feat: kickstart cli

docs/source/api.rst

@@ -3,10 +3,10 @@
 API
 ====
 
-momics.Momics
+momics.api
 -------------
 
-.. automodule:: momics.Momics
+.. automodule:: momics.api
    :members:
    :undoc-members:
    :show-inheritance:

docs/source/conf.py

@@ -58,12 +58,12 @@
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = "furo"
 # html_theme = "pydata_sphinx_theme"
 html_static_path = ["_static"]
 htmlhelp_basename = "momicsdoc"
 html_last_updated_fmt = "%b %d, %Y"
 html_title = "momics"
+html_theme = "furo"
 html_theme_options = {
     "source_repository": "https://github.com/js2264/momics/",
     "source_branch": "devel",

pyproject.toml

@@ -32,6 +32,7 @@ dependencies = [
     "numpy", 
     "pandas", 
     "pyarrow>=1.0",
+    "click>=7",
 ]
 
 [project.urls]

src/momics/__init__.py

@@ -9,9 +9,11 @@
 
 """
 
+from .api import Momics
 from .version import __format_version__, __version__
 
 __all__ = [
     "__version__",
     "__format_version__",
+    "Momics",
 ]

src/momics/cli/__init__.py

@@ -0,0 +1,27 @@
+import click
+
+from ..version import __version__
+
+CONTEXT_SETTINGS = {"help_option_names": ["-h", "--help"]}
+
+
+class UnsortedGroup(click.Group):
+    """A click Group that lists commands in the order they were added."""
+
+    def list_commands(self, ctx):
+        return list(self.commands)
+
+
+@click.version_option(__version__, "-V", "--version")
+@click.group(context_settings=CONTEXT_SETTINGS, cls=UnsortedGroup)
+def cli():
+    """
+    Type -h or --help after any subcommand for more information.
+
+    """
+
+
+# Load and register cli subcommands
+from . import (  # noqa: E402,F401
+    dump,
+)

src/momics/cli/dump.py

@@ -0,0 +1,21 @@
+import click
+
+from .. import api
+from . import cli
+
+
+@cli.command()
+@click.argument("momics", metavar="MOMICS_PATH")
+@click.option(
+    "--table",
+    "-t",
+    help="Which table to dump.",
+    type=click.Choice(["chroms", "tracks"]),
+    default="chroms",
+    show_default=True,
+)
+def dump(momics, table):
+    if table == "tracks":
+        print(api.Momics(momics).tracks())
+    if table == "chroms":
+        print(api.Momics(momics).chroms())