Merge branch 'master' into fix#504

Author: blankirigaya

CONTRIBUTING.md

@@ -200,15 +200,6 @@ poetry run pytest -v tests --typeguard-packages=malariagen_data,malariagen_data.
 - Address review feedback by pushing new commits to your branch
 - Once approved, a maintainer will merge your PR
 
-## AI-assisted contributions
-
-We welcome contributions that involve AI tools (like GitHub Copilot, ChatGPT, or similar). If you use AI assistance:
-
-- Review and understand any AI-generated code before submitting
-- Ensure the code follows project conventions and passes all tests
-- You remain responsible for the quality and correctness of the contribution
-- Disclosure of AI usage is optional. Regardless of tools used, contributors remain responsible for the quality and correctness of their submissions.
-
 ## Communication
 
 - **Issues**: Use [GitHub Issues](https://github.com/malariagen/malariagen-data-python/issues) for bug reports and feature requests

malariagen_data/anoph/describe.py

@@ -0,0 +1,115 @@
+import inspect
+from typing import Optional
+
+import pandas as pd
+from numpydoc_decorator import doc  # type: ignore
+
+from .base import AnophelesBase
+
+
+class AnophelesDescribe(AnophelesBase):
+    """Mixin class providing API introspection and discovery functionality."""
+
+    @doc(
+        summary="""
+            List all available public API methods with their descriptions.
+        """,
+        returns="""
+            A dataframe with one row per public method, containing the method
+            name, a short summary description, and its category (data access,
+            analysis, or plotting).
+        """,
+        parameters=dict(
+            category="""
+                Optional filter to show only methods of a given category.
+                Supported values are "data", "analysis", "plot", or None to
+                show all methods.
+            """,
+        ),
+    )
+    def describe_api(
+        self,
+        category: Optional[str] = None,
+    ) -> pd.DataFrame:
+        methods_info = []
+
+        # Walk through all public methods on this instance.
+        for name in sorted(dir(self)):
+            # Skip private/dunder methods.
+            if name.startswith("_"):
+                continue
+
+            attr = getattr(type(self), name, None)
+            if attr is None:
+                continue
+
+            # Only include callable methods and non-property attributes.
+            if isinstance(attr, property):
+                continue
+            if not callable(attr):
+                continue
+
+            # Extract the docstring summary.
+            summary = self._extract_summary(attr)
+
+            # Determine category.
+            method_category = self._categorize_method(name)
+
+            methods_info.append(
+                {
+                    "method": name,
+                    "summary": summary,
+                    "category": method_category,
+                }
+            )
+
+        df = pd.DataFrame(methods_info)
+
+        # Apply category filter if specified.
+        if category is not None:
+            valid_categories = {"data", "analysis", "plot"}
+            if category not in valid_categories:
+                raise ValueError(
+                    f"Invalid category: {category!r}. "
+                    f"Must be one of {valid_categories}."
+                )
+            df = df[df["category"] == category].reset_index(drop=True)
+
+        return df
+
+    @staticmethod
+    def _extract_summary(method) -> str:
+        """Extract the first line of the docstring as a summary."""
+        docstring = inspect.getdoc(method)
+        if not docstring:
+            return ""
+        # Take the first non-empty line as the summary.
+        for line in docstring.strip().splitlines():
+            line = line.strip()
+            if line:
+                return line
+        return ""
+
+    @staticmethod
+    def _categorize_method(name: str) -> str:
+        """Categorize a method based on its name."""
+        if name.startswith("plot_"):
+            return "plot"
+        data_prefixes = (
+            "sample_",
+            "snp_",
+            "hap_",
+            "cnv_",
+            "genome_",
+            "open_",
+            "lookup_",
+            "read_",
+            "general_",
+            "sequence_",
+            "cohorts_",
+            "aim_",
+            "gene_",
+        )
+        if name.startswith(data_prefixes):
+            return "data"
+        return "analysis"

malariagen_data/anoph/fst.py

@@ -235,7 +235,7 @@ def plot_fst_gwss_track(
             height=height,
             toolbar_location="above",
             x_range=x_range,
-            y_range=(0, 1),
+            y_range=(clip_min, 1),
             output_backend=output_backend,
         )
 
@@ -252,7 +252,7 @@ def plot_fst_gwss_track(
 
         # tidy up the plot
         fig.yaxis.axis_label = "Fst"
-        fig.yaxis.ticker = [0, 1]
+        fig.yaxis.ticker = sorted(set([clip_min, 0, 1]))
         self._bokeh_style_genome_xaxis(fig, contig)
 
         if show:  # pragma: no cover

malariagen_data/anopheles.py

@@ -44,6 +44,7 @@
 from .anoph.phenotypes import AnophelesPhenotypeData
 from .mjn import _median_joining_network, _mjn_graph
 from .anoph.hapclust import AnophelesHapClustAnalysis
+from .anoph.describe import AnophelesDescribe
 from .anoph.dipclust import AnophelesDipClustAnalysis
 from .util import (
     CacheMiss,
@@ -95,6 +96,7 @@ class AnophelesDataResource(
     AnophelesSampleMetadata,
     AnophelesGenomeFeaturesData,
     AnophelesGenomeSequenceData,
+    AnophelesDescribe,
     AnophelesBase,
     AnophelesPhenotypeData,
 ):