@pikaa-ai/pikaa 0.3.22 → 0.3.24

package/skills/vaex/SKILL.md

@@ -1,204 +0,0 @@
----
-name: vaex
-description: Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that do not fit in memory.
-allowed-tools: Read Write Edit Bash Grep Glob
-license: MIT license
-metadata:
-  version: "1.0"
-  skill-author: K-Dense Inc.
-compatibility: Requires Python 3.10+ (3.12+ recommended with vaex 4.19.0). Install with uv pip install vaex. Optional s3fs/gcsfs/adlfs for cloud I/O.
----
-
-# Vaex
-
-## Overview
-
-Vaex is a high-performance Python library designed for lazy, out-of-core DataFrames to process and visualize tabular datasets that are too large to fit into RAM. Vaex can process over a billion rows per second, enabling interactive data exploration and analysis on datasets with billions of rows.
-
-## Installation
-
-Install the full meta-package (recommended):
-
-```bash
-uv pip install vaex
-```
-
-Minimal install (pick only what you need):
-
-```bash
-uv pip install vaex-core vaex-viz vaex-hdf5 vaex-ml
-```
-
-The `vaex` package is a meta-package that pulls in `vaex-core`, `vaex-viz`, `vaex-hdf5`, `vaex-ml`, and other sub-packages. Arrow support is built into `vaex-core` (the separate `vaex-arrow` package is deprecated). `vaex-distributed` is deprecated in favor of vaex-enterprise.
-
-**Version notes (vaex 4.19.0+):** Python 3.12 and NumPy v2 require vaex >= 4.19.0. On Windows, you may need Python dev headers to build the `annoy` dependency.
-
-## When to Use This Skill
-
-Use Vaex when:
-- Processing tabular datasets larger than available RAM (gigabytes to terabytes)
-- Performing fast statistical aggregations on massive datasets
-- Creating visualizations and heatmaps of large datasets
-- Building machine learning pipelines on big data
-- Converting between data formats (CSV, HDF5, Arrow, Parquet)
-- Needing lazy evaluation and virtual columns to avoid memory overhead
-- Working with astronomical data, financial time series, or other large-scale scientific datasets
-
-**Vaex vs alternatives:** Use **polars** when data fits in RAM and you need maximum in-memory speed. Use **dask** when you need distributed pandas/NumPy across a cluster. Use **vaex** for single-machine, out-of-core analytics on tabular data that exceeds RAM via memory-mapped HDF5/Arrow files.
-
-## Core Capabilities
-
-Vaex provides six primary capability areas, each documented in detail in the references directory:
-
-### 1. DataFrames and Data Loading
-
-Load and create Vaex DataFrames from various sources including files (HDF5, CSV, Arrow, Parquet), pandas DataFrames, NumPy arrays, and dictionaries. Reference `references/core_dataframes.md` for:
-- Opening large files efficiently
-- Converting from pandas/NumPy/Arrow
-- Working with example datasets
-- Understanding DataFrame structure
-
-### 2. Data Processing and Manipulation
-
-Perform filtering, create virtual columns, use expressions, and aggregate data without loading everything into memory. Reference `references/data_processing.md` for:
-- Filtering and selections
-- Virtual columns and expressions
-- Groupby operations and aggregations
-- String operations and datetime handling
-- Working with missing data
-
-### 3. Performance and Optimization
-
-Leverage Vaex's lazy evaluation, caching strategies, and memory-efficient operations. Reference `references/performance.md` for:
-- Understanding lazy evaluation
-- Using `delay=True` for batching operations
-- Materializing columns when needed
-- Caching strategies
-- Asynchronous operations
-
-### 4. Data Visualization
-
-Create interactive visualizations of large datasets including heatmaps, histograms, and scatter plots. Reference `references/visualization.md` for:
-- Creating 1D and 2D plots
-- Heatmap visualizations
-- Working with selections
-- Customizing plots and subplots
-
-### 5. Machine Learning Integration
-
-Build ML pipelines with transformers, encoders, and integration with scikit-learn, XGBoost, and other frameworks. Reference `references/machine_learning.md` for:
-- Feature scaling and encoding
-- PCA and dimensionality reduction
