Clean up existing rmarkdown files before rendering quarto stage (#57)

* Clean up existing rmarkdown filese before rendering quarto stage

* update changelog

CHANGELOG.md

@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning][].
 ### Fixes
 -   Remove vendored `hiyapyco` code since required changes were released upstream in v0.7.0 ([#45](https://github.com/Boehringer-Ingelheim/dso/pull/45)).
 -   `None` values in `params.in.yaml` can now be used to override anything, e.g. to disable watermarking only in a specific stage ([#45](https://github.com/Boehringer-Ingelheim/dso/pull/45)).
+-   Clean up existing `*.rmarkdown` files in quarto stage before running `quarto render`. This fixes issues with re-running quarto stages that failed in the previous attempt ([#57](https://github.com/Boehringer-Ingelheim/dso/pull/57)).
 -   DSO now respects a `DSO_SKIP_CHECK_ASK_PRE_COMMIT` environment variable.  If it is set
     to anything that evaluates as `True`, we skip the check if pre-commit is installed. This was a
     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)).

src/dso/exec.py

@@ -29,6 +29,16 @@ def _render_quarto(quarto_dir: Path, report_dir: Path, before_script: str, cwd:
     before_script = indent(before_script, " " * 8)
     report_dir = report_dir.absolute()
     report_dir.mkdir(exist_ok=True)
+
+    # 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()
+
     pandocfilter = "--filter dso_pandocfilter" if with_pandocfilter else ""
     # propagate quiet setting to quarto
     quiet = "--quiet" if bool(int(os.environ.get("DSO_QUIET", 0))) else ""