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task_compile_documents.py
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import getpass
import subprocess
import shutil
from pathlib import Path
import pytask
ROOT = Path(__file__).parent
BLD = ROOT / "bld"
SRC = ROOT / "src"
_DEPENDENCIES = [*SRC.rglob("*.tex"), *(BLD / "param_tables").rglob("*.tex")]
@pytask.mark.latex(
[
"--pdf",
"--interaction=nonstopmode",
"--synctex=1",
"--cd",
"--shell-escape",
"-f",
]
)
@pytask.mark.depends_on([SRC / "paper.tex", *_DEPENDENCIES])
@pytask.mark.produces(BLD / "paper.pdf")
def task_compile_paper():
pass
@pytask.mark.latex(
[
"--pdf",
"--interaction=nonstopmode",
"--synctex=1",
"--cd",
"--shell-escape",
"-f",
]
)
@pytask.mark.depends_on([SRC / "sars-cov-2-spread-policies-pres.tex", *_DEPENDENCIES])
@pytask.mark.produces(BLD / "sars-cov-2-spread-policies-pres.pdf")
def task_compile_pres():
pass
@pytask.mark.latex(
[
"--pdf",
"--interaction=nonstopmode",
"--synctex=1",
"--cd",
"--shell-escape",
"-f",
]
)
@pytask.mark.depends_on([SRC / "science" / "paper.tex", *_DEPENDENCIES])
@pytask.mark.produces(BLD / "science" / "paper.pdf")
def task_compile_science_report():
pass
@pytask.mark.latex(
[
"--pdf",
"--interaction=nonstopmode",
"--synctex=1",
"--cd",
"--shell-escape",
"-f",
]
)
@pytask.mark.depends_on([SRC / "science" / "cover_letter.tex", *_DEPENDENCIES])
@pytask.mark.produces(BLD / "cover_letter.pdf")
def task_compile_cover_letter():
pass
@pytask.mark.depends_on(BLD / "paper.pdf")
@pytask.mark.produces(ROOT / "paper.pdf")
def task_copy_pdf_to_root(depends_on, produces):
shutil.copy(depends_on, produces)
@pytask.mark.skipif(shutil.which("qpdf") is None, reason="Extraction needs qpdf.")
@pytask.mark.depends_on(BLD / "paper.pdf")
@pytask.mark.produces(BLD / "supplementary_material.pdf")
def task_extract_supplementary_material(depends_on, produces):
subprocess.run(
[
"qpdf",
"--empty",
"--pages",
depends_on.as_posix(),
"12-78",
"--",
produces.as_posix(),
]
)
@pytask.mark.depends_on(
{
"paper": SRC / "science" / "paper.tex",
"scicite": SRC / "science" / "scicite.sty",
"model_graph_top_left": SRC / "figures" / "model-graph-top-left.pdf",
"model_graph_top_right": SRC / "figures" / "model-graph-top-right.pdf",
"model_graph_bottom_left": SRC / "figures" / "model-graph-bottom-left.pdf",
"model_graph_bottom_right": SRC / "figures" / "model-graph-bottom-right.pdf",
"full_new_known_case": SRC
/ "figures"
/ "results"
/ "figures"
/ "scenario_comparisons"
/ "combined_fit"
/ "full_new_known_case.pdf",
"stringency2_with_seasonality": SRC
/ "figures"
/ "results"
/ "figures"
/ "data"
/ "stringency2_with_seasonality.pdf",
"full_share_b117": SRC
/ "figures"
/ "results"
/ "figures"
/ "scenario_comparisons"
/ "combined_fit"
/ "full_share_b117.pdf",
"full_share_rapid_test_in_last_week_and_vaccinated": SRC
/ "figures"
/ "results"
/ "figures"
/ "scenario_comparisons"
/ "combined_fit"
/ "full_share_rapid_test_in_last_week_and_vaccinated.pdf",
"full_new_known_case_": SRC
/ "figures"
/ "results"
/ "figures"
/ "scenario_comparisons"
/ "effect_of_channels_on_pessimistic_scenario"
/ "full_new_known_case.pdf",
"full_newly_infected_": SRC
/ "figures"
/ "results"
/ "figures"
/ "scenario_comparisons"
/ "effect_of_channels_on_pessimistic_scenario"
/ "full_newly_infected.pdf",
