@rubix0270/arboris 1.0.1 → 1.0.3

package/prisma/skills/scientific-pkg-gget/SKILL.md

@@ -1,167 +0,0 @@
----
-name: gget
-description: gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.
-metadata:
-  origin: community
----
-
-# gget
-
-Use this skill when a task needs quick bioinformatics lookup across genomic
-reference databases with the `gget` CLI or Python package.
-
-## When to Use
-
-- Finding Ensembl IDs, gene metadata, transcript details, or sequences.
-- Running quick BLAST or BLAT lookups without building a full local pipeline.
-- Fetching reference genome links and annotations from Ensembl.
-- Querying protein structure, pathway, cancer, expression, or disease-association
-  modules through a single interface.
-- Creating a reproducible first-pass evidence log before moving to heavier
-  tools such as Biopython, Snakemake, Nextflow, BLAST+, or database-specific
-  clients.
-
-Use a dedicated workflow instead of `gget` when the task requires regulated
-clinical interpretation, high-throughput production pipelines, or fine-grained
-control over database versions and local indexes.
-
-## Installation
-
-Use a clean Python environment.
-
-```bash
-python -m venv .venv
-. .venv/bin/activate
-python -m pip install --upgrade pip
-python -m pip install --upgrade gget
-gget --help
-```
-
-If `uv` is available:
-
-```bash
-uv venv
-. .venv/bin/activate
-uv pip install gget
-```
-
-Before relying on an older environment, upgrade `gget` and re-check the module
-docs. The upstream databases queried by `gget` change over time.
-
-## Basic Patterns
-
-CLI shape:
-
-```bash
-gget <module> [arguments] [options]
-```
-
-Python shape:
-
-```python
-import gget
-
-result = gget.search(["BRCA1"], species="human")
-print(result)
-```
-
-Common workflow:
-
-1. Identify the species, assembly, gene ID type, and database needed.
-2. Check the current module documentation for arguments.
-3. Run a small query first.
-4. Save output with an explicit filename and date.
-5. Record module name, version, arguments, and database assumptions.
-
-## Common Modules
-
-Use current upstream docs for exact arguments. These modules are common first
-choices:
-
-- `gget search`: find Ensembl IDs from search terms.
-- `gget info`: retrieve metadata for Ensembl, UniProt, or related IDs.
-- `gget seq`: fetch nucleotide or amino-acid sequences.
-- `gget ref`: retrieve reference genome download links.
-- `gget blast`: run a quick BLAST query.
-- `gget blat`: locate a sequence against supported genome assemblies.
-- `gget muscle`: run multiple sequence alignment.
-- `gget diamond`: run local sequence alignment against reference sequences.
-- `gget alphafold` and `gget pdb`: inspect protein-structure references.
-- `gget enrichr`, `gget opentargets`, `gget archs4`, `gget bgee`, `gget cbio`,
-  and `gget cosmic`: explore enrichment, target, expression, cancer, and disease
-  association data.
-
-Do not assume every module supports every Python version or dependency set.
-Some optional scientific dependencies have narrower version support than the
-core package.
-
-## Quick Examples
-
-Find genes:
-
-```bash
-gget search -s human brca1 dna repair -o brca1-search.json
-```
-
-Fetch gene metadata:
-
-```bash
-gget info ENSG00000012048 -o brca1-info.json
-```
-
-Fetch a sequence:
-
-```bash
-gget seq ENSG00000012048 -o brca1-seq.fa
-```
-
-Run a small BLAST query:
-
-```bash
-gget blast "MEEPQSDPSVEPPLSQETFSDLWKLLPEN" -l 10 -o blast-results.json
-```
-
-Python example:
-
-```python
-import gget
-
-genes = gget.search(["BRCA1", "DNA repair"], species="human")
-info = gget.info(["ENSG00000012048"])
-sequence = gget.seq("ENSG00000012048")
-```
-
-## Reproducibility Log
-
-For scientific outputs, include enough metadata to replay the query.
-
-```markdown
-| Date | gget version | Module | Query | Species/assembly | Output | Notes |
-| --- | --- | --- | --- | --- | --- | --- |
-| 2026-05-11 | `gget --version` | search | `BRCA1 DNA repair` | human | `brca1-search.json` | Docs checked before run |
-```
-
-Also record:
-
-- Python version and environment manager.
-- Any optional dependency installed through `gget setup`.
-- Database-specific identifiers returned by the query.
-- Whether output is JSON, CSV, FASTA, or a DataFrame export.
-- Any failures that were resolved by upgrading `gget`.
-
-## Review Checklist
-
-- Did you upgrade or verify the installed `gget` version?
