Merge pull request #103 from cokelaer/main

removed old deprecated option --use-singularity

.github/workflows/main.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.8,3.9,'3.10']
+        python: [3.8,3.9,'3.10', '3.11']
       fail-fast: false
 
 

README.rst

@@ -313,6 +313,9 @@ Changelog
 ========= ======================================================================
 Version   Description
 ========= ======================================================================
+0.17.1    * remove the --use-singulariry (replaced by --use-apptainer in
+            previous release)
+          * slight updates on logging and slight update on slurm module
 0.17.0    * Remove deprecated options and deprecated functions. More tests.
 0.16.9    * Fix slurm sys exit (replaced by print)
           * upadte doc

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "poetry.core.masonry.api"
 #maintainer ?#maintainer email
 [tool.poetry]
 name = "sequana_pipetools"
-version = "0.17.0"
+version = "0.17.1"
 description = "A set of tools to help building or using Sequana pipelines"
 authors = ["Sequana Team"]
 license = "BSD-3"
@@ -34,7 +34,6 @@ packages = [
 
 [tool.poetry.dependencies]
 python = ">=3.8,<4.0"
-deprecated = ">=1.2.13"
 easydev = ">=0.12.1"
 parse = ">=1.19.0"
 "ruamel.yaml" = ">=0.18.5"

sequana_pipetools/options.py

@@ -250,18 +250,6 @@ def __init__(self, working_directory="analysis", caller=None):
 
         _default_jobs = 40 if guess_scheduler() == "slurm" else 4
 
-        if "--use-singularity" in sys.argv:  # pragma: no cover
-            print("--use-singularity is deprecated, use --use-apptainer instead.")
-            sys.exit(1)
-
-        if "--singularity-prefix" in sys.argv:  # pragma: no cover
-            print("--singularity-prefix is deprecated, use --apptainer-prefix instead.")
-            sys.exit(1)
-
-        if "--singularity-args" in sys.argv:  # pragma: no cover
-            print("--singularity-args is deprecated, use --apptainer-args instead.")
-            sys.exit(1)
-
         self.options = [
             click.option(
                 "--apptainer-prefix",

sequana_pipetools/scripts/main.py

@@ -246,6 +246,7 @@ def main(**kwargs):
         cfg = SequanaConfig(config_file)
         cfg.create_draft_schema()
     elif kwargs["slurm_diag"]:
+        click.echo("Looking for slurm files")
         p = PipeError()
         p.status(".")
 

sequana_pipetools/sequana_manager.py

@@ -11,6 +11,7 @@
 #  Contributors:  https://github.com/sequana/sequana/graphs/contributors
 ##############################################################################
 import asyncio
+import datetime
 import glob
 import os
 import shutil
@@ -241,7 +242,7 @@ def _create_directories(self):
         # Now we create the directory to store the config/pipeline
         if self.workdir.exists():
             if self.options.force:
-                logger.warning(f"Path {self.workdir} exists already but you set --force to overwrite it")
+                logger.warning(f"\u2757 Path {self.workdir} exists already but you set --force to overwrite it")
             else:  # pragma: no cover
                 logger.error(f"Output path {self.workdir} exists already. Use --force to overwrite")
                 sys.exit()
@@ -260,11 +261,13 @@ def check_input_files(self, stop_on_error=True):
 
         filenames = glob.glob(cfg.input_directory + os.sep + cfg.input_pattern)
         logger.info(
-            f"Found {len(filenames)} files matching your input  pattern ({cfg.input_pattern}) in {cfg.input_directory}"
+            f"\u2705 Found {len(filenames)} files matching your input  pattern ({cfg.input_pattern}) in {cfg.input_directory}"
         )
 
