Merge pull request #19 from cokelaer/main

Fix workflow, update version, verbosity

.github/workflows/main.yml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.8, 3.9, '3.10', '3.11']
+        python: [3.8, 3.9, '3.10', '3.11', '3.12']
       fail-fast: false
 
     steps:
@@ -54,13 +54,6 @@ jobs:
         pip install .
         pip install pytest pytest-cov coverage coveralls pytest-subprocess pytest-mock
 
-    - name: Install Damona using pip
-      run: |
-        bash
-        pip install damona
-        damona
-        echo " source ~/.config/damona/damona.sh" >> ~/.bashrc
-
     - name: testing
       run: |
         pytest --cov-report term --cov=versionix

README.rst

@@ -15,7 +15,7 @@ Versionix
 .. image:: https://zenodo.org/badge/658721856.svg
    :target: https://zenodo.org/badge/latestdoi/658721856
 
-:Python version: Python 3.8, 3.9, 3.10, 3.11
+:Python version: Python 3.8, 3.9, 3.10, 3.11, 3.12
 :Source: See  `http://github.com/sequana/versionix <https://github.com/sequana/versionix/>`__.
 :Issues: Please fill a report on `github <https://github.com/sequana/versionix/issues>`__
 
@@ -36,11 +36,18 @@ This is pure Python so no need for fancy libraries.
 Usage
 -----
 
-Then, just type **versionix** followed by an executable installed on your system, e.g::
+Then, just type **versionix** followed by an executable installed on your system, e.g for linux users::
+
+    versionix ls
+
+where **ls** is a standard command. In bioinformatics, **fastqc** is quite common. You can check its version as
+follows::
 
     versionix fastqc
 
-**versionix** prints the version as X.Y.Z string. Most tools would work. However, a registry is available for complex cases. Registered tools can be obtained with and if your favorite tool is not there, create a PR or an issue::
+**versionix** prints the version as X.Y.Z string.
+
+Most tools would work. However, a registry is available for complex cases. Registered tools can be obtained with the following command. If your favorite tool is not there, create a PR or an issue::
 
     versionix --registered
 
@@ -68,6 +75,7 @@ Changelog
 ========= ========================================================================
 Version   Description
 ========= ========================================================================
+0.99.0    Final version before 1.0.0
 0.3.0     Refactor to use regular expression and registry only if needed. This
           make versionix quite generic.
 0.2.4     More tools in the registry and added precommit

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "versionix"
-version = "0.3.0"
+version = "0.99.0"
 description = "Get version of any tools"
 authors = ["Sequana Team"]
 license = "BSD-3"
@@ -22,6 +22,7 @@ classifiers = [
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
         "Topic :: Software Development :: Libraries :: Python Modules",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Information Analysis",
@@ -34,6 +35,7 @@ packages = [
 python = "^3.8"
 click = "^8.1.7"
 rich-click = "^1.7.1"
+colorlog = "^6.8.2"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.0.1"

versionix/parser.py

@@ -87,7 +87,8 @@ def get_version(standalone, verbose=True):
 
     # let us check that the standalone exists locally
     if shutil.which(standalone) is None:
-        logger.error(f"ERROR: {standalone} command not found in your environment")
+        if verbose:
+            logger.warning(f"{standalone} command not found in your environment")
         sys.exit(1)
 
     # is it registered ?