From 4b041d2b521b014115d461abbc45b68a8160d43c Mon Sep 17 00:00:00 2001
From: js2264 <jacquesserizay@gmail.com>
Date: Thu, 1 Aug 2024 19:45:26 +0200
Subject: [PATCH] feat: kickstart cli

---
 docs/source/api.rst                 |  4 ++--
 docs/source/conf.py                 |  2 +-
 pyproject.toml                      |  1 +
 src/momics/__init__.py              |  2 ++
 src/momics/{Momics.py => api.py}    |  0
 src/momics/cli/__init__.py          | 27 +++++++++++++++++++++++++++
 src/momics/cli/dump.py              | 21 +++++++++++++++++++++
 tests/{test_main.py => test_api.py} |  0
 8 files changed, 54 insertions(+), 3 deletions(-)
 rename src/momics/{Momics.py => api.py} (100%)
 create mode 100644 src/momics/cli/__init__.py
 create mode 100644 src/momics/cli/dump.py
 rename tests/{test_main.py => test_api.py} (100%)

diff --git a/docs/source/api.rst b/docs/source/api.rst
index feeb3df..acb7f31 100644
--- a/docs/source/api.rst
+++ b/docs/source/api.rst
@@ -3,10 +3,10 @@
 API
 ====
 
-momics.Momics
+momics.api
 -------------
 
-.. automodule:: momics.Momics
+.. automodule:: momics.api
    :members:
    :undoc-members:
    :show-inheritance:
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 937e949..4ceaa3a 100644
--- a/docs/source/conf.py
+++ b/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",
diff --git a/pyproject.toml b/pyproject.toml
index 660d878..82e15b4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,6 +32,7 @@ dependencies = [
     "numpy", 
     "pandas", 
     "pyarrow>=1.0",
+    "click>=7",
 ]
 
 [project.urls]
diff --git a/src/momics/__init__.py b/src/momics/__init__.py
index 1cd2fdb..2210c08 100644
--- a/src/momics/__init__.py
+++ b/src/momics/__init__.py
@@ -9,9 +9,11 @@
 
 """
 
+from .api import Momics
 from .version import __format_version__, __version__
 
 __all__ = [
     "__version__",
     "__format_version__",
+    "Momics",
 ]
diff --git a/src/momics/Momics.py b/src/momics/api.py
similarity index 100%
rename from src/momics/Momics.py
rename to src/momics/api.py
diff --git a/src/momics/cli/__init__.py b/src/momics/cli/__init__.py
new file mode 100644
index 0000000..ce3442b
--- /dev/null
+++ b/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,
+)
diff --git a/src/momics/cli/dump.py b/src/momics/cli/dump.py
new file mode 100644
index 0000000..90239e6
--- /dev/null
+++ b/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())
diff --git a/tests/test_main.py b/tests/test_api.py
similarity index 100%
rename from tests/test_main.py
rename to tests/test_api.py