John’s Tasks

September 21, 2026

• Playwright migration
  • galaxy#23621 — Run history panel collection tests under Playwright
  • galaxy#23622 — Run history panel tests under Playwright
  • galaxy#23623 — Run admin app tests under Playwright; fix stale GTable selectors
  • galaxy#23624 — Run published histories tests under Playwright
  • galaxy#23644 — Run integration Selenium tests under Playwright
  • galaxy#23706 — Run dataset tests under Playwright
  • galaxy#23707 — Make more drag-and-drop tests work under Playwright
• Pulsar path handling
  • galaxy#23620 — Read the remote job and tool directories from the Pulsar job config
  • pulsar#515 — Remove the __PULSAR_JOBS_DIRECTORY__ destination token (merged 2026-09-22; closes pulsar#29)
• Pulsar staging and postprocessing
  • pulsar#517 — Let file actions declare what they need from the destination (draft)
  • pulsar#518 — Record file staging metrics for Galaxy job metrics (draft)
  • pulsar#519 — Implement recovery of postprocessing (draft)
• Galaxy fixes
  • galaxy#23618 — Enforce enable_account_interface server-side
  • galaxy#23619 — Harden tool framework infinity handling (redux)
  • galaxy#23628 — Return serializable data validation errors
  • galaxy#23629 — Allow <requirements> children in any order in the tool XSD
  • galaxy#23630 — Report unparseable tool expression templates as author errors
  • galaxy#23651 — Throw more specific exceptions in workflow extraction
  • galaxy#23652 — Trim non-code changes from merged data table validation work
  • galaxy#19937 — Add a redirect for an old Tool Shed URL pattern (draft)
• Workflow semantics — workflow_semantics
  • galaxy#23659 — Refactor collection handling toward reuse
  • galaxy#23676 — Bring subworkflow mapping inline between the workflow editor and backend (draft)
  • galaxy#23681 — Refactor workflow evaluation ahead of subworkflow mapping
• Workflow and tool state
  • galaxy#23699 — Make tool-util model package imports lightweight
  • galaxy#23705 — Refactor schema states for lazy downstream imports
  • gxformat2#255 — Preserve numeric workflow input bounds in conversions
• Galaxy package test infrastructure
  • galaxy#23697 — Include unit tests in Python package sdists (draft)
  • galaxy#23698 — Allow the packaged test driver to work (draft)
• Tool Shed — toolshed
  • galaxy#23663 — Upgrade client-side csv-parse
  • galaxy#23665 — Upgrade client Vitest dependencies to 4.1.11
  • galaxy#23666 — Bump Quasar to 2.33.1 in the Tool Shed frontend
  • galaxy#23668 — Implement CI for the Tool Shed frontend
  • galaxy#23672 — Upgrade Tool Shed Vitest
  • galaxy#23704 — Overhaul Tool Shed publish permissions (draft)
• Planemo workflow testing
  • planemo#1723 — Fix silently skipped collection output assertions
  • planemo#1724 — Sanitize invocation labels used as filenames
  • planemo#1725 — Make --test_data resolve tool test inputs
  • planemo#1726 — Skip tests when external services are down
  • planemo#1727 — Exit non-zero when autoupdate fails to update a tool (draft)
  • planemo#1728 — Preserve collected outputs when a test names an undefined output
• Foundry
  • foundry#598 — Clarify evaluation plan and scenario boundaries
  • foundry#599 — Add Foundry documentation and content review skills
  • foundry#600 — Explain the CWL-to-Galaxy pipeline journey
  • foundry#601 — Guide paper-to-Galaxy pipeline use
  • foundry#602 — Guide paper-to-CWL pipeline use
  • foundry#603 — Guide Nextflow-to-CWL pipeline use
  • foundry#604 — Clarify Galaxy tabular pattern choices
  • foundry#605 — Keep Workflow Brief planning opt-in and clarify build routes
  • foundry#606 — Clarify Galaxy collection pattern choices
  • foundry#607 — Ignore private workspaces in changeset checks
  • foundry#608 — Clarify Galaxy conditional pattern choices
  • foundry#609 — Refresh IWC corpus integration guidance
  • foundry#610 — Clarify CWL test-plan translation
  • foundry#611 — Update IWC test data conventions
  • foundry#612 — Ground IWC test shortcut guidance in evidence
  • foundry#613 — Choose Planemo assertions by failure mode and stability
  • foundry#614 — Clarify Galaxy workflow testability design
  • foundry#615 — Clarify gxformat2 structural schema limits