-- K-means clustering
-- Integration with scikit-learn/XGBoost/CatBoost
-- Model serialization and deployment
-
-### 6. I/O Operations
-
-Efficiently read and write data in various formats with optimal performance. Reference `references/io_operations.md` for:
-- File format recommendations
-- Export strategies
-- Working with Apache Arrow
-- CSV handling for large files
-- Server and remote data access
-
-## Quick Start Pattern
-
-For most Vaex tasks, follow this pattern:
-
-```python
-import vaex
-
-# 1. Open or create DataFrame
-df = vaex.open('large_file.hdf5')  # or .csv, .arrow, .parquet
-# OR
-df = vaex.from_pandas(pandas_df)
-
-# 2. Explore the data
-print(df)  # Shows first/last rows and column info
-df.describe()  # Statistical summary
-
-# 3. Create virtual columns (no memory overhead)
-df['new_column'] = df.x ** 2 + df.y
-
-# 4. Filter with selections
-df_filtered = df[df.age > 25]
-
-# 5. Compute statistics (fast, lazy evaluation)
-mean_val = df.x.mean()
-stats = df.groupby('category').agg({'value': 'sum'})
-
-# 6. Visualize (df.viz is the recommended accessor since vaex 4.0)
-df.viz.heatmap(df.x, df.y, limits='99.7%', show=True)
-# Legacy: df.plot1d() and df.plot() still work on the DataFrame
-
-# 7. Export if needed
-df.export_hdf5('output.hdf5')
-```
-
-## Working with References
-
-The reference files contain detailed information about each capability area. Load references into context based on the specific task:
-
-- **Basic operations**: Start with `references/core_dataframes.md` and `references/data_processing.md`
-- **Performance issues**: Check `references/performance.md`
-- **Visualization tasks**: Use `references/visualization.md`
-- **ML pipelines**: Reference `references/machine_learning.md`
-- **File I/O**: Consult `references/io_operations.md`
-
-## Best Practices
-
-1. **Use HDF5 or Apache Arrow formats** for optimal performance with large datasets
-2. **Leverage virtual columns** instead of materializing data to save memory
-3. **Batch operations** using `delay=True` when performing multiple calculations
-4. **Export to efficient formats** rather than keeping data in CSV
-5. **Use expressions** for complex calculations without intermediate storage
-6. **Profile with `df.describe()` and `df.nbytes`** to understand data shape and memory usage
-
-## Common Patterns
-
-### Pattern: Converting Large CSV to HDF5
-```python
-import vaex
-
-# Open large CSV lazily (vaex 4.14+), or use from_csv to convert to HDF5
-df = vaex.open('large_file.csv')
-# df = vaex.from_csv('large_file.csv', convert='large_file.hdf5')
-
-# Export to HDF5 for faster future access
-df.export_hdf5('large_file.hdf5')
-
-# Future loads are instant
-df = vaex.open('large_file.hdf5')
-```
-
-### Pattern: Efficient Aggregations
-```python
-# Use delay=True to batch multiple operations
-mean_x = df.x.mean(delay=True)
-std_y = df.y.std(delay=True)
-sum_z = df.z.sum(delay=True)
-
-# Execute all at once
-results = vaex.execute([mean_x, std_y, sum_z])
-```
-
-### Pattern: Virtual Columns for Feature Engineering
-```python
-# No memory overhead - computed on the fly
-df['age_squared'] = df.age ** 2
-df['full_name'] = df.first_name + ' ' + df.last_name
-df['is_adult'] = df.age >= 18
-```
-
-## Resources
-
-This skill includes reference documentation in the `references/` directory:
-
-- `core_dataframes.md` - DataFrame creation, loading, and basic structure
-- `data_processing.md` - Filtering, expressions, aggregations, and transformations
-- `performance.md` - Optimization strategies and lazy evaluation
-- `visualization.md` - Plotting and interactive visualizations
-- `machine_learning.md` - ML pipelines and model integration
-- `io_operations.md` - File formats and data import/export
-

package/skills/venue-templates/SKILL.md

@@ -1,269 +0,0 @@
----
-name: venue-templates
-description: Prepare journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting guidance and bundled LaTeX scaffolds. Use when selecting an official template, checking current page or anonymity rules, adapting academic writing to a venue, or inspecting a submission PDF.
