Replace myst_parser with myst_nb

CHANGELOG.md

@@ -1,8 +1,9 @@
 # Changelog
 
-## Version 0.1.1
+## Version 0.1.1 - 0.1.2
 
-Minor changes to improve user experience.
+- Minor changes to improve user experience.
+- Replace `myst_nb` and `myst_parser`.
 
 ## Version 0.1.0
 

README.md

@@ -46,7 +46,10 @@ create_repository(
 
 ## After setup
 
-- (Optional) Enable [pre-commit.ci](https://pre-commit.ci/) bot for your new repository.
+- Add a secret variable, `PYPI_API_TOKEN`, to your repository containing the token for publishing the package to PyPI.
+  - Tagging the repository will trigger an action to test, generate documentation, and publish the package to PyPI.
+- Install [tox](https://tox.wiki/en/4.23.2/) to handle package tasks. GitHub Actions relies on the tox configuration to test, generate documentation, and publish packages.
+- (Optional) Enable the [pre-commit.ci](https://pre-commit.ci/) bot for your repository.
 - (Optional) Install [ruff](https://docs.astral.sh/ruff/) for code formatting.
 
 <!-- pyscaffold-notes -->

docs/conf.py

@@ -79,7 +79,7 @@
 
 
 # Enable markdown
-extensions.append("myst_parser")
+extensions.append("myst_nb")
 
 # Configure MyST-Parser
 myst_enable_extensions = [
@@ -305,9 +305,6 @@
 
 # -- Biocsetup configuration -------------------------------------------------
 
-# Enable execution of code chunks in markdown
-extensions.append('myst_nb')
-
 # Less verbose api documentation
 extensions.append('sphinx_autodoc_typehints')
 

docs/requirements.txt

@@ -1,9 +1,9 @@
 furo
+myst-nb
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
 sphinx>=3.2.1
-myst-nb
-sphinx-autodoc-typehints
+sphinx-autodoc-typehints

src/biocsetup/create_repository.py

@@ -73,6 +73,7 @@ def create_repository(
 # -- Biocsetup configuration -------------------------------------------------
 
 # Enable execution of code chunks in markdown
+extensions.remove('myst_parser')
 extensions.append('myst_nb')
 
 # Less verbose api documentation
@@ -86,9 +87,11 @@ def create_repository(
 
 autosummary_generate = True
 autosummary_imported_members = True
+
+html_theme = "furo"
 """
 
-    conf_content = conf_content.replace("alabaster", "furo")
+    # conf_content = conf_content.replace("alabaster", "furo")
 
     with open(conf_py_path, "w") as f:
         f.write(conf_content + myst_config)