opencode-skills-collection 4.1.14 → 4.1.16

package/bundled-skills/scanpy/scripts/qc_analysis.py

@@ -0,0 +1,200 @@
+#!/usr/bin/env python3
+"""
+Quality Control Analysis Script for Scanpy
+
+Performs comprehensive quality control on single-cell RNA-seq data,
+including calculating metrics, generating QC plots, and filtering cells.
+
+Usage:
+    python qc_analysis.py <input_file> [--output <output_file>]
+"""
+
+import argparse
+import scanpy as sc
+import matplotlib.pyplot as plt
+
+
+def calculate_qc_metrics(adata, mt_threshold=5, min_genes=200, min_cells=3):
+    """
+    Calculate QC metrics and filter cells/genes.
+
+    Parameters:
+    -----------
+    adata : AnnData
+        Annotated data matrix
+    mt_threshold : float
+        Maximum percentage of mitochondrial genes (default: 5)
+    min_genes : int
+        Minimum number of genes per cell (default: 200)
+    min_cells : int
+        Minimum number of cells per gene (default: 3)
+
+    Returns:
+    --------
+    AnnData
+        Filtered annotated data matrix
+    """
+    # Identify mitochondrial genes (assumes gene names follow standard conventions)
+    adata.var['mt'] = adata.var_names.str.startswith(('MT-', 'mt-', 'Mt-'))
+
+    # Calculate QC metrics
+    sc.pp.calculate_qc_metrics(adata, qc_vars=['mt'], percent_top=None,
+                                log1p=False, inplace=True)
+
+    print("\n=== QC Metrics Summary ===")
+    print(f"Total cells: {adata.n_obs}")
+    print(f"Total genes: {adata.n_vars}")
+    print(f"Mean genes per cell: {adata.obs['n_genes_by_counts'].mean():.2f}")
+    print(f"Mean counts per cell: {adata.obs['total_counts'].mean():.2f}")
+    print(f"Mean mitochondrial %: {adata.obs['pct_counts_mt'].mean():.2f}")
+
+    return adata
+
+
+def generate_qc_plots(adata, output_prefix='qc'):
+    """
+    Generate comprehensive QC plots.
+
+    Parameters:
+    -----------
+    adata : AnnData
+        Annotated data matrix
+    output_prefix : str
+        Prefix for saved figure files
+    """
+    # Create figure directory if it doesn't exist
+    import os
+    os.makedirs('figures', exist_ok=True)
+
+    # Violin plots for QC metrics
+    sc.pl.violin(adata, ['n_genes_by_counts', 'total_counts', 'pct_counts_mt'],
+                 jitter=0.4, multi_panel=True, save=f'_{output_prefix}_violin.pdf')
+
+    # Scatter plots
+    sc.pl.scatter(adata, x='total_counts', y='pct_counts_mt',
+                  save=f'_{output_prefix}_mt_scatter.pdf')
+    sc.pl.scatter(adata, x='total_counts', y='n_genes_by_counts',
+                  save=f'_{output_prefix}_genes_scatter.pdf')
+
+    # Highest expressing genes
+    sc.pl.highest_expr_genes(adata, n_top=20,
+                              save=f'_{output_prefix}_highest_expr.pdf')
+
+    print(f"\nQC plots saved to figures/ directory with prefix '{output_prefix}'")
+
+
+def filter_data(adata, mt_threshold=5, min_genes=200, max_genes=None,
+                min_counts=None, max_counts=None, min_cells=3):
+    """
+    Filter cells and genes based on QC thresholds.
+
+    Parameters:
+    -----------
+    adata : AnnData
+        Annotated data matrix
+    mt_threshold : float
+        Maximum percentage of mitochondrial genes
+    min_genes : int
+        Minimum number of genes per cell
+    max_genes : int, optional
+        Maximum number of genes per cell
+    min_counts : int, optional
+        Minimum number of counts per cell
+    max_counts : int, optional
+        Maximum number of counts per cell