  • foundry#616 — Clarify gxformat2 workflow input guidance
• claude-jmchilton-plugins#2 — Add shared writing and documentation skills
• docker-galaxy#638 — Build the Galaxy 26.1 image with HTCondor and ARM64 support
• PRs Reviewed
  • Galaxy
    • galaxy#23703 itisAliRH — Remove duplicate scoped base.scss copies from the CSS bundle
    • galaxy#23700 nsoranzo — Report which mypy errors a PR introduces instead of their count
    • galaxy#23694 mvdbeek — Fix user-defined tool references in workflow steps
    • galaxy#23692 nsoranzo — Prevent growth of the mypy untyped-code backlog
    • galaxy#23683 davelopez — Hide upload size when unknown or zero bytes
    • galaxy#23682 davelopez — Improve URL validation feedback on small screens
    • galaxy#23679 ahmedhamidawan — Hide history dropdown options for unowned histories
    • galaxy#23677 mvdbeek — Fix connection-reset race in the interactor POST retry test
    • galaxy#23674 mvdbeek — Merge release 26.1 into dev
    • galaxy#23673 mvdbeek — Fix unusable admin quota forms on large instances
    • galaxy#23671 nsoranzo — Grow the mypy green list with four near-miss packages
    • galaxy#23670 dannon — Cap keyed and quoted terms in index search filtering
    • galaxy#23664 mvdbeek — Fix workflow scheduler history updates committed mid-attempt
    • galaxy#23653 davelopez — Add warc.gz with WARC-aware upload content checks
    • galaxy#23650 mvdbeek — Return 400 for non-integer dataset IDs in /root/display_as
    • galaxy#23647 mvdbeek — Serialize the Rucio test container’s WSGI workers
    • galaxy#23641 mvdbeek — Preserve numeric encoded history IDs in form submissions
    • galaxy#23640 mvdbeek — Replace external fixture downloads with the test HTTP server
    • galaxy#23639 davelopez — Make upload history changes obvious and show the URL in progress
    • galaxy#23638 mvdbeek — Merge release 26.1 into dev
    • galaxy#23637 mvdbeek — Fix data selector pagination inside repeat inputs
    • galaxy#23636 mvdbeek — Report failed staged inputs in tool test errors
    • galaxy#23635 mvdbeek — Preserve early local job process failure diagnostics
    • galaxy#23634 mvdbeek — Use consistent filenames for dataset display and downloads
    • galaxy#23633 mvdbeek — Fix unavailable toolbox filters in user preferences
    • galaxy#23631 mvdbeek — Preserve diagnostics when job stdout or stderr cannot be read
    • galaxy#23617 ksuderman — Fix doubled URL prefix on the workflow preview Run button
    • galaxy#23615 mvdbeek — Advertise annotation limits and fix library collection annotation lookup
    • galaxy#23614 mvdbeek — Fix dangling discriminator mapping in standalone tool state JSON schemas
    • galaxy#23587 davelopez — Improve upload state tracking in the progress view
    • galaxy#23583 mvdbeek — Use the bundle index for chained data-manager metadata
    • galaxy#23536 mvdbeek — Add password reset to the Tool Shed
    • galaxy#23534 guerler — Let visualizations target frozen and tagged release branches
    • galaxy#23508 arash77 — Add GitLab and ARC file sources
    • galaxy#23485 ahmedhamidawan — Simplify/refactor Filtering by tokenizing the filter text once
    • galaxy#23464 itisAliRH — Restore styling and behavior lost in the GButton adoption sweep
    • galaxy#23365 mvdbeek — Add embedded authoring reference for user-defined tools
    • galaxy#23342 ahmedhamidawan — Wrap tooltips instead of overflowing their width
    • galaxy#22128 mvdbeek — Track scheduling dependencies for workflow invocations
    • galaxy#18455 Delphine-L — Sanitize spaces in the export tool
    • galaxy#18017 mvdbeek — Don’t catch ParameterValueError after persisting values in the database
    • galaxy#17164 mvdbeek — Containerize set metadata
  • Docker Galaxy
    • docker-galaxy#635 bgruening — Galaxy 26.1 release
    • docker-galaxy#634 bgruening — ARM64 support
  • Foundry
    • foundry#593 nekrut — Add shared Antigravity support for Foundry skills
  • gxformat2
    • gxformat2#254 mvdbeek — Preserve a user-defined tool step’s state when converting to format2
  • Planemo
    • planemo#1130 bernt-matthias — Include subdirectories and parent directories in ci_find
  • Pulsar
    • pulsar#514 dSizovs — Use the manager name returned by compute-resource registration

