Fix/replace asserts with runtime validation

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)

malariagen_data/anoph/hap_frq.py

@@ -100,7 +100,11 @@ def haplotypes_frequencies(
             hap_dict = {k: 0 for k in f_all.keys()}
 
             n_samples = np.count_nonzero(loc_coh)
-            assert n_samples >= min_cohort_size
+            if n_samples < min_cohort_size:
+                raise ValueError(
+                    f"Not enough samples ({n_samples}) for minimum "
+                    f"cohort size ({min_cohort_size})"
+                )
             gt_coh = gt.compress(loc_coh, axis=1)
             gt_hap = gt_coh.to_haplotypes()
             f, _, _ = _haplotype_frequencies(gt_hap)
@@ -224,7 +228,11 @@ def haplotypes_frequencies_advanced(
             hap_freq = {k: 0 for k in f_all.keys()}
             hap_count = {k: 0 for k in f_all.keys()}
             hap_nob = {k: 2 * n_samples for k in f_all.keys()}
-            assert n_samples >= min_cohort_size
+            if n_samples < min_cohort_size:
+                raise ValueError(
+                    f"Not enough samples ({n_samples}) for minimum "
+                    f"cohort size ({min_cohort_size})"
+                )
             sample_indices = group_samples_by_cohort.indices[cohort_key]
             gt_coh = gt.take(sample_indices, axis=1)
             gt_hap = gt_coh.to_haplotypes()

malariagen_data/anoph/sample_metadata.py

@@ -594,8 +594,16 @@ def _aim_analysis(self):
     def _parse_aim_metadata(
         self, sample_set: str, data: Union[bytes, Exception]
     ) -> pd.DataFrame:
-        assert self._aim_metadata_columns is not None
-        assert self._aim_metadata_dtype is not None
+        if self._aim_metadata_columns is None:
+            raise RuntimeError(
+                "Internal error: AIM metadata columns are not configured. "
+                "This should not happen; please open a GitHub issue."
+            )
+        if self._aim_metadata_dtype is None:
+            raise RuntimeError(
+                "Internal error: AIM metadata dtypes are not configured. "
+                "This should not happen; please open a GitHub issue."
+            )
         if isinstance(data, bytes):
             # Parse CSV data but don't apply the dtype yet.
             df = pd.read_csv(io.BytesIO(data), na_values="")

malariagen_data/anoph/snp_data.py

@@ -103,6 +103,14 @@ def site_mask_ids(self) -> Tuple[str, ...]:
         """
         return tuple(self.config.get("SITE_MASK_IDS", ()))  # ensure tuple
 
+    def site_mask_def(self) -> str:
+        """Return the default site mask identifier for this data resource."""
+        if self._default_site_mask is None:
+            raise RuntimeError(
+                "No default site mask configured. Please specify the 'site_mask' parameter explicitly."
+            )
+        return self._default_site_mask
+
     @property
     def _site_annotations_zarr_path(self) -> str:
         return self.config["SITE_ANNOTATIONS_ZARR_PATH"]
@@ -114,7 +122,11 @@ def _prep_site_mask_param(
     ) -> base_params.site_mask:
         if site_mask == base_params.DEFAULT:
             # Use whatever is the default site mask for this data resource.
-            assert self._default_site_mask is not None
+            if self._default_site_mask is None:
+                raise RuntimeError(
+                    "No default site mask configured. "
+                    "Please specify the 'site_mask' parameter explicitly."
+                )
             return self._default_site_mask
         elif site_mask in self.site_mask_ids:
             return site_mask
@@ -214,7 +226,9 @@ def _site_filters_for_contig(
         *,
         contig: str,
         mask: base_params.site_mask,
-        field: base_params.field,
+        # Field identifies which per-variant filter array to read (e.g. "filter_pass").
+        # Default kept for backwards compatibility with internal callers/tests.
+        field: base_params.field = "filter_pass",
         inline_array: base_params.inline_array,
         chunks: base_params.chunks,
     ) -> da.Array:
@@ -234,7 +248,11 @@ def _site_filters_for_contig(
             return d
 
         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_site_filters(mask=mask)
             z = root[f"{contig}/variants/{field}"]
             d = _da_from_zarr(z, inline_array=inline_array, chunks=chunks)
@@ -336,12 +354,32 @@ def _snp_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_snp_sites()
             z = root[f"{contig}/variants/{field}"]
             ret = _da_from_zarr(z, inline_array=inline_array, chunks=chunks)
             return ret
 
+    # Backwards compatible alias for internal callers/tests.
+    def snp_sites_for_contig(
+        self,
+        *,
+        contig: base_params.contig,
+        field: base_params.field,
+        inline_array: base_params.inline_array,
+        chunks: base_params.chunks,
+    ) -> da.Array:
+        return self._snp_sites_for_contig(
+            contig=contig,
+            field=field,
+            inline_array=inline_array,
+            chunks=chunks,
+        )
+
     def _snp_sites_for_region(
         self,
         *,
@@ -445,7 +483,11 @@ def _snp_genotypes_for_contig(
             return da.concatenate(arrs)
 
         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_snp_genotypes(sample_set=sample_set)
             z = root[f"{contig}/calldata/{field}"]
             d = _da_from_zarr(z, inline_array=inline_array, chunks=chunks)
@@ -601,7 +643,11 @@ def _snp_variants_for_contig(
             return ret
 
         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}"
+                )
             coords = dict()
             data_vars = dict()
             sites_root = self.open_snp_sites()
@@ -721,6 +767,40 @@ def _site_annotations_raw(
 
         return ds
 
+    def _site_annotations_for_contig(
+        self,
+        *,
+        contig,
+        inline_array: base_params.inline_array,
+        chunks: base_params.chunks,
+    ) -> xr.Dataset:
+        """
+        Backwards compatible internal helper.
+
+        Raises a ValueError with a consistent message when the contig is unknown,
+        matching expectations in tests and existing error-handling behavior.
+        """
+        if contig in getattr(self, "virtual_contigs", {}):
+            contigs = self.virtual_contigs[contig]
+            ds_parts = [
+                self._site_annotations_raw(
+                    contig=c,
+                    inline_array=inline_array,
+                    chunks=chunks,
+                )
+                for c in contigs
+            ]
+            return _simple_xarray_concat(ds_parts, dim=DIM_VARIANT)
+
+        if contig not in self.contigs:
+            raise ValueError(
+                f"Contig {contig!r} not found. Available contigs: {self.contigs}"
+            )
+
+        return self._site_annotations_raw(
+            contig=contig, inline_array=inline_array, chunks=chunks
+        )
+
     @_check_types
     @doc(
         summary="Load site annotations.",
@@ -977,7 +1057,11 @@ def _snp_calls_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}"
+                )
 
             coords = dict()
             data_vars = dict()
@@ -1159,7 +1243,12 @@ def _raw_snp_calls(
                         inline_array=inline_array,
                         chunks=chunks,
                     )
-                    assert x.sizes["variants"] == loc_ann.shape[0]
+                    if x.sizes["variants"] != loc_ann.shape[0]:
+                        raise RuntimeError(
+                            f"Variants dimension mismatch: dataset has "
+                            f"{x.sizes['variants']} variants but annotation "
+                            f"mask has {loc_ann.shape[0]}"
+                        )
                     x = x.isel(variants=loc_ann)
 
                 lx.append(x)