+    min_cells : int
+        Minimum number of cells per gene
+
+    Returns:
+    --------
+    AnnData
+        Filtered annotated data matrix
+    """
+    n_cells_before = adata.n_obs
+    n_genes_before = adata.n_vars
+
+    # Filter cells
+    sc.pp.filter_cells(adata, min_genes=min_genes)
+    if max_genes:
+        adata = adata[adata.obs['n_genes_by_counts'] < max_genes, :]
+    if min_counts:
+        adata = adata[adata.obs['total_counts'] >= min_counts, :]
+    if max_counts:
+        adata = adata[adata.obs['total_counts'] < max_counts, :]
+
+    # Filter by mitochondrial percentage
+    adata = adata[adata.obs['pct_counts_mt'] < mt_threshold, :]
+
+    # Filter genes
+    sc.pp.filter_genes(adata, min_cells=min_cells)
+
+    print(f"\n=== Filtering Results ===")
+    print(f"Cells: {n_cells_before} -> {adata.n_obs} ({adata.n_obs/n_cells_before*100:.1f}% retained)")
+    print(f"Genes: {n_genes_before} -> {adata.n_vars} ({adata.n_vars/n_genes_before*100:.1f}% retained)")
+
+    return adata
+
+
+def main():
+    parser = argparse.ArgumentParser(description='QC analysis for single-cell data')
+    parser.add_argument('input', help='Input file (h5ad, 10X mtx, csv, etc.)')
+    parser.add_argument('--output', default='qc_filtered.h5ad',
+                        help='Output file name (default: qc_filtered.h5ad)')
+    parser.add_argument('--mt-threshold', type=float, default=5,
+                        help='Max mitochondrial percentage (default: 5)')
+    parser.add_argument('--min-genes', type=int, default=200,
+                        help='Min genes per cell (default: 200)')
+    parser.add_argument('--min-cells', type=int, default=3,
+                        help='Min cells per gene (default: 3)')
+    parser.add_argument('--skip-plots', action='store_true',
+                        help='Skip generating QC plots')
+
+    args = parser.parse_args()
+
+    # Configure scanpy
+    sc.settings.verbosity = 2
+    sc.settings.set_figure_params(dpi=300, facecolor='white')
+    sc.settings.figdir = './figures/'
+
+    print(f"Loading data from: {args.input}")
+
+    # Load data based on file extension
+    if args.input.endswith('.h5ad'):
+        adata = sc.read_h5ad(args.input)
+    elif args.input.endswith('.h5'):
+        adata = sc.read_10x_h5(args.input)
+    elif args.input.endswith('.csv'):
+        adata = sc.read_csv(args.input)
+    else:
+        # Try reading as 10X mtx directory
+        adata = sc.read_10x_mtx(args.input)
+
+    print(f"Loaded data: {adata.n_obs} cells x {adata.n_vars} genes")
+
+    # Calculate QC metrics
+    adata = calculate_qc_metrics(adata, mt_threshold=args.mt_threshold,
+                                  min_genes=args.min_genes, min_cells=args.min_cells)
+
+    # Generate QC plots (before filtering)
+    if not args.skip_plots:
+        print("\nGenerating QC plots (before filtering)...")
+        generate_qc_plots(adata, output_prefix='qc_before')
+
+    # Filter data
+    adata = filter_data(adata, mt_threshold=args.mt_threshold,
+                        min_genes=args.min_genes, min_cells=args.min_cells)
+
+    # Generate QC plots (after filtering)
+    if not args.skip_plots:
+        print("\nGenerating QC plots (after filtering)...")
+        generate_qc_plots(adata, output_prefix='qc_after')
+
+    # Save filtered data
+    print(f"\nSaving filtered data to: {args.output}")
+    adata.write_h5ad(args.output)
+
+    print("\n=== QC Analysis Complete ===")
+
+
+if __name__ == "__main__":
+    main()