September 14, 2026

• Foundry
  • foundry#523 — Flag issues missing roadmap/priority labels or valid substep parentage
  • foundry#524 — Verify four more pattern claims with test workflows
  • foundry#525 — Add issue-backed Foundry roadmap
  • foundry#526 — Refine roadmap issue presentation
  • foundry#527 — Verify four more pattern claims with test workflows
  • foundry#528 — Document Nextflow test case selection policy
  • foundry#529 — Classify Nextflow profiles by kind
  • foundry#530 — Make the conversion worker Planemo-ready
  • foundry#533 — Remove conversion Mold revision history
  • foundry#536 — Clean up the nf-core conversion Mold
  • foundry#537 — Ground nf-core conversion datatype mapping
  • foundry#545 — Make Nextflow evidence optional in Galaxy UDT authoring
  • foundry#567 — Initial Workflow Brief pipelines
• Embed Galaxy in Planemo — embedded_galaxy_in_planemo
  • planemo#1703 — List invocations across all workflows
  • planemo#1704 — Pin Galaxy virtualenvs to an explicit Python version
  • planemo#1707 — Write inline test jobs outside source directories (draft)
  • planemo#1708 — Keep managed Galaxy running after tests (draft)
  • planemo#1711 — Use galaxy.util.wait.wait_on
  • planemo#1712 — Fix no-wait Galaxy tool execution
  • planemo#1713 — Report standalone engine errors without crashing
• Linting Overhaul
  • planemo#1706 — Modernize Planemo-specific tool linters
  • planemo#1710 — Fix shed_lint fail-fast behavior (draft)
• Pulsar
  • pulsar#503 — Send tool stdout and stderr to Galaxy while the job is running
  • pulsar#504 — Better error handling when setting up environment statements
  • pulsar#505 — Fail the job when a transport error blocks work-dir stage out
  • pulsar#506 — Run the resilience suite on ubuntu-24.04
  • pulsar#507 — Replace flake8 with ruff
  • pulsar#508 — Move the lint and test jobs to ubuntu-24.04
  • pulsar#509 — Extract the resilience harness and recorder into pulsar.testing
• Playwright migration
  • galaxy#23574 — Add a keyboard abstraction to enable more Playwright testing
  • galaxy#23598 — Drop more selenium_only test markers
  • galaxy#23601 — Run tool form tests under Playwright
  • galaxy#23602 — Run upload tests under Playwright
  • galaxy#23603 — Run workflow management tests under Playwright
  • galaxy#23607 — Unlock test_workflow_run for Playwright
  • galaxy#23611 — Run collection builder tests under Playwright
• Tool and test reporting
  • galaxy#23600 — Report test-case state-building errors instead of raising
  • galaxy#23605 — Report tool-model and test-parse failures in test-case validation
  • galaxy#23608 — Report unresolvable job markdown labels instead of returning 500
  • galaxy#23599 — Fix 500 on the dataset tool-markdown report endpoint
• Galaxy fixes and maintenance
  • galaxy#23593 — Fix counterintuitive has_n_cols behavior for CSV (redux)
  • galaxy#23594 — Drop broken annotation indices and limit annotation sizes
  • galaxy#23606 — Expose implicit_collection_jobs_id on the job details and search APIs
  • galaxy#23610 — Rebuild config on dev and add CI to keep it current
  • SergeyYakubov/galaxy#1 — Harden Docker identity resolution from OIDC claims
  • fairytalesbykcc/galaxy#1 — Fix Parquet converter headers, inference, and safe text round trips
• Workflow state tooling
  • galaxy-tool-util-ts#183 — Convert statefully by default when the tool cache is populated
• Planemo maintenance
  • planemo#1709 — Replace Perl documentation example with Python
  • planemo#1714 — Apply Click conversion to configured option values
• PRs Reviewed
  • galaxy#23550 guerler — Add varri visualization
  • galaxy#23543 ksuderman — Add k8s_fs_group_change_policy to the Kubernetes job runner
  • galaxy#23542 nsoranzo — Add AbstractTool class to tool_util
  • galaxy#23541 mvdbeek — Backport mulled cache seeding to fix flaky integration tests
  • galaxy#23540 mvdbeek — Record shed install panel placement before the cached toolbox reload
  • galaxy#23539 mvdbeek — Deliver SSE control tasks to webapp processes only
  • galaxy#23537 mvdbeek — Fix two flaky API tests
  • galaxy#23533 mvdbeek — Fix zero defaults for YAML numeric tool parameters
  • galaxy#23517 afgane — Reuse connections and bound the connect timeout in the test interactor
  • galaxy#23516 davelopez — Add Common Crawl file source
  • galaxy#23515 afgane — Make the tool-test polling cadence configurable
  • galaxy#23388 mvdbeek — Harden user-defined tool output declarations
  • galaxy#23387 mvdbeek — Require top-level containers for user-defined tools
  • galaxy#23283 guerler — Reject generating parameter models for upload_dataset inputs

