Adopt lastest cmdy

.pylintrc

@@ -297,9 +297,19 @@ function-naming-style=snake_case
 good-names=i,
            j,
            k,
+           x,
+		   y,
+           z,
+           np,
+           nn,
+           t,
+           t0,
            ex,
            rc,
            eq,
+           do,
+           by,
+           tf,
            Run,
            _
 
@@ -498,7 +508,7 @@ max-attributes=7
 max-bool-expr=5
 
 # Maximum number of branch for function / method body.
-max-branches=12
+max-branches=15
 
 # Maximum number of locals for function / method body.
 max-locals=15

tests/test_init.py

@@ -9,8 +9,8 @@
 def vcffile(tmp_path):
 	ovcf = HERE.parent.joinpath('examples', 'sample.vcf')
 	nvcf = tmp_path.with_suffix('.vcf.gz')
-	c = cmdy.bgzip(ovcf, c = True, _out = nvcf)
-	cmdy.tabix(p = 'vcf', _ = nvcf, _fg = True)
+	c = cmdy.bgzip(ovcf, c=True).r > nvcf
+	cmdy.tabix(p='vcf', _=nvcf).fg
 	return nvcf
 
 def test_get_vcf_by_regions(vcffile):
@@ -82,7 +82,7 @@ def test_load_config(tmp_path):
 
 def test_main(vcffile, tmp_path):
 	# help
-	cmd = cmdy.vcfstats(_raise = False)
+	cmd = cmdy.vcfstats(_raise=False)
 	assert 'Show help message and exit.' in cmd.stderr
 
 	macrofile = tmp_path.with_suffix('.macromain.py')
@@ -93,7 +93,9 @@ def DEMO(variant):
 	'''Some demo macro'''
 	return variant.CHROM
 """)
-	cmd = cmdy.vcfstats(l = True, macro = macrofile, _raise = False)
+	cmd = cmdy.vcfstats(vcf=True, l=True,
+						o=True, f=True, t=True,
+					    macro=macrofile, _raise=False)
 	assert 'Return 1 for a variant' in cmd.stderr
 	assert 'Some demo macro' in cmd.stderr