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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,62 +1,4 @@ | ||
| import logging | ||
| import os | ||
| from ._metadata import __version__ # noqa | ||
| from .api import here, read_params, set_stage, stage_here | ||
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| import rich_click as click | ||
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| from ._logging import log | ||
| from ._metadata import __version__ | ||
| from .compile_config import cli as compile_config_cli | ||
| from .create import cli as create_cli | ||
| from .exec import cli as exec_cli | ||
| from .get_config import cli as get_config_cli | ||
| from .init import cli as init_cli | ||
| from .lint import cli as lint_cli | ||
| from .repro import cli as repro_cli | ||
| from .watermark import cli as watermark_cli | ||
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| click.rich_click.USE_MARKDOWN = True | ||
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| @click.group() | ||
| @click.option( | ||
| "-q", | ||
| "--quiet", | ||
| count=True, | ||
| help=( | ||
| "Reduce verbosity. `-q` disables info messages, `-qq` disables warnings. Errors messages cannot be disabled. " | ||
| "The same can be achieved by setting the env var `DSO_QUIET=1` or `DSO_QUIET=2`, respectively." | ||
| ), | ||
| default=int(os.environ.get("DSO_QUIET", 0)), | ||
| ) | ||
| @click.option( | ||
| "-v", | ||
| "--verbose", | ||
| help=( | ||
| "Increase logging verbosity to include debug messages. " | ||
| "The same can be achieved by setting the env var `DSO_VERBOSE=1`." | ||
| ), | ||
| default=bool(int(os.environ.get("DSO_VERBOSE", 0))), | ||
| is_flag=True, | ||
| ) | ||
| @click.version_option(version=__version__, prog_name="dso") | ||
| def cli(quiet: int, verbose: bool): | ||
| """Root command""" | ||
| if quiet >= 2: | ||
| log.setLevel(logging.ERROR) | ||
| os.environ["DSO_QUIET"] = "2" | ||
| elif quiet == 1: | ||
| log.setLevel(logging.WARNING) | ||
| os.environ["DSO_QUIET"] = "1" | ||
| elif verbose: | ||
| log.setLevel(logging.DEBUG) | ||
| os.environ["DSO_VERBOSE"] = "1" | ||
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| cli.add_command(create_cli) | ||
| cli.add_command(init_cli) | ||
| cli.add_command(compile_config_cli) | ||
| cli.add_command(repro_cli) | ||
| cli.add_command(exec_cli) | ||
| cli.add_command(lint_cli) | ||
| cli.add_command(get_config_cli) | ||
| cli.add_command(watermark_cli) | ||
| __all__ = ["read_params", "here", "stage_here", "set_stage"] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| """Helper functions for rendering quarto documents""" | ||
|
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||
| import os | ||
| import stat | ||
| import subprocess | ||
| import sys | ||
| import tempfile | ||
| from contextlib import contextmanager | ||
| from pathlib import Path | ||
| from textwrap import dedent, indent | ||
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| from ruamel.yaml import YAML | ||
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| def render_quarto(quarto_dir: Path, report_dir: Path, before_script: str, cwd: Path, with_pandocfilter: bool = False): | ||
| """ | ||
| Render a quarto project | ||
| Parameters | ||
| ---------- | ||
| quarto_dir | ||
| Path that contains the _quarto.yml document | ||
| report_dir | ||
| Output directory of the rendered document | ||
| before_script | ||
| Bash snippet to execute before running quarto (e.g. to setup the enviornment) | ||
| """ | ||
| before_script = indent(before_script, " " * 8) | ||
| report_dir = report_dir.absolute() | ||
| report_dir.mkdir(exist_ok=True) | ||
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| # clean up existing `.rmarkdown` files that may interfere with rendering | ||
| # these are leftovers from a previous, failed `quarto render` attempt. If they still exist, the next attempt | ||
| # fails. We remove them *before* the run instead of cleaning them up *after* the run, because they | ||
| # may be usefule for debugging failures. | ||
| # see https://github.com/Boehringer-Ingelheim/dso/issues/54 | ||
| for f in quarto_dir.glob("*.rmarkdown"): | ||
| if f.is_file(): | ||
| f.unlink() | ||
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| # Enable pandocfilter if requested. | ||
| # We create a temporary script that then calls the current python binary with the dso.pandocfilter module | ||
| # This may seem cumbersome, but we do it this way because | ||
| # * pandoc only supports a single binary for `--filter`, referring to subcommands or `-m` is not possible here | ||
| # * we want to ensure that exactly the same python/dso version is used for the pandocfilter as for the | ||
| # parent command (important when running through dso-mgr) | ||
| filter_script = None | ||
| if with_pandocfilter: | ||
| with tempfile.NamedTemporaryFile(delete=False, mode="w") as f: | ||
| f.write("#!/bin/bash\n") | ||
| f.write(f'{sys.executable} -m dso.pandocfilter "$@"\n') | ||
| filter_script = Path(f.name) | ||
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| filter_script.chmod(filter_script.stat().st_mode | stat.S_IEXEC) | ||
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| pandocfilter = f"--filter {filter_script}" | ||
| else: | ||
| pandocfilter = "" | ||
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| # propagate quiet setting to quarto | ||
| quiet = "--quiet" if bool(int(os.environ.get("DSO_QUIET", 0))) else "" | ||
| script = dedent( | ||
| f"""\ | ||
| #!/bin/bash | ||
| set -euo pipefail | ||
| # this flags enables building larger reports with embedded resources | ||
| export QUARTO_DENO_V8_OPTIONS=--max-old-space-size=8192 | ||
| {before_script} | ||
| quarto render "{quarto_dir}" --output-dir "{report_dir}" {quiet} {pandocfilter} | ||
| """ | ||
| ) | ||
| res = subprocess.run(script, shell=True, executable="/bin/bash", cwd=cwd) | ||
|
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| # clean up | ||
| if filter_script is not None: | ||
| filter_script.unlink() | ||
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| if res.returncode: | ||
| sys.exit(res.returncode) | ||
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| @contextmanager | ||
| def quarto_config_yml(quarto_config: dict | None, quarto_dir: Path): | ||
| """Context manager that temporarily creates a _quarto.yml file and cleans up after itself""" | ||
| if quarto_config is None: | ||
| quarto_config = {} | ||
| config_file = quarto_dir / "_quarto.yml" | ||
| yaml = YAML(typ="safe") | ||
| yaml.dump(quarto_config, config_file) | ||
| try: | ||
| yield | ||
| finally: | ||
| config_file.unlink() |
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