@yeyuan98/opencode-bioresearcher-plugin 1.6.7 → 1.6.8-alpha.1

package/dist/skills/pzfx-io/guides/convert.md

@@ -1,102 +0,0 @@
-# Converting PZFX Files
-
-## Convert to CSV
-
-```bash
-uv run python pzfx.py convert <file.pzfx> --format csv
-```
-
-Creates `<basename>.csv` next to the original file.
-
-## Convert to TSV
-
-```bash
-uv run python pzfx.py convert <file.pzfx> --format tsv
-```
-
-## Convert to JSON
-
-```bash
-uv run python pzfx.py convert <file.pzfx> --format json
-```
-
-JSON output includes full structured data:
-```json
-{
-  "success": true,
-  "table_id": "Table0",
-  "table_type": "OneWay",
-  "columns": [...],
-  "row_titles": [...],
-  "source_file": "/path/to/file.pzfx"
-}
-```
-
-## Convert Specific Table
-
-For multi-table files, convert a single table:
-```bash
-uv run python pzfx.py convert <file.pzfx> --table 0 --format csv
-```
-
-## Convert All Tables
-
-Without `--table`, all tables are converted. For CSV/TSV, each table gets a separate file:
-```
-basename_Table0.csv
-basename_Table1.csv
-```
-
-## Custom Output Path
-
-```bash
-uv run python pzfx.py convert <file.pzfx> --format csv --output /path/to/output.csv
-```
-
-Note: `--output` is only used when converting a single table (or the last table).
-
-## Excluded Data Modes
-
-```bash
-uv run python pzfx.py convert <file.pzfx> --exclude-mode keep
-uv run python pzfx.py convert <file.pzfx> --exclude-mode star
-```
-
-| Mode | Effect |
-|------|--------|
-| `exclude` (default) | Excluded values omitted (empty cells) |
-| `keep` | Excluded values preserved as raw numbers |
-| `star` | Excluded values marked with asterisk (e.g., `90*`) |
-
-## Convert Output Includes
-
-By default, converted output includes:
-- Row titles (if present)
-- X column data (if present, for XY/Survival tables)
-- All Y column subcolumns with proper naming
-
-Column naming follows YFormat conventions:
-- Replicates: `Title_1`, `Title_2`
-- SD: `Title_MEAN`, `Title_SD`
-- SE: `Title_MEAN`, `Title_SE`
-- etc.
-
-## Batch Conversion Example
-
-Convert all PZFX files in a directory:
-```bash
-for f in *.pzfx; do
-  uv run python pzfx.py convert "$f" --format csv
-done
-```
-
-## Comparison with `read` Command
-
-| Feature | `read` | `convert` |
-|---------|--------|-----------|
-| Output to stdout | Yes | No (writes file) |
-| Write to file | No | Yes |
-| Include row titles | `--include-row-titles` | Always included |
-| Include X column | `--include-x` | Always included |
-| Multi-table | One at a time (`--table`) | All or one |
-| Use case | Quick inspection, piping | File export, batch processing |

