pylocuszoom 0.6.0__tar.gz → 1.0.0__tar.gz

{pylocuszoom-0.6.0 → pylocuszoom-1.0.0}/.github/workflows/ci.yml

@@ -44,14 +44,9 @@ jobs:
         run: uv sync --extra dev --extra all
 
       - name: Run tests
-        run: uv run pytest --cov=pylocuszoom --cov-report=xml
-
-      - name: Upload coverage
-        uses: codecov/codecov-action@v4
-        if: matrix.python-version == '3.11'
-        with:
-          files: ./coverage.xml
-          fail_ci_if_error: false
+        # Verbose shows pytest-randomly seed for reproduction
+        # To reproduce: pytest --randomly-seed=<seed>
+        run: uv run pytest -v
 
   build:
     runs-on: ubuntu-latest

{pylocuszoom-0.6.0 → pylocuszoom-1.0.0}/.github/workflows/publish.yml

@@ -58,8 +58,13 @@ jobs:
   update-bioconda:
     needs: publish
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
     steps:
       - uses: actions/checkout@v4
+        with:
+          ref: main
 
       - name: Update bioconda/meta.yaml
         env:
@@ -88,21 +93,71 @@ jobs:
 
           cat bioconda/meta.yaml
 
-      - name: Create Pull Request
+      - name: Create local PR for bioconda/meta.yaml
         uses: peter-evans/create-pull-request@v6
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          commit-message: "chore: update bioconda recipe for new release"
+          commit-message: "chore: update bioconda recipe for v${{ needs.publish.outputs.version }}"
           branch: bioconda-update
-          title: "Update bioconda recipe"
+          title: "Update bioconda recipe for v${{ needs.publish.outputs.version }}"
           body: |
             Automated update of bioconda/meta.yaml after PyPI release.
 
-            **Next steps:**
-            1. Review this PR
-            2. Merge to main
-            3. Copy `bioconda/meta.yaml` to your fork of bioconda-recipes
-            4. Submit PR to bioconda-recipes
+            This PR updates the local recipe. The bioconda-recipes PR is created automatically below.
           labels: |
             bioconda
             automated
+
+  submit-bioconda-pr:
+    needs: [publish, update-bioconda]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout bioconda-recipes fork
+        uses: actions/checkout@v4
+        with:
+          repository: michael-denyer/bioconda-recipes
+          token: ${{ secrets.BIOCONDA_PAT }}
+          path: bioconda-recipes
+
+      - name: Checkout pyLocusZoom
+        uses: actions/checkout@v4
+        with:
+          ref: main
+          path: pylocuszoom
+
+      - name: Update recipe and create PR
+        env:
+          GH_TOKEN: ${{ secrets.BIOCONDA_PAT }}
+          PKG_VERSION: ${{ needs.publish.outputs.version }}
+        run: |
+          cd bioconda-recipes
+
+          # Sync fork with upstream
+          git remote add upstream https://github.com/bioconda/bioconda-recipes.git
+          git fetch upstream
+          git checkout master
+          git reset --hard upstream/master
+          git push origin master --force
+
+          # Create branch for this version
+          BRANCH="pylocuszoom-$PKG_VERSION"
+          git checkout -b "$BRANCH"
+
+          # Copy updated recipe
+          mkdir -p recipes/pylocuszoom
+          cp ../pylocuszoom/bioconda/meta.yaml recipes/pylocuszoom/meta.yaml
+
+          # Commit and push
+          git add recipes/pylocuszoom/meta.yaml
+          git commit -m "Update pylocuszoom to $PKG_VERSION"
+          git push -u origin "$BRANCH" --force
+
+          # Create PR to bioconda/bioconda-recipes
+          gh pr create \
+            --repo bioconda/bioconda-recipes \
+            --title "Update pylocuszoom to $PKG_VERSION" \
+            --body "Automated update of pylocuszoom to version $PKG_VERSION.
+
+          Changes: https://github.com/michael-denyer/pyLocusZoom/releases/tag/v$PKG_VERSION" \
+            --head "michael-denyer:$BRANCH" \
+            --base master || echo "PR may already exist"

