Add a "demo_mode" to CladeTime

It's difficult to do live demos of CladeTime because it's
designed to operatate against Nextstrain's full set of sequence
and sequence metadata. This changeset adds an option that will
use a smaller dataset instead:
https://docs.nextstrain.org/projects/ncov/en/latest/reference/remote_inputs.html#k-subsamples

The "demo mode" is controlled by an environment variable
CLADETIME_DEMO

src/cladetime/util/config.py

@@ -1,3 +1,4 @@
+import os
 from dataclasses import InitVar, asdict, dataclass
 from datetime import datetime, timezone
 from pathlib import Path
@@ -60,5 +61,10 @@ def __post_init__(
         else:
             self.data_path = Path(".").home() / "covid_variant" / self.run_time
 
+        # For demo purposes, use Nextstrain's 100k sample dataset
+        if os.environ.get("CLADETIME_DEMO") == "true":
+            self.nextstrain_genome_metadata_key = "files/ncov/open/100k/metadata.tsv.xz"
+            self.nextstrain_genome_sequence_key = "files/ncov/open/100k/sequences.fasta.xz"
+
     def __repr__(self):
         return str(pprint(asdict(self)))

tests/conftest.py

@@ -11,6 +11,14 @@
 from cladetime.util.config import Config
 
 
+@pytest.fixture(scope="function")
+def demo_mode(monkeypatch):
+    "Set demo mode to True for tests using the Nextstrain 100K sequence files."
+    demo_mode = "true"
+    monkeypatch.setenv("CLADETIME_DEMO", demo_mode)
+    yield demo_mode
+
+
 @pytest.fixture
 def test_sequences():
     """Return a set of sequences for testing.

tests/integration/test_cladetime_integration.py

@@ -1,60 +1,28 @@
-import lzma
 from datetime import datetime, timezone
 from unittest.mock import MagicMock, patch
 
 import polars as pl
 import pytest
-import requests
 from freezegun import freeze_time
 from polars.testing import assert_frame_equal, assert_frame_not_equal
 
 from cladetime import CladeTime, sequence
 from cladetime.exceptions import CladeTimeSequenceWarning
-from cladetime.util.config import Config
-from cladetime.util.reference import _docker_installed, _get_s3_object_url
+from cladetime.util.reference import _docker_installed
 
 docker_enabled = _docker_installed()
 
 
-@pytest.fixture()
-def metadata_100k(tmp_path) -> pl.LazyFrame:
-    "Return metadata for Nextstain's 100k samples as of 2024-11-01"
-    config = Config()
-    metadata_url = _get_s3_object_url(
-        bucket_name=config.nextstrain_ncov_bucket,
-        object_key="files/ncov/open/100k/metadata.tsv.xz",
-        date=datetime(2024, 11, 1, tzinfo=timezone.utc),
-    )[1]
-
-    # download test metadata for Nextstrain's 100k samples (we can't use polars to scan it from
-    # s3 like we usually do, because the 100k samples don't have ZSTD-compressed versions
-    # and lmza.open doesn't support https)
-    response = requests.get(metadata_url)
-    response.raise_for_status()
-    with open(tmp_path / "metadata.tsv.xz", "wb") as file:
-        file.write(response.content)
-    metadata = pl.read_csv(lzma.open(tmp_path / "metadata.tsv.xz"), separator="\t", infer_schema_length=100000).lazy()
-
-    return metadata
-
-
 @pytest.mark.skipif(not docker_enabled, reason="Docker is not installed")
-def test_cladetime_assign_clades(tmp_path, metadata_100k):
-    config = Config()
+def test_cladetime_assign_clades(tmp_path, demo_mode):
+    # demo_mode fixture overrides CladeTime config to use Nextstrain's 100k sample
+    # sequence and sequence metadata instead of the entire universe of SARS-CoV-2 sequences
     assignment_file = tmp_path / "assignments.csv"
 
     with freeze_time("2024-11-01"):
         ct = CladeTime()
 
-        # override link to sequence .fasta to test against the 100k sample dataset
-        sequence_url = _get_s3_object_url(
-            bucket_name=config.nextstrain_ncov_bucket,
-            object_key="files/ncov/open/100k/sequences.fasta.xz",
-            date=datetime(2024, 11, 1, tzinfo=timezone.utc),
-        )[1]
-        ct.url_sequence = sequence_url
-
-        metadata_filtered = sequence.filter_metadata(metadata_100k, collection_min_date="2024-10-01")
+        metadata_filtered = sequence.filter_metadata(ct.sequence_metadata, collection_min_date="2024-10-01")
 
         # store clade assignments as they exist on the metadata file downloaded from Nextstrain
         original_clade_assignments = metadata_filtered.select(["strain", "clade"])