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#!/usr/bin/env python
"""
This takes doctest files and turns them into standalone scripts.
"""
import pathlib
import re
import click
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2022, The Cogent Project"
__contributors__ = ["Gavin Huttley", "Peter Maxwell"]
__license__ = "BSD-3"
__version__ = "2020.2.7a"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
not_wsp = re.compile(r"^\S+")
code_eval = re.compile(r"(?<=\s{4})([>]{3}|[.]{3})\s")
code_block = re.compile(r".. (jupyter-execute|doctest)::")
block_option = re.compile(r"\s+:[a-z\-]+:")
raise_option = re.compile(r"\s+:raises:")
plotly_show = re.compile(r"\s*[a-z]+.*\.show\(")
def get_error_type(line):
if raise_option.search(line) is None:
return None
return raise_option.sub("", line).strip()
def get_path_update(rootdir: pathlib.Path) -> str:
"""returns code block to allow import set_working_directory"""
swd_script = pathlib.Path("set_working_directory.py").absolute()
assert swd_script.exists()
block = [
"import sys",
f"sys.path.append({str(swd_script.parent)!r})",
"import os",
f"os.chdir({str(rootdir)!r})",
'os.environ["OMP_NUM_THREADS"] = "1"',
'os.environ["OPENBLAS_NUM_THREADS"] = "1"',
'os.environ["MKL_NUM_THREADS"] = "1"',
'os.environ["VECLIB_MAXIMUM_THREADS"] = "1"',
'os.environ["NUMEXPR_NUM_THREADS"] = "1"',
]
return "\n".join(block)
def deindent(line):
if line.startswith(" " * 4):
line = line[4:]
return line
def get_code_block_line_numbers(doc):
"""returns the (start, end) of codeblock sections"""
lines = []
in_code_block = False
start = None
for i, line in enumerate(doc):
if code_block.search(line):
if in_code_block:
lines.append((start, i - 1))
start = i
in_code_block = True
continue
if in_code_block and not_wsp.search(line):
lines.append((start, i))
in_code_block = False
continue
if in_code_block:
if i == len(doc) - 1:
i += 1
lines.append((start, i))
return lines
def format_block(block):
"""handles exceptions, de-indent, etc..."""
error_type = get_error_type(block[0])
format_line = (lambda x: x) if error_type else deindent
code = [format_line(l) for l in block if not block_option.search(l)]
if error_type:
code.insert(0, "try:")
code.extend([f"except {error_type}:", " pass"])
for i, l in enumerate(code):
if plotly_show.search(l):
# comment out as cannot be executed in script
code[i] = f"# {l}"
return code
def get_code_blocks(doc: list[str], working_dir: pathlib.Path) -> str:
coords = get_code_block_line_numbers(doc)
refactored = [get_path_update(working_dir)]
for start, end in coords:
code = format_block(doc[start + 1 : end])
refactored.extend([""] + code)
return "\n".join(refactored)
def _rst_path(*args):
path = pathlib.Path(args[-1])
assert path.suffix == ".rst"
if not path.exists():
click.secho(f"ERROR: {str(path)} does not exist", fg="red")
exit(1)
return path
@click.command(no_args_is_help=True, context_settings={"show_default": True})
@click.argument("rst_path", callback=_rst_path)
@click.option(
"-wd",
"--working_dir",
type=pathlib.Path,
help="Set the working directory. Defaults to dir containing this script.",
)
@click.option("-t", "--test", is_flag=True, help="don't write script, print it")
def main(rst_path, working_dir, test):
"""extracts code under jupyter_execute or doctest blocks to python script"""
outpath = f"{rst_path.stem}.py"
outpath = (working_dir / outpath) if working_dir else (rst_path.parent / outpath)
doc = rst_path.read_text()
doc = doc.splitlines()
working_dir = working_dir or pathlib.Path(__file__).parent
just_code = get_code_blocks(doc, working_dir)
if test:
print(just_code)
exit()
outpath.write_text(just_code)
if __name__ == "__main__":
main()
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