Issue¶
open (67)¶
biblio_pdf_fetch_oa: html_fallback should be a clear failure
created: 2026-05-05 · status: open · confidence: 1.0
biblio_merge: dedup by DOI, not just citekey
created: 2026-05-05 · status: open · confidence: 1.0
Packaging & install-path cleanup: make uv tool install work, slim the umbrella repo
created: 2026-04-21 · status: open
report_build preflight fails on projects with no bibliography (quarto-reports ph
created: 2026-04-20 · status: open · confidence: 1.0
Implement quarto-reports phase 1: report_init + report_build MCP tools
created: 2026-04-20 · status: open · confidence: 1.0
_scan_deliverables in src/projio/mcp/questio
created: 2026-04-19 · status: open · confidence: 1.0
pipeio_run_kill: "Failed to kill screen session" despite the screen existing
created: 2026-04-17 · status: open · confidence: 1.0
pipeio_run MCP: targets array only passes first target to snakemake
created: 2026-04-17 · status: open · confidence: 1.0
pipeio_run env resolution bug: _resolve_snakemake_cmd() finds snakemake on PAT
created: 2026-04-14 · status: open · confidence: 1.0
Cross-project biblio sharing: no way to import papers with processed derivati
created: 2026-04-11 · status: open · confidence: 1.0
projio_init study profile should pre-configure pixecog-like layout
created: 2026-04-11 · status: open · confidence: 1.0
pipeio_run wildcards parameter doesn't filter snakebids sessions
created: 2026-04-11 · status: open · confidence: 1.0
pipeio_registry_scan should support mod grouping hints
created: 2026-04-11 · status: open · confidence: 1.0
Retro skill should offer to dispatch follow-up tasks
created: 2026-04-10 · status: open · confidence: 1.0
pipeio_flow_new should auto-register flow (or prompt for registry_scan)
created: 2026-04-10 · status: open · confidence: 1.0
pipeio_dag_export SVG: dot binary permission/PATH issues after install
created: 2026-04-10 · status: open · confidence: 1.0
pipeio_dag_export SVG fails with Permission denied on dot
created: 2026-04-10 · status: open · confidence: 1.0
_work_to_minimal() in openalex_resolve
created: 2026-04-10 · status: open · confidence: 1.0
biblio_extract: YAML parsing fails when LLM output contains colons in summary
created: 2026-04-10 · status: open · confidence: 1.0
Citekey generation mangles diacritics in author names
created: 2026-04-09 · status: open · confidence: 1.0
biblio_pdf_fetch_oa reports "html_fallback: 15" but downloads 0 files
created: 2026-04-09 · status: open · confidence: 1.0
biblio_enrich silently returns 0 when resolution is missing
created: 2026-04-09 · status: open · confidence: 1.0
Missing MCP tool: biblio_openalex_resolve
created: 2026-04-09 · status: open · confidence: 1.0
questio docs_collect: cross-sub-site relative links break in monorepo layout
created: 2026-04-09 · status: open · confidence: 1.0
pipeio docs_collect: top-level pipelines index should include architecture me
created: 2026-04-09 · status: open · confidence: 1.0
Commit pipeio fixes + add input stage resolution to PipelineContext
created: 2026-04-07 · status: open · confidence: 1.0
pipeio_nb_sync nb2py fails for demo workspace notebooks — "Paired notebook not f
created: 2026-04-06 · status: open · confidence: 1.0
Implement: biblio CLI commands for zotero and pool promote
created: 2026-04-04 · status: open · confidence: 1.0
Implement: Register Zotero + pool tools in MCP server and update CLAUDE
created: 2026-04-04 · status: open · confidence: 1.0
Implement: Topic enrichment pipeline — persist OpenAlex topics per citekey
created: 2026-04-04 · status: open · confidence: 1.0
Implement: OpenAlex API P1 fixes from audit
created: 2026-04-04 · status: open · confidence: 1.0
Implement: biblio zotero push-tags — write enrichments back to Zotero
created: 2026-04-03 · status: open · confidence: 1.0
Implement: biblio zotero pull — read items + PDFs from Zotero via API
created: 2026-04-03 · status: open · confidence: 1.0
Implement: biblio pool promote — move project-local papers to a pool
created: 2026-04-03 · status: open · confidence: 1.0
codio + indexio MCP friction points discovered during labpy session
created: 2026-04-03 · status: open · confidence: 1.0
biblio pdf_fetch_oa saves HTML paywall pages as
created: 2026-04-02 · status: open · confidence: 1.0
projio: Update MCP tools and CLAUDE
created: 2026-04-02 · status: open · confidence: 1.0
projio: Ship CSL files and update render paths
created: 2026-04-02 · status: open · confidence: 1.0
biblio: New biblio_compile tool — merge intermediates into compiled
created: 2026-04-02 · status: open · confidence: 1.0
biblio: Move merge output, config, and logs to
created: 2026-04-02 · status: open · confidence: 1.0
