feat(python): add CLI option

python/cookiecutter.json

@@ -7,5 +7,6 @@
     "your_name": "",
     "your_email": "",
     "add_docs": [false, true],
+    "add_cli": [false, true],
     "add_fastapi": [false, true]
 }

python/hooks/post_gen_project.py

@@ -8,10 +8,16 @@
     shutil.rmtree("docs")
     Path(".readthedocs.yaml").unlink()
 
+if not {{ cookiecutter.add_cli }}:
+    Path("./src/{{ cookiecutter.project_slug }}/cli.py").unlink()
+    if {{ cookiecutter.add_docs }}:
+        Path("./docs/source/cli_reference.rst").unlink()
 
 if not {{ cookiecutter.add_fastapi }}:
     Path("tests/test_api.py").unlink()
     Path("src/{{ cookiecutter.project_slug }}/api.py").unlink()
     Path("src/{{ cookiecutter.project_slug }}/models.py").unlink()
     Path("src/{{ cookiecutter.project_slug }}/config.py").unlink()
-    Path("src/{{ cookiecutter.project_slug }}/logging.py").unlink()
+
+if (not {{ cookiecutter.add_fastapi }}) and (not {{ cookiecutter.add_cli }}):
+    Path("./src/{{ cookiecutter.project_slug }}/logging.py").unlink()

python/{{cookiecutter.project_slug}}/docs/source/cli_reference.rst

@@ -0,0 +1,8 @@
+.. _cli-reference:
+
+Command-line interface
+----------------------
+
+.. click:: {{ cookiecutter.project_slug }}.cli:cli
+   :prog: {{ cookiecutter.project_slug | replace("_", "-") }}
+   :nested: full

python/{{cookiecutter.project_slug}}/docs/source/conf.py

@@ -77,3 +77,106 @@ def linkcode_resolve(domain, info):
 # -- code block style --------------------------------------------------------
 pygments_style = "default"
 pygements_dark_style = "monokai"
+
+
+# -- sphinx-click ------------------------------------------------------------
+# These functions let us write descriptions/docstrings in a way that doesn't look
+# weird in the Click CLI, but get additional formatting in the sphinx-click autodocs for
+# better readability.
+import re
+
+from click.core import Context
+from sphinx.application import Sphinx
+from sphinx_click.ext import _get_usage, _indent
+
+
+CMD_PATTERN = r"--[^ ]+"
+STR_PATTERN = r"\"[^ ]+\""
+SNAKE_PATTERN = r"[A-Z]+_[A-Z_]*[A-Z][., ]"
+
+
+def _add_formatting_to_string(line: str) -> str:
+    """Add fixed-width code formatting to span sections in lines:
+
+    * shell options, eg `--update_all`
+    * double-quoted strings, eg `"HGNC"`
+    * all caps SNAKE_CASE env vars, eg `GENE_NORM_REMOTE_DB_URL`
+    """
+    for pattern in (CMD_PATTERN, STR_PATTERN, SNAKE_PATTERN):
+        line = re.sub(pattern, lambda x: f"``{x.group()}``", line)
+    return line
+
+
+def process_description(app: Sphinx, ctx: Context, lines: list[str]):
+    """Add custom formatting to sphinx-click autodoc descriptions.
+
+    * remove :param: :return: etc
+    * add fixed-width (code) font to certain words
+    * add code block formatting to example shell commands
+    * move primary usage example to the top of the description
+
+    Because we have to modify the lines list in place, we have to make multiple passes
+    through it to format everything correctly.
+    """
+    if not lines:
+        return
+
+    # chop off params
+    param_boundary = None
+    for i, line in enumerate(lines):
+        if ":param" in line:
+            param_boundary = i
+            break
+    if param_boundary is not None:
+        del lines[param_boundary:]
+        lines[-1] = ""
+
+    # add code formatting to strings, commands, and env vars
+    lines_to_fmt = []
+    for i, line in enumerate(lines):
+        if line.startswith(("   ", ">>> ", "|")):
+            continue  # skip example code blocks
+        if any(
+            [
+                re.findall(CMD_PATTERN, line),
+                re.findall(STR_PATTERN, line),
+                re.findall(SNAKE_PATTERN, line),
+            ]
+        ):
+            lines_to_fmt.append(i)
+    for line_num in lines_to_fmt:
+        lines[line_num] = _add_formatting_to_string(lines[line_num])
+
+    # add code block formatting to example console commands
+    for i in range(len(lines) - 1, -1, -1):
+        if lines[i].startswith(("    ", "|     ")):
+            if lines[i].startswith("|     "):
+                lines[i] = lines[i][3:]
+            if (i == 0 or lines[i - 1] == "\b" or lines[i - 1] == ""):
+                lines.insert(i, "")
+                lines.insert(i, ".. code-block:: console")
+
+    # put usage at the top of the description
+    lines.insert(0, "")
+    for usage_line in _get_usage(ctx).splitlines()[::-1]:
+        lines.insert(0, _indent(usage_line))
+    lines.insert(0, "")
+    lines.insert(0, ".. code-block:: shell")
+
+
+def process_option(app: Sphinx, ctx: Context, lines: list[str]):
+    """Add fixed-width formatting to strings in sphinx-click autodoc options."""
+    for i, line in enumerate(lines):
+        if re.findall(STR_PATTERN, line):
+            lines[i] = re.sub(STR_PATTERN, lambda x: f"``{x.group()}``", line)
+
+
+def setup(app):
+    """Used to hook format customization into sphinx-click build.
+
+    In particular, since we move usage to the top of the command description, we need
+    an extra hook here to silence the built-in usage section.
+    """
+    app.connect("sphinx-click-process-description", process_description)
+    app.connect("sphinx-click-process-options", process_option)
+    app.connect("sphinx-click-process-usage", lambda app, ctx, lines: lines.clear())