{pylocuszoom-0.6.0 → pylocuszoom-1.0.0}/.gitignore

@@ -26,3 +26,5 @@ htmlcov/
 
 # Project instructions (private)
 CLAUDE.md
+docs/plans/
+.planning/

pylocuszoom-1.0.0/.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.1
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: local
+    hooks:
+      - id: pytest-cov
+        name: pytest with coverage
+        entry: uv run python -m pytest -n auto -q
+        language: system
+        types: [python]
+        pass_filenames: false
+        always_run: true

{pylocuszoom-0.6.0 → pylocuszoom-1.0.0}/CHANGELOG.md

@@ -5,6 +5,72 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+## [1.0.0] - 2026-01-28
+
+### Added
+- Unified exception hierarchy with `PyLocusZoomError` base class
+- Custom exceptions: `ValidationError`, `DownloadError`, `LiftoverError`, `DataError`, `PLINKError`, `ConfigurationError`
+- Internal Pydantic validation for plot parameters (validates kwargs at call time)
+- Error path tests for download failures and validation edge cases
+- CI ordering validation for forest plots (`ci_lower <= effect <= ci_upper`)
+- P-value validation warnings for NaN and out-of-range values
+- Vectorized eQTL/PheWAS scatter calls for better performance
+
+### Changed
+- All validation errors now raise `ValidationError` (also a `ValueError` for backward compatibility)
+- Test randomization enabled via pytest-randomly (visible in CI output)
+- Config classes (`PlotConfig`, `StackedPlotConfig`) are now internal implementation details, not part of public API
+- Capped pytest-xdist workers at 8 to prevent terminal issues
+
+### Fixed
+- Recombination overlay now uses correct twin axis for matplotlib (no longer distorts GWAS y-limits)
+- Mb formatting now applied to gene track axis for interactive backends (Plotly/Bokeh)
+- Gene track row assignment algorithm now correctly prevents overlapping genes in same row
+- Handle all-NaN p-values in stacked plot lead SNP detection
+- Replaced broad `except Exception` blocks with specific exception types (only 1 justified fallback remains)
+- Download error handling now catches specific HTTP/network errors
+
+## [0.8.0] - 2026-01-28
+
+### Added
+- `set_yticks()` backend method for consistent y-axis labels across all backends
+- Shared `convert_latex_to_unicode()` utility for interactive backends
+- Automatic gene annotation fetching from Ensembl REST API (`auto_genes=True`)
+- `get_genes_for_region()` function to fetch genes from Ensembl with disk caching
+- `fetch_genes_from_ensembl()` and `fetch_exons_from_ensembl()` low-level API functions
+- `clear_ensembl_cache()` utility to clear cached Ensembl data
+- Support for human, mouse, rat, and any Ensembl species
+- Retry logic with exponential backoff for Ensembl API resilience
+- 5Mb region size validation (Ensembl API limit)
+- `DataFrameValidator` builder class for consistent validation across modules
+- `filter_by_region()` shared utility for chromosome/position filtering
+- `HoverDataBuilder` for constructing hover tooltips across backends
+- Backend capability system with `supports_*` properties for feature detection
+- Backend registration system with `get_backend()` and automatic fallback
+- Pre-commit hook for pytest with coverage enforcement (70% minimum)
+
+### Changed
+- Forest plot example now uses odds ratios with `null_value=1.0` (more representative)
+- PheWAS and forest plot y-axis labels now work correctly in Plotly and Bokeh backends
+- Gene track styling: arrows now 75% height and 10% wider for better proportions
+- Gene track labels increased from 5.5pt to 7pt for improved readability
+- Migrated eQTL, finemapping, phewas, and forest validation to `DataFrameValidator`
+- Plotter now uses capability-based dispatch instead of backend name checks
+- Removed empty `__init__` methods from backend classes
+- Removed unused matplotlib imports from plotter (now backend-agnostic)
+
+### Fixed
+- `load_gwas()` now forwards `**kwargs` to format-specific loaders
+- Forest plot validator now checks that effect and CI columns are numeric
+- PheWAS validator now checks that p-values are numeric and within (0, 1] range
+
+### Security
+- Tar extraction now includes path traversal protection for recombination map downloads
+
+## [0.7.0] - 2026-01-27
+
 ## [0.6.0] - 2026-01-27
 
