Merge pull request #26 from CCBR/fix-cli-citation

Fix cli citation flag

CITATION.cff

@@ -0,0 +1,15 @@
+cff-version: 1.2.0
+message: "Please cite LOGAN as below." # TODO set up Zenodo to archive your tool and assign a DOI. Or if it gets published in a journal, include the citation here.
+authors:
+  - family-names: Nousome
+    given-names: Darryl
+  - family-names: Sovacool
+    given-names: Kelly
+    orcid: https://orcid.org/0000-0003-3283-829X
+  - family-names: Koparde
+    given-names: Vishal
+    orcid: https://orcid.org/0000-0001-8978-8495
+title: "LOGAN: whoLe genOme-sequencinG Analysis pipeliNe"
+url: https://ccbr.github.io/LOGAN/
+repository-code: https://github.com/CCBR/LOGAN
+license: MIT

src/__main__.py

@@ -31,7 +31,14 @@ def common_options(func):
     cls=OrderedCommands, context_settings=dict(help_option_names=["-h", "--help"])
 )
 @click.version_option(get_version(), "-v", "--version", is_flag=True)
-@click.option("--citation", is_flag=True, callback=print_citation, expose_value=False, help="Print the citation in bibtex format and exit.")
+@click.option(
+    "--citation",
+    is_flag=True,
+    callback=print_citation,
+    expose_value=False,
+    is_eager=True,
+    help="Print the citation in bibtex format and exit.",
+)
 def cli():
     """whoLe genOme-sequencinG Analysis pipeliNe
 

src/util.py

@@ -25,6 +25,8 @@ def get_version():
 
 
 def print_citation(context, param, value):
+    if not value or context.resilient_parsing:
+        return
     citation = create_citation(nek_base("CITATION.cff"), None)
     # click.echo(citation._implementation.cffobj['message'])
     validate_or_write_output(None, "bibtex", False, citation)