Add script

Author: cthoyt

src/semra/landscape/anatomy.py

@@ -28,7 +28,7 @@
 Web Application
 ***************
 The pre-built artifacts for this mapping database can be downloaded from Zenodo
-at |anatomy| and unzipped. The web application can be run
+at |anatomyimg| and unzipped. The web application can be run
 locally on Docker from inside the folder where the data was unzipped with:
 
 .. code-block:: console
@@ -46,7 +46,7 @@
 Finally, navigate in your web browser to http://localhost:8773 to see the web
 application.
 
-.. |anatomy| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091803.svg
+.. |anatomyimg| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091803.svg
     :target: https://doi.org/10.5281/zenodo.11091803
 
 """  # noqa:D205,D400

src/semra/landscape/cell.py

@@ -32,7 +32,7 @@
 Web Application
 ***************
 The pre-built artifacts for this mapping database can be downloaded from Zenodo
-at |cell| and unzipped. The web application can be run
+at |cellimg| and unzipped. The web application can be run
 locally on Docker from inside the folder where the data was unzipped with:
 
 .. code-block:: console
@@ -50,7 +50,7 @@
 Finally, navigate in your web browser to http://localhost:8773 to see the web
 application.
 
-.. |cell| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091581.svg
+.. |cellimg| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091581.svg
     :target: https://doi.org/10.5281/zenodo.11091581
 
 """  # noqa:D205,D400

src/semra/landscape/complex.py

@@ -30,7 +30,7 @@
 Web Application
 ***************
 The pre-built artifacts for this mapping database can be downloaded from Zenodo
-at |complex| and unzipped. The web application can be run
+at |compleximg| and unzipped. The web application can be run
 locally on Docker from inside the folder where the data was unzipped with:
 
 .. code-block:: console
@@ -48,7 +48,7 @@
 Finally, navigate in your web browser to http://localhost:8773 to see the web
 application.
 
-.. |complex| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091422.svg
+.. |compleximg| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091422.svg
     :target: https://doi.org/10.5281/zenodo.11091422
 
 """  # noqa:D205,D400

src/semra/landscape/disease.py

@@ -41,7 +41,7 @@
 Web Application
 ***************
 The pre-built artifacts for this mapping database can be downloaded from Zenodo
-at |disease| and unzipped. The web application can be run
+at |diseaseimg| and unzipped. The web application can be run
 locally on Docker from inside the folder where the data was unzipped with:
 
 .. code-block:: console
@@ -59,7 +59,7 @@
 Finally, navigate in your web browser to http://localhost:8773 to see the web
 application.
 
-.. |disease| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091886.svg
+.. |diseaseimg| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11091886.svg
     :target: https://doi.org/10.5281/zenodo.11091886
 
 """  # noqa:D205,D400

src/semra/landscape/gene.py

@@ -35,7 +35,7 @@
 Web Application
 ***************
 The pre-built artifacts for this mapping database can be downloaded from Zenodo
-at |gene| and unzipped. The web application can be run
+at |geneimg| and unzipped. The web application can be run
 locally on Docker from inside the folder where the data was unzipped with:
 
 .. code-block:: console
@@ -53,7 +53,7 @@
 Finally, navigate in your web browser to http://localhost:8773 to see the web
 application.
 
-.. |gene| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11092013.svg
+.. |geneimg| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11092013.svg
     :target: https://doi.org/10.5281/zenodo.11092013
 
 """  # noqa:D205,D400

src/semra/landscape/taxrank.py

@@ -35,7 +35,7 @@
 Finally, navigate in your web browser to http://localhost:8773 to see the web
 application.
 
-.. |taxrank| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.None.svg
+.. |taxrankimg| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.None.svg
     :target: https://doi.org/10.5281/zenodo.None
 
 """  # noqa:D205,D400

src/semra/landscape/update_docs.py

@@ -0,0 +1,28 @@
+"""Update the module level docstrings for landscape configurations."""
+
+from semra.landscape import CONFIGURATIONS
+
+from pathlib import Path
+import click
+
+__all__ = [
+    "update_landscape_module_docstrings",
+]
+
+HERE = Path(__file__).parent.resolve()
+
+
+@click.command()
+def update_landscape_module_docstrings() -> None:
+    """Update the module level docstrings for landscape configurations."""
+    for conf in CONFIGURATIONS:
+        path = HERE.joinpath(conf.key).with_suffix(".py")
+        text = path.read_text()
+        lines = text.splitlines()
+        idx = min(i for i, line in enumerate(lines[1:], start=1) if line.startswith('"""'))
+        new = conf._get_header_text()
+        path.write_text(new + "\n".join(lines[idx + 1:]) + "\n")
+
+
+if __name__ == '__main__':
+    update_landscape_module_docstrings()