package/dist/skills/pzfx-io/guides/read-parse.md

@@ -1,116 +0,0 @@
-# Reading and Parsing PZFX Files
-
-## Quick Inspect
-
-Get file metadata without extracting data:
-
-```bash
-uv run python pzfx.py inspect <file.pzfx>
-```
-
-Output includes: table IDs, types, formats, row counts, column titles and subcolumn counts.
-
-## Read Table Data
-
-### JSON format (default)
-```bash
-uv run python pzfx.py read <file.pzfx> --format json --include-x --include-row-titles
-```
-
-JSON structure:
-```json
-{
-  "table_id": "Table0",
-  "table_type": "XY",
-  "columns": [
-    {
-      "title": "X Title",
-      "subcolumn_names": ["X Title"],
-      "data": [[1.0, 2.0, 3.0]]
-    },
-    {
-      "title": "Sample",
-      "subcolumn_names": ["Sample_1", "Sample_2"],
-      "data": [[100.0, 90.0, 80.0], [50.0, 60.0, 70.0]]
-    }
-  ],
-  "row_titles": ["A", "B", "C"]
-}
-```
-
-### CSV/TSV format
-```bash
-uv run python pzfx.py read <file.pzfx> --format csv --include-x --include-row-titles
-uv run python pzfx.py read <file.pzfx> --format tsv --include-x
-```
-
-Output:
-```
-ROWTITLE,XX,Ya_1,Ya_2,Yb_1,Yb_2
-A,1.0,100.0,50.0,1.0,10.0
-B,2.0,90.0,60.0,2.0,9.0
-C,3.0,80.0,70.0,3.0,8.0
-```
-
-## Multi-Table Files
-
-Specify table index (0-based):
-```bash
-uv run python pzfx.py read <file.pzfx> --table 1 --format csv
-```
-
-Use `inspect` first to see how many tables exist.
-
-## Excluded Data Handling
-
-Prism supports "excluding" (striking through) data points. Control with `--exclude-mode`:
-
-| Mode | Effect | Example |
-|------|--------|---------|
-| `exclude` (default) | Excluded values → `null`/empty | `[100, null, 80]` |
-| `keep` | Excluded values kept as-is | `[100, 90, 80]` |
-| `star` | Append asterisk to excluded | `[100, "90*", 80]` |
-
-```bash
-uv run python pzfx.py read <file.pzfx> --exclude-mode star --format csv
-```
-
-## Value Normalization
-
-Values are automatically normalized:
-- `"42."` → integer `42`
-- `"3.14"` → float `3.14`
-- `"3,5"` → float `3.5` (comma-decimal notation)
-- `""` or empty → `null`
-- Non-numeric text → kept as string
-
-## Reading Specific Table Types
-
-### XY Tables (with X column)
-```bash
-uv run python pzfx.py read <file.pzfx> --include-x --format csv
-```
-
-### Contingency Tables (with row titles)
-```bash
-uv run python pzfx.py read <file.pzfx> --include-row-titles --format csv
-```
-
-### Date-Formatted X Columns
-XColumn stores fractional years; XAdvancedColumn stores formatted date strings. Both are included with `--include-x`.
-
-### HugeTable Files
-Handled identically to regular Tables. `inspect` shows `"is_huge": true`.
-
-## Error Output Format
-
-On failure, JSON error is returned:
-```json
-{
-  "success": false,
-  "error": "CATEGORY: message",
-  "hint": "Suggested fix"
-}
-```
-
-Error categories: `FILE_NOT_FOUND`, `PARSE_ERROR`, `VALIDATION_ERROR`

