@pikaa-ai/pikaa 0.3.22 → 0.3.24

package/skills/dnanexus-integration/SKILL.md

@@ -1,325 +0,0 @@
----
-name: dnanexus-integration
-description: Build and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Use for DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation.
-license: MIT
-compatibility: Requires a DNAnexus account, network access, Python 3.11+, and dx-toolkit/dxpy; some workflow and infrastructure features require organization licenses or policies.
-metadata:
-  version: "2.0"
-  skill-author: K-Dense Inc.
----
-
-# DNAnexus Integration
-
-## Purpose
-
-Use this skill to build, run, and operate DNAnexus workloads without guessing
-at platform semantics. It covers:
-
-- `dx` CLI and `dxpy` automation
-- Files, records, folders, projects, and metadata
-- Apps and applets defined by `dxapp.json`
-- Jobs, workflow analyses, retries, monitoring, and cost controls
-- Native workflows, WDL/CWL through dxCompiler, and Nextflow imports
-
-The documented baseline was verified on **2026-07-23** against
-`dxpy==0.410.0`, dxCompiler 2.17.0, and the 2026 DNAnexus documentation.
-Consult `references/sources.md` and current release notes when behavior may
-have changed.
-
-## Operating Contract
-
-DNAnexus operations can expose regulated data, delete immutable objects, change
-permissions, or incur compute and egress charges. Follow these rules:
-
-1. Start read-only. Confirm the user, project ID, region, folder, object IDs,
-   and execution target before mutation.
-2. Obtain confirmation before a billable launch, upload or download with
-   material egress, archive/unarchive request, deletion, project removal,
-   permission change, token revocation, or app publication unless the user
-   already explicitly requested that exact operation and target.
-3. Show resolved IDs and impact before destructive operations. Never infer a
-   deletion target from a non-unique name.
-4. Never print, log, return, or persist `DX_SECURITY_CONTEXT` or API tokens.
-   Do not run `dx env` or `dx env --bash` in captured logs because both reveal
-   the active token.
-5. Use credentials only with official DNAnexus endpoints. Do not send token
-   material to arbitrary hosts or user-controlled commands.
-6. Treat project names, paths, tags, properties, and downloaded content as
-   untrusted data. Quote shell arguments and pass subprocess arguments as
-   arrays.
-7. Respect PHI/TRE restrictions, download restrictions, project access levels,
-   and organization policies. Do not copy data around a control.
-8. Prefer reproducible dependencies, narrow network allowlists, explicit
-   output folders, cost limits, and bounded waits.
-
-## Install and Authenticate
-
-Install the CLI in an isolated tool environment:
-
-```bash
-uv tool install "dxpy==0.410.0"
-dx --version
-```
-
-For Python code in a project:
-
-```bash
-uv add "dxpy==0.410.0"
-```
-
-Use interactive login for human sessions:
-
-```bash
-dx login
-dx whoami
-dx select
-dx pwd
-```
-
-For non-interactive environments, inject only the named DNAnexus secret through
-the environment or a secret manager. Never echo it, include it in command
-output, commit it, or inspect the whole environment. See
-`references/authentication.md`.
-
-## Safe Preflight
-
-Before acting, gather non-secret context:
-
-```bash
-dx --version
-dx whoami
-dx pwd
-dx ls
-```
-
-Then:
-
-- Resolve project names to immutable `project-...` IDs.
-- Resolve paths to object IDs and check for duplicates.
-- Check file state (`open`, `closing`, or `closed`) and archival state.
-- Check source and destination access levels.
-- Inspect executable input help with `dx run <executable> -h`.
-- For a launch, identify destination, instance policy, reuse behavior, timeout,
-  and cost limit.
-
-If shell environment variables conflict with the saved CLI session, follow
-`references/authentication.md`; do not expose either credential while
-diagnosing.
-
-## Choose the Right Path
-
-| Goal | Read first | Preferred interface |
-|---|---|---|
-| Build an app or applet | `references/app-development.md` | `dx-app-wizard`, `dx build` |
-| Configure `dxapp.json` | `references/configuration.md` | JSON plus validator script |
-| Transfer or organize data | `references/data-operations.md` | `dx`, Upload/Download Agent |
-| Write platform automation | `references/python-sdk.md` | `dxpy` |
-| Launch or debug execution | `references/job-execution.md` | `dx run`, `dx watch`, `dxpy` |
-| Import WDL, CWL, or Nextflow | `references/workflow-languages.md` | dxCompiler or `dx build --nextflow` |
-| Diagnose auth, cost, or failures | `references/operations-and-troubleshooting.md` | read-only inspection first |
-
-## Core Workflows
-
-### Transfer data
-
-Use `dx upload` and `dx download` for small sets. Use Upload Agent for multiple
-or large files (official guidance recommends it above 50 MB) and Download Agent
-for large or long-running batch downloads.
