Fix mypy errors outside of lib/

Author: nsoranzo

doc/source/conf.py

@@ -25,7 +25,7 @@
 ]
 
 templates_path = ["_templates"]
-exclude_patterns = ()
+exclude_patterns: list[str] = []
 
 
 # -- Options for HTML output -------------------------------------------------

scripts/bed_coverage.py

@@ -10,12 +10,16 @@
 
 import fileinput
 import sys
+from typing import (
+    TextIO,
+    Union,
+)
 
 from bx.bitset_builders import binned_bitsets_from_file
 
 bed_filenames = sys.argv[1:]
 if bed_filenames:
-    input = fileinput.input(bed_filenames)
+    input: Union[fileinput.FileInput, TextIO] = fileinput.input(bed_filenames)
 else:
     input = sys.stdin
 

scripts/bed_merge_overlapping.py

@@ -10,12 +10,16 @@
 
 import fileinput
 import sys
+from typing import (
+    TextIO,
+    Union,
+)
 
 from bx.bitset_builders import binned_bitsets_from_bed_file
 
 bed_filenames = sys.argv[1:]
 if bed_filenames:
-    input = fileinput.input(bed_filenames)
+    input: Union[fileinput.FileInput, TextIO] = fileinput.input(bed_filenames)
 else:
     input = sys.stdin
 

scripts/bnMapper.py

@@ -20,7 +20,7 @@
 import numpy as np
 
 from bx.align import epo
-from bx.align.epo import bed_union as elem_u
+from bx.align.epo import bed_union as elem_u  # type: ignore[attr-defined]
 from bx.intervals.intersection import (
     Interval,
     IntervalTree,
@@ -427,6 +427,6 @@ def loadFeatures(path, opt):
             outpath = os.path.join(opt.output, os.path.basename(inpath))
             if os.path.isfile(outpath):
                 log.warning("overwriting %s ...", outpath)
-            transform_file(loadFeatures(inpath), outpath, EPO, TREE, opt)
+            transform_file(loadFeatures(inpath, opt), outpath, EPO, TREE, opt)
     else:
         transform_file(loadFeatures(opt.input[0], opt), opt.output, EPO, TREE, opt)

scripts/gene_fourfold_sites.py

@@ -94,13 +94,13 @@ def translate(codon, genetic_code):
 
 
 """ parse the doc string to hash the genetic code"""
-GEN_CODE = {}
+GEN_CODE: dict[str, dict[str, dict[str, str]]] = {}
 for line in GENETIC_CODE.split("\n"):
     if line.strip() == "":
         continue
     f = re.split(r"\s|\(|\)|\/", line)
     codon = f[0]
-    c1, c2, c3 = codon
+    c1, c2, c3 = list(codon)
     aminoacid = f[3]
     if c1 not in GEN_CODE:
         GEN_CODE[c1] = {}

scripts/maf_col_counts.py

@@ -14,7 +14,7 @@
 
 import bx.align.maf
 
-counts = {}
+counts: dict[tuple, int] = {}
 
 nspecies = None
 
@@ -31,8 +31,8 @@
         except Exception:
             counts[col] = 1
 
-counts = sorted((value, key) for key, value in counts.items())
-counts.reverse()
+sorted_counts = sorted((value, key) for key, value in counts.items())
+sorted_counts.reverse()
 
-for count, col in counts:
+for count, col in sorted_counts:
     print("".join(col), count)

scripts/maf_col_counts_all.py

@@ -22,24 +22,25 @@
     doc_optparse,
 )
 
-counts = {}
+counts: dict[str, int] = {}
 
 nspecies = None
 
 for block in bx.align.maf.Reader(sys.stdin):
     # Ensure all blocks have the same number of rows
-    if nspecies:
+    if nspecies is not None:
         assert len(block.components) == nspecies
     else:
         nspecies = len(block.components)
     # Increment count for each column
-    for col in zip(*[iter(comp.text.upper()) for comp in block.components]):
-        col = "".join(col)
+    for col_tuple in zip(*[iter(comp.text.upper()) for comp in block.components]):
+        col = "".join(col_tuple)
         try:
             counts[col] += 1
         except Exception:
             counts[col] = 1
 
+assert nspecies is not None
 options, args = doc_optparse.parse(__doc__)
 
 wildcard = False
@@ -54,8 +55,8 @@
 if wildcard:
     nucs += "*"
 
-for col in cross_lists(*([nucs] * nspecies)):
-    col = "".join(col)
+for col_list in cross_lists(*([nucs] * nspecies)):
+    col = "".join(col_list)
     if wildcard and col.count("*") > max_wildcard:
         continue
     if col.count("-") == nspecies:

scripts/tfloc_summary.py

@@ -10,7 +10,7 @@
 import sys
 from collections import defaultdict
 
-counts = defaultdict(int)
+counts: dict[int, int] = defaultdict(int)
 
 max_index = -1
 

scripts/wiggle_to_simple.py

@@ -7,16 +7,17 @@
 """
 
 import sys
+from typing import TextIO
 
 import bx.wiggle
 
 if len(sys.argv) > 1:
-    in_file = open(sys.argv[1])
+    in_file: TextIO = open(sys.argv[1])
 else:
     in_file = sys.stdin
 
 if len(sys.argv) > 2:
-    out_file = open(sys.argv[2], "w")
+    out_file: TextIO = open(sys.argv[2], "w")
 else:
     out_file = sys.stdout
 

tox.ini

@@ -8,7 +8,7 @@ commands =
     lint: flake8 .
     lint: black --check --diff .
     lint: isort --check --diff .
-    lint: mypy lib/
+    lint: mypy .
 deps =
     test: Cython
     test: numpy