feat: improve dump cli

docs/source/cli.rst

@@ -3,3 +3,7 @@
 CLI
 ====
 
+.. click:: momics.cli.dump:dump
+  :prog: momics dump
+  :show-nested:
+

docs/source/conf.py

@@ -37,6 +37,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
+    "sphinx_click.ext",
     "recommonmark",
 ]
 

pyproject.toml

@@ -76,6 +76,7 @@ docs = [
     "recommonmark",
     "Sphinx>=1.6",
     "sphinx-autobuild",
+    "sphinx-click",
     "furo",
 ]
 

src/momics/api.py

@@ -185,25 +185,31 @@ def add_chroms(self, chr_lengths: dict, genome_version: str = ""):
             array.meta["genome_assembly_version"] = genome_version
             array.meta["timestamp"] = datetime.now().isoformat()
 
-    def __init__(self, path: str):
+    def __init__(self, path: str, create=True):
         """
         Initialize the Momics class.
 
         Parameters
         ----------
         path : str
             Path to a `.momics` repository.
+
+        create : bool
+            If not found, should the repository be initiated?
         """
 
         self.path = path
-        genome_path = os.path.join(path, "genome")
-        seq_path = os.path.join(path, "genome", "sequence")
-        coverage_path = os.path.join(path, "coverage")
-        features_path = os.path.join(path, "features")
 
         if not os.path.exists(path):
-            tiledb.group_create(path)
-            tiledb.group_create(genome_path)
-            tiledb.group_create(coverage_path)
-            tiledb.group_create(features_path)
-            tiledb.group_create(seq_path)
+            if create:
+                genome_path = os.path.join(path, "genome")
+                seq_path = os.path.join(path, "genome", "sequence")
+                coverage_path = os.path.join(path, "coverage")
+                features_path = os.path.join(path, "features")
+                tiledb.group_create(path)
+                tiledb.group_create(genome_path)
+                tiledb.group_create(coverage_path)
+                tiledb.group_create(features_path)
+                tiledb.group_create(seq_path)
+            else:
+                raise OSError("`momics repository not found.")

src/momics/cli/dump.py

@@ -9,13 +9,13 @@
 @click.option(
     "--table",
     "-t",
-    help="Which table to dump.",
+    help="Which supporting 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())
+        print(api.Momics(momics, create=False).tracks())
     if table == "chroms":
-        print(api.Momics(momics).chroms())
+        print(api.Momics(momics, create=False).chroms())