 ### Added
@@ -140,7 +206,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - bokeh >= 3.8.2
 - kaleido >= 0.2.0
 
-[Unreleased]: https://github.com/michael-denyer/pyLocusZoom/compare/v0.6.0...HEAD
+[Unreleased]: https://github.com/michael-denyer/pyLocusZoom/compare/v0.8.0...HEAD
+[0.8.0]: https://github.com/michael-denyer/pyLocusZoom/compare/v0.7.0...v0.8.0
+[0.7.0]: https://github.com/michael-denyer/pyLocusZoom/compare/v0.6.0...v0.7.0
 [0.6.0]: https://github.com/michael-denyer/pyLocusZoom/compare/v0.5.0...v0.6.0
 [0.5.0]: https://github.com/michael-denyer/pyLocusZoom/compare/v0.4.0...v0.5.0
 [0.4.0]: https://github.com/michael-denyer/pyLocusZoom/compare/v0.3.0...v0.4.0

{pylocuszoom-0.6.0 → pylocuszoom-1.0.0}/PKG-INFO

@@ -1,15 +1,15 @@
 Metadata-Version: 2.4
 Name: pylocuszoom
-Version: 0.6.0
+Version: 1.0.0
 Summary: Publication-ready regional association plots with LD coloring, gene tracks, and recombination overlays
 Project-URL: Homepage, https://github.com/michael-denyer/pylocuszoom
 Project-URL: Documentation, https://github.com/michael-denyer/pylocuszoom#readme
 Project-URL: Repository, https://github.com/michael-denyer/pylocuszoom
-Author: Michael Denyer
+Author-email: Michael Denyer <code.denyer@gmail.com>
 License-Expression: GPL-3.0-or-later
 License-File: LICENSE.md
 Keywords: genetics,gwas,locus-zoom,locuszoom,regional-plot,visualization
-Classifier: Development Status :: 3 - Alpha
+Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Classifier: Programming Language :: Python :: 3
@@ -44,20 +44,18 @@ Requires-Dist: pyspark>=3.0.0; extra == 'spark'
 Description-Content-Type: text/markdown
 
 [![CI](https://github.com/michael-denyer/pyLocusZoom/actions/workflows/ci.yml/badge.svg)](https://github.com/michael-denyer/pyLocusZoom/actions/workflows/ci.yml)
-[![codecov](https://codecov.io/gh/michael-denyer/pyLocusZoom/graph/badge.svg)](https://codecov.io/gh/michael-denyer/pyLocusZoom)
 [![PyPI](https://img.shields.io/pypi/v/pylocuszoom)](https://pypi.org/project/pylocuszoom/)
-[![Bioconda](https://img.shields.io/conda/vn/bioconda/pylocuszoom)](https://anaconda.org/bioconda/pylocuszoom)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-red.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Matplotlib](https://img.shields.io/badge/Matplotlib-3.5+-11557c.svg)](https://matplotlib.org/)
-[![Plotly](https://img.shields.io/badge/Plotly-5.0+-3F4F75.svg)](https://plotly.com/python/)
+[![Plotly](https://img.shields.io/badge/Plotly-5.15+-3F4F75.svg)](https://plotly.com/python/)
 [![Bokeh](https://img.shields.io/badge/Bokeh-3.8+-E6526F.svg)](https://bokeh.org/)
 [![Pandas](https://img.shields.io/badge/Pandas-1.4+-150458.svg)](https://pandas.pydata.org/)
 <img src="logo.svg" alt="pyLocusZoom logo" width="120" align="right">
 # pyLocusZoom
 
-Publication-ready regional association plots with LD coloring, gene tracks, and recombination overlays.
+Designed for publication-ready GWAS visualization with regional association plots, gene tracks, eQTL, PheWAS, fine-mapping, and forest plots.
 
 Inspired by [LocusZoom](http://locuszoom.org/) and [locuszoomr](https://github.com/myles-lewis/locuszoomr).
 