September 7, 2026

• Galaxy fixes and maintenance
  • galaxy#23465 — Fix some package test warnings on dev
  • galaxy#23459 — Reject output-only format_source references in the XML linter
  • guerler/galaxy#36 — Handle output discovery failures consistently
  • galaxy#23482 — Default missing workflow comment colors
  • galaxy#23498 — Use TRS IDs as fallback names for GalaxyAI workflow suggestions
  • galaxy#23513 — Set Galaxy memory variables in GB and support memory overhead
  • galaxy#23514 — Add the Galaxy Conda environment hash to mulled-hash
• IUC Standards Docs
  • standards#85 — Add Pulsar / remote-execution compatibility best-practices docs
  • standards#86 — Add security corpus-research deep-dives
• Foundry
  • foundry#486 — Fix commented Nextflow workflow parsing
  • foundry#521 — Bump planemo pin to 0.75.47
  • foundry#522 — Verify four more pattern claims with test workflows
  • iwc-lab#3 — Read workflow descriptors as YAML so Format-2 works
  • foundry#489 — Add linear Pi Pipeline evaluation controller
  • foundry#490 — Vendor IWC workflow review prompts
  • iwc#1364 — Skip combine_outputs when there is nothing to combine
  • iwc#1365 — Only report deploy status when deploy actually failed
  • iwc#1366 — Expanded Agent Review Command
  • planemo#1695 — Require workflow tests under the IWC lint profile
  • planemo#1696 — Fix Dockstore names for Galaxy workflow suffixes
  • planemo#1697 — Validate dates in IWC changelog headings
  • planemo#1698 — Skip Zenodo-dependent tests when the API is unavailable
  • foundry#495 — Resolve bundled Foundry validator in Pi harness
  • foundry#497 — Add lifecycle taxonomy for review and publication pipelines
  • foundry#498 — Add IWC workflow maturation Mold
  • foundry#502 — The gallery shows the badge a note page shows, not a copy of it
  • foundry#506 — Single-source the planemo pin behind a check
  • foundry#508 — Add GALAXY WORKFLOW MATURATION pipeline
  • foundry#509 — Add GALAXY WORKFLOW REVIEW pipeline and review-galaxy-workflow Mold
  • foundry-pattern#59 — Add the edge of human knowledge to the Case (draft)
  • foundry#488 — Add Pi-backed clean-room skill evaluation harness
  • foundry-lib#133 — A contested wiki-link address says so
• Embed Galaxy in Planemo — embedded_galaxy_in_planemo
  • planemo#1701 — Run package-installed Galaxy through Gravity (draft)
• Tool Shed — toolshed
  • galaxy#23500 — More Tool Shed Dead Code Removal.
  • galaxy#23502 — Prevent dependency cache failures from rolling back Tool Shed installs
• Pulsar
  • pulsar#494 — Fix daemon handling in webless mode
  • pulsar#495 — Fix typos and grammar in documentation
  • pulsar#496 — Fix job recovery startup race