-license: MIT license
-compatibility: Requires Python 3.11+ for helper scripts; LaTeX and Poppler command-line tools are optional for compilation and PDF inspection.
-metadata:
-  version: "1.2"
-  skill-author: K-Dense Inc.
----
-
-# Venue Templates
-
-Prepare publication and funding documents without treating stale formatting details as authoritative. This skill combines:
-
-- a verification-first workflow for current venue rules;
-- bundled LaTeX scaffolds for a small, explicit set of document types;
-- writing-style and reviewer-expectation guides; and
-- local helpers for discovering, copying, and inspecting templates.
-
-## Mandatory Currency Rule
-
-Venue requirements are time-sensitive. Before giving exact page limits, deadlines, style-file names, anonymity rules, or required sections:
-
-1. Identify the exact venue, year or funding cycle, track, and article or proposal type.
-2. Open the official author instructions, call, solicitation, notice of funding opportunity (NOFO), or policy guide.
-3. Record the source URL and the date checked.
-4. Distinguish initial submission, revision/rebuttal, and camera-ready rules.
-5. Treat bundled files as scaffolds unless this skill explicitly says they are a copy of an official template.
-
-Never infer a current style-file name by changing the year in an old filename. Never present a generic scaffold as an official venue template.
-
-## When to Use
-
-Use this skill for:
-
-- locating official journal or conference author instructions;
-- checking page limits, required sections, anonymity, supplemental-material rules, or citation style;
-- choosing and adapting a bundled LaTeX scaffold;
-- preparing NSF, NIH, DOE, DARPA, or foundation proposal documents;
-- designing a research poster after checking event-specific dimensions;
-- adapting prose to a venue's audience and reviewer expectations; or
-- inspecting a PDF's page count and embedded fonts.
-
-## Verification-First Workflow
-
-### 1. Resolve the exact target
-
-Ask for or derive:
-
-- venue or funding agency;
-- year/cycle and track;
-- document type, such as research article, short paper, main track, R01, or R21;
-- submission stage; and
-- authoring format, such as LaTeX or Word.
-
-Do not combine rules from similarly named venues or tracks.
-
-### 2. Consult the right reference
-
-| Need | Reference |
-|---|---|
-| Journal submission and official publisher resources | `references/journals_formatting.md` |
-| Conference rules and 2026 verified snapshots | `references/conferences_formatting.md` |
-| Poster sizes, layout, and accessibility | `references/posters_guidelines.md` |
-| NSF, NIH, DOE, DARPA, and foundation proposals | `references/grants_requirements.md` |
-| Cross-venue writing comparison | `references/venue_writing_styles.md` |
-| Nature and Science writing | `references/nature_science_style.md` |
-| Cell Press writing | `references/cell_press_style.md` |
-| Medical journal writing | `references/medical_journal_styles.md` |
-| ML and computer-vision conference writing | `references/ml_conference_style.md` |
-| ACL, EMNLP, CHI, and other CS writing | `references/cs_conference_style.md` |
-| Review criteria and rebuttals | `references/reviewer_expectations.md` |
-
-Reference files summarize rules but do not override the current official source.
-
-### 3. Capture a compliance note
-
-Before editing, write a short note in the working document or task log:
-
-```text
-Target: ICML 2026 main track, initial submission
-Official source: https://icml.cc/Conferences/2026/AuthorInstructions
-Checked: 2026-07-20
-Main-text limit: 8 pages
-References/appendices: additional pages allowed in the same PDF
-Anonymity: required
-Official template: ICML 2026 style package linked by the author instructions
-```
-
-This makes later validation reproducible.
