Merge pull request #118 from cokelaer/main

Fixing #116

Author: cokelaer

.github/workflows/pypi.yml

@@ -11,10 +11,10 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
     - uses: actions/checkout@main
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: '3.10'
 
     - name: Install package 
       run: |

README.rst

@@ -317,6 +317,9 @@ Changelog
 ========= ======================================================================
 Version   Description
 ========= ======================================================================
+1.2.1     * create apptainer directory if it does not exist
+          * --use-apptainer set to True internally is --apptainer-prefix is used
+          * do not store conda env anymore since we are using containers
 1.2.0     * update to be compatible with poetry 2.0
           * print container size when initiating a pipeline
 1.1.1     * symlink creation on apptainers skipped if permission error (file

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "sequana_pipetools"
-version = "1.2.0"
+version = "1.2.1"
 description = "A set of tools to help building or using Sequana pipelines"
 authors = [{name="Sequana Team", email="[email protected]"}]
 license = "BSD-3"

sequana_pipetools/info.py

@@ -18,7 +18,7 @@
 
 
 sequana_epilog = Colors().purple(
-"""\U00002139\U0000FE0F  To use completion, type 'sequana_pipetools --completion NAME'
+    """\U00002139\U0000FE0F  To use completion, type 'sequana_pipetools --completion {name}'
 
 \u2705 If you use or like the Sequana project,
 please consider citing us (visit sequana.readthedocs.io for details) or use this
@@ -33,8 +33,8 @@
 
 sequana_prolog = """Welcome to Sequana project (https://sequana.readthedocs.io)
 
-This script prepares the pipeline sequana_{name}. It stores the pipeline and its 
-configuration file in the requested working directory ({name} by default). 
+This script prepares the pipeline sequana_{name}. It stores the pipeline and its
+configuration file in the requested working directory ({name} by default).
 Please check out the documentation carefully. In case of issues, please report
 on https://github.com/sequana/sequana/issues or https://github.com/sequana/{name}/issues
 

sequana_pipetools/options.py

@@ -67,6 +67,7 @@ def main(**kwargs):
 
     """
     click.rich_click.HEADER_TEXT = sequana_prolog.format(name=NAME)
+    click.rich_click.FOOTER_TEXT = sequana_epilog.format(name=NAME)
     click.rich_click.OPTION_GROUPS[f"sequana_{NAME}"] = []
 
     click.rich_context.RichContext.NAME = NAME

sequana_pipetools/sequana_manager.py

@@ -139,9 +139,11 @@ def __init__(self):
 
         if self.options.apptainer_prefix:  # pragma: no cover
             self.apptainer_prefix = Path(self.options.apptainer_prefix).resolve()
+            self.options.use_apptainer = True
+
             if self.apptainer_prefix.exists() is False:
-                logger.error(f"{self.apptainer_prefix} does not exist")
-                sys.exit(1)
+                logger.warning(f"Creating {self.apptainer_prefix} to store containers (does not exist)")
+                os.makedirs(self.apptainer_prefix)
             self.local_apptainers = False
         else:  # pragma: no cover
             self.apptainer_prefix = os.environ.get("SEQUANA_SINGULARITY_PREFIX", f"{self.workdir}/.sequana/apptainers")
@@ -444,22 +446,11 @@ def teardown(self, check_schema=True, check_input_files=True):
         with open(self.workdir / "unlock.sh", "w") as fout:
             fout.write(f"#!/bin/sh\nsnakemake -s {snakefilename} --unlock -j 1")
 
-        # save environment
-        if shutil.which("conda"):
-            print(self.colors.purple("Saving current conda environment information"))
-            cmd = "conda list"
-            with open(f"{self.workdir}/.sequana/env.yml", "w") as fout:
-                subprocess.call(cmd.split(), stdout=fout)
-            logger.debug("Saved your conda environment into env.yml")
-        else:
-            with open(f"{self.workdir}/.sequana/env.yml", "w") as fout:
-                fout.write("Conda standalone not found")
-
         if shutil.which("pip"):
             cmd = f"{sys.executable} -m pip freeze"
             with open(f"{self.workdir}/.sequana/pip.yml", "w") as fout:
                 subprocess.call(cmd.split(), stdout=fout)
-            logger.debug("Saved your pip environment into pip.txt (conda not found)")
+            logger.debug("Saved your pip environment into pip.txt")
         else:  # pragma: no cover
             with open(f"{self.workdir}/.sequana/pip.yml", "w") as fout:
                 fout.write("pip not found")

sequana_pipetools/snaketools/dot_parser.py

@@ -53,7 +53,7 @@ class DOTParser:
 
     """
 
-    _name_to_drops = {"dag", "conda", "rulegraph", "copy_multiple_files"}
+    _name_to_drops = {"dag", "rulegraph", "copy_multiple_files"}
 
     def __init__(self, filename):
         """.. rubric:: constructor

sequana_pipetools/snaketools/module.py

@@ -255,17 +255,12 @@ def check(self, mode="warning"):
             # _ = self.is_executable()
             missing = " ".join(missing)
             txt = f"""Some executable or Python packages are not available: {missing}
-Some functionalities may not work. Consider adding them with conda or set the --use-apptainer options.
+Some functionalities may not work. Consider using apptainer by setting a host directory with --apptainer-prefix
 
             """
 
             if mode == "warning":
                 logger.critical(txt)
-            elif mode == "error":  # pragma: no cover
-                txt += "you may want to use \n conda install {missing};"
-                for this in missing:
-                    txt += "- %s\n" % this
-                raise ValueError(txt)
 
     def md5(self):
         """return md5 of snakefile and its default configuration file