Make sure dso_pandocfilter version matches parent dso command version (…

…#61)

* Make pandocfilter independent of binary

* Update CHANGELOG

* Autoformat

* fix traversable import

CHANGELOG.md

@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning][].
     requirement introduced by the R API package, see [#50](https://github.com/Boehringer-Ingelheim/dso/issues/50) ([#58](https://github.com/Boehringer-Ingelheim/dso/pull/58)).
 -   Improve logging for "missing path" warning during `compile-config` ([#59](https://github.com/Boehringer-Ingelheim/dso/pull/59)).
 -   Improve logging for missing parameters in `dvc.yaml` during `get-config` ([#59](https://github.com/Boehringer-Ingelheim/dso/pull/59)).
+-   Make sure internal calls to the dso pandocfilter use the same python and dso version as the parent command. This is important for the upcoming `dso-mgr` feature ([#61](https://github.com/Boehringer-Ingelheim/dso/pull/61)).
 
 ## v0.9.0
 

pyproject.toml

@@ -67,7 +67,6 @@ urls.Documentation = "https://github.com/Boehringer-Ingelheim/dso"
 urls.Home-page = "https://github.com/Boehringer-Ingelheim/dso"
 urls.Source = "https://github.com/Boehringer-Ingelheim/dso"
 scripts.dso = "dso:cli"
-scripts.dso_pandocfilter = "dso.pandocfilter:main"
 
 [tool.hatch.version]
 source = "vcs"

src/dso/_util.py

@@ -5,7 +5,13 @@
 from collections.abc import Sequence
 from functools import cache
 from importlib import resources
-from importlib.abc import Traversable
+
+try:
+    # has been added in Python 3.11
+    from importlib.resources.abc import Traversable
+except ImportError:
+    # will be removed in Python 3.14
+    from importlib.abc import Traversable
 from os import environ
 from pathlib import Path
 from typing import Literal

src/dso/exec.py

@@ -1,6 +1,8 @@
 import os
+import stat
 import subprocess
 import sys
+import tempfile
 from contextlib import contextmanager
 from pathlib import Path
 from textwrap import dedent, indent
@@ -39,7 +41,25 @@ def _render_quarto(quarto_dir: Path, report_dir: Path, before_script: str, cwd:
         if f.is_file():
             f.unlink()
 
-    pandocfilter = "--filter dso_pandocfilter" if with_pandocfilter else ""
+    # 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)
+
+        filter_script.chmod(filter_script.stat().st_mode | stat.S_IEXEC)
+
+        pandocfilter = f"--filter {filter_script}"
+    else:
+        pandocfilter = ""
+
     # propagate quiet setting to quarto
     quiet = "--quiet" if bool(int(os.environ.get("DSO_QUIET", 0))) else ""
     script = dedent(
@@ -56,6 +76,11 @@ def _render_quarto(quarto_dir: Path, report_dir: Path, before_script: str, cwd:
         """
     )
     res = subprocess.run(script, shell=True, executable="/bin/bash", cwd=cwd)
+
+    # clean up
+    if filter_script is not None:
+        filter_script.unlink()
+
     if res.returncode:
         sys.exit(res.returncode)
 

src/dso/pandocfilter.py

@@ -3,6 +3,8 @@
 
  * warning box at the top
  * watermark to all PNG images
+
+Called internally by `dso exec quarto`.
 """
 
 import sys
@@ -89,10 +91,5 @@ def action(elem, doc):
     return elem
 
 
-def main(doc=None):
-    """
-    A pandoc filter to add warning boxes to documents and watermarks to plots
-
-    Called internally by `dso exec quarto`.
-    """
-    return run_filter(action, prepare=prepare, doc=doc)
+if __name__ == "__main__":
+    run_filter(action, prepare=prepare, doc=None)