-
-### 4. Start from the official template
-
-For annual conferences and publisher-managed workflows:
-
-1. Download the template from the official source.
-2. Keep its class/style files unchanged.
-3. Add content without overriding margins, font sizes, spacing, or headers.
-4. Use a bundled scaffold only for drafting or when the official source explicitly permits it.
-
-For grants, many components are entered or uploaded separately. Do not submit a combined bundled `.tex` file as if it were an agency-issued form.
-
-### 5. Validate manually and mechanically
-
-Verify at least:
-
-- main-text and total-file page rules;
-- font, margin, line-spacing, and paper-size rules;
-- anonymity and metadata;
-- required sections, statements, checklists, and disclosures;
-- figure/table placement and accessibility;
-- reference and supplemental-material treatment; and
-- source-package and PDF requirements.
-
-The helper can inspect page totals and embedded fonts, but it cannot prove that margins, font sizes, excluded sections, or hidden metadata comply.
-
-## Bundled Assets
-
-The repository intentionally bundles only the following templates. Other venues listed in references require an official external template.
-
-### Journal and conference scaffolds
-
-| File | Status |
-|---|---|
-| `assets/journals/nature_article.tex` | Generic Nature-oriented writing scaffold; not an official Nature template |
-| `assets/journals/plos_one.tex` | PLOS ONE-oriented scaffold; compare with the current official PLOS LaTeX package |
-| `assets/journals/neurips_article.tex` | NeurIPS 2026 wrapper; requires the official `neurips_2026.sty` |
-| `assets/journals/elsarticle-template-num.tex` | Elsevier `elsarticle` numeric example |
-| `assets/journals/elsarticle-template-num-names.tex` | Elsevier `elsarticle` numbered/name example |
-| `assets/journals/elsarticle-template-harv.tex` | Elsevier `elsarticle` author-year example |
-
-The matching Elsevier `.bst` files are in `assets/journals/`.
-
-### Grant scaffolds
-
-| File | Status |
-|---|---|
-| `assets/grants/nsf_proposal_template.tex` | Planning scaffold for common NSF narrative components; upload components separately |
-| `assets/grants/nih_specific_aims.tex` | Writing scaffold for a one-page NIH Specific Aims attachment |
-
-Use SciENcv and agency-provided common forms where required. Do not recreate biosketch or current-support forms in LaTeX.
-
-### Poster scaffold
-
-| File | Status |
-|---|---|
-| `assets/posters/beamerposter_academic.tex` | Venue-agnostic beamerposter scaffold; set dimensions from the event's current presenter instructions |
-
-## Common Workflows
-
-### Annual conference paper
-
-1. Open `references/conferences_formatting.md`.
-2. Follow the official link for the exact year and track.
-3. Download the official author kit.
-4. Draft in the official template.
-5. Keep identifying information out of every submitted file when review is blind.
-6. Check the paper checklist, supplement, rebuttal, and camera-ready rules separately.
-
-For NeurIPS 2026, the bundled wrapper can be copied after downloading the official style file:
-
-```bash
-python scripts/customize_template.py \
-  --template neurips_article.tex \
-  --output my_neurips_2026_paper.tex
-```
-
-### Journal manuscript
-
-1. Resolve the exact journal and article type.
-2. Determine whether initial submission is format-flexible.
-3. Use the journal's official template or submission format when required.
-4. Apply the appropriate writing-style reference.
-5. Recheck final-production instructions only after acceptance or revision.
-
-Do not apply a publisher-wide template when the journal provides its own Guide for Authors.
-
-### Grant proposal
-
-1. Read the solicitation or NOFO before general agency guidance.
-2. Confirm the effective policy guide and form set.
-3. Map every required component to its page limit and upload field.
