From afb47983ed77b7fac519e797170db7a781c73d1b Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Thu, 28 Mar 2024 17:59:35 +0100
Subject: [PATCH] write in tmp file instead
---
.../df-wiki-cli/df_wiki_cli/content/main.py | 25 ++++++++-----------
1 file changed, 11 insertions(+), 14 deletions(-)
diff --git a/packages/df-wiki-cli/df_wiki_cli/content/main.py b/packages/df-wiki-cli/df_wiki_cli/content/main.py
index 751e7d48..319089d3 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/content/main.py
@@ -4,6 +4,7 @@ import json
import pandas as pd
import shutil
import csv
+import tempfile
import matplotlib.pyplot as plt
from pandas.errors import ParserError
from typing_extensions import Annotated
@@ -426,30 +427,26 @@ def markdown(
help="Dir where all systems article are",
),
],
- # output: Annotated[
- # Path,
- # typer.Option(
- # file_okay=True,
- # dir_okay=False,
- # writable=True,
- # resolve_path=True,
- # ),
- # ],
):
-
for file in dir.iterdir():
if file.suffix == ".md":
console.rule(f"[bold blue]{file.name}", style="blue")
- with open(file, "r+") as f:
+ # make a copy of file
+ _, tmp_path = tempfile.mkstemp()
+ # with open(dst, "w") as tmp_f:
+ dst = Path(tmp_path)
+ dst.write_bytes(file.read_bytes())
+
+ with open(dst, "r+") as f:
new_f = re.sub(
- r"##\s+Structure\n.+##\s+Experimental\s+validation",
+ r"##\s+Structure\n.*##\s+Experimental\s+validation",
"## Structure\n\n::article-structure\n::\n\n## Experimental validation",
f.read(),
flags=re.DOTALL,
)
- f.seek(0, 0)
- f.write(new_f)
+ with open(file, "w") as f_out:
+ f_out.write(new_f)
def remove_version(assembly):
--
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