Cleanup code and enhance test suite with Codacy integration

.codacy.yaml

@@ -0,0 +1,2 @@
+exclude_paths:
+  - "test/**"

.github/workflows/main.yml

@@ -15,7 +15,7 @@ on:
 
 jobs:
   build-linux:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       max-parallel: 5
       matrix:
@@ -29,7 +29,7 @@ jobs:
         sudo rm -rf /usr/share/dotnet
         sudo rm -rf "$AGENT_TOOLSDIRECTORY"
 
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: docker-practice/actions-setup-docker@master
     - name: Test docker
       run: |
@@ -45,7 +45,7 @@ jobs:
         singularity version
 
     - name: Set up Python 3.X
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python }}
 

.github/workflows/pypi.yml

@@ -1,5 +1,5 @@
 name: Publish to PyPI
-on: 
+on:
   workflow_dispatch:
   push:
     tags:
@@ -8,29 +8,31 @@ on:
 jobs:
   build-n-publish:
     name: Build and publish to PyPI and TestPyPI
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@main
+    - uses: actions/checkout@v4
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.8
 
-    - name: Install package 
+    - name: Install package
       run: |
           pip install build poetry
 
     - name: Build source tarball
       run: |
           rm -rf dist;
           poetry build
- 
+
     - name: Publish distribution to Test PyPI
+      if: startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.TEST_PYPI_API_TOKEN }}
         repository_url: https://test.pypi.org/legacy/
+
     - name: Publish distribution to PyPI
       if: startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@release/v1

README.rst

@@ -21,6 +21,10 @@ Versionix
     :target: https://coveralls.io/github/sequana/versionix?branch=main
     :alt: Coverage
 
+.. image:: https://app.codacy.com/project/badge/Grade/7828229d14404f02b14eae651f8a5b20
+    :target: https://app.codacy.com/gh/cokelaer/versionix/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
+    :alt: Codacy grade
+
 .. image:: https://img.shields.io/badge/license-BSD--3--Clause-blue.svg
     :target: https://github.com/sequana/versionix/blob/main/LICENSE
     :alt: License
@@ -62,6 +66,7 @@ Key features
 - 🐍 **Pure Python** — no compiled dependencies; works on any platform
 - ⚡ **Fast** — single subprocess call, minimal overhead
 - 🔗 **Library API** — importable ``get_version()`` function for use in your own code
+- 📦 **Container support** — introspect versions from local Singularity/Apptainer image files
 
 Installation
 ============
@@ -98,16 +103,36 @@ Full help::
 .. image:: doc/versionix_usage.png
    :alt: versionix --help output
 
+Container introspection
+-----------------------
+
+You can retrieve the version of a tool that is packaged inside a local
+Singularity/Apptainer image file (``.img`` or ``.sif``) using the ``--from``
+option::
+
+    versionix sniffles --from sniffles_2.7.3.img
+    versionix fastqc --from fastqc.sif
+
+If ``apptainer`` is available it is preferred over ``singularity``; both are
+tried automatically.
+
 Python API
 ----------
 
 You can also call ``get_version`` directly from Python::
 
-    from versionix.parser import get_version
+    from versionix import get_version
 
     version = get_version("fastqc")
     print(version)  # e.g. "0.11.9"
 
+Pass a ``container`` argument to introspect a tool inside a local image file::
+
+    from versionix import get_version
+
+    version = get_version("sniffles", container="sniffles_2.7.3.img")
+
+
 How it works
 ============
 
@@ -148,6 +173,7 @@ Changelog
 ========= ========================================================================
 Version   Description
 ========= ========================================================================
+0.99.5    Update doc
 0.99.4    allow introspection of apptainers
 0.99.3    Maintenance release
 0.99.2    Handle cases where e.g. --version is returned to the stderr (instead of

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "versionix"
-version = "0.99.4"
+version = "0.99.5"
 description = "Get version of any tools"
 authors = ["Sequana Team"]
 license = "BSD-3"
@@ -45,6 +45,9 @@ ipython = "^8.0.1"
 pytest-mock = "^3.7.0"
 pytest-subprocess = "^1.5.0"
 
+[tool.pytest.ini_options]
+addopts = "-p no:asyncio"
+
 [tool.poetry.scripts]
 versionix = "versionix.scripts:main"
 

test/test_misc.py

@@ -1 +1,5 @@
 from versionix import version
+
+
+def test_version():
+    assert isinstance(version, str) and len(version) > 0

test/test_parser.py

@@ -1,6 +1,8 @@
 import sys
 
-from versionix.parser import get_version as get_version
+import pytest
+
+from versionix.parser import get_version
 from versionix.scripts import main
 