created: 2026-04-02 · status: open · confidence: 1.0
Spec: Document new bib architecture — sources vs artifacts separation
created: 2026-04-02 · status: open · confidence: 1.0
biblio needs a batch docling command that processes all (or filtered) citekeys w
created: 2026-04-02 · status: open · confidence: 1.0
projio: model project code tiers in config (core_library + project_utils)
created: 2026-04-01 · status: open · confidence: 1.0
Background agents running queued tasks in a project cannot read files outside th
created: 2026-04-01 · status: open · confidence: 1.0
pipeio_config_read bids_signatures show bids() calls, not resolved path patterns
created: 2026-03-31 · status: open
pipeio_run: no wildcard filtering — need --filter-wildcards for single-session scoping
created: 2026-03-31 · status: open
pipeio_run_status / log_parse: conda run buffers stdout, logs empty during BIDS indexing
created: 2026-03-31 · status: open
Fix for pipeio_run --directory issue: cd into flow directory before launching sn
created: 2026-03-31 · status: open · confidence: 1.0
DAG tool returns 0 edges for ecephys despite clear rule dependencies
created: 2026-03-31 · status: open · confidence: 1.0
config_patch produces spurious formatting diffs (YAML round-trip fidelity)
created: 2026-03-31 · status: open · confidence: 1.0
Execution failed: task-arash-20260330-175554-840850
created: 2026-03-30 · status: open · confidence: 1.0
indexio CLI missing --update flag: The MCP indexio_build(update=True) works bu
created: 2026-03-28 · status: open · confidence: 1.0
Address the 4 open indexio/CLI bug reports filed today
created: 2026-03-28 · status: open · confidence: 1.0
indexio build should have a smart incremental mode:
created: 2026-03-28 · status: open · confidence: 1.0
indexio status command fails when called from projio MCP context:
created: 2026-03-28 · status: open · confidence: 1.0
projio CLI is silent — all subcommands produce no output:
created: 2026-03-28 · status: open · confidence: 1.0
indexio_build_status bug: progress file only updates between sources, not during
created: 2026-03-28 · status: open · confidence: 1.0
Add MCP tool for biblio graph expansion
created: 2026-03-28 · status: open · confidence: 1.0
created: 2026-03-28 · status: open · confidence: 1.0
Feature request: inject git-annex into PATH for git subprocess calls
created: 2026-03-27 · status: open · confidence: 1.0
created: 2026-03-26 · status: open · confidence: 1.0
Close issue-arash-20260326-185507 (module_context → pipeio): decided not worth g
created: 2026-03-26 · status: open · confidence: 1.0
Absorb module_context extraction into pipeio (merge with pipeio_mod_resolve or a
created: 2026-03-26 · status: open · confidence: 1.0
Absorb smk_logging into pipeio as standardized Snakemake script logging
created: 2026-03-26 · status: open · confidence: 1.0
Absorb toc-index note directory indexing into notio
created: 2026-03-26 · status: open · confidence: 1.0
Feature request: Slim down notio note types and add structural primitives
created: 2026-03-26 · status: open · confidence: 1.0
scheduled (1)¶
Add hook scaffolding support to projio add claude and a new `projio claude upd
created: 2026-03-31 · status: scheduled · confidence: 1.0
partial (1)¶
Notio manuscript: dual-render master files and mkdocs transclusion setup
created: 2026-04-02 · status: partial · confidence: 1.0
done (33)
Test coverage audit + expansion: figio package (via projio MCP wrappers)
created: 2026-04-12 · status: done · confidence: 1.0
Test coverage audit + expansion: indexio package
created: 2026-04-12 · status: done · confidence: 1.0
Test coverage audit + expansion: codio package (via projio MCP wrappers)
created: 2026-04-12 · status: done · confidence: 1.0
Test coverage audit + expansion: notio package (via projio MCP wrappers)
created: 2026-04-12 · status: done · confidence: 1.0
Test coverage audit + expansion: biblio package (via projio MCP wrappers)
created: 2026-04-12 · status: done · confidence: 1.0
Test coverage audit + expansion: pipeio package
created: 2026-04-12 · status: done · confidence: 1.0
created: 2026-04-12 · status: done · confidence: 1.0
created: 2026-04-12 · status: done · confidence: 1.0
created: 2026-04-12 · status: done · confidence: 1.0
created: 2026-04-12 · status: done · confidence: 1.0
created: 2026-04-12 · status: done · confidence: 1.0
created: 2026-04-12 · status: done · confidence: 1.0
pipeio_docs_collect produces duplicate notebook HTMLs alongside pipeio_nb_pub
created: 2026-04-10 · status: done · confidence: 1.0
Create pipeio-flow-create skill and pixecog-flow-setup skill
created: 2026-04-10 · status: done · confidence: 1.0
created: 2026-04-07 · status: done · confidence: 1.0
