add defensefinder version

CONTRIBUTING.md

@@ -20,9 +20,9 @@ A [Github action](https://github.com/mdmparis/defense-finder/actions) is setup t
 Note that you don't need to publish defense-finder everytime the models change: only changes in this repository are relevant.
 
 Here are the steps to follow in order to publish defense-finder:
-- find the current version in the `setup` function of `setup.py`.
+- find the current version in `defense_finder_cli/_version.py`
 - get a new version number according to [semantic versionning](https://semver.org/)
-- update the version un `setup.py`
+- update the version un `defense_finder_cli/_version.py`
 - commit this change, and tag the commit with `git tag -a v<your version number> -m '<your version number> <an optional message>'`
 - push your commits to master
 - run `git push origin v<your version>` to sync the tags

defense_finder_cli/_version.py

@@ -0,0 +1 @@
+__version__ = "1.2.2"

defense_finder_cli/main.py

@@ -15,6 +15,7 @@
 except AttributeError:
     logging = colorlog.wrappers.logging
 
+from ._version import __version__
 
 @click.group(context_settings=dict(help_option_names=["-h", "--help"]))
 def cli():
@@ -32,6 +33,12 @@ def cli():
     """
     pass
 
+@cli.command()
+def version():
+    """Get the version of DefenseFinder (software)
+    """
+    print(f"Using DefenseFinder version {__version__}")
+
 
 @cli.command()
 @click.option('--models-dir', 'models_dir', required=False, help='Specify a directory containing your models.')
@@ -68,8 +75,6 @@ def update(models_dir=None, force_reinstall: bool = False):
 @click.option('--log-level', 'loglevel', default="INFO",
               help='set the logging level among DEBUG, [INFO], WARNING, ERROR, CRITICAL')
 @click.option('--index-dir', 'index_dir', required=False, help='Specify a directory to write the index files required by macsyfinder when the input file is in a read-only folder')
-
-
 def run(file: str, outdir: str, dbtype: str, workers: int, coverage: float, preserve_raw: bool, 
         no_cut_ga: bool, models_dir: str = None, loglevel : str = "INFO",
         index_dir: str = None):
@@ -146,7 +151,7 @@ def run(file: str, outdir: str, dbtype: str, workers: int, coverage: float, pres
         else:
             protein_file_name = filename
 
-    logger.info("Running DefenseFinder")
+    logger.info(f"Running DefenseFinder version {__version__}")
     defense_finder.run(protein_file_name, dbtype, workers, coverage, tmp_dir, models_dir, no_cut_ga, loglevel, index_dir)
     logger.info("Post-treatment of the data")
     defense_finder_posttreat.run(tmp_dir, outdir, os.path.splitext(os.path.basename(filename))[0])
@@ -168,6 +173,8 @@ def run(file: str, outdir: str, dbtype: str, workers: int, coverage: float, pres
 Tesson F., Hervé A. , Mordret E., Touchon M., d’Humières C., Cury J., Bernheim A., 2022, Nature Communication
 Systematic and quantitative view of the antiviral arsenal of prokaryotes
 
+Using DefenseFinder version {__version__}.
+
 DefenseFinder relies on MacSyFinder : 
 
 {get_version_message().split("and don't")[0]}

setup.py

@@ -11,9 +11,10 @@ def read_md(f):
 def read_req(req: str):
     return [i for i in [l.strip() for l in open(req).read().split('\n')] if i]
 
+exec(open('defense_finder_cli/_version.py').read())
 
 setup(name='mdmparis-defense-finder',
-        version='1.2.2',
+        version=__version__, # from 'defense_finder_cli/_version.py'
         description="Defense Finder: allow for a systematic search of all known anti-phage systems.",
         long_description=read_md('README.md'),
         long_description_content_type="text/markdown",