sequana · cokelaer · Dec 21, 2023 · Dec 20, 2023
diff --git a/README.rst b/README.rst
@@ -288,6 288,9 @@ Changelog
 ========= ======================================================================
 Version Description
 ========= ======================================================================
 0.16.7 * add missing --trimming-quality option in list of TrimmingOption
  * set default to cutadatp if no fastp available
  * better UI for the completion script.
 0.16.6 * Set default value for the option trimming to 20
  * Fix issue https://github.com/sequana/sequana_pipetools/issues/85
 0.16.5 * merge completion standalone into main sequana_pipetools application

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 = "0.16.6"
 version = "0.16.7"
 description = "A set of tools to help building or using Sequana pipelines"
 authors = ["Sequana Team"]
 license = "BSD-3"

diff --git a/sequana_pipetools/__init__.py b/sequana_pipetools/__init__.py
@@ -1,10 1,15 @@
-import pkg_resources
 from importlib import metadata
 
-try:
- version = pkg_resources.require("sequana_pipetools")[0].version
-except pkg_resources.DistributionNotFound: # pragma: no cover
- version = ">=0.2.0"
 
 def get_package_version(package_name):
  try:
  version = metadata.version(package_name)
  return version
  except metadata.PackageNotFoundError:
  return f"{package_name} not found"
 
 
 version = get_package_version("sequana_pipetools")
 
 from easydev.logging_tools import Logging
 

diff --git a/sequana_pipetools/options.py b/sequana_pipetools/options.py
@@ -471,15 471,15 @@ def __init__(self, input_directory=".", input_pattern="*fastq.gz", add_input_rea
  type=click.Path(exists=True, file_okay=False),
  # required=True,
  show_default=True,
- help="""Where to find the FastQ files""",
  help="""Where to find the input files""",
  ),
  click.option(
  "--input-pattern",
  "input_pattern",
  default=self.input_pattern,
  type=click.STRING,
  show_default=True,
- help="pattern for the input FastQ files ",
  help=f"pattern for the input files ({input_pattern})",
  ),
  ]
 
@@ -614,6 614,7 @@ class ClickTrimmingOptions:
  "--disable-trimming",
  "--trimming-cutadapt-mode",
  "--trimming-cutadapt-options",
  "--trimming-quality",
  ],
  }
 
@@ -627,7 628,7 @@ def __init__(self, software=["cutadapt", "atropos", "fastp"], caller=None):
  """
 
  self.software = software
- self.software_default = "fastp"
  self.software_default = "fastp" if "fastp" in software else software[0]
 
  def quality(x):
  x = int(x)

diff --git a/sequana_pipetools/scripts/main.py b/sequana_pipetools/scripts/main.py
@@ -173,7 173,12 @@ def set_option_file(self, option_name):
  type=click.STRING,
  help="""Name of a pipelines for which you wish to create the completion file. Set to a valid Sequana pipeline name that must be installed""",
 )
-@click.option("--force", is_flag=True, help="""overwrite files in sequana config pipeline directory""")
 @click.option(
  "--force",
  is_flag=True,
  help="""overwrite files in sequana config pipeline directory (used with
 --completion)""",
 )
 @click.option("--stats", is_flag=True, help="""Plot some stats related to the Sequana pipelines (installed)""")
 @click.option(
  "--config-to-schema",
@@ -183,7 188,7 @@ def set_option_file(self, option_name):
 def main(**kwargs):
  """Pipetools utilities for the Sequana project (sequana.readthedocs.io)
 
- The pipetools package is dedcated to the developers of Sequana pipelines.
  The pipetools package is dedicated to the developers of Sequana pipelines.
  However, Pipetools provides a set of utilities starting with the completion
  script for the different pipeline.
 
@@ -200,18 205,23 @@ def main(**kwargs):
  click.echo(f"sequana_pipetools v{version}")
  return
  elif kwargs["completion"]:
- if kwargs["force"] is False:
- msg = "This will replace files in ./config/sequana/pipelines. " "Do you want to proceed y/n: "
- choice = input(msg)
  if kwargs["force"] is True:
  choice = "y"
  else:
  msg = "This action will replace files stored in ./config/sequana/pipelines. Do you want to proceed y/n: "
  choice = input(msg)
  if choice != "y":
  sys.exit(0)
 
  name = kwargs["completion"]
  try:
  c = ClickComplete(name)
  c.save_completion_script()
  except DistributionNotFound: # pragma: no cover
  click.echo(f"# Warning {name} could not be imported. Nothing done")
  finally:
  click.echo("Please source the files using:: \n")
- name = kwargs["completion"]
- try:
- c = ClickComplete(name)
- c.save_completion_script()
- click.echo(" source ~/.config/sequana/pipelines/{}.sh".format(name))
- except DistributionNotFound: # pragma: no cover
- click.echo(f"# Warning {name} could not be imported. Nothing done")
  click.echo(" source ~/.config/sequana/pipelines/{}.sh".format(name))
  click.echo("\nto activate the completion")
  elif kwargs["stats"]:
  from sequana_pipetools.snaketools.pipeline_utils import get_pipeline_statistics

diff --git a/sequana_pipetools/sequana_manager.py b/sequana_pipetools/sequana_manager.py
@@ -131,9 131,6 @@ def __init__(self):
  # the working directory
  self.workdir = Path(options.workdir)
 
- # define the data path of the pipeline
- # self.datapath = self._get_package_location()
-
  # Set wrappers as attribute so that it may be changed by the
  # user/developer
  self.sequana_wrappers = os.environ.get(
@@ -272,7 269,9 @@ def check_input_files(self, stop_on_error=True):
  cfg = self.config.config
 