  • pulsar#497 — Clarify real-user job configuration documentation
  • pulsar#499 — Limit stdout and stderr in status responses
  • pulsar#500 — Close leaked file and transport handles
  • pulsar#502 — Support configuring the AMQP heartbeat interval, or disabling heartbeats
• Planemo
  • planemo#1700 — Allow anonymous access to external Galaxy instances
  • planemo#1702 — Add --use_cache to planemo test, off by default
• Research and prototypes
  • galaxy#22860 — Empower Researches to Extract Workflows with Reproducible Narratives from a Notebook
  • galaxy-skills#26 — Add project-review skill (stub)
  • statistical-genomics-foundry#164 — Adopt the shared source-note frontmatter contract
  • topoqa-interface-quality-replication#1 — Name the benchmark as the papers do
  • crypt4gh-recryptor-service#3 — Harden CORS per service mode
• PRs Reviewed
  • Galaxy
    • galaxy#23526 mvdbeek — Keep the center GalaxyAI view mounted across its own route changes
    • galaxy#23525 mvdbeek — Use pydantic-aware serializer for celery control replies
    • galaxy#23524 mvdbeek — Keep collection input form state local until undo or redo
    • galaxy#23512 mvdbeek — Prevent mapper deferrals from starving later ready jobs
    • galaxy#23511 nsoranzo — Document configuration schema and Python dependency workflows in CONTRIBUTING.md
    • galaxy#23510 mvdbeek — Return rate-limit rejections as Galaxy error responses
    • galaxy#23506 afgane — Accept a directory as a fetch src=path target
    • galaxy#23494 ahmedhamidawan — Prevent ScrollList from doing infinite fetches on error
    • galaxy#23491 nsoranzo — Remove remaining Reports webapp config and docs
    • galaxy#23490 afgane — Upload test files the server cannot see, even with —force_path_paste
    • galaxy#23488 mvdbeek — Document unique server names for multi-instance Gunicorn deployments
    • galaxy#23483 afgane — Retry not-ready dataset downloads and surface HTTP status in the tool test client
    • galaxy#23481 davelopez — Add support to cancel file uploads
    • galaxy#23476 guerler — Fail the job when output discovery fails
    • galaxy#23467 afgane — Don’t set job state to OK before finish_job runs in the GCP Batch runner
    • galaxy#23460 nsoranzo — Add pkg-resources-backport dependency for fs
    • galaxy#23450 ahmedhamidawan — Migrate ToolForm to Composition API and TypeScript
    • galaxy#23401 afgane — Forward force_path_paste for non-composite test inputs
    • galaxy#23329 guerler — Enable tool request by default
    • galaxy#23245 Rajioba1 — Populate AnnData spec version metadata
    • galaxy#23171 pauldg — Retry transient connection errors on idempotent iRODS reads
  • Pulsar
    • pulsar#427 bernt-matthias — Add typing for managers

