Fixes bug in profile creation

sequana · Apr 5, 2024 · 1eb4474 · 1eb4474
1 parent 5fca981
commit 1eb4474
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Showing 3 changed files with 10 additions and 8 deletions.
diff --git a/README.rst b/README.rst
@@ -313,6 313,8 @@ Changelog
 ========= ======================================================================
 Version Description
 ========= ======================================================================
 1.0.1 * hot fix in the profile creation (regression)
 1.0.0 * Stable release
 0.17.3 * remove useless code and fix a requirement
 0.17.2 * simpler logging
 0.17.1 * remove the --use-singulariry (replaced by --use-apptainer in

diff --git a/pyproject.toml b/pyproject.toml
@@ -6,7 6,7 @@ build-backend = "poetry.core.masonry.api"
 #maintainer ?#maintainer email
 [tool.poetry]
 name = "sequana_pipetools"
-version = "1.0.0"
 version = "1.0.1"
 description = "A set of tools to help building or using Sequana pipelines"
 authors = ["Sequana Team"]
 license = "BSD-3"

diff --git a/sequana_pipetools/snaketools/profile.py b/sequana_pipetools/snaketools/profile.py
@@ -13,16 13,16 @@
 def create_profile(workdir: Path, profile: str, **kwargs) -> str:
  """Create profile config in working directory."""
  try:
- slurm_file = resources.files("sequana_pipetools.resources").joinpath(f"{profile}.yaml")
- with open(slurm_file, "r") as fin:
- slurm_text = fin.read()
- slurl_text = slurm_text.format(**kwargs)
  profile_file = resources.files("sequana_pipetools.resources").joinpath(f"{profile}.yaml")
  with open(profile_file, "r") as fin:
  profile_text = fin.read()
  profile_text = profile_text.format(**kwargs)
  except AttributeError:
  # python 3.8 support for back compatibility
- with resources.path("sequana_pipetools.resources", f"{profile}.yaml") as slurm_file:
- slurm_text = slurm_file.read_text().format(**kwargs)
  with resources.path("sequana_pipetools.resources", f"{profile}.yaml") as profile_file:
  profile_text = profile_file.read_text().format(**kwargs)
 
  outfile = workdir / f".sequana/profile_{profile}" / "config.yaml"
  outfile.parent.mkdir(parents=True, exist_ok=True)
- outfile.write_text(slurm_text)
  outfile.write_text(profile_text)
  return f".sequana/profile_{profile}"