-- Did you check the current upstream module docs before using arguments?
-- Is the species or assembly explicit?
-- Are identifiers preserved exactly, including Ensembl/UniProt prefixes?
-- Is the result labeled as database output rather than clinical interpretation?
-- Is the query reproducible from the saved command or Python snippet?
-- Are optional dependencies installed in an isolated environment?
-
-## References
-
-- [gget documentation](https://pachterlab.github.io/gget/)
-- [gget updates](https://pachterlab.github.io/gget/en/updates.html)
-- [gget GitHub repository](https://github.com/pachterlab/gget)
-- [gget Bioinformatics paper](https://doi.org/10.1093/bioinformatics/btac836)

package/prisma/skills/scientific-thinking-literature-review/SKILL.md

@@ -1,193 +0,0 @@
----
-name: literature-review
-description: Systematic literature-review workflow for academic, biomedical, technical, and scientific topics, including search planning, source screening, synthesis, citation checks, and evidence logging.
-metadata:
-  origin: community
----
-
-# Literature Review
-
-Use this skill when the task is to find, screen, synthesize, and cite a body of
-academic or technical literature.
-
-## When to Use
-
-- Building a systematic, scoping, or narrative literature review.
-- Synthesizing the state of the art for a research question.
-- Finding gaps, contradictions, or future-work directions.
-- Preparing citation-backed background sections for papers or reports.
-- Comparing evidence across peer-reviewed papers, preprints, patents, and
-  technical reports.
-
-## Review Types
-
-- **Narrative review**: broad synthesis; useful for orientation.
-- **Scoping review**: maps concepts, methods, and evidence gaps.
-- **Systematic review**: predefined protocol, reproducible search, explicit
-  screening and exclusion.
-- **Meta-analysis**: systematic review plus quantitative effect aggregation.
-
-Ask the user which level of rigor is needed. If unspecified, default to a
-scoping review for exploratory work and a systematic review for publication or
-clinical claims.
-
-## Workflow
-
-### 1. Define the Question
-
-Convert the prompt into a searchable research question.
-
-For clinical or biomedical work, use PICO:
-
-- Population
-- Intervention or exposure
-- Comparator
-- Outcome
-
-For technical work, use:
-
-- system or domain
-- method or intervention
-- comparison baseline
-- evaluation metric
-
-### 2. Plan the Search
-
-Create a search protocol before collecting sources:
-
-- databases to search
-- date range
-- languages
-- publication types
-- inclusion criteria
-- exclusion criteria
-- exact search strings
-
-Minimum useful database set:
-
-- PubMed for biomedical and life-sciences literature.
-- arXiv for CS, math, physics, quantitative biology, and preprints.
-- Semantic Scholar or Crossref for broad academic discovery.
-- Domain-specific sources when relevant, such as clinical-trial registries,
-  patent databases, standards bodies, or official technical docs.
-
-### 3. Search and Log Evidence
-
-Keep a search log that makes the review reproducible:
-
-```markdown
-| Database | Date searched | Query | Filters | Results | Export |
-| --- | --- | --- | --- | ---: | --- |
-| PubMed | 2026-05-11 | `("CRISPR"[tiab] OR "Cas9"[tiab]) AND "sickle cell"[tiab]` | 2020:2026, English | 86 | PMID list |
-| arXiv | 2026-05-11 | `CRISPR sickle cell gene editing` | q-bio, 2020:2026 | 9 | BibTeX |
-```
-
-Save raw IDs, URLs, DOIs, abstracts, and notes separately from the final prose.
-
-### 4. Deduplicate
-
-Deduplicate in this order:
-
-1. DOI
-2. PMID or arXiv ID
-3. exact title
-4. normalized title plus first author and year
-
-Record how many duplicates were removed.
-
-### 5. Screen Sources
-
-Screen in stages:
-
-1. title
-2. abstract
-3. full text
-
-For systematic work, record exclusion reasons:
-
-- wrong population
-- wrong intervention
-- wrong outcome
-- not primary research
-- duplicate
-- unavailable full text
-- outside date range
-
-### 6. Extract Data
-
-Use a structured extraction table:
-
-```markdown
-| Study | Design | Population/Data | Method | Comparator | Outcome | Key finding | Limitations |
-| --- | --- | --- | --- | --- | --- | --- | --- |
-| Author Year | RCT/cohort/review/etc. | sample or corpus | method | baseline | measured outcome | result | caveat |
-```
-
-For technical papers, include dataset, benchmark, metric, baseline, and
-reproducibility notes.
-
-### 7. Synthesize
-
-Group evidence by theme rather than summarizing papers one by one.