August 31, 2026

• Ekkk - Chicago.
• Embed Galaxy in Planemo
  • planemo#1691 — [WIP] Run package-installed Galaxy through Gravity
• Linting Overhaul
  • galaxy#23229 — Repository-level data-table linting for data-manager / reference-data bundles
• Kubernetes
  • galaxy#23324 — Refactor Kubernetes PV/PVC setup between integration test classes for reuse
  • galaxy#23325 — Fix stale Kubernetes job naming docs
• Pick Value
  • galaxy#23433 — Bug fix - pick_values inputs need to be available before picking.
  • galaxy#23455 — Add a failure-tolerant Pick Value mode (draft)
• Job Finishing
  • galaxy#23436 — Add FINISHING job state and pulsar recovery for restart safety (redo)
  • galaxy#23448 — Move metadata handling into finish_job on the work queue
• galaxy#23334 — Warn when a post job action cannot run on a step with no job
• galaxy#23340 — Accumulated review nits - 2026-08-21
• pulsar#493 — Size GCP Batch jobs from requested resources

August 24, 2026

• iwc-lab
• Foundry FAQ
• Handle Foundry Prompt
• Handle Foundry Feedback
• Optional Input
  • [ ]
• Embed Galaxy in Planemo
  • Wheel Fixes PR
  • Research and Plan
  • Implement
  • planemo#1690 — [WIP] Add an embedded Galaxy engine for package-installed Galaxy
• Linting Overhaul
• planemo#1683 — Document running Planemo workflows on Slurm clusters (rebase + fixes)

August 17, 2026

• Register for Conference.
• Add Application kind to topo-bio-foundry.
• Pulsar Review - Docs from mvdbeek.
• Hand-off iwc-lab
• Pulsar Review - missing state.
• Fix Tool Submission Errors
  • PR
  • Usher
• Pulsar HTCondor2
  • pulsar#486 — Add a queued_htcondor manager on the htcondor2 bindings, shared with Galaxy
  • galaxy#23326 — Share HTCondor mechanics with Pulsar via util/condor (draft)
• Many Pulsar and Planemo PRs.
• galaxy#23330 — Don’t apply PJAs to skipped elements of mapped over outputs (draft)
• planemo#1679 — Various fixes for targeting postgres in singularity (rebase)
• planemo#1684 — Drop dead interactor.VERBOSE_GALAXY_ERRORS assignment
• foundry-pattern#64 — One route is the rule; the key as the segment is the preference
• statistical-genomics-foundry#168 — A summary is shown wherever a note has one
• ksuderman/galaxy#10 — Review suggestions for #23295: self-enforcing seam, three-tier resolution

July 27, 2026

• PR the Data Validation Work
• PR the Tool Dependency Stuff
• [ ]
• tools-iuc#8255 — Fix ARTIC data table declaration and protocol URL
• statistical-genomics-foundry#134 — Read ScientistOne’s Chain-of-Evidence against our probes
• joachimwolff/galaxy#1 — Collection panel selection: one identity per row, keyed by element occurrence

July 13, 2026

• WES PR Update
• Extract https://github.com/galaxyproject/galaxy/pull/22996/changes/ef93b9f6bcfe9686069b9af2c9efadc9501a1d35 into its own PR.
• 1. The CLI —preserve/—strip flags oversell the same way (they promise per-category selection clean.py doesn’t implement, documented in wf_tooling.md). Fix in scope, file separately, or ignore?

July 6, 2026

• Workflow state stuff
  • Clean export in Galaxy for gxformat2 and ga files.
  • Tool Parsing in galaxy-tool-util-ts
• Publish some foundry workflows - foundry-experiments
• Decide Next Steps on Notebook Paper
• Update two Notebook PRs.
• DRS PR

June 29, 2026

• Auto-layout in gxformat2
• Clean export in Galaxy for gxformat2 and ga files.
• Tool Parsing in galaxy-tool-util-ts
• Linting Overhaul
• FAIR Foundries and Licensing Details.
• Better Unit tests.