tests: address issue #16 (fixes #16)

README.md

@@ -1,2 +1,104 @@
-# deepevents.ai
-deepevents.ai main codebase
+# AI-Powered Research Assistant Suite
+
+A self-contained toolkit that augments scientific workflows with an embedded
+analyst, reviewer, and strategist. The suite is dependency-free (Python
+standard library only) and ships with a full pytest suite.
+
+## Capabilities
+
+### 1. Auto Peer Review Reports — `scibase.review`
+
+Analyzes a manuscript and generates structured, category-based review
+suggestions:
+
+- **Clarity and coherence** checks (jargon, vague wording, sentence length)
+- **Statistical red flags** (unreported p-values, sample sizes, correlations)
+- **Methodological red flags** (e.g. missing survey response rates)
+- **Missing citations** and scope misalignment
+- **Claims vs. evidence alignment** (unsupported or thinly-evidenced claims)
+
+Templates are adaptable per domain (`molecular-biology`, `quantum-physics`,
+`clinical-trials`); unknown domains fall back to a generic template. Each
+review produces a 0-100 score.
+
+```python
+from scibase import Manuscript, generate_peer_review
+
+ms = Manuscript(
+    title="My study",
+    abstract="A significant p-value was observed.",
+    claims=[("The treatment works.", None)],
+    citations=["Smith et al., 2021"],
+    domain="clinical-trials",
+)
+report = generate_peer_review(ms)
+print(report.summary)
+print(report.score)   # 0-100
+for issue in report.issues:
+    print(issue.category, issue.severity, issue.message, issue.suggestion)
+```
+
+### 2. Reproducibility Checker — `scibase.reproducibility`
+
+Inspects a project directory and verifies:
+
+- **Pipeline presence** — source/notebook files exist
+- **Raw data present** — data files under `data/`
+- **Tests present** — `test_*` files
+- **Output consistency** — reported results match actual file contents
+- **Dependency/version integrity** — every dependency is pinned
+- **Determinism** — byte-identical outputs across `reproducibility/runs/`
+
+Each check contributes a reproducibility confidence score from 0.0 to 1.0.
+
+```python
+from pathlib import Path
+from scibase import Project, ReproducibilityChecker
+
+project = Project(
+    name="example",
+    root=Path("my_research"),
+    reported_results={"results.txt": "accuracy=0.94"},
+    dependencies={"numpy": "1.26.4", "pandas": None},  # None => unpinned
+)
+report = ReproducibilityChecker().check(project)
+print(report.score, report.reproducible)
+for issue in report.issues:
+    print(issue.code, issue.message)
+```
+
+### 3. Research Gap Finder — `scibase.gap_finder`
+
+Scans a corpus of papers and identifies:
+
+- **Under-studied intersections** — topic combinations where each topic is
+  individually active but the combination rarely (or never) co-occurs
+- **Frequently cited unresolved questions** — extracted from limitations
+  sections, ranked by citation count
+- A personalized **research opportunities feed** ranked against the user's
+  interests and project history
+
+```python
+from scibase import GapFinder, Paper
+
+papers = [
+    Paper(id="p1", title="...", topics=["CRISPR", "Alzheimer's"], citations=40,
+          open_questions=["The role of glia remains unclear."]),
+    # ...
+]
+finder = GapFinder(papers)
+for opp in finder.under_studied_intersections():
+    print(opp.topics, opp.rationale, opp.score)
+
+for question, papers, citations in finder.unresolved_questions():
+    print(question, papers, citations)
+
+feed = finder.research_opportunities_feed(
+    interests=["single-cell RNA-seq"], project_history=["CRISPR"])
+```
+
+## Running the tests
+
+```bash
+python -m pytest tests/ -q
+```

scibase/__init__.py

@@ -0,0 +1,44 @@
+"""AI-Powered Research Assistant Suite.
+
+A self-contained toolkit that augments scientific workflows with:
+
+- Auto peer review reports (:mod:`scibase.review`)
+- A reproducibility checker (:mod:`scibase.reproducibility`)
+- A research gap finder (:mod:`scibase.gap_finder`)
+
+All modules use only the Python standard library so the suite runs anywhere.
+"""
+
+from .gap_finder import GapFinder, Paper, ResearchOpportunity
+from .reproducibility import (
+    Project,
+    ReproducibilityIssue,
+    ReproducibilityReport,
+    ReproducibilityChecker,
+)
+from .review import (
+    Manuscript,
+    ReviewCategory,
+    ReviewIssue,
+    ReviewReport,
+    generate_peer_review,
+    peer_review_score,
+)
+
+__all__ = [
+    "GapFinder",
+    "Manuscript",
+    "Paper",
+    "Project",
+    "ReproducibilityChecker",
+    "ReproducibilityIssue",
+    "ReproducibilityReport",
+    "ResearchOpportunity",
+    "ReviewCategory",
+    "ReviewIssue",
+    "ReviewReport",
+    "generate_peer_review",
+    "peer_review_score",
+]
+
+__version__ = "0.1.0"