@@ -68,20 +66,22 @@ Inspired by [LocusZoom](http://locuszoom.org/) and [locuszoomr](https://github.c
     - **Multi-species support**: Built-in reference data for *Canis lupus familiaris* (CanFam3.1/CanFam4) and *Felis catus* (FelCat9), or optionally provide your own for any species
     - **LD coloring**: SNPs colored by linkage disequilibrium (R²) with lead variant
     - **Gene tracks**: Annotated gene/exon positions below the association plot
-    - **Recombination rate**: Overlay showing recombination rate across region (*Canis lupus familiaris* only)
-    - **SNP labels (matplotlib)**: Automatic labeling of lead SNPs with RS ID
-    - **Tooltips (Bokeh and Plotly)**: Mouseover for detailed SNP data
+    - **Recombination rate**: Optional overlay across region (*Canis lupus familiaris* built-in, not shown in example image)
+    - **SNP labels (matplotlib)**: Automatic labeling of top SNPs by p-value (RS IDs)
+    - **Hover tooltips (Plotly and Bokeh)**: Detailed SNP data on hover
 
-![Example regional association plot](examples/regional_plot.png)
+![Example regional association plot with LD coloring and gene track](examples/regional_plot.png)
+*Regional association plot with LD coloring, gene/exon track, and top SNP labels (recombination overlay disabled in example).*
 
 2. **Stacked plots**: Compare multiple GWAS/phenotypes vertically
 3. **eQTL plot**: Expression QTL data aligned with association plots and gene tracks
 4. **Fine-mapping plots**: Visualize SuSiE credible sets with posterior inclusion probabilities
 5. **PheWAS plots**: Phenome-wide association study visualization across multiple phenotypes
 6. **Forest plots**: Meta-analysis effect size visualization with confidence intervals
-7. **Multiple charting libraries**: matplotlib (static), plotly (interactive), bokeh (dashboards)
+7. **Multiple backends**: matplotlib (publication-ready), plotly (interactive), bokeh (dashboard integration)
 8. **Pandas and PySpark support**: Works with both Pandas and PySpark DataFrames for large-scale genomics data
 9. **Convenience data file loaders**: Load and validate common GWAS, eQTL and fine-mapping file formats
+10. **Automatic gene annotations**: Fetch gene/exon data from Ensembl REST API with caching (human, mouse, rat, canine, feline, and any Ensembl species)
 
 ## Installation
 
@@ -109,15 +109,14 @@ from pylocuszoom import LocusZoomPlotter
 # Initialize plotter (loads reference data for canine)
 plotter = LocusZoomPlotter(species="canine")
 
-# Create regional plot
+# Plot with parameters passed directly
 fig = plotter.plot(
-    gwas_df,                    # DataFrame with ps, p_wald, rs columns
+    gwas_df,                        # DataFrame with ps, p_wald, rs columns
     chrom=1,
     start=1000000,
     end=2000000,
-    lead_pos=1500000,           # Highlight lead SNP
+    lead_pos=1500000,               # Highlight lead SNP
 )
-
 fig.savefig("regional_plot.png", dpi=150)
 ```
 
@@ -137,9 +136,7 @@ fig = plotter.plot(
     start=1000000,
     end=2000000,
     lead_pos=1500000,
-    ld_reference_file="genotypes.bed",  # For LD calculation
-    genes_df=genes_df,                  # Gene annotations
-    exons_df=exons_df,                  # Exon annotations
+    ld_reference_file="genotypes",      # PLINK fileset (without extension)
     show_recombination=True,            # Overlay recombination rate
     snp_labels=True,                    # Label top SNPs
     label_top_n=5,                      # How many to label
@@ -147,6 +144,8 @@ fig = plotter.plot(
     p_col="p_wald",                     # Column name for p-value
     rs_col="rs",                        # Column name for SNP ID
     figsize=(12, 8),
+    genes_df=genes_df,                  # Gene annotations
+    exons_df=exons_df,                  # Exon annotations
 )
 ```
 