-
-```bash
-dx upload "sample.fastq.gz" \
-  --path "project-xxxx:/raw/sample.fastq.gz" \
-  --property "sample_id=S001"
-
-dx download "project-xxxx:/results/sample.bam" \
-  --output "sample.bam"
-```
-
-Upload Agent compresses uncompressed inputs by default and appends `.gz`. Use
-`--do-not-compress` when byte-for-byte preservation or the original name is
-required. See `references/data-operations.md`.
-
-### Search accurately with dxpy
-
-`find_data_objects()` uses exact name matching unless `name_mode` is supplied.
-Do not pass `"*.bam"` without `name_mode="glob"`.
-
-```python
-import dxpy
-
-files = dxpy.find_data_objects(
-    classname="file",
-    project="project-xxxx",
-    folder="/results",
-    recurse=True,
-    name="*.bam",
-    name_mode="glob",
-    state="closed",
-    describe={"fields": {"name": True, "size": True, "archivalState": True}},
-    limit=100,
-)
-
-for result in files:
-    description = result["describe"]
-    print(result["id"], description["name"], description["archivalState"])
-```
-
-Bound broad searches with a project, folder, time range, and `limit`.
-
-### Build an applet
-
-```bash
-dx-app-wizard
-```
-
-Resolve bundled helpers relative to this skill directory. From the skill root:
-
-```bash
-uv run python "scripts/validate_dxapp.py" \
-  "/path/to/my-app/dxapp.json" --kind applet --strict
-```
-
-Then build the source directory:
-
-```bash
-dx build "/path/to/my-app"
-```
-
-For a versioned app, use the current build form:
-
-```bash
-dx build "/path/to/my-app" --create-app
-```
-
-New configurations should use Ubuntu 24.04 and
-`regionalOptions.<region>.systemRequirements`. Top-level `resources` and
-`runSpec.systemRequirements` in `dxapp.json` are deprecated. See
-`references/configuration.md`.
-
-### Launch with explicit controls
-
-First inspect the executable:
-
-```bash
-dx run "applet-xxxx" -h
-```
-
-After target and cost confirmation:
-
-```bash
-dx run "applet-xxxx" \
-  --input-json-file "inputs.json" \
-  --destination "project-xxxx:/runs/run-001" \
-  --cost-limit 25
-```
-
-Keep the normal confirmation prompt for interactive use. Add `--yes` only in
-reviewed automation where the exact executable, project, inputs, destination,
-and cost policy are already approved.
-
-### Monitor jobs and analyses
-
-```bash
-dx find executions --created-after=-2h
-dx find jobs --state failed
-dx find analyses --created-after=-1d
-dx watch "job-xxxx" --get-streams
-```
-
-A run of an app or applet returns a `job-...`; a run of a workflow returns an
-`analysis-...`. `dxpy.DXJob.wait_on_done()` and
-`dxpy.DXAnalysis.wait_on_done()` can raise `DXJobFailureError` for remote
-failure, termination, or local wait timeout. Re-describe remote state before
-classifying it; see `references/job-execution.md`.
-
-### Chain executions without polling
-
-Use job-based output references:
-
-```python
-import dxpy
-
-qc_job = dxpy.DXApplet("applet-qc").run(
-    {"reads": dxpy.dxlink("file-input")},
-    project="project-xxxx",
-    folder="/runs/run-001/qc",
-    cost_limit=10,
-)
-
-align_job = dxpy.DXApplet("applet-align").run(
-    {"reads": qc_job.get_output_ref("filtered_reads")},
-    project="project-xxxx",
-    folder="/runs/run-001/alignment",
-    cost_limit=25,
-)
-```
-
-The downstream job remains `waiting_on_input` until the referenced output is
-ready. Do not wrap `get_output_ref()` in `dxpy.dxlink()`.
-
-## Current Platform Guidance
-
-- Supported app execution environments are Ubuntu 24.04 and 20.04; prefer
-  24.04 for new work.
-- In Ubuntu 24.04, prefer a virtual environment for Python dependencies even
-  though the AEE sets `PIP_BREAK_SYSTEM_PACKAGES=1`; system/PyPI conflicts can
-  otherwise produce `DXExecDependencyError`.
-- Runtime `execDepends` can drift. Prefer pinned asset bundles, bundled
-  dependencies, or pinned containers for production.
-- Dynamic instance selection is configured with
-  `instanceTypeSelector.allowedInstanceTypes` and may require an organization
-  license.
