Issues

• Running notebooks in VScode leads to diffs in volatile data picked up by git

  low hanging fruit 🍎low prioritytriage
  malariagen/malariagen-data-python#1357 · Filter by author kebarr opened on Sep 29, 2026

• to_vcf - sample_sets and sample_query are optional. Inefficiencies due to using multiple dask.compute calls

  bugperformancetriageusability
  malariagen/malariagen-data-python#1356 · Filter by author kebarr opened on Sep 29, 2026

• Haplotype clustering without a cut height in plot_haplotype_clustering_advanced

  triage
  malariagen/malariagen-data-python#1353 · Filter by author sanjaynagi opened on Sep 16, 2026

• Use poetry for dependency management on Mac

  triage
  malariagen/malariagen-data-python#1350 · Filter by author kebarr opened on Sep 10, 2026

• wgs_run_accessions() not found in docs

  bug
  malariagen/malariagen-data-python#1349 · Filter by author ahernank opened on Sep 7, 2026
  2

  

• Add support for Python 3.13

  malariagen/malariagen-data-python#1344 · Filter by author ahernank opened on Aug 24, 2026
  12

  

• Incompatibility following Google colab upgrade to Python 3.13

  bughigh priority
  malariagen/malariagen-data-python#1343 · Filter by author ahernank opened on Aug 24, 2026
  8

• Proposal: Out-of-core Random Forest Classifier for Ag1000G using Dask

  triage
  malariagen/malariagen-data-python#1342 · Filter by author Schronding opened on Aug 17, 2026

• custom colours in ag3.plot_haplotype_network

  triage
  malariagen/malariagen-data-python#1340 · Filter by author EricRLucas opened on Aug 7, 2026
  

• Computing kinship coefficients

  triage
  Feature

  malariagen/malariagen-data-python#1337 · Filter by author tristanpwdennis opened on Jul 8, 2026

• PCA downsampling not behaving as expected.

  triage
  malariagen/malariagen-data-python#1336 · Filter by author KellyLBennett opened on Jul 7, 2026
  1

  

• pca's cohorts argument does not work the way it is expected to

  bug
  malariagen/malariagen-data-python#1328 · Filter by author jonbrenas opened on May 27, 2026
  4

• Test access to BAMs and VCFs on ENA/EVA with IGV

  low prioritymaintenanceusability
  malariagen/malariagen-data-python#1325 · Filter by author jonbrenas opened on May 8, 2026
  

• Add missing stacklevel to warnings

  triage
  malariagen/malariagen-data-python#1317 · Filter by author 31puneet opened on Apr 22, 2026

• ipinfo Location Check Silently Swallows All Network Errors With No Logging or Fallback Notification

  triage
  malariagen/malariagen-data-python#1311 · Filter by author kunal-10-cloud opened on Apr 18, 2026
  1

• dask.config.set() at Module Import Time in ag3.py Silently Modifies Global Dask Configuration

  triage
  malariagen/malariagen-data-python#1308 · Filter by author khushthecoder opened on Apr 17, 2026
  1

• CI Coverage Workflow Has Two Blind Spots — Excludes Root Modules and Uses Outdated Codecov Action

  triage
  malariagen/malariagen-data-python#1301 · Filter by author kunal-10-cloud opened on Apr 15, 2026
  1

• Integration Test and Notebook CI Workflows Use Hardcoded GCS Cache Key From September 2024

  triage
  malariagen/malariagen-data-python#1296 · Filter by author kunal-10-cloud opened on Apr 14, 2026
  1

• No Public API to Clear or Inspect In-Memory Caches — Users Cannot Reclaim Memory in Long-Running Sessions

  triage
  malariagen/malariagen-data-python#1289 · Filter by author khushthecoder opened on Apr 13, 2026
  2

• diversity_stats doesn't have a max_cohort_size parameter

  triage
  malariagen/malariagen-data-python#1288 · Filter by author jonbrenas opened on Apr 13, 2026
  3

• snp_calls_to_vcf() silently drops requested FORMAT fields when underlying data arrays don't exist

  triage
  malariagen/malariagen-data-python#1283 · Filter by author Yashsingh045 opened on Apr 10, 2026
  1

• geneset() and snp_dataset() are deprecated but don't warn users

  triage
  malariagen/malariagen-data-python#1273 · Filter by author ZiadXI opened on Apr 3, 2026
  1

• plot_samples_interactive_map returns an error when the data contains colony data and no other unassigned samples

  bugtriage
  malariagen/malariagen-data-python#1268 · Filter by author jonbrenas opened on Apr 1, 2026
  1

  

• Improve API and methods discoverability for agents and natural‑language interfaces

  triage
  malariagen/malariagen-data-python#1262 · Filter by author caiocrocha opened on Mar 31, 2026
  1

• Improve LRU cache test coverage by validating eviction order in load_genome_seq (test_veff.py)

  triage
  malariagen/malariagen-data-python#1244 · Filter by author simplyshree opened on Mar 29, 2026