Merge branch 'master' into fix/issue-1280-vcf-performance

Author: khushthecoder

docs/source/_static/custom.css

@@ -0,0 +1,6 @@
+/* Fix version switcher dropdown overflow - GitHub issue #578 */
+.version-switcher__menu {
+    max-height: 60vh;
+    overflow-y: auto !important;
+    overflow-x: hidden;
+}

docs/source/conf.py

@@ -46,5 +46,6 @@
     ],
 }
 html_static_path = ["_static"]
+html_css_files = ["custom.css"]
 html_logo = "_static/logo.svg"
 html_favicon = "_static/favicon.ico"

malariagen_data/__init__.py

@@ -7,6 +7,7 @@
 from .anopheles import AnophelesDataResource, Region
 from .pf7 import Pf7
 from .pf8 import Pf8
+from .pf9 import Pf9
 from .pv4 import Pv4
 from .util import SiteClass
 

malariagen_data/anoph/aim_data.py

@@ -254,14 +254,24 @@ def plot_aim_heatmap(
             gn = np.take(gn, ix_sorted, axis=1)
             samples = np.take(samples, ix_sorted, axis=0)
 
+        species = aims.split("_vs_")
+
         # Set up colors for genotypes
         if palette is None:
-            assert self._aim_palettes is not None
+            if self._aim_palettes is None:
+                raise RuntimeError(
+                    "AIM palettes are not available for this data resource. "
+                    "Please provide the 'palette' parameter explicitly (4 colors)."
+                )
             palette = self._aim_palettes[aims]
-            assert len(palette) == 4
+            if len(palette) != 4:
+                raise RuntimeError(
+                    "Expected AIM palette to have 4 colors "
+                    f"(missing, {species[0]}/{species[0]}, {species[0]}/{species[1]}, {species[1]}/{species[1]}), "
+                    f"got {len(palette)}"
+                )
             # Expect 4 colors, in the order:
             # missing, hom taxon 1, het, hom taxon 2
-        species = aims.split("_vs_")
 
         # Create subplots.
         fig = go_make_subplots(

malariagen_data/anoph/cnv_frq.py

@@ -597,7 +597,11 @@ def _gene_cnv_frequencies_advanced(
             if nobs_mode == "called":
                 nobs[:, cohort_index] = np.repeat(cohort_n_called, 2)
             else:
-                assert nobs_mode == "fixed"
+                if nobs_mode != "fixed":
+                    raise RuntimeError(
+                        f"Internal error: expected nobs_mode='fixed', got {nobs_mode!r}. "
+                        "This should not happen; please open a GitHub issue."
+                    )
                 nobs[:, cohort_index] = cohort.size
 
         debug("compute frequency")

malariagen_data/anoph/frq_base.py

@@ -417,14 +417,6 @@ def plot_frequencies_heatmap(
                 `aa_allele_frequencies_advanced()` or
                 `gene_cnv_frequencies_advanced()`.
             """,
-            taxa="""
-                Taxon or list of taxa to include in the plot. If None,
-                all taxa are shown.
-            """,
-            areas="""
-                Area or list of areas to include in the plot. If None,
-                all areas are shown.
-            """,
             kwargs="Passed through to `px.line()`.",
         ),
         returns="""

malariagen_data/anoph/genome_features.py

@@ -110,7 +110,11 @@ def _genome_features_for_contig(self, *, contig: str, attributes: Tuple[str, ...
 
         # Handle normal contigs in the reference genome.
         else:
-            assert contig in self.contigs
+            if contig not in self.contigs:
+                raise ValueError(
+                    f"Contig {contig!r} not found. "
+                    f"Available contigs: {self.contigs}"
+                )
             df = self._genome_features(attributes=attributes)
 
             # Apply contig query.
@@ -561,7 +565,8 @@ def plot_genes(
 
             # Increase the figure height by a certain factor, to accommodate labels.
             height_increase_factor = 1.3
-            assert fig.height is not None
+            if fig.height is None:
+                raise RuntimeError("Figure height is unexpectedly None")
             fig.height = int(fig.height * height_increase_factor)
 
             # Get the original y_range.

malariagen_data/anoph/genome_sequence.py

@@ -86,7 +86,11 @@ def _genome_sequence_for_contig(self, *, contig, inline_array, chunks):
 
         # Handle normal contigs in the reference genome.
         else:
-            assert contig in self.contigs
+            if contig not in self.contigs:
+                raise ValueError(
+                    f"Contig {contig!r} not found. "
+                    f"Available contigs: {self.contigs}"
+                )
             root = self.open_genome()
             z = root[contig]
             d = _da_from_zarr(z, inline_array=inline_array, chunks=chunks)

malariagen_data/anoph/h1x.py

@@ -403,8 +403,17 @@ def _moving_h1x(ha, hb, size, start=0, stop=None, step=None):
         H1X values (sum of squares of joint haplotype frequencies).
     """
 
-    assert ha.ndim == hb.ndim == 2
-    assert ha.shape[0] == hb.shape[0]
+    if ha.ndim != 2 or hb.ndim != 2:
+        raise ValueError(
+            "Expected both haplotype arrays to be 2-dimensional "
+            "(n_variants, n_haplotypes), "
+            f"got ndim=({ha.ndim}, {hb.ndim})"
+        )
+    if ha.shape[0] != hb.shape[0]:
+        raise ValueError(
+            "Expected both haplotype arrays to have the same number of variants "
+            f"(axis 0), got ({ha.shape[0]}, {hb.shape[0]})"
+        )
 
     # Construct moving windows.
     windows = allel.index_windows(ha, size, start, stop, step)

malariagen_data/anoph/hap_data.py

@@ -58,7 +58,11 @@ def phasing_analysis_ids(self) -> Tuple[str, ...]:
     def _prep_phasing_analysis_param(self, *, analysis: hap_params.analysis) -> str:
         if analysis == base_params.DEFAULT:
             # Use whatever is the default phasing analysis for this data resource.
-            assert self._default_phasing_analysis is not None
+            if self._default_phasing_analysis is None:
+                raise RuntimeError(
+                    "No default phasing analysis configured. "
+                    "Please specify the 'analysis' parameter explicitly."
+                )
             return self._default_phasing_analysis
         elif analysis in self.phasing_analysis_ids:
             return analysis
@@ -118,7 +122,11 @@ def _haplotype_sites_for_contig(
 
         # Handle contig in the reference genome.
         else:
-            assert contig in self.contigs
+            if contig not in self.contigs:
+                raise ValueError(
+                    f"Contig {contig!r} not found. "
+                    f"Available contigs: {self.contigs}"
+                )
             root = self.open_haplotype_sites(analysis=analysis)
             z = root[f"{contig}/variants/{field}"]
             ret = _da_from_zarr(z, inline_array=inline_array, chunks=chunks)
@@ -251,7 +259,11 @@ def _haplotypes_for_contig(
 
         # Handle contig in the reference genome.
         else:
-            assert contig in self.contigs
+            if contig not in self.contigs:
+                raise ValueError(
+                    f"Contig {contig!r} not found. "
+                    f"Available contigs: {self.contigs}"
+                )
 
             # Open haplotypes zarr.
             root = self.open_haplotypes(sample_set=sample_set, analysis=analysis)