-
-Useful synthesis lenses:
-
-- strongest evidence
-- conflicting evidence
-- methodological weaknesses
-- population or dataset limits
-- recency and replication
-- practical implications
-- unanswered questions
-
-Separate claims by confidence:
-
-- **High confidence**: replicated, high-quality evidence across sources.
-- **Medium confidence**: plausible but limited by sample, method, or recency.
-- **Low confidence**: early, speculative, single-source, or weakly measured.
-
-### 8. Verify Citations
-
-Before finalizing:
-
-- verify DOI, PMID, arXiv ID, or official URL
-- check author names and publication year
-- do not cite a paper for a claim it does not make
-- mark preprints as preprints
-- distinguish reviews from primary evidence
-
-## Output Template
-
-```markdown
-# Literature Review: <Topic>
-
-Generated: <date>
-Review type: <narrative | scoping | systematic | meta-analysis>
-Search window: <dates>
-Databases: <list>
-
-## Research Question
-
-## Search Strategy
-
-## Inclusion and Exclusion Criteria
-
-## Evidence Summary
-
-## Thematic Synthesis
-
-## Gaps and Limitations
-
-## References
-
-## Search Log
-```
-
-## Pitfalls
-
-- Do not treat search snippets as evidence.
-- Do not mix preprints, reviews, and primary studies without labeling them.
-- Do not omit negative or conflicting findings.
-- Do not claim systematic-review rigor without a reproducible protocol.
-- Do not use a single database for a broad claim unless the scope is explicitly
-  limited to that database.

package/prisma/skills/scientific-thinking-scholar-evaluation/SKILL.md

@@ -1,161 +0,0 @@
----
-name: scholar-evaluation
-description: Structured scholarly-work evaluation for papers, proposals, literature reviews, methods sections, evidence quality, citation support, and research-writing feedback.
-metadata:
-  origin: community
----
-
-# Scholar Evaluation
-
-Use this skill to evaluate academic or scientific work with a repeatable rubric.
-
-## When to Use
-
-- Reviewing a research paper, proposal, thesis chapter, or literature review.
-- Checking whether claims are supported by cited evidence.
-- Evaluating methodology, study design, analysis, or limitations.
-- Comparing two or more papers for quality or relevance.
-- Producing structured feedback for revision.
-
-## Evaluation Scope
-
-Start by identifying the artifact:
-
-- empirical research paper
-- theoretical paper
-- technical report
-- systematic or narrative literature review
-- research proposal
-- thesis or dissertation chapter
-- conference abstract or short paper
-
-Then choose scope:
-
-- **comprehensive**: all rubric dimensions
-- **targeted**: one or two dimensions, such as method or citations
-- **comparative**: rank multiple works against the same rubric
-
-## Rubric
-
-Score each applicable dimension from 1 to 5:
-
-- 5: excellent; clear, rigorous, and publication-ready
-- 4: good; minor improvements needed
-- 3: adequate; meaningful gaps but usable
-- 2: weak; substantial revision needed
-- 1: poor; major validity or clarity problems
-
-Use `N/A` for dimensions that do not apply.
-
-### 1. Problem and Research Question
-
-- Is the problem clear and specific?
-- Is the contribution meaningful?
-- Are scope and assumptions explicit?
-- Does the question match the claimed contribution?
-
-### 2. Literature and Context
-
-- Is relevant prior work covered?
-- Does the work synthesize rather than merely list sources?
-- Are gaps accurately identified?
-- Are recent and foundational sources balanced?
-
-### 3. Methodology
-
-- Does the method answer the research question?
-- Are design choices justified?
-- Are variables, datasets, participants, or materials described clearly?
-- Could another researcher reproduce the work?
-- Are ethical and practical constraints acknowledged?
-
-### 4. Data and Evidence
-
-- Are data sources credible and appropriate?
-- Is sample size or corpus coverage adequate?
-- Are inclusion, exclusion, and preprocessing decisions documented?
-- Are missing data and bias risks discussed?
-
-### 5. Analysis
-
-- Are statistical, qualitative, or computational methods appropriate?
-- Are baselines and controls fair?
-- Are uncertainty, sensitivity, or robustness checks included when needed?
-- Are alternative explanations considered?
-
-### 6. Results and Interpretation
-
-- Are results clearly presented?
-- Do claims stay within the evidence?
-- Are figures, tables, and metrics understandable?
-- Are negative or null results handled honestly?
-
-### 7. Limitations and Threats to Validity
-
-- Are limitations specific rather than generic?
-- Are internal, external, construct, and conclusion-validity risks addressed?