 # for testing we do not want to install all those tools/software so
@@ -112,12 +114,9 @@ def test_script(fp, mocker):
 
 def test_DESeq2_error(fp, mocker):
     # registered tool but if not installed, should raise a SystemExit error
-    try:
-        mocker.patch("shutil.which", return_value=None)
+    mocker.patch("shutil.which", return_value=None)
+    with pytest.raises(SystemExit):
         get_version("DESeq2")
-        assert False
-    except SystemExit:
-        assert True
 
 
 def test_DESeq2_uses_rscript_caller(fp, mocker):
@@ -127,28 +126,22 @@ def which_side_effect(cmd):
 
     mocker.patch("versionix.parser.shutil.which", side_effect=which_side_effect)
     fp.register(
-        'Rscript -e "library(DESeq2);packageVersion(\'DESeq2\')"',
+        "Rscript -e \"library(DESeq2);packageVersion('DESeq2')\"",
         stdout=["[1] '1.42.0'"],
     )
     assert get_version("DESeq2") == "1.42.0"
 
 
 def test_empty_parsers(fp, mocker):
-    try:
-        mocker.patch("shutil.which", return_value=True)
+    mocker.patch("shutil.which", return_value=True)
+    with pytest.raises(ValueError):
         get_version("for_testing_empty_parsers")
-        assert False
-    except ValueError:
-        assert True
 
 
 def test_no_parser(fp, mocker):
-    try:
-        mocker.patch("shutil.which", return_value=True)
+    mocker.patch("shutil.which", return_value=True)
+    with pytest.raises(ValueError):
         get_version("for_testing_no_parsers")
-        assert False
-    except ValueError:
-        assert True
 
 
 def test_from_singularity_img(fp, mocker):
@@ -213,6 +206,20 @@ def which_side_effect(cmd):
     assert get_version("dot", container="sequana_0.18.img") == "2.40.1"
 
 
+def test_no_singularity_or_apptainer_in_path(fp, mocker):
+    mocker.patch("versionix.parser.shutil.which", return_value=None)
+    mocker.patch("versionix.parser.os.path.isfile", return_value=False)
+    with pytest.raises(SystemExit):
+        get_version("fastqc", container="myimage.sif")
+
+
+def test_no_docker_in_path(fp, mocker):
+    mocker.patch("versionix.parser.shutil.which", return_value=None)
+    mocker.patch("versionix.parser.os.path.isfile", return_value=False)
+    with pytest.raises(SystemExit):
+        get_version("fastqc", container="myimage:latest")
+
+
 def test_script_from_container(fp, mocker):
     from click.testing import CliRunner
 

versionix/logging.py

@@ -1,15 +1,13 @@
-# -*- python -*-
 #
-#  This file is part of easydev software
+#  This file is part of Versionix software
 #
-#  Copyright (c) 2011-2024
+#  Copyright (c) 2023 - Sequana Dev Team (https://sequana.readthedocs.io)
 #
-#  File author(s): Thomas Cokelaer <[email protected]>
-#
-#  Distributed under the BSD3 License.
-#
-#  Website: https://github.com/cokelaer/easydev
+#  Distributed under the terms of the 3-clause BSD license.
+#  The full license is in the LICENSE file, distributed with this software.
 #
+#  Website:       https://github.com/sequana/versionix
+#  Contributors:  https://github.com/sequana/versionix/graphs/contributors
 ##############################################################################
 # import logging
 import colorlog

versionix/parser.py

@@ -18,9 +18,7 @@
 
 import colorlog
 
-from versionix import logger
-
-logger = colorlog.getLogger(logger.name)
+logger = colorlog.getLogger("versionix")
 
 
 from .blacklist import blacklist
@@ -149,7 +147,7 @@ def get_version(standalone, verbose=True, container=None):
             sys.exit(1)
 
     # is it registered ?
-    if standalone in metadata.keys():
+    if standalone in metadata:
         version = search_registered(standalone, container_runner=container_runner)
         return version
 

versionix/scripts.py

@@ -12,7 +12,6 @@
 """.. rubric:: Standalone application (CLI entry point) for Versionix"""
 import sys
 
-import colorlog
 import rich_click as click
 
 from versionix import version
@@ -26,8 +25,6 @@
 click.rich_click.STYLE_ERRORS_SUGGESTION = "magenta italic"
 click.rich_click.SHOW_ARGUMENTS = True
 
-logger = colorlog.getLogger(__name__)
-
 
 @click.command()
 @click.argument("standalone", required=False, type=click.STRING, default=None)
@@ -75,8 +72,8 @@ def main(**kwargs):
             click.echo(f"{name}")
     else:
         if kwargs["standalone"] is None:
-            from rich.panel import Panel
             from rich.console import Console
+            from rich.panel import Panel
 
             console = Console()
             console.print(