package/bundled-skills/scarcity-urgency-psychologist/SKILL.md

@@ -1,16 +1,22 @@
 ---
 name: scarcity-urgency-psychologist
-description: "One sentence - what this skill does and when to invoke it"
+description: "Design honest scarcity and urgency messaging when verified inventory, capacity, or deadlines justify a timely decision."
 risk: safe
 source: community
 date_added: "2026-04-04"
 ---
-You are a **Behavioral Psychologist specializing in motivation, reactance, and temporal decision-making**. Your task is to engineer genuine scarcity and urgency mechanics that create real psychological motivation to act now.
+Use a marketing planning and audience-research lens. Your task is to engineer genuine scarcity and urgency mechanics that create real psychological motivation to act now.
 
 ## When to Use
 - Use when you need urgency or scarcity messaging that feels credible instead of manipulative.
 - Use when timing, stock, access, or deadlines should push action without damaging trust.
 
+## Evidence and scope
+
+Use observed audience research and verified product facts. Psychological interpretations and the author-year references below are inherited conceptual context, not validated evidence for this exact workflow or a guaranteed conversion effect. Before using a scientific claim externally, verify the actual publication, method and applicability; omit unsupported claims. This is marketing planning, not clinical diagnosis. Do not infer sensitive traits or exploit vulnerabilities.
+
+Original contribution: [PR 451](https://github.com/sickn33/agentic-awesome-skills/pull/451) by MMEHDI0606; [immutable source snapshot](https://github.com/MMEHDI0606/antigravity-awesome-skills/blob/9c61357e3e6bb167946036f52ac1e28fc82e04d0/skills/scarcity-urgency-psychologist/SKILL.md). This identifies the contributed instructions, not scientific validation or a new upstream endorsement.
+
 ## CONTEXT GATHERING
 
 Before designing scarcity, establish:
@@ -31,23 +37,23 @@ Scarcity works when the audience believes the opportunity is genuinely limited a
 
 **Step 1 - Verify the scarcity is real**
 Check whether the limit is inventory, capacity, time, access, or attention.
-*Research basis: fake scarcity destroys trust when detected (Omar et al., 2021; Wang et al., 2025).*
+*Planning hypothesis (verify before presenting as research): fake scarcity destroys trust when detected (Omar et al., 2021; Wang et al., 2025).*
 
 **Step 2 - Decide whether urgency is needed**
 Not every scarce offer needs a deadline.
-*Research basis: urgency is effective only when delay has a real cost (temporal discounting research; Brehm).*
+*Planning hypothesis (verify before presenting as research): urgency is effective only when delay has a real cost (temporal discounting research; Brehm).*
 
 **Step 3 - Match the frame to cynicism**
 Use softer language when the audience is skeptical and stronger language when the limit is obvious.
-*Research basis: reactance increases as the audience perceives pressure or manipulation (Grandpre et al., 2003; Quick et al., 2018).*
+*Planning hypothesis (verify before presenting as research): reactance increases as the audience perceives pressure or manipulation (Grandpre et al., 2003; Quick et al., 2018).*
 
 **Step 4 - State the consequence clearly**
 Explain what happens if the user waits.
-*Research basis: visible opportunity cost increases action more than vague urgency (Houdek, 2016; Suvarna & Malagi, 2025).*
+*Planning hypothesis (verify before presenting as research): visible opportunity cost increases action more than vague urgency (Houdek, 2016; Suvarna & Malagi, 2025).*
 
 **Step 5 - Keep the tone calm**
 Avoid panic language.
-*Research basis: high-pressure scarcity can trigger avoidance and doubt (Brehm; Lavoie & Quick, 2013).*
+*Planning hypothesis (verify before presenting as research): high-pressure scarcity can trigger avoidance and doubt (Brehm; Lavoie & Quick, 2013).*
 
 ## DECISION MATRIX
 
@@ -95,7 +101,7 @@ The line between persuasion and manipulation is making a real opportunity timely
 
 ## SKILL CHAINING
 
-Before invoking this skill, the agent should have completed:
+Optional context from related skills (equivalent supplied research is sufficient; do not create a prerequisite cycle):
 - [ ] `@loss-aversion-designer`
 - [ ] `@trust-calibrator`
 
@@ -119,6 +125,8 @@ Before finalizing output, the agent asks:
 
 > Rewrite this urgency message so the deadline is credible, specific, and persuasive without manipulation.
 
+**Illustrative output:** If an authorized inventory check confirms three seats at a stated time, mention that snapshot; if the quantity or deadline cannot be verified, omit the urgency claim.
+
 ## Limitations
 - Use this skill only when the task clearly matches the scope described above.
 - Do not treat the output as a substitute for environment-specific validation, testing, or expert review.

package/bundled-skills/score-eval/SKILL.md

@@ -5,31 +5,42 @@ source_repo: neondatabase/agent-skills
 source_type: official
 source: neondatabase
 date_added: '2026-09-21'
-risk: unknown
-description: Imported skill `score-eval` from upstream source.
+risk: critical
+description: "Use when scoring an evaluation diff against a supplied rubric and baseline fixture: retain evidence for detected/fixed findings and report unscorable or unexecuted checks."
 ---
+
+# Score an Evaluation Diff
+
 ## When to Use
+- You have an evaluation diff, rubric, and baseline fixture and need to assess detected and fixed problems.
 