-- Does the paper distinguish speculation from demonstrated results?
-
-### 8. Writing and Structure
-
-- Is the argument easy to follow?
-- Are sections organized around the research question?
-- Are definitions and notation clear?
-- Is the tone precise and scholarly?
-
-### 9. Citations
-
-- Do cited papers support the claims attached to them?
-- Are primary sources used where possible?
-- Are reviews labeled as reviews?
-- Are preprints labeled as preprints?
-- Are citation metadata and links correct?
-
-## Review Process
-
-1. Read the abstract, introduction, figures, and conclusion for claimed
-   contribution.
-2. Read methods and results for evidence quality.
-3. Check the strongest claims against cited sources.
-4. Score each applicable dimension.
-5. Separate critical blockers from revision suggestions.
-6. End with concrete next edits.
-
-## Output Template
-
-```markdown
-# Scholar Evaluation: <Artifact>
-
-## Overall Assessment
-
-- Overall score: <1-5 or N/A>
-- Confidence: <high | medium | low>
-- Summary: <3-5 sentences>
-
-## Dimension Scores
-
-| Dimension | Score | Evidence | Revision priority |
-| --- | ---: | --- | --- |
-| Problem and question |  |  |  |
-| Literature and context |  |  |  |
-| Methodology |  |  |  |
-| Data and evidence |  |  |  |
-| Analysis |  |  |  |
-| Results and interpretation |  |  |  |
-| Limitations |  |  |  |
-| Writing and structure |  |  |  |
-| Citations |  |  |  |
-
-## Critical Issues
-
-## Recommended Revisions
-
-## Evidence Checks Needed
-```
-
-## Pitfalls
-
-- Do not use the score as a substitute for concrete feedback.
-- Do not penalize a paper for omitting a dimension outside its scope.
-- Do not treat citation count, venue, or author reputation as proof of quality.
-- Do not accept unsupported claims just because they appear in the abstract.

package/prisma/skills/search-first/SKILL.md

@@ -1,183 +0,0 @@
----
-name: search-first
-description: Research-before-coding workflow. Search for existing tools, libraries, and patterns before writing custom code. Invokes the researcher agent.
-metadata:
-  origin: ECC
----
-
-# /search-first — Research Before You Code
-
-Systematizes the "search for existing solutions before implementing" workflow.
-
-## Trigger
-
-Use this skill when:
-- Starting a new feature that likely has existing solutions
-- Adding a dependency or integration
-- The user asks "add X functionality" and you're about to write code
-- Before creating a new utility, helper, or abstraction
-
-## Workflow
-
-```
-┌─────────────────────────────────────────────┐
-│  0. TOOL AVAILABILITY PREFLIGHT             │
-│     Check search channels before relying on │
-│     them; report skipped channels honestly   │
-├─────────────────────────────────────────────┤
-│  1. NEED ANALYSIS                           │
-│     Define what functionality is needed      │
-│     Identify language/framework constraints  │
-├─────────────────────────────────────────────┤
-│  2. PARALLEL SEARCH (researcher agent)      │
-│     ┌──────────┐ ┌──────────┐ ┌──────────┐  │
-│     │  npm /   │ │  MCP /   │ │  GitHub / │  │
-│     │  PyPI    │ │  Skills  │ │  Web      │  │
-│     └──────────┘ └──────────┘ └──────────┘  │
-├─────────────────────────────────────────────┤
-│  3. EVALUATE                                │
-│     Score candidates (functionality, maint, │
-│     community, docs, license, deps)         │
-├─────────────────────────────────────────────┤
-│  4. DECIDE                                  │
-│     ┌─────────┐  ┌──────────┐  ┌─────────┐  │
-│     │  Adopt  │  │  Extend  │  │  Build   │  │
-│     │ as-is   │  │  /Wrap   │  │  Custom  │  │
-│     └─────────┘  └──────────┘  └─────────┘  │
-├─────────────────────────────────────────────┤
-│  5. IMPLEMENT                               │
-│     Install package / Configure MCP /       │
-│     Write minimal custom code               │
-└─────────────────────────────────────────────┘
-```
-
-## Decision Matrix
-
-| Signal | Action |
-|--------|--------|
-| Exact match, well-maintained, MIT/Apache | **Adopt** — install and use directly |
-| Partial match, good foundation | **Extend** — install + write thin wrapper |
-| Multiple weak matches | **Compose** — combine 2-3 small packages |
-| Nothing suitable found | **Build** — write custom, but informed by research |
-
-## How to Use
-
-### Step 0: Tool Availability Preflight
-
-This is agent guidance, not an executable setup script. Check only the channels
-that are relevant to the task and project in front of you.