created: 2026-04-07 · status: done · confidence: 1.0
Move runtime env configuration into
created: 2026-04-07 · status: done · confidence: 1.0
pipeio_nb_exec: python_bin as string breaks subprocess
created: 2026-04-07 · status: done · confidence: 1.0
pipeio_nb_exec: add kernel/env option and fix papermill resolution
created: 2026-04-07 · status: done · confidence: 1.0
Study: biblio-glutton — high-performance bibliographic matching for reference
created: 2026-04-04 · status: done · confidence: 1.0
Study: Unpaywall/oadoi internals — improve biblio's OA PDF cascade
created: 2026-04-04 · status: done · confidence: 1.0
Spec: GROBID citation context — beyond simple citation networks
created: 2026-04-04 · status: done · confidence: 1.0
Implement: biblio GUI — OpenAlex outbound links in corpus table
created: 2026-04-03 · status: done · confidence: 1.0
Spec: biblio ↔ Zotero integration model
created: 2026-04-03 · status: done · confidence: 1.0
Spec: biblio enrichment pipeline redesign
created: 2026-04-03 · status: done · confidence: 1.0
Audit: biblio concept tagging vs OpenAlex topic classification — overlap anal
created: 2026-04-03 · status: done · confidence: 1.0
Audit: biblio OpenAlex API usage vs actual API capabilities
created: 2026-04-03 · status: done · confidence: 1.0
created: 2026-03-31 · status: done · confidence: 1.0
Update CLI reference docs — 4 subcommands missing
created: 2026-03-31 · status: done · confidence: 1.0
Update MCP tools reference docs — 61 of 95 tools undocumented
created: 2026-03-31 · status: done · confidence: 1.0
Implement notio reindex — generate/update index
created: 2026-03-26 · status: done · confidence: 1.0
pipeio_mod_resolve: fill doc_path gap and add modkey
created: 2026-03-26 · status: done · confidence: 1.0
MCP tools missing for index setup and source registration
created: 2026-03-26 · status: done · confidence: 1.0
resolved (25)
pipeio_nb_exec output convention unclear — `_executed
created: 2026-04-10 · status: resolved · confidence: 1.0
pipeio_nb_update cannot move notebooks between flows
created: 2026-04-10 · status: resolved · confidence: 1.0
pipeio_run passes unrecognized --filter-* flags to snakemake
created: 2026-04-09 · status: resolved · confidence: 1.0
pipeio_run_status crashes with name 'pipe' is not defined
created: 2026-04-09 · status: resolved · confidence: 1.0
pipeio_nb_exec runs papermill from MCP server env, not notebook kernel env
created: 2026-04-09 · status: resolved · confidence: 1.0
pipeio docs: two navigation/embedding issues
created: 2026-04-09 · status: resolved · confidence: 1.0
questio docs_collect generates both README
created: 2026-04-09 · status: resolved · confidence: 1.0
pipeio docs_collect generates bare directory links instead of dir/index
created: 2026-04-09 · status: resolved · confidence: 1.0
questio docs_collect generates wrong relative path depth and missing
created: 2026-04-09 · status: resolved · confidence: 1.0
notio note_resolve generates malformed cross-references (missing dot before
created: 2026-04-09 · status: resolved · confidence: 1.0
pipeio docs_collect does not collect overview
created: 2026-04-09 · status: resolved · confidence: 1.0
note_create MCP tool requires 3 round-trips for agent use: create empty template
created: 2026-04-09 · status: resolved · confidence: 1.0
created: 2026-04-08 · status: resolved · confidence: 1.0
created: 2026-04-08 · status: resolved · confidence: 1.0
pipeio docs_collect: mod docs collected but not included in nav YAML
created: 2026-04-08 · status: resolved · confidence: 1.0
created: 2026-04-08 · status: resolved · confidence: 1.0
created: 2026-04-08 · status: resolved · confidence: 1.0
pipeio registry_scan: has_docs always false despite flow-local docs/ existing
created: 2026-04-08 · status: resolved · confidence: 1.0
Bug: pipeio_run doesn't pass --configfile or --directory to snakemake
created: 2026-03-31 · status: resolved · confidence: 1.0
pipeio_run does not activate cogpy conda env — snakemake not found
created: 2026-03-31 · status: resolved
Two pipeio bugs discovered during ttl_removal mod creation:
created: 2026-03-30 · status: resolved · confidence: 1.0
Issue: pipeio_config_patch apply=True destroys YAML comments, anchors, and forma
created: 2026-03-29 · status: resolved · confidence: 1.0
Bug: projio note_read tool requires path param but note_list only returns m
created: 2026-03-28 · status: resolved · confidence: 1.0
codio: three bugs in codio_rag_sync + unclear MCP docs
created: 2026-03-27 · status: resolved · confidence: 1.0
**Feature request: biblio-gui should resolve git-annex symlinks when serving fil
created: 2026-03-26 · status: resolved · confidence: 1.0