"full_decomposition_channels_area": SRC
/ "figures"
/ "results"
/ "figures"
/ "full_decomposition_channels_area.pdf",
"full_decomposition_rapid_tests_area": SRC
/ "figures"
/ "results"
/ "figures"
/ "full_decomposition_rapid_tests_area.pdf",
}
)
@pytask.mark.produces(
{
"paper": BLD / "science" / "paper.tex",
"scicite": BLD / "science" / "scicite.sty",
"model_graph_top_left": BLD
/ "science"
/ "figures"
/ "model-graph-top-left.pdf",
"model_graph_top_right": BLD
/ "science"
/ "figures"
/ "model-graph-top-right.pdf",
"model_graph_bottom_left": BLD
/ "science"
/ "figures"
/ "model-graph-bottom-left.pdf",
"model_graph_bottom_right": BLD
/ "science"
/ "figures"
/ "model-graph-bottom-right.pdf",
"full_new_known_case": BLD
/ "science"
/ "figures"
/ "results"
/ "figures"
/ "scenario_comparisons"
/ "combined_fit"
/ "full_new_known_case.pdf",
"stringency2_with_seasonality": BLD
/ "science"
/ "figures"
/ "results"
/ "figures"
/ "data"
/ "stringency2_with_seasonality.pdf",
"full_share_b117": BLD
/ "science"
/ "figures"
/ "results"
/ "figures"
/ "scenario_comparisons"
/ "combined_fit"
/ "full_share_b117.pdf",
"full_share_rapid_test_in_last_week_and_vaccinated": BLD
/ "science"
/ "figures"
/ "results"
/ "figures"
/ "scenario_comparisons"
/ "combined_fit"
/ "full_share_rapid_test_in_last_week_and_vaccinated.pdf",
"full_new_known_case_": BLD
/ "science"
/ "figures"
/ "results"
/ "figures"
/ "scenario_comparisons"
/ "effect_of_channels_on_pessimistic_scenario"
/ "full_new_known_case.pdf",
"full_newly_infected_": BLD
/ "science"
/ "figures"
/ "results"
/ "figures"
/ "scenario_comparisons"
/ "effect_of_channels_on_pessimistic_scenario"
/ "full_newly_infected.pdf",
"full_decomposition_channels_area": BLD
/ "science"
/ "figures"
/ "results"
/ "figures"
/ "full_decomposition_channels_area.pdf",
"full_decomposition_rapid_tests_area": BLD
/ "science"
/ "figures"
/ "results"
/ "figures"
/ "full_decomposition_rapid_tests_area.pdf",
}
)
def task_prepare_submission_material(depends_on, produces):
for name in depends_on:
if name == "paper":
text = depends_on[name].read_text()
# Fix figure paths
text = text.replace("../figures", "figures")
produces[name].write_text(text)
else:
shutil.copy(depends_on[name], produces[name])
@pytask.mark.skipif(shutil.which("qpdf") is None, reason="Combination needs qpdf.")
@pytask.mark.depends_on(
[BLD / "science" / "paper.pdf", BLD / "supplementary_material.pdf"]
)
@pytask.mark.produces(BLD / "science" / "full_paper.pdf")
def task_create_combined_report(depends_on, produces):
subprocess.run(
[
"qpdf",
"--empty",
"--pages",
depends_on[0].as_posix(),
depends_on[1].as_posix(),
"--",
produces.as_posix(),
]
)
@pytask.mark.skipif(shutil.which("qpdf") is None, reason="Extraction needs qpdf.")
@pytask.mark.depends_on(BLD / "paper.pdf")
@pytask.mark.produces(ROOT / "paper-no-appendix.pdf")
def task_extract_paper(depends_on, produces):
subprocess.run(
[
"qpdf",
"--empty",
"--pages",
depends_on.as_posix(),
"1-14",
"--",
produces.as_posix(),
]
)
@pytask.mark.skipif(getpass.getuser() != "hmg", reason="Need UniBN letter basics.")
@pytask.mark.latex(
[
"--pdf",
"--interaction=nonstopmode",
"--synctex=1",
"--cd",
"--shell-escape",
"-f",
]
)
@pytask.mark.depends_on([SRC / "cover-letter.tex"])
@pytask.mark.produces(BLD / "cover-letter.pdf")
def task_compile_cover_letter():
pass