Merge branch 'master' into docs/add-contributing-md

Author: jonbrenas

.github/workflows/integration_tests.yml

@@ -3,9 +3,6 @@ on:
   push:
     branches:
       - master
-  pull_request:
-    branches:
-      - master
 jobs:
   integration_tests:
     strategy:

.github/workflows/notebooks.yml

@@ -3,9 +3,6 @@ on:
   push:
     branches:
       - master
-  pull_request:
-    branches:
-      - master
 jobs:
   notebooks:
     strategy:

README.md

@@ -142,7 +142,7 @@ modifying the `docs/source/_static/switcher.json` file accordingly.
 
 If you use the `malariagen_data` package in a publication
 or include any of its functions or code in other materials (_e.g._ training resources),
-please cite: [doi.org/10.5281/zenodo.11173411](doi.org/10.5281/zenodo.11173411)
+please cite: [doi.org/10.5281/zenodo.11173411](https://doi.org/10.5281/zenodo.11173411)
 
 Some functions may require additional citations to acknowledge specific contributions. These are indicated in the description for each relevant function.
 

docs/source/Ag3.rst

@@ -15,7 +15,7 @@ All the functions below can then be accessed as methods on the ``ag3`` object. E
     df_samples = ag3.sample_metadata()
 
 For more information about the data and terms of use, please see the
-`MalariaGEN Anopheles gambiae genomic surveillance project <https://www.malariagen.net/anopheles-gambiae-genomic-surveillance-project>`_
+`MalariaGEN Anopheles gambiae genomic surveillance project <https://www.malariagen.net/project/anopheles-gambiae-genomic-surveillance-project>`_
 home page.
 
 .. currentmodule:: malariagen_data.ag3.Ag3

malariagen_data/anoph/cnv_data.py

@@ -886,11 +886,13 @@ def plot_cnv_hmm_heatmap_track(
         width: gplt_params.width = gplt_params.width_default,
         row_height: gplt_params.row_height = 7,
         height: Optional[gplt_params.height] = None,
-        palette: Optional[gplt_params.colors] = cnv_params.colorscale_default,
+        palette: Optional[gplt_params.colors] = None,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
     ) -> gplt_params.optional_figure:
         debug = self._log.debug
+        if palette is None:
+            palette = cnv_params.colorscale_default
 
         import bokeh.models as bkmod
         import bokeh.plotting as bkplt
@@ -1028,13 +1030,15 @@ def plot_cnv_hmm_heatmap(
         width: gplt_params.width = gplt_params.width_default,
         row_height: gplt_params.row_height = 7,
         track_height: Optional[gplt_params.track_height] = None,
-        palette: Optional[gplt_params.colors] = cnv_params.colorscale_default,
+        palette: Optional[gplt_params.colors] = None,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         gene_labels: Optional[gplt_params.gene_labels] = None,
         gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.optional_figure:
         debug = self._log.debug
+        if palette is None:
+            palette = cnv_params.colorscale_default
 
         import bokeh.layouts as bklay
         import bokeh.plotting as bkplt

malariagen_data/anoph/dipclust.py

@@ -622,7 +622,7 @@ def plot_diplotype_clustering_advanced(
         snp_filter_min_maf: float = 0.05,
         snp_query: Optional[base_params.snp_query] = AA_CHANGE_QUERY,
         cnv_region: Optional[base_params.regions] = None,
-        cnv_colorscale: plotly_params.color_continuous_scale = cnv_params.colorscale_default,
+        cnv_colorscale: plotly_params.color_continuous_scale = None,
         cnv_max_coverage_variance: cnv_params.max_coverage_variance = 0.2,
         site_mask: Optional[base_params.site_mask] = None,
         sample_sets: Optional[base_params.sample_sets] = None,
@@ -657,6 +657,8 @@ def plot_diplotype_clustering_advanced(
         chunks: base_params.chunks = base_params.native_chunks,
         inline_array: base_params.inline_array = base_params.inline_array_default,
     ):
+        if cnv_colorscale is None:
+            cnv_colorscale = cnv_params.colorscale_default
         if cohort_size and snp_transcript:
             cohort_size = None
             print(