@@ -163,6 +162,8 @@ Recombination maps are automatically lifted over from CanFam3.1 to CanFam4 coord
 ## Using with Other Species
 
 ```python
+from pylocuszoom import LocusZoomPlotter
+
 # Feline (LD and gene tracks, user provides recombination data)
 plotter = LocusZoomPlotter(species="feline")
 
@@ -172,37 +173,61 @@ plotter = LocusZoomPlotter(
     recomb_data_dir="/path/to/recomb_maps/",
 )
 
-# Or provide data per-plot
+# Provide data per-plot
 fig = plotter.plot(
     gwas_df,
-    chrom=1, start=1000000, end=2000000,
+    chrom=1,
+    start=1000000,
+    end=2000000,
     recomb_df=my_recomb_dataframe,
     genes_df=my_genes_df,
 )
 ```
 
+## Automatic Gene Annotations
+
+pyLocusZoom can automatically fetch gene annotations from Ensembl for any species:
+
+```python
+from pylocuszoom import LocusZoomPlotter
+
+# Enable automatic gene fetching
+plotter = LocusZoomPlotter(species="human", auto_genes=True)
+
+# No need to provide genes_df - fetched automatically
+fig = plotter.plot(gwas_df, chrom=13, start=32000000, end=33000000)
+```
+
+Supported species aliases: `human`, `mouse`, `rat`, `canine`/`dog`, `feline`/`cat`, or any Ensembl species name.
+Data is cached locally for fast subsequent plots. Maximum region size is 5Mb (Ensembl API limit).
+
 ## Backends
 
-pyLocusZoom supports multiple rendering backends:
+pyLocusZoom supports multiple rendering backends (set at initialization):
 
 ```python
+from pylocuszoom import LocusZoomPlotter
+
 # Static publication-quality plot (default)
-fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="matplotlib")
+plotter = LocusZoomPlotter(species="canine", backend="matplotlib")
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000)
 fig.savefig("plot.png", dpi=150)
 
 # Interactive Plotly (hover tooltips, pan/zoom)
-fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="plotly")
+plotter = LocusZoomPlotter(species="canine", backend="plotly")
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000)
 fig.write_html("plot.html")
 
 # Interactive Bokeh (dashboard-ready)
-fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="bokeh")
+plotter = LocusZoomPlotter(species="canine", backend="bokeh")
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000)
 ```
 
 | Backend | Output | Best For | Features |
 |---------|--------|----------|----------|
-| `matplotlib` | Static PNG/PDF/SVG | Publications, presentations | Full feature set with SNP labels |
-| `plotly` | Interactive HTML | Web reports, data exploration | Hover tooltips, pan/zoom |
-| `bokeh` | Interactive HTML | Dashboards, web apps | Hover tooltips, pan/zoom |
+| `matplotlib` | Static PNG/PDF/SVG | Publication-ready figures | Full feature set with SNP labels |
+| `plotly` | Interactive HTML | Web reports, exploration | Hover tooltips, pan/zoom |
+| `bokeh` | Interactive HTML | Dashboard integration | Hover tooltips, pan/zoom |
 
 > **Note:** All backends support scatter plots, gene tracks, recombination overlay, and LD legend. SNP labels (auto-positioned with adjustText) are matplotlib-only; interactive backends use hover tooltips instead.
 
@@ -211,6 +236,10 @@ fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="bokeh"
 Compare multiple GWAS results vertically with shared x-axis:
 
 ```python
+from pylocuszoom import LocusZoomPlotter
+
+plotter = LocusZoomPlotter(species="canine")
+
 fig = plotter.plot_stacked(
     [gwas_height, gwas_bmi, gwas_whr],
     chrom=1,
@@ -221,22 +250,29 @@ fig = plotter.plot_stacked(
 )
 ```
 
-![Example stacked plot](examples/stacked_plot.png)
+![Example stacked plot comparing two phenotypes](examples/stacked_plot.png)
+*Stacked plot comparing two phenotypes with LD coloring and shared gene track.*
 
 ## eQTL Overlay
 
 Add expression QTL data as a separate panel:
 
 ```python
+from pylocuszoom import LocusZoomPlotter
+
 eqtl_df = pd.DataFrame({
     "pos": [1000500, 1001200, 1002000],
     "p_value": [1e-6, 1e-4, 0.01],
     "gene": ["BRCA1", "BRCA1", "BRCA1"],
 })
 
+plotter = LocusZoomPlotter(species="canine")
+
 fig = plotter.plot_stacked(
     [gwas_df],
-    chrom=1, start=1000000, end=2000000,
+    chrom=1,
+    start=1000000,
+    end=2000000,
     eqtl_df=eqtl_df,
     eqtl_gene="BRCA1",
     genes_df=genes_df,
@@ -244,21 +280,28 @@ fig = plotter.plot_stacked(
 ```
 
