Move sequence file and rename filter function

Documenting the filter_covid_genome_metadata function made it
clear that its name should better align with the CladeTime
vernacular ('sequence metadata'). Additionally, it makes more
sense to move sequence.py out of the utility folder, since
sequence-related functions are integral to the package.

util/sequence.py remains in the code base for now, so we can
import the filtering function with its old name for backward
compatibility.

docs/reference/index.rst

@@ -4,6 +4,6 @@ API Reference
 .. toctree::
 
    cladetime
-   filter_covid_genome_metadata
+   sequence
    types
 

docs/reference/sequence.rst

@@ -0,0 +1,6 @@
+=========
+sequence
+=========
+
+.. autofunction:: cladetime.sequence.filter_sequence_metadata
+

docs/reference/types.rst

@@ -1,5 +1,5 @@
 =====
-Types
+types
 =====
 
 

src/cladetime/assign_clades.py

@@ -8,13 +8,13 @@
 import rich_click as click
 import structlog
 
-from cladetime.util.config import Config
-from cladetime.util.reference import get_nextclade_dataset
-from cladetime.util.sequence import (
+from cladetime.sequence import (
     _unzip_sequence_package,
     get_covid_genome_data,
     parse_sequence_assignments,
 )
+from cladetime.util.config import Config
+from cladetime.util.reference import get_nextclade_dataset
 
 logger = structlog.get_logger()
 

src/cladetime/cladetime.py

@@ -7,9 +7,9 @@
 import structlog
 
 from cladetime.exceptions import CladeTimeFutureDateWarning, CladeTimeInvalidDateError, CladeTimeInvalidURLError
+from cladetime.sequence import _get_ncov_metadata, get_covid_genome_metadata
 from cladetime.util.config import Config
 from cladetime.util.reference import _get_s3_object_url
-from cladetime.util.sequence import _get_ncov_metadata, get_covid_genome_metadata
 
 logger = structlog.get_logger()
 

src/cladetime/get_clade_list.py

@@ -7,13 +7,13 @@
 import structlog
 from cloudpathlib import AnyPath
 
-from cladetime.util.config import Config
-from cladetime.util.sequence import (
+from cladetime.sequence import (
     download_covid_genome_metadata,
-    filter_covid_genome_metadata,
+    filter_sequence_metadata,
     get_clade_counts,
     get_covid_genome_metadata,
 )
+from cladetime.util.config import Config
 from cladetime.util.session import _get_session
 from cladetime.util.timing import time_function
 
@@ -107,7 +107,7 @@ def main(
         data_dir,
     )
     lf_metadata = get_covid_genome_metadata(genome_metadata_path)
-    lf_metadata_filtered = filter_covid_genome_metadata(lf_metadata)
+    lf_metadata_filtered = filter_sequence_metadata(lf_metadata)
     counts = get_clade_counts(lf_metadata_filtered)
     clade_list = get_clades(counts, threshold, threshold_weeks, max_clades)