=False, action="store_true", help="Do not print header"
     )
-    p.add_option_group(g4)
     opts, args, iopts = p.set_image_options(args, figsize="12x6", style="white")
 
     return opts, args, iopts