-4. Use agency systems and common forms for biosketches and support disclosures.
-5. Use bundled `.tex` files only as drafting aids.
-6. Have the institution's sponsored-research office review the final package.
-
-### Research poster
-
-1. Read the event's presenter instructions.
-2. Confirm physical dimensions, orientation, file format, and upload deadline.
-3. Set the poster dimensions in the scaffold.
-4. Use readable type, high contrast, color-independent encodings, and a logical reading order.
-5. Export and inspect the PDF at final size.
-
-## Helper Scripts
-
-Run scripts from the skill directory.
-
-### List bundled templates
-
-```bash
-python scripts/query_template.py --list-all
-python scripts/query_template.py --venue NeurIPS --requirements
-python scripts/query_template.py --type grants
-```
-
-The query helper reports only assets that exist in this skill and includes source/currency notes.
-
-### Copy and customize a scaffold
-
-```bash
-python scripts/customize_template.py \
-  --template nature_article.tex \
-  --title "Your Paper Title" \
-  --authors "First Author, Second Author" \
-  --affiliations "Institution Name" \
-  --output my_paper.tex
-```
-
-Review every replacement and compile before adding substantial content. User-provided text may need LaTeX escaping.
-
-### Inspect a PDF
-
-Use a verified preset:
-
-```bash
-python scripts/validate_format.py \
-  --file paper.pdf \
-  --venue icml-2026 \
-  --content-pages 8 \
-  --check page-count,fonts
-```
-
-Or provide an explicit limit and source:
-
-```bash
-python scripts/validate_format.py \
-  --file proposal.pdf \
-  --max-pages 15 \
-  --content-pages 15 \
-  --source-url "https://www.nsf.gov/policies/pappg" \
-  --check page-count,fonts \
-  --report validation.txt
-```
-
-`--content-pages` must be counted according to the official rule. The script does not infer where references or appendices begin.
-
-## Final Compliance Checklist
-
-- [ ] Exact venue, year/cycle, track, article type, and stage identified
-- [ ] Official source URL recorded with date checked
-- [ ] Official template or form used where required
-- [ ] Page-limit scope understood, including excluded sections
-- [ ] Required statements, checklists, and disclosures present
-- [ ] Blind-review files and PDF metadata checked for identity leaks
-- [ ] Figures and tables are legible and accessible
-- [ ] References, appendices, and supplements follow current rules
-- [ ] PDF and source package compile cleanly
-- [ ] Submission portal preview reviewed before final submission
-
-## Maintenance
-
-This skill was reviewed on 2026-07-20. Annual conference snapshots are labeled with their year. When updating:
-
-1. replace year-specific claims only after checking official sources;
-2. avoid adding links to assets that are not bundled;
-3. keep generic guidance separate from official requirements;
-4. update helper presets and examples together; and
-5. increment `metadata.version`.

package/skills/verification-before-completion/SKILL.md

@@ -1,22 +0,0 @@
----
-name: verification-before-completion
-description: "Mandatory pre-completion verification protocol: execute automated tests, linter, and type checks before reporting completion."
-risk: low
-source: built-in
----
-
-# Verification Before Completion
-
-## The Iron Rule of Completion
-
-```
-NEVER REPORT A TASK COMPLETE WITHOUT RUNNING RUNNABLE VERIFICATION FIRST
-```
-
-Before declaring any task or ticket completed to the user:
-
-1. **Run Unit Tests**: Execute `bun test` / `npm test` and verify 0 failures.
-2. **Run Typecheck & Linter**: Ensure no compile or type errors exist.
-3. **Verify Edge Cases**: Check boundary conditions and error paths.
-4. **Clean up Scratch Artifacts & Verify Zero-Residue**: Remove any temporary debug logs, test outputs, or stray files. Run `git status --short` to ensure only intended project modifications exist.
-5. **Enforce Guardian Rails**: Verify no `tmp_*`, `scratch_*`, or detached preview files remain in the workspace.