-
-| Channel | Check | If missing |
-|---------|-------|------------|
-| Repository search | `rg --files` and targeted `rg` queries | State that only visible files were inspected |
-| Package registry | `npm --version`, `python -m pip --version`, or project package manager | Use web/docs search and avoid claiming registry coverage |
-| GitHub CLI | `gh auth status` | Use public web or local git history only |
-| MCP/docs tools | Available tool list or local MCP config | Fall back to official docs/web search |
-| Skills directory | `ls ~/.claude/skills ~/.codex/skills` where applicable | Say no local skill catalog was available |
-
-### Quick Mode (inline)
-
-Before writing a utility or adding functionality, mentally run through:
-
-0. Does this already exist in the repo? → `rg` through relevant modules/tests first
-1. Is this a common problem? → Search npm/PyPI
-2. Is there an MCP for this? → Check `~/.claude/settings.json` and search
-3. Is there a skill for this? → Check `~/.claude/skills/`
-4. Is there a GitHub implementation/template? → Run GitHub code search for maintained OSS before writing net-new code
-
-### Full Mode (agent)
-
-For non-trivial functionality, launch the researcher agent:
-
-```
-Agent(subagent_type="general-purpose", prompt="
-  Research existing tools for: [DESCRIPTION]
-  Language/framework: [LANG]
-  Constraints: [ANY]
-
-  Search: npm/PyPI, MCP servers, Claude Code skills, GitHub
-  Return: Structured comparison with recommendation
-")
-```
-
-Older Claude Code docs may call this `Task(...)`; use the current agent/subagent
-tool name exposed by the active harness.
-
-## Search Shortcuts by Category
-
-### Development Tooling
-- Linting → `eslint`, `ruff`, `textlint`, `markdownlint`
-- Formatting → `prettier`, `black`, `gofmt`
-- Testing → `jest`, `pytest`, `go test`
-- Pre-commit → `husky`, `lint-staged`, `pre-commit`
-
-### AI/LLM Integration
-- Claude SDK → Context7 for latest docs
-- Prompt management → Check MCP servers
-- Document processing → `unstructured`, `pdfplumber`, `mammoth`
-
-### Data & APIs
-- HTTP clients → `httpx` (Python), `ky`/`undici` (Node)
-- Validation → `zod` (TS), `pydantic` (Python)
-- Database → Check for MCP servers first
-
-### Content & Publishing
-- Markdown processing → `remark`, `unified`, `markdown-it`
-- Image optimization → `sharp`, `imagemin`
-
-## Integration Points
-
-### With planner agent
-The planner should invoke researcher before Phase 1 (Architecture Review):
-- Researcher identifies available tools
-- Planner incorporates them into the implementation plan
-- Avoids "reinventing the wheel" in the plan
-
-### With architect agent
-The architect should consult researcher for:
-- Technology stack decisions
-- Integration pattern discovery
-- Existing reference architectures
-
-### With iterative-retrieval skill
-Combine for progressive discovery:
-- Cycle 1: Broad search (npm, PyPI, MCP)
-- Cycle 2: Evaluate top candidates in detail
-- Cycle 3: Test compatibility with project constraints
-
-## Examples
-
-### Example 1: "Add dead link checking"
-```
-Need: Check markdown files for broken links
-Search: npm "markdown dead link checker"
-Found: textlint-rule-no-dead-link (score: 9/10)
-Action: ADOPT — npm install textlint-rule-no-dead-link
-Result: Zero custom code, battle-tested solution
-```
-
-### Example 2: "Add HTTP client wrapper"
-```
-Need: Resilient HTTP client with retries and timeout handling
-Search: npm "http client retry", PyPI "httpx retry"
-Found: got (Node) with retry plugin, httpx (Python) with built-in retry
-Action: ADOPT — use got/httpx directly with retry config
-Result: Zero custom code, production-proven libraries
-```
-
-### Example 3: "Add config file linter"
-```
-Need: Validate project config files against a schema
-Search: npm "config linter schema", "json schema validator cli"
-Found: ajv-cli (score: 8/10)
-Action: ADOPT + EXTEND — install ajv-cli, write project-specific schema
-Result: 1 package + 1 schema file, no custom validation logic
-```
-
-## Anti-Patterns
-
-- **Jumping to code**: Writing a utility without checking if one exists
-- **Ignoring MCP**: Not checking if an MCP server already provides the capability
-- **Silent skipping**: Reporting "nothing found" when a search channel was unavailable
-- **Over-customizing**: Wrapping a library so heavily it loses its benefits
-- **Dependency bloat**: Installing a massive package for one small feature