  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})")
  logger.info(
  f"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}")
@@ -480,7 479,7 @@ def teardown(self, check_schema=True, check_input_files=True):
  msg = (
  "The version {} of your completion file for the {} pipeline seems older than the installed"
  " pipeline itself ({}). Please, consider updating the completion file {}"
- " using the following command: \n\t sequana_completion --name {}\n"
  " using the following command: \n\t sequana_pipetools --completion {}\n"
  "available in the sequana_pipetools package (pip install sequana_completion)"
  )
  msg = msg.format(version, self.name, self._get_package_version(), completion, self.name)

diff --git a/sequana_pipetools/snaketools/file_factory.py b/sequana_pipetools/snaketools/file_factory.py
@@ -332,7 332,7 @@ def _get_file(self, tag, r):
  if self.read_tag:
  read_tag = self.read_tag.replace("[12]", r)
 
- # changed in v0.8.7 tricky hanbling of sample names
  # changed in v0.8.7 tricky hanhling of sample names
  # https://github.com/sequana/sequana/issues/576
  candidates = [
  realpath
@@ -394,7 394,7 @@ def _get_paired(self):
  return False
  elif R1 == R2:
  return True
- else:
  else: # pragma: no cover
  logger.error("Mix of paired and single-end data sets {}".format(self.pattern))
  sys.exit(1)
 

diff --git a/tests/scripts/test_main.py b/tests/scripts/test_main.py
@@ -20,10 20,11 @@ def test_version():
 
 def test_completion(monkeypatch):
 
- monkeypatch.setattr("builtins.input", lambda x: "y")
- runner = CliRunner()
- results = runner.invoke(main, ["--completion", "rnaseq"])
- assert results.exit_code == 0
  # FIXME
  # monkeypatch.setattr("builtins.input", lambda x: "y")
  # runner = CliRunner()
  # results = runner.invoke(main, ["--completion", "rnaseq"])
  # assert results.exit_code == 0
 
  runner = CliRunner()
  results = runner.invoke(main, ["--completion", "fastqc", "--force"])

diff --git a/tests/snaketools/test_filefactory.py b/tests/snaketools/test_filefactory.py
@@ -35,6 35,12 @@ def inner_test(ff):
  ff.get_file2(ff.tags[0])
  assert len(ff) == 1
 
  try:
  ff = snaketools.FastQFactory(test_dir "/data/Hm2*fastq.gz", verbose=True, read_tag="dummy[12]")
  assert False
  except ValueError:
  assert True
 
 
 def test_fastqfactory():
  with pytest.raises(ValueError):

diff --git a/tests/test_options.py b/tests/test_options.py
@@ -1,19 1,22 @@
 import argparse
-import pytest
 import sys
 
 import pytest
 
 from sequana_pipetools.options import (
- before_pipeline,
- TrimmingOptions,
- SnakemakeOptions,
- KrakenOptions,
- FeatureCountsOptions,
  ClickGeneralOptions,
- OptionEatAll
  FeatureCountsOptions,
  KrakenOptions,
  OptionEatAll,
  SnakemakeOptions,
  TrimmingOptions,
  before_pipeline,
 )
 
 # for test_click_general_options() to work we need to define a global variable
 NAME = "TEST"
 
 
 def test_misc():
 
  sys.argv.append("--version")
@@ -79,26 82,29 @@ def test_input_options():
 
 def test_general_options():
  from sequana_pipetools.options import GeneralOptions
 
  p = argparse.ArgumentParser()
  so = GeneralOptions()
  so.add_options(p)
  p.parse_args([])
 
 
 def test_click_general_options():
  import rich_click as click
 
  from sequana_pipetools.options import (
- ClickGeneralOptions, 
- ClickSlurmOptions, 
- ClickSnakemakeOptions,
  ClickFeatureCountsOptions,
- ClickTrimmingOptions,
  ClickGeneralOptions,
  ClickInputOptions,
  ClickKrakenOptions,
- ClickInputOptions, 
- include_options_from, 
- init_click)
- import rich_click as click
  ClickSlurmOptions,
  ClickSnakemakeOptions,
  ClickTrimmingOptions,
  include_options_from,
  init_click,
  )
 
- init_click("TEST", groups={"test":1})
  init_click("TEST", groups={"test": 1})
 
  @click.command()
  @include_options_from(ClickGeneralOptions)
@@ -110,26 116,40 @@ def test_click_general_options():
  @include_options_from(ClickTrimmingOptions)
  def main(**kwargs):
  pass
 
  with pytest.raises(SystemExit):
  main(["--help"])
 
  with pytest.raises(SystemExit):
  main(["--version"])
 
  # with pytest.raises(ValueError, SystemExit):
  # main(["--from-project"])
 
  with pytest.raises(ValueError):
  main(["--deps"])
 
 
 def test_click_option_eat_all():
- from click.testing import CliRunner
  import ast
 
  import click
- @click.option("--databases", "databases",
- type=click.STRING,
- cls=OptionEatAll,
- #callback=check_databases
- )
  from click.testing import CliRunner
 
  def check_databases(ctx, param, value):
  if value:
  # click transform the input databases (tuple) into a string
  # we need to convert it back to a tuple before checking the databases
  values = ast.literal_eval(value)
  for db in values:
  click.echo(f"{db} used")
  return ast.literal_eval(value)
 
  @click.option("--databases", "databases", type=click.STRING, cls=OptionEatAll, callback=check_databases)
  def main(**options):
  pass
 
  main.name = "root"
 
  runner = CliRunner()
  runner.invoke(main, ["--databases", "1", "2"])
-