 ![Example eQTL overlay plot](examples/eqtl_overlay.png)
+*eQTL overlay with effect direction (up/down triangles) and magnitude binning.*
 
 ## Fine-mapping Visualization
 
 Visualize SuSiE or other fine-mapping results with credible set coloring:
 
 ```python
+from pylocuszoom import LocusZoomPlotter
+
 finemapping_df = pd.DataFrame({
     "pos": [1000500, 1001200, 1002000, 1003500],
     "pip": [0.85, 0.12, 0.02, 0.45],  # Posterior inclusion probability
     "cs": [1, 1, 0, 2],               # Credible set assignment (0 = not in CS)
 })
 
+plotter = LocusZoomPlotter(species="canine")
+
 fig = plotter.plot_stacked(
     [gwas_df],
-    chrom=1, start=1000000, end=2000000,
+    chrom=1,
+    start=1000000,
+    end=2000000,
     finemapping_df=finemapping_df,
     finemapping_cs_col="cs",
     genes_df=genes_df,
@@ -266,6 +309,7 @@ fig = plotter.plot_stacked(
 ```
 
 ![Example fine-mapping plot](examples/finemapping_plot.png)
+*Fine-mapping visualization with PIP line and credible set coloring (CS1/CS2).*
 
 ## PheWAS Plots
 
@@ -286,6 +330,7 @@ fig = plotter.plot_phewas(
 ```
 
 ![Example PheWAS plot](examples/phewas_plot.png)
+*PheWAS plot showing associations across phenotype categories with significance threshold.*
 
 ## Forest Plots
 
@@ -308,19 +353,18 @@ fig = plotter.plot_forest(
 ```
 
 ![Example forest plot](examples/forest_plot.png)
+*Forest plot with effect sizes, confidence intervals, and weight-proportional markers.*
 
 ## PySpark Support
 
-For large-scale genomics data, pass PySpark DataFrames directly:
+For large-scale genomics data, convert PySpark DataFrames with `to_pandas()` before plotting:
 
 ```python
 from pylocuszoom import LocusZoomPlotter, to_pandas
 
-# PySpark DataFrame (automatically converted)
-fig = plotter.plot(spark_gwas_df, chrom=1, start=1000000, end=2000000)
-
-# Or convert manually with sampling for very large data
+# Convert PySpark DataFrame (optionally sampled for very large data)
 pandas_df = to_pandas(spark_gwas_df, sample_size=100000)
+fig = plotter.plot(pandas_df, chrom=1, start=1000000, end=2000000)
 ```
 
 Install PySpark support: `uv add pylocuszoom[spark]`
@@ -393,7 +437,7 @@ gwas_df = pd.DataFrame({
 |--------|------|----------|-------------|
 | `chr` | str or int | Yes | Chromosome identifier. Accepts "1", "chr1", or 1. The "chr" prefix is stripped for matching. |
 | `start` | int | Yes | Gene start position (bp, 1-based). Transcript start for strand-aware genes. |
-| `end` | int | Yes | Gene end position (bp, 1-based). Must be ≥ start. |
+| `end` | int | Yes | Gene end position (bp, 1-based). Must be >= start. |
 | `gene_name` | str | Yes | Gene symbol displayed in track (e.g., "BRCA1", "TP53"). Keep short for readability. |
 
 Example:
@@ -495,6 +539,7 @@ Optional:
 ## Documentation
 
 - [User Guide](docs/USER_GUIDE.md) - Comprehensive documentation with API reference
+- [Code Map](docs/CODEMAP.md) - Architecture diagram with source code links
 - [Architecture](docs/ARCHITECTURE.md) - Design decisions and component overview
 - [Example Notebook](examples/getting_started.ipynb) - Interactive tutorial
 - [CHANGELOG](CHANGELOG.md) - Version history