python/{{cookiecutter.project_slug}}/docs/source/index.rst

@@ -25,6 +25,9 @@
     Installation<install>
     Usage<usage>
     API Reference<reference/index>
+{%- if cookiecutter.add_cli %}
+    CLI Reference<cli>
+{%- endif %}
     Changelog<changelog>
     Contributing<contributing>
     License<license>

python/{{cookiecutter.project_slug}}/pyproject.toml

@@ -18,14 +18,15 @@ classifiers = [
 requires-python = ">=3.11"
 description = "{{ cookiecutter.description }}"
 license = {file = "LICENSE"}
-{%- if cookiecutter.add_fastapi %}
 dependencies = [
+{%- if cookiecutter.add_cli %}
+    "click",
+{%- endif %}
+{%- if cookiecutter.add_fastapi %}
     "fastapi",
     "pydantic~=2.1",
+{%- endif %}
 ]
-{% else %}
-dependencies = []
-{% endif -%}
 dynamic = ["version"]
 
 [project.optional-dependencies]
@@ -48,9 +49,12 @@ docs = [
     "sphinx-copybutton==0.5.2",
     "sphinxext-opengraph==0.8.2",
     "furo==2023.3.27",
-    "sphinx-github-changelog==1.2.1"
+    "sphinx-github-changelog==1.2.1",
+{%- if cookiecutter.add_cli %}
+    "sphinx-click==5.0.1",
+{%- endif %}
 ]
-{% endif %}
+{%- endif %}
 
 [project.urls]
 Homepage = "https://github.com/{{ cookiecutter.org }}/{{ cookiecutter.repo }}"
@@ -60,6 +64,9 @@ Source = "https://github.com/{{ cookiecutter.org }}/{{ cookiecutter.repo }}"
 "Bug Tracker" = "https://github.com/{{ cookiecutter.org }}/{{ cookiecutter.repo }}/issues"
 
 [project.scripts]
+{%- if cookiecutter.add_cli %}
+{{ cookiecutter.project_slug | replace("_", "-") }} = "{{ cookiecutter.project_slug }}.cli:cli"
+{%- endif %}
 
 [build-system]
 requires = ["setuptools>=64", "setuptools_scm>=8"]
@@ -79,7 +86,9 @@ branch = true
 
 [tool.ruff]
 src = ["src"]
-{% if cookiecutter.add_docs %}exclude = ["docs/source/conf.py"]{% endif %}
+{%- if cookiecutter.add_docs %}
+exclude = ["docs/source/conf.py"]
+{%- endif %}
 
 [tool.ruff.lint]
 select = [

python/{{cookiecutter.project_slug}}/src/{{cookiecutter.project_slug}}/cli.py

@@ -0,0 +1,21 @@
+"""Provide CLI for application."""
+
+import click
+
+from {{ cookiecutter.project_slug }} import __version__
+from {{ cookiecutter.project_slug }}.logging import initialize_logs
+
+
+@click.group()
+@click.version_option(__version__)
+def cli() -> None:
+    """Short description of CLI.
+
+    \b
+        $ echo "provide a multiline description with a leading \\b"
+        $ echo "more commands here"
+        $ echo "otherwise, a single indent will pick up proper formatting"
+
+    Conclude by summarizing additional commands
+    """  # noqa: D301
+    initialize_logs()