Merge branch 'feat_nftemplate' of https://github.com/CCBR/LOGAN into …

…feat_nftemplate

.pre-commit-config.yaml

@@ -3,7 +3,8 @@ default_stages: [pre-commit]
 exclude: |
   (?x)(
       ^assets/|
-      ^docs/.*.html
+      ^docs/.*.html|
+      ^_extensions/
    )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -12,6 +13,7 @@ repos:
       - id: check-added-large-files
       - id: end-of-file-fixer
       - id: trailing-whitespace
+      - id: check-json
   # spell check
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.4

.prettierrc

@@ -1,4 +1,7 @@
 overrides:
-  - files: "*.md"
+  - files:
+      - "*.md"
+      - "*.cff"
+      - ".prettierrc"
     options:
       tabWidth: 2

CITATION.cff

@@ -1,16 +1,19 @@
 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 TOOL_NAME gets published in a journal, include the citation here.
-authors: # TODO: author names should match those in pyproject.toml
+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
     orcid: https://orcid.org/0000-0002-5259-8599
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
   - family-names: Sovacool
     given-names: Kelly
     orcid: https://orcid.org/0000-0003-3283-829X
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
   - family-names: Koparde
     given-names: Vishal
     orcid: https://orcid.org/0000-0001-8978-8495
-title: "LOGAN: whoLe genOme-sequencinG Analysis pipeliNe" # TODO: citation title should match pyproject.toml
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
+title: "LOGAN: whoLe genOme-sequencinG Analysis pipeliNe"
 url: https://ccbr.github.io/LOGAN/
 repository-code: https://github.com/CCBR/LOGAN
-license: MIT
+license: MIT

src/__main__.py

@@ -31,11 +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)