Add CITATION.cff file with main contributors (#159)

* Add CITATION.cff file with main contributors
* Add script to bump version in README.md and CITATION.cff

.dev/bump_date.py

@@ -0,0 +1,67 @@
+from datetime import datetime
+from typing import Callable, Dict
+import re
+
+citation_regex = lambda new_date, content: re.sub(
+    r"date-released: \d{4}-\d{2}-\d{2}", f"date-released: {new_date}", content
+)
+
+readme_regexes = {
+    "bibtex_year": lambda year, content: re.sub(r"\{\d{4}\}", str(year), content),  # {2023} in bibtex
+    "bibtex_month": lambda month, content: re.sub(r"\{\d{1,2}\}", str(month), content),  # {5} or {12} in bibtex
+    "plain_bib_year": lambda year, content: re.sub(r"(\d{4})", str(year), content),  # (2023) in the plain bibliography
+}
+
+
+def bump_citation_file(
+    new_date: str,
+    filename: str = "CITATION.cff",
+    regex_function: Callable = citation_regex,
+) -> None:
+    """
+    Runs a specific regex function on the defined citation file
+    """
+    with open(filename, "r") as f:
+        content = f.read()
+
+    with open(filename, "w") as f:
+        content = regex_function(new_date, content)
+        f.write(content)
+
+
+def bump_readme_file(
+    year: str,
+    month: str,
+    regex_functions: Dict[str, Callable] = readme_regexes,
+    filename: str = "README.md",
+) -> None:
+    """
+    Runs the required regex functions on the README file
+    """
+    with open(filename, "r") as f:
+        content = f.read()
+
+    with open(filename, "w") as f:
+        content = regex_functions["bibtex_year"](year, content)
+        content = regex_functions["bibtex_month"](month, content)
+        content = regex_functions["plain_bib_year"](year, content)
+        f.write(content)
+
+
+def bump_date() -> None:
+    """
+    A developer function to bump the date when a version is bumped.
+
+    Run after bump2version is run, since bump2version doesn't allow updating
+    the date in e.g. README.md and CITATION.cff.
+    """
+    new_date = datetime.now().strftime("%Y-%m-%d")
+    year = str(datetime.now().year)
+    month = str(datetime.now().month)
+
+    bump_citation_file(new_date=new_date)
+    bump_readme_file(year=year, month=month)
+
+
+if __name__ == "__main__":
+    bump_date()

CITATION.cff

@@ -0,0 +1,21 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Teuwen"
+  given-names: "Jonas"
+  orcid: "https://orcid.org/0000-0002-1825-1428"
+- family-names: "Romor"
+  given-names: "Leonardo"
+- family-names: "Pai"
+  given-names: "Ajey"
+  orcid: "https://orcid.org/0009-0003-3970-9236"
+- family-names: "Schirris"
+  given-names: "Yoni"
+  orcid: "https://orcid.org/0000-0003-0217-8737"
+- family-names: "Marcus"
+  given-names: "Eric"
+  orchid: "https://orcid.org/0000-0002-3375-6248"
+title: "DLUP: Deep Learning Utilities for Pathology"
+version: 0.3.29
+date-released: 2023-10-10
+url: "https://github.com/nki-ai/dlup"

CONTRIBUTING.rst

@@ -129,6 +129,7 @@ Make sure all your changes are committed. Then run:
 .. code-block:: console
 
     $ bump2version patch # possible: major / minor / patch
+    $ python .dev/bump_date.py
     $ git push
 
 

README.md

@@ -21,3 +21,23 @@ The package can be installed using `python -m pip install dlup`.
 
 ## Used by
 - [ahcore](https://github.com/NKI-AI/ahcore.git): a pytorch lightning based-library for computational pathology
+
+## Citing DLUP
+If you use DLUP in your own research, please use the following BiBTeX entry:
+
+```
+@software{dlup,
+  author = {Teuwen, J., Romor, L., Pai, A., Schirris, Y., Marcus, E.},
+  month = {5},
+  title = {{DLUP: Deep Learning Utilities for Pathology}},
+  url = {https://github.com/nki-ai/dlup},
+  version = {0.3.29},
+  year = {2023}
+}
+```
+
+or the following plain bibliography:
+
+```
+Teuwen, J., Romor, L., Pai, A., Schirris, Y., Marcus E. (2023). DLUP: Deep Learning Utilities for Pathology (Version 0.3.29) [Computer software]. https://github.com/nki-ai/dlup
+```

setup.cfg

@@ -18,6 +18,14 @@ values =
 search = {current_version}
 replace = {new_version}
 
+[bumpversion:file:README.md]
+search = {current_version}
+replace = {new_version}
+
+[bumpversion:file:CITATION.cff]
+search = {current_version}
+replace = {new_version}
+
 [aliases]
 test = pytest