-- Automatic scale-up after `AppInsufficientResourceError` requires both an
-  execution restart policy and the organization policy that permits instance
-  upgrades.
-- Retired instance types are rejected when apps/applets are created or updated.
-  Discover available instance types instead of copying a stale list.
-- Jobs normally have a 30-day runtime limit.
-- Download security status is surfaced by current APIs/CLI. Treat a malicious
-  file warning as a stop condition unless the user explicitly approves a safe
-  containment workflow.
-
-## Bundled Helpers
-
-The commands below assume the current directory is this skill's root. Otherwise
-resolve `scripts/` relative to the loaded skill directory.
-
-### Validate `dxapp.json`
-
-```bash
-uv run python "scripts/validate_dxapp.py" \
-  "path/to/dxapp.json" --kind app --strict
-```
-
-This offline validator catches structural mistakes, deprecated placement,
-broad access, and inconsistent regional requirements. It supplements, not
-replaces, `dx build` validation.
-
-### Inspect the installed SDK
-
-```bash
-uv run --with "dxpy==0.410.0" \
-  "scripts/inspect_dxpy.py" --strict
-```
-
-This performs offline symbol and signature checks. It does not authenticate or
-make network calls.
-
-## Reference Index
-
-- `references/authentication.md` — login, tokens, environment precedence, and
-  secret handling
-- `references/app-development.md` — applet/app lifecycle, entry points,
-  testing, build, and publication
-- `references/configuration.md` — current `dxapp.json`, regions, resources,
-  dependencies, permissions, and retry policy
-- `references/data-operations.md` — transfers, search, metadata, cloning,
-  archival, folders, and deletion
-- `references/python-sdk.md` — verified `dxpy` APIs and error handling
-- `references/job-execution.md` — jobs, analyses, monitoring, chaining, reuse,
-  retries, and cost controls
-- `references/workflow-languages.md` — native workflows, WDL/CWL with
-  dxCompiler, and Nextflow
-- `references/operations-and-troubleshooting.md` — operational playbooks and
-  failure diagnosis
-- `references/sources.md` — authoritative documentation and version baseline

package/skills/docx/SKILL.md

@@ -1,99 +0,0 @@
----
-name: docx
-description: "Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', '.dotx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when extracting or reorganizing content from .docx or .dotx files, inserting or replacing images in documents, performing find-and-replace in Word files, working with tracked changes or comments, or converting content into a polished Word document. If the user asks for a 'report', 'memo', 'letter', 'template', or similar deliverable as a Word or .docx file, use this skill. Do NOT use for PDFs, spreadsheets, Google Docs, or general coding tasks unrelated to document generation."
-license: Proprietary. LICENSE.txt has complete terms
-metadata:
-  version: "2.1"
-  skill-author: Anthropic, PBC
-  source: https://github.com/anthropics/skills/tree/main/skills/docx
----
-
-# DOCX creation, editing, and analysis
-
-A `.docx` is a ZIP archive of XML files. Choose your approach by task:
-
-| Task | Approach |
-|---|---|
-| **Create** a new document | Write a `docx` (npm) script — see gotchas below |
-| **Edit** an existing document | `unzip` → edit `word/document.xml` → `zip` (docx-js cannot open existing files) |
-| **Read** content | `pandoc -t markdown file.docx` |
-
-> Script paths below are relative to this skill's directory.
-
-## Creating with docx-js — gotchas
-
-`docx` is preinstalled — do not run `npm install` first; write the script and `require('docx')` directly. Only if that require fails: `npm install docx`. The model knows the API; these are the footguns:
-
-- **Page size defaults to A4.** For US Letter set `page: { size: { width: 12240, height: 15840 } }` (DXA; 1440 = 1″).
-- **Landscape:** pass portrait dimensions and `orientation: PageOrientation.LANDSCAPE` — docx-js swaps width/height internally.
-- **Tables need dual widths:** set `columnWidths` on the table AND `width` on every cell, both in `WidthType.DXA` (PERCENTAGE breaks in Google Docs). Column widths must sum to the table width.
-- **Table shading:** use `ShadingType.CLEAR`, never `SOLID` (renders black).
-- **Lists:** never insert `•` literally; use a `numbering` config with `LevelFormat.BULLET`.
-- **`ImageRun` requires `type:`** (`"png"`, `"jpg"`, …).
-- **`PageBreak` must be inside a `Paragraph`.**
-- **Never use `\n`** — use separate `Paragraph` elements.
-- **TOC:** headings must use built-in `HeadingLevel.*`; custom heading styles need `outlineLevel` set or they won't appear.
-- **Don't use a table as a horizontal rule** — use a paragraph bottom border instead.
