Merge remote-tracking branch 'origin/master'

Resolve conflicts in g123.py and test_g123.py:
- Keep DEFAULT_SITE_PARAMETER approach in all 4 function signatures
- Drop remote's base_params.DEFAULT fallback blocks (now dead code)
- Fix pre=False for adir1/amin1 fixtures (not pre-release datasets)

Author: blankkiri

README.md

@@ -10,6 +10,22 @@ package index (PyPI) and can be installed via `pip`, e.g.:
 ```bash
 pip install malariagen-data
 ```
+## Quick Start
+
+Once installed, you can begin accessing MalariaGEN datasets directly
+from Python.
+
+For example, to work with the Pf8 dataset:
+
+```python
+import malariagen_data
+
+# Instantiate dataset
+pf8 = malariagen_data.Pf8()
+
+# Load sample metadata
+df = pf8.sample_metadata()
+print(df.head())
 
 ## Documentation
 

malariagen_data/anoph/g123.py

@@ -276,6 +276,12 @@ def g123_calibration(
         # invalidate any previously cached data.
         name = "g123_calibration_v1"
 
+        valid_sites = self.phasing_analysis_ids + ("all", "segregating")
+        if sites not in valid_sites:
+            raise ValueError(
+                f"Invalid value for `sites` parameter, must be one of {valid_sites}."
+            )
+
         params = dict(
             contig=contig,
             sites=sites,

tests/anoph/test_g123.py

@@ -163,8 +163,9 @@ def test_g123_gwss_with_default_sites(fixture, api: AnophelesG123Analysis):
 
 @parametrize_with_cases("fixture,api", cases=".")
 def test_g123_gwss_with_phased_sites(fixture, api: AnophelesG123Analysis):
+    # Skip if this dataset has no phasing analyses (e.g., Adir1, Amin1).
     if not api.phasing_analysis_ids:
-        pytest.skip("No phasing analysis available")
+        pytest.skip("No phasing analyses available for this dataset.")
 
     # Set up test parameters.
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
@@ -233,8 +234,9 @@ def test_g123_gwss_with_bad_sites(fixture, api: AnophelesG123Analysis):
 
 @parametrize_with_cases("fixture,api", cases=".")
 def test_g123_calibration(fixture, api: AnophelesG123Analysis):
+    # Skip if this dataset has no phasing analyses (e.g., Adir1, Amin1).
     if not api.phasing_analysis_ids:
-        pytest.skip("No phasing analysis available")
+        pytest.skip("No phasing analyses available for this dataset.")
 
     # Set up test parameters.
     all_sample_sets = api.sample_sets()["sample_set"].to_list()