update docstrings to pass the doctest

pyproject.toml

@@ -23,3 +23,16 @@ classifiers = [
 [tool.poetry.dependencies]
 python = "^3.8"
 weasyprint = ">=52.5"
+
+[tool.pytest.ini_options]
+addopts = [
+    "--doctest-modules",
+    "--doctest-glob=README.md",
+    "--ignore=examples",
+    "--verbose",
+    "-ra",
+    "--color=yes",
+]
+doctest_optionflags = "NORMALIZE_WHITESPACE"
+pythonpath = "src"
+testpaths = ["tests"]

src/cstag/consensus.py

@@ -146,7 +146,7 @@ def consensus(cs_tags: list[str], positions: list[int], prefix: bool = False) ->
         >>> cs_tags = ["=ACGT", "=AC*gt=T", "=C*gt=T", "=C*gt=T", "=ACT+ccc=T"]
         >>> positions = [1,1,1,2,1]
         >>> cstag.consensus(cs_tags, positions)
-        =AC*gt=T
+        '=AC*gt=T'
     """
     if not (len(cs_tags) == len(positions) > 0):
         raise ValueError("Element numbers of each argument must be the same")

src/cstag/lengthen.py

@@ -21,7 +21,7 @@ def lengthen(cs_tag: str, cigar: str, seq: str, prefix: bool = False) -> str:
         >>> cigar = "8M"
         >>> seq = "ACGTACGT"
         >>> cstag.lengthen(cs, cigar, seq)
-        =ACGT*ag=CGT
+        '=ACGT*ag=CGT'
     """
     validate_cs_tag(cs_tag)
     validate_short_format(cs_tag)

src/cstag/mask.py

@@ -20,8 +20,8 @@ def mask(cs_tag: str, cigar: str, qual: str, threshold: int = 10, prefix: bool =
         >>> cs_tag = "=ACGT*ac+gg-cc=T"
         >>> cigar = "5M2I2D1M"
         >>> qual = "AA!!!!AA"
-        >>> cstag.mask(cs_tag, qual)
-        =ACNN*an+ng-cc=T
+        >>> cstag.mask(cs_tag, cigar, qual)
+        '=ACNN*an+ng-cc=T'
     """
     validate_cs_tag(cs_tag)
     validate_long_format(cs_tag)

src/cstag/revcomp.py

@@ -35,7 +35,7 @@ def revcomp(cs_tag: str, prefix: bool = False) -> str:
         >>> import cstag
         >>> cs = "=AAAA*ag=CTG"
         >>> cstag.revcomp(cs)
-        =CAG*tc=TTTT
+        '=CAG*tc=TTTT'
     """
     pattern = r"(\=[ACGTN]+|:[0-9]+|\*[acgtn][acgtn]|\+[acgtn]+|\-[acgtn]+|\~[acgtn]{2}[0-9]+[acgtn]{2})"
     cs_tag_revcomp = []

src/cstag/shorten.py

@@ -14,7 +14,7 @@ def shorten(cs_tag: str, prefix: bool = False) -> str:
         >>> import cstag
         >>> cs = "=ACGT*ag=CGT"
         >>> cstag.shorten(cs, prefix=True)
-        cs:Z::4*ag:3
+        'cs:Z::4*ag:3'
     """
     cstags = re.split(r"([-+*~=])", cs_tag.replace("cs:Z:", ""))[1:]
     cstags = [i + j for i, j in zip(cstags[0::2], cstags[1::2])]

src/cstag/split.py

@@ -15,7 +15,7 @@ def split(cs_tag: str, prefix: bool = False) -> list[str]:
         >>> import cstag
         >>> cs = ":4*ag:3"
         >>> cstag.split(cs)
-        [":4", "*ag", ":3"]
+        [':4', '*ag', ':3']
     """
     cs_tag = cs_tag.replace("cs:Z:", "")
 

src/cstag/to_html.py

@@ -144,7 +144,7 @@ def to_html(cs_tag: str, description: str = "") -> str:
         HTML string
     Example:
         >>> import cstag
-        >>> cs_tag = "=AC+GGG=T-ACGT*at~gt10cg=GNNN"
+        >>> cs_tag = "=AC+ggg=T-acgt*at~gt10cg=GNNN"
         >>> description = "Example"
         >>> html_string = cstag.to_html(cs_tag, description)
     """

src/cstag/to_pdf.py

@@ -23,7 +23,7 @@ def to_pdf(cs_tag: str, description: str, path_out: str | Path) -> None:
 
     Examples:
         >>> import cstag
-        >>> cs_tag = "=AC+GGG=T-ACGT*at~gt10cg=GNNN"
+        >>> cs_tag = "=AC+ggg=T-acgt*at~gt10cg=GNNN"
         >>> description = "Example"
         >>> path_out = "report.pdf"
         >>> to_pdf(cs_tag, description, path_out)

src/cstag/to_sequence.py

@@ -17,7 +17,7 @@ def to_sequence(cs_tag: str) -> str:
         >>> import cstag
         >>> cs_tag = "=AC*gt=T-gg=C+tt=A"
         >>> cstag.to_sequence(cs_tag)
-        "ACTTCTTA"
+        'ACTTCTTA'
     """
     validate_cs_tag(cs_tag)
     validate_long_format(cs_tag)

src/cstag/to_vcf.py

@@ -333,7 +333,7 @@ def to_vcf(cs_tags: str | list[str], chroms: str | int | list[str] | list[int],
         >>> cs_tag = "=AC*gt=T-gg=C+tt=A"
         >>> chrom = "chr1"
         >>> pos = 1
-        >>> print(cstag.to_vcf(cstag, chrom, pos))
+        >>> print(cstag.to_vcf(cs_tag, chrom, pos))
         ##fileformat=VCFv4.2
         #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
         chr1	3	.	G	T	.	.	.