Add entry points for scripts (#39)

* Try fixing the docs pipeline.

* Add entry point

* Fix CLI configuration

* Minor refactoring

* Finish the script

mkdocs.yml

@@ -45,3 +45,32 @@ repo_url: https://github.com/cbg-ethz/covvfit
 
 watch:
   - src/covvfit
+
+extra:
+  social:
+    - icon: fontawesome/brands/github-alt
+      link: https://github.com/cbg-ethz/covvfit
+
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - admonition
+  - pymdownx.arithmatex:
+      generic: true
+  - footnotes
+  - pymdownx.details
+  - pymdownx.superfences
+  - pymdownx.mark
+  - attr_list
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+
+
+extra_javascript:
+  - javascripts/mathjax.js
+  - https://polyfill.io/v3/polyfill.min.js?features=es6
+  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

pyproject.toml

@@ -21,7 +21,10 @@ seaborn = "^0.13.2"
 numpyro = "^0.14.0"
 subplots-from-axsize = "^0.1.9"
 pango-aliasor = "^0.3.0"
+typer = "^0.15.1"
 
+[tool.poetry.scripts]
+covvfit = "covvfit.cli:main"
 
 [tool.poetry.group.dev]
 optional = true
@@ -32,9 +35,9 @@ ruff = "^0.1.3"
 black = "==23.12.1"
 pre-commit = "^3.5.0"
 pyright = "^1.1.333"
-mkdocstrings = {extras = ["python"], version = "^0.23.0"}
+mkdocs-material = "^9.5.50"
+mkdocstrings = {extras = ["python-legacy"], version = "^0.21.2"}
 mkdocs = "^1.5.3"
-mkdocs-material = "^9.4.7"
 jupytext = "^1.16.1"
 jupyterlab = "^4.1.6"
 

src/covvfit/_cli/__init__.py

@@ -0,0 +1 @@
+"""Subpackage with scripts."""

src/covvfit/_cli/freyja.py

@@ -0,0 +1,18 @@
+"""Script gathering Freyja files into one CSV."""
+from typing import Annotated
+
+import typer
+
+
+def freyja_gather(
+    directory: Annotated[str, typer.Argument(help="Directory with Freyja output")],
+    metadata: Annotated[str, typer.Argument(help="Metadata")],
+    output: Annotated[str, typer.Argument(help="Desired output location")],
+):
+    """Gathers Freyja-demixed files from the given directory into the output CSV,
+    adding the metadata."""
+    typer.echo(
+        "This function is not implemented yet. It will be added at a later time."
+    )
+    typer.Exit(code=1)
+    # Add your processing logic here