package/dist/skills/pzfx-io/guides/schema-reference.md

@@ -1,167 +0,0 @@
-# PZFX Schema Reference
-
-## File Structure
-
-Every PZFX file follows this layout:
-
-```xml
-<?xml version="1.0" encoding="UTF-8"?>
-<GraphPadPrismFile PrismXMLVersion="5.00">
-  <Created>...</Created>
-  <InfoSequence><Ref ID="Info0" Selected="1"></Ref></InfoSequence>
-  <Info ID="Info0">...</Info>
-  <TableSequence><Ref ID="Table0" Selected="1"></Ref></TableSequence>
-  <Table ...>...</Table>
-  <!--Analyses, graphs and layouts as compressed binary. Don't edit this part of the file.-->
-  <Template dt:dt="bin.base64" xmlns:dt="urn:schemas-microsoft-com:datatypes">base64...</Template>
-</GraphPadPrismFile>
-```
-
-The `<Template>` block is an opaque base64-encoded zlib blob containing graphs, analyses, and layouts. It must never be modified.
-
-## XML Style Variants
-
-| Variant | Prism Version | Features |
-|---------|---------------|----------|
-| Classic | 6-7 | Closing tags (`</Subcolumn></YColumn>`), no xmlns |
-| Modern  | 8+  | Self-closing tags (`<Subcolumn/>`), `xmlns="http://graphpad.com/prism/Prism.htm"` on root |
-
-Both variants are handled by stripping XML namespaces at parse time.
-
-## Table Element Attributes
-
-```xml
-<Table ID="Table0" XFormat="numbers" YFormat="replicates" Replicates="2"
-       TableType="XY" EVFormat="AsteriskAfterNumber">
-```
-
-| Attribute | Required | Values |
-|-----------|----------|--------|
-| ID | Yes | Unique table identifier (e.g. "Table0") |
-| TableType | Yes | `OneWay`, `TwoWay`, `XY`, `Survival`, `Contingency`, `PartsOfWhole` |
-| XFormat | Yes | `none`, `numbers`, `date`, `error` |
-| YFormat | Conditional | `replicates`, `SD`, `SE`, `CV`, `SDN`, `SEN`, `CVN`, `low-high`, `upper-lower-limits` |
-| Replicates | Conditional | Integer, required when YFormat="replicates" |
-| EVFormat | Yes | Always `AsteriskAfterNumber` |
-
-### TableType to XFormat Mapping
-
-| TableType | Required XFormat |
-|-----------|-----------------|
-| OneWay | none |
-| TwoWay | none |
-| Contingency | none |
-| PartsOfWhole | none |
-| XY | numbers (or date, error) |
-| Survival | numbers |
-
-## Column Types
-
-### XColumn (XY/Survival tables only)
-
-```xml
-<XColumn Width="199" Subcolumns="1" Decimals="8">
-  <Title>X Title</Title>
-  <Subcolumn>
-    <d>1.0</d>
-    <d>2.0</d>
-  </Subcolumn>
-</XColumn>
-```
-
-- When XFormat="error", has 2 subcolumns (value ± error)
-- Subcolumns count is always 1 for numbers/date formats
-
-### XAdvancedColumn (Date-formatted X columns)
-
-```xml
-<XAdvancedColumn Version="1" Width="199" Decimals="8" Subcolumns="1">
-  <Title>Date X</Title>
-  <Subcolumn>
-    <d>2023-01-15</d>
-  </Subcolumn>
-</XAdvancedColumn>
-```
-
-- Stores formatted date strings alongside XColumn fractional years
-- Always paired with an XColumn when XFormat="date"
-
-### YColumn
-
-```xml
-<YColumn Width="89" Decimals="0" Subcolumns="2">
-  <Title>Sample</Title>
-  <Subcolumn><d>1.</d><d>2.</d></Subcolumn>
-  <Subcolumn><d>3.</d><d>4.</d></Subcolumn>
-</YColumn>
-```
-
-Subcolumn count depends on YFormat:
-
-| YFormat | Subcolumns | Naming Convention |
-|---------|------------|-------------------|
-| replicates | = Replicates | `{Title}_1`, `{Title}_2`, ... |
-| SD | 2 | `{Title}_MEAN`, `{Title}_SD` |
-| SE | 2 | `{Title}_MEAN`, `{Title}_SE` |
-| CV | 2 | `{Title}_MEAN`, `{Title}_CV` |
-| SDN | 3 | `{Title}_MEAN`, `{Title}_SD`, `{Title}_N` |
-| SEN | 3 | `{Title}_MEAN`, `{Title}_SEM`, `{Title}_N` |
-| CVN | 3 | `{Title}_MEAN`, `{Title}_CV`, `{Title}_N` |
-| low-high | 3 | `{Title}_MEAN`, `{Title}_PLUSERROR`, `{Title}_MINUSERROR` |
-| upper-lower-limits | 3 | `{Title}_MEAN`, `{Title}_UPPERLIMIT`, `{Title}_LOWERLIMIT` |
-
-### RowTitlesColumn (Contingency tables)
-
-```xml
-<RowTitlesColumn Width="81">
-  <Subcolumn>
-    <d>Male</d>
-    <d>Female</d>
-  </Subcolumn>
-</RowTitlesColumn>
-```
-
-## Cell Data (`<d>` Elements)
-
-```xml
-<d>42.5</d>                        <!-- Normal value -->
-<d>3,5</d>                         <!-- Comma decimal (3.5) -->
-<d Excluded="1">99.0</d>           <!-- Excluded/strikethrough value -->
-<d></d>                            <!-- Empty cell -->
-<d><TextAlign>Label</TextAlign></d> <!-- Text cell (non-numeric) -->
-```
-
-- Comma-as-decimal: values like `3,5` are normalized to `3.5`
-- Excluded cells have `Excluded="1"` attribute
-- Empty `<d></d>` or `<d/>` represents missing data
-
-## Other Elements
-
-### Info Block
-```xml
-<Info ID="Info0">
-  <Title>Project info 1</Title>
-  <Notes></Notes>
-  <Constant><Name>Experiment Date</Name><Value>2024-01-01</Value></Constant>
-</Info>
-```
-
-### HugeTable
-Identical to `Table` internally, just uses `<HugeTable>` tag for large datasets.
-
-### FloatingNote
-```xml
-<FloatingNote ID="#0" Width="262" Height="137" Left="451" Top="33" Expanded="1">
-  <Title>Note</Title>
-  <Content>Some annotation text</Content>
-</FloatingNote>
-```
-
-## Validation Rules
-
-1. PartsOfWhole tables must have exactly 1 YColumn
-2. Contingency tables must have a RowTitlesColumn
-3. YColumn titles must be unique within a table
-4. SD/SE/CV format requires exactly 2 subcolumns per YColumn
-5. SDN/SEN/CVN/low-high/upper-lower-limits requires exactly 3 subcolumns
-6. XY tables require XFormat in (numbers, date, error)