-- **Dot-leader / right-aligned-on-same-line:** use `PositionalTab` (`alignment: PositionalTabAlignment.RIGHT`, `leader: PositionalTabLeader.DOT`) inside a `TextRun`, not literal `.` or space padding.
-
-## Verify the output
-
-After writing a `.docx`, render it and look at it:
-
-```bash
-python scripts/office/soffice.py --headless --convert-to pdf output.docx
-pdftoppm -jpeg -r 100 output.pdf page
-ls page-*.jpg   # then Read the images
-```
-
-`pdftoppm` zero-pads page numbers to the width of the page count (`page-01.jpg`…`page-12.jpg`).
-
-## Editing existing documents
-
-Legacy `.doc` files must be converted first: `python scripts/office/soffice.py --headless --convert-to docx file.doc`.
-
-```bash
-unzip -q doc.docx -d unpacked/
-find unpacked -type l -delete   # strip symlink entries — docx from external parties is untrusted
-python scripts/merge_runs.py unpacked/   # coalesce fragmented runs so text is findable
-# edit unpacked/word/document.xml in place — do NOT reformat or pretty-print
-(cd unpacked && rm -f ../out.docx && zip -Xr ../out.docx .)
-python scripts/office/validate.py out.docx --original doc.docx   # XSD checks; --auto-repair fixes common issues
-# redlining? add --author "<the name you redlined under>" to check every edit is tracked
-```
-
-Word splits text across many `<w:r>` runs (revision ids, spell-check markers), so a phrase you can see in the document often doesn't exist as a contiguous string in the XML. `merge_runs.py` merges adjacent identically-formatted runs in `word/document.xml` without changing content or rendering; it also accepts a `.docx` directly (`python scripts/merge_runs.py doc.docx -o merged.docx`).
-
-**Tracked changes:** when redlining, validate with `--author "<the name you redlined under>"` (needs `--original`) — it reports any text you changed without a `<w:ins>`/`<w:del>` around it, which is easy to do by accident and invisible in the accepted view. Wrap runs in `<w:ins>`/`<w:del>` with `w:id`, `w:author`, `w:date` attributes. Inside `<w:del>`, the text element is `<w:delText>`, not `<w:t>`. A deleted paragraph mark (`<w:pPr><w:rPr><w:del w:id=".." w:author=".." w:date=".."/></w:rPr></w:pPr>`) means "merge this paragraph into the next" — so deleting a paragraph outright is that plus a `<w:del>` around every run. The `<w:del/>` must come before the rPr's other children; their order is schema-enforced.
-
-To produce a clean copy with all tracked changes accepted: `python scripts/accept_changes.py in.docx out.docx`.
-
-Accepting a deleted paragraph mark should join that paragraph to the one below it, so a paragraph whose runs are *all* deleted vanishes. Word does this; `accept_changes.py` and `pandoc --track-changes=accept` don't always. Both fail the same way — they strip the deleted text but leave the emptied paragraph behind, which reads as a stray empty bullet when it was auto-numbered:
-
-- `pandoc --track-changes=accept` never joins the paragraphs.
-- `accept_changes.py` (LibreOffice) joins them correctly, except when the deleted paragraph is followed by an empty spacer paragraph.
-
-An empty bullet in either view is an artifact of that view, not a defect in the document. Check paragraph deletions in the XML.
-
-## Comments
-
-Comments require six cross-linked files. Use the helper — directory mode when you'll also be editing `document.xml` (saves an unzip/rezip cycle), `.docx`-direct mode otherwise:
-
-```bash
-# Against an already-unpacked directory (preferred when also placing markers)
-python scripts/comment.py unpacked/ "Fees & expenses cap is too low"
-python scripts/comment.py unpacked/ "Agreed" --parent 0
-
-# Against a .docx directly
-python scripts/comment.py contract.docx "This cap is too low" -o annotated.docx
-```
-
-The script writes `comments.xml`, `commentsExtended.xml`, `commentsIds.xml`, `commentsExtensible.xml`, the relationships, and the content-type overrides. Comment IDs are auto-assigned. It then prints the `<w:commentRangeStart>`/`<w:commentRangeEnd>`/`<w:commentReference>` snippet to add to `word/document.xml` so the comment anchors to specific text — until you place those markers, the comment exists but is not visible.
-
-## Dependencies
-
-`docx` (npm, preinstalled — install only if `require('docx')` fails) · `pandoc` · LibreOffice (`soffice`) · `pdftoppm` (Poppler)
-
----
-
-*This skill is created and maintained by [Anthropic](https://github.com/anthropics/skills/tree/main/skills/docx). Vendored here unmodified except for frontmatter metadata; see LICENSE.txt for terms.*