-- Use when this upstream workflow matches the user's stated goal.
-- Use when the task requires the procedures documented in this skill.
+## Required Inputs
+- The diff file to score.
+- The evaluation rubric, including each problem ID, scoring questions, and output columns.
+- The original fixture directory or immutable baseline revision.
+- An authorized destination for the results.
 
-Score the eval diff at $ARGUMENTS against the eval rubric.
+These are inputs from the evaluation project, not files bundled in this catalog entry. Resolve the paths from the supplied task; do not assume eval-rubric.md, fixtures/hono-drizzle-app/, or results.csv exists in the skill directory.
 
-1. Read the diff file at the path provided
-2. Read the eval rubric at eval-rubric.md
-3. Read the original fixture app in fixtures/hono-drizzle-app/ for comparison
-4. For each problem P1-P5, answer the Detected? and Fixed? questions from the rubric as yes or no
-5. Append a row to results.csv — fill in all fields you can determine from the diff and context. Leave fields you can't determine empty.
+## Procedure
+1. Confirm all required inputs are readable and refer to the same evaluation task. If a rubric or baseline is missing, stop scoring and name the missing input.
+2. Read the diff, rubric, and relevant baseline files. Use the rubric's actual problem IDs; do not invent P1-P5 or a replacement grading policy.
+3. For each problem, answer the rubric's detected/fixed questions and cite concrete diff or file evidence. Record uncertainty using the rubric's permitted representation; do not substitute absence of evidence for a verified fix.
+4. Run only the task's authorized validation when required for a fixed claim. Review fixture code and scripts before execution, isolate them from production credentials/data, and honor resource/network limits. A supplied fixture is not automatically trusted. Clearly distinguish static inspection from executed checks.
+5. Prepare one result row using the rubric's exact column schema. Preserve existing results; append only to the supplied destination and leave unsupported fields empty if the rubric permits it.
+6. Report the completed row, evidence, and any unexecuted checks or unscorable questions.
 
+## Example
+> Score work/change.diff against work/rubric.md and the baseline fixture, then append the reviewed row to work/results.csv. Do not infer missing grading criteria.
 
-## Examples
+## Risk boundary
 
-```text
-User: Apply this skill to my current task.
-Assistant: Follow the workflow in this skill, cite limitations, and ask before risky steps.
-```
+The critical label covers optional execution of supplied fixture code and appending
+to evaluation results. Static reading alone stays read-only. Neither a diff nor a
+rubric authorizes production changes, installing dependencies or running arbitrary
+fixture scripts outside the evaluation scope.
 
 ## Limitations
-
-- Imported upstream skill; verify credentials, permissions, and safety boundaries before execution.
-- Does not replace environment-specific validation, testing, or maintainer review.
+- This skill does not provide the upstream evaluation fixture or rubric.
+- Scoring depends on the supplied rubric; a diff alone does not prove runtime behavior.
+- Result writes and test execution must remain within the user's authorized evaluation scope.

package/bundled-skills/search-specialist/SKILL.md

@@ -21,7 +21,6 @@ date_added: "2026-02-27"
 - Clarify goals, constraints, and required inputs.
 - Apply relevant best practices and validate outcomes.
 - Provide actionable steps and verification.
-- If detailed examples are required, open `resources/implementation-playbook.md`.
 
 You are a search specialist expert at finding and synthesizing information from the web.
 

package/bundled-skills/security-bluebook-builder/SKILL.md

@@ -5,6 +5,14 @@ risk: safe
 source: community
 date_added: "2026-09-04"
 ---
+## Supporting material availability
+
+This catalog copy contains the inline guidance below, but does not include the following supporting paths. They are external prerequisites, not bundled files:
+
+- `<support-root>/references/bluebook_template.md`
+
+Ask for the original supporting material or an existing installation before using a step that depends on these paths; this catalog does not identify a verified download source for them. Resolve each path relative to that installation, inspect its contents, and verify any applicable license and execution prerequisites. Do not run a command or claim a referenced procedure was followed until its required file exists. Do not fabricate the missing scripts or treat an unrelated file with the same name as equivalent. Independent steps fully documented here can proceed within the user’s authorized scope; report any dependent step as unavailable.
+
 
 # Security Bluebook Builder
 
@@ -51,7 +59,7 @@ Confirm the Blue Book includes:
 - Security gates + go/no-go checklist
 
 ## Resources
-- `references/bluebook_template.md`
+- `<support-root>/references/bluebook_template.md`
 
 ## Example