package/dist/skills/pzfx-io/guides/write-edit.md

@@ -1,150 +0,0 @@
-# Writing and Editing PZFX Files
-
-## Creating New PZFX Files
-
-### From CSV/TSV data
-```bash
-uv run python pzfx.py write output.pzfx \
-  --data-file data.csv \
-  --data-format csv \
-  --table-type OneWay
-```
-
-### From TSV data
-```bash
-uv run python pzfx.py write output.pzfx \
-  --data-file data.tsv \
-  --data-format tsv \
-  --table-type XY \
-  --x-format numbers \
-  --y-format replicates \
-  --replicates 2
-```
-
-### From JSON data
-```bash
-uv run python pzfx.py write output.pzfx \
-  --data-file data.json \
-  --data-format json \
-  --table-type TwoWay \
-  --y-format SD
-```
-
-### Input CSV/TSV Format
-
-Headers determine column assignment. For XY tables, the first non-ROWTITLE column becomes the X column:
-
-```csv
-ROWTITLE,Xconc,Ya,Yb
-A,1.0,100,50
-B,2.0,90,60
-C,3.0,80,70
-```
-
-For non-XY tables (XFormat=none), all columns become YColumns:
-
-```csv
-Aa,Bb
-1,100
-2,90
-3,80
-```
-
-### Dry Run (validate without writing)
-```bash
-uv run python pzfx.py write output.pzfx \
-  --data-file data.csv --data-format csv \
-  --table-type OneWay --dry-run
-```
-
-## Editing Existing Files
-
-### Modify cell values
-```bash
-uv run python pzfx.py edit <file.pzfx> \
-  --column-title "Aa" \
-  --subcolumn 0 \
-  --values '[10,20,30,40]'
-```
-
-### Edit with exclusion flags
-```bash
-uv run python pzfx.py edit <file.pzfx> \
-  --column-title "Sample" \
-  --subcolumn 0 \
-  --values '[100,90,80]' \
-  --exclude-values '[false,true,false]'
-```
-
-### Edit and save to different file
-```bash
-uv run python pzfx.py edit <file.pzfx> \
-  --column-title "Aa" \
-  --subcolumn 0 \
-  --values '[10,20,30,40]' \
-  --output modified.pzfx
-```
-
-### Preview changes without writing
-```bash
-uv run python pzfx.py edit <file.pzfx> \
-  --column-title "Aa" \
-  --subcolumn 0 \
-  --values '[10,20,30,40]' \
-  --dry-run
-```
-
-## Adding Columns
-
-### Add a single-subcolumn column
-```bash
-uv run python pzfx.py add-column <file.pzfx> \
-  --title "NewCol" \
-  --subcolumns 1 \
-  --values '[[1,2,3,4]]' \
-  --output modified.pzfx
-```
-
-### Add a multi-subcolumn column (e.g., Mean ± SD)
-```bash
-uv run python pzfx.py add-column <file.pzfx> \
-  --title "Treatment" \
-  --subcolumns 2 \
-  --values '[[100,110,120],[10,20,30]]' \
-  --output modified.pzfx
-```
-
-The `--values` is a JSON array of arrays: one inner array per subcolumn.
-
-### Dry run
-```bash
-uv run python pzfx.py add-column <file.pzfx> \
-  --title "NewCol" --subcolumns 1 \
-  --values '[[1,2,3]]' --dry-run
-```
-
-## Table Type Constraints
-
-| TableType | XFormat | YColumns | Special |
-|-----------|---------|----------|---------|
-| OneWay | none | >= 1 | Default column type |
-| TwoWay | none | >= 1 | Supports error formats |
-| XY | numbers/date/error | >= 1 | Requires XColumn |
-| Survival | numbers | >= 1 | X = time, Y = event |
-| Contingency | none | >= 1 | Requires RowTitlesColumn |
-| PartsOfWhole | none | exactly 1 | Pie chart data |
-
-## Template Preservation
-
-All write/edit operations preserve the original `<Template>` base64 blob unchanged. This ensures graphs, analyses, and layouts survive round-trips.
-
-## Round-Trip Safety
-
-Read → edit → write preserves:
-- All columns not being edited
-- XColumn and XAdvancedColumn data
-- RowTitlesColumn data
-- FloatingNote annotations
-- Table metadata (ID, type, format, replicates)
-- The complete Template blob
-- Info block data

package/dist/skills/pzfx-io/pyproject.toml

@@ -1,6 +0,0 @@
-[project]
-name = "pzfx-io-skill"
-version = "0.1.0"
-description = "GraphPad Prism PZFX file read/write skill"
-requires-python = ">=3.10"
-dependencies = []