Make the Clade class public (#72)

Having Clade as a public class means we can use it
for type checking. For example, the target data
scripts we're writing for the variant-nowcast-hub
will benefit from typing the object returned by
CladeTime.assign_clades().

docs/reference/clade.rst

@@ -2,5 +2,5 @@
 Clade
 ==========
 
-.. autoclass:: cladetime._clade.Clade
+.. autoclass:: cladetime.clade.Clade
     :members:

src/cladetime/__init__.py

@@ -5,10 +5,11 @@
 
 # must import Tree before CladeTime
 from cladetime.tree import Tree
+from cladetime.clade import Clade
 from cladetime.cladetime import CladeTime
 from cladetime.util.reference import _docker_installed
 
-__all__ = ["CladeTime", "Tree"]
+__all__ = ["Clade", "CladeTime", "Tree"]
 
 # tells us package to consider DC a state
 os.environ["DC_STATEHOOD"] = "1"

src/cladetime/cladetime.py

@@ -9,7 +9,7 @@
 import structlog
 
 from cladetime import Tree, sequence
-from cladetime._clade import Clade
+from cladetime.clade import Clade
 from cladetime.exceptions import CladeTimeDateWarning, CladeTimeInvalidURLError, CladeTimeSequenceWarning
 from cladetime.util.config import Config
 from cladetime.util.reference import _get_clade_assignments, _get_date, _get_nextclade_dataset, _get_s3_object_url
@@ -235,7 +235,7 @@ def assign_clades(self, sequence_metadata: pl.LazyFrame, output_file: str | None
 
         Returns
         -------
-        :class:`cladetime._clade.Clade`
+        :class:`cladetime.clade.Clade`
             A Clade object that contains detailed and summarized information
             about clades assigned to the sequences in sequence_metadata.