         if len(filenames) == 0:
-            logger.critical(f"Found no files with your matching pattern ({cfg.input_pattern}) in {cfg.input_directory}")
+            logger.critical(
+                f"\u2757 Found no files with your matching pattern ({cfg.input_pattern}) in {cfg.input_directory}"
+            )
             if "*" not in cfg.input_pattern and "?" not in cfg.input_pattern:
                 logger.critical("No wildcard used in your input pattern, please use a * or ? character")
             if stop_on_error:
@@ -426,6 +429,9 @@ def teardown(self, check_schema=True, check_input_files=True):
             fout.write(f"# sequana_pipetools version: {version}\n")
             fout.write(f"# sequana_{self.name} version: {self._get_package_version()}\n")
             fout.write(f"# sequana version: {self._get_sequana_version()}\n")
+
+            fout.write(f"# python version: {sys.version.split()[0]}\n")
+            fout.write(f"# Date: {datetime.datetime.now()}\n")
             cmd1 = os.path.basename(sys.argv[0])
             fout.write(" ".join([cmd1] + sys.argv[1:]))
 

sequana_pipetools/snaketools/errors.py

@@ -12,7 +12,6 @@
 ##############################################################################
 from pathlib import Path
 
-from sequana_pipetools.options import guess_scheduler
 from sequana_pipetools.snaketools.slurm import SlurmParsing
 
 
@@ -24,11 +23,10 @@ def __init__(self, *args, **kwargs):
 
     def status(self, working_directory="./", logs_directory="logs"):
 
-        if guess_scheduler == "slurm":
-            try:  # let us try to introspect the slurm files
-                dj = SlurmParsing(working_directory, logs_directory)
-                print(dj)
-            except Exception as err:  # pragma: no cover
-                print(err)
-        else:
-            pass
+        # we allows slurm to be detected even though we are not on a cluster
+        # this allows users to debug slurm job through NFS mounting
+        try:  # let us try to introspect the slurm files
+            dj = SlurmParsing(working_directory, logs_directory)
+            print(dj)
+        except Exception as err:  # pragma: no cover
+            print(err)

sequana_pipetools/snaketools/pipeline_manager.py

@@ -15,15 +15,14 @@
 import shutil
 
 import colorlog
-from deprecated import deprecated
 
 from sequana_pipetools import get_package_version
 from sequana_pipetools.misc import PipetoolsException
 from sequana_pipetools.snaketools.errors import PipeError
 
 from .file_factory import FastQFactory, FileFactory
 from .module import Pipeline
-from .pipeline_utils import OnSuccessCleaner, message
+from .pipeline_utils import OnSuccessCleaner
 from .sequana_config import SequanaConfig
 
 logger = colorlog.getLogger(__name__)
@@ -95,10 +94,6 @@ def getrawdata(self):
             )
         return lambda wildcards: self.samples[wildcards.sample]
 
-    @deprecated(version="1.0", reason="will be removed in v1.0. Update your pipelines.")
-    def message(self, msg):  # pragma: no cover
-        message(msg)
-
     def setup(self, namespace=None, mode="error"):
         """
 

sequana_pipetools/snaketools/slurm.py

@@ -89,7 +89,7 @@ def __repr__(self):
     def _report(self):
         N = len(self.errors)
         message = "#" * 33 + " DEBUG REPORT " + "#" * 33 + "\n\n"
-        message += f"The analysis reached {self.percent}%. A total of {N} errors has been found.\n"
+        message += f"The analysis reached {self.percent}. A total of {N} error(s) has been found.\n"
         message += f"Errors are comming from rule(s): {','.join(set([e['rule'] for e in self.errors]))}\n\n"
 
         for e in self.errors:
@@ -112,8 +112,11 @@ def _get_percent(self):
         with open(self.master, "r") as f:
             data = f.read()
             last_percent_parse = [x for x in parse.findall(step_percent, data)]
-
-        return last_percent_parse[-1]["percent"]
+            if last_percent_parse:
+                pct = last_percent_parse[-1]["percent"]
+                pct = f"{pct}%"
+            else:
+                return "undefined status"
 
     def _get_rules_with_errors(self):
         """Return name and log files of rules which returned an error.,"""
@@ -132,7 +135,6 @@ def _get_rules_with_errors(self):
                     ID = filename.name.strip(".out").split("-")[-1]
                     rule = filename.name.split("-")[0]
                     for k in self.registry.keys():
-                        print(k)
                         if k in data:
                             errors.append({"rule": rule, "slurm_id": ID})
                             break