Read files with oxbow

.claude/settings.local.json

@@ -0,0 +1,12 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(python -m build:*)",
+      "Bash(python:*)",
+      "Bash(git rm:*)",
+      "Bash(make:*)"
+    ],
+    "deny": [],
+    "ask": []
+  }
+}

.github/workflows/docker-publish.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v1
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
 

.github/workflows/docs.yml

@@ -0,0 +1,91 @@
+name: Build and Deploy Documentation
+
+on:
+  push:
+    branches:
+      - master
+      - oxbow  # Build docs for development branch as well
+    paths:
+      - 'docs/**'
+      - 'coolbox/**'
+      - '.github/workflows/docs.yml'
+  pull_request:
+    branches:
+      - master
+    paths:
+      - 'docs/**'
+      - 'coolbox/**'
+  workflow_dispatch:  # Allow manual trigger
+
+permissions:
+  contents: write  # Required for pushing to gh-pages branch
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Fetch full history for version info
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          # Install project with documentation dependencies
+          pip install -e ".[doc]"
+
+      - name: Build documentation
+        run: |
+          cd docs
+          # Clean old build artifacts if any
+          rm -rf build/
+          # Build documentation with Sphinx
+          sphinx-build -b html source build/html -W --keep-going
+          # Create .nojekyll file to tell GitHub Pages not to ignore underscore-prefixed directories
+          touch build/html/.nojekyll
+        env:
+          SPHINXOPTS: "-W --keep-going"
+
+      - name: Check documentation
+        run: |
+          cd docs/build/html
+          echo "Documentation build completed successfully!"
+          echo "Generated files:"
+          ls -lh
+          echo ""
+          echo "Total size:"
+          du -sh .
+
+      # Only deploy when pushing to master branch
+      - name: Deploy to GitHub Pages
+        if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/build/html
+          publish_branch: gh-pages
+          force_orphan: true  # Create orphan gh-pages branch without history
+          user_name: 'github-actions[bot]'
+          user_email: 'github-actions[bot]@users.noreply.github.com'
+          commit_message: 'Deploy documentation from ${{ github.sha }}'
+
+      - name: Upload documentation artifact
+        if: github.event_name == 'pull_request'
+        uses: actions/upload-artifact@v4
+        with:
+          name: documentation
+          path: docs/build/html
+          retention-days: 7

.github/workflows/python-package-conda.yml

@@ -10,9 +10,9 @@ jobs:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
     - name: Update Conda

.github/workflows/python-publish.yml

@@ -1,5 +1,5 @@
 # This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
 
 name: Upload Python Package
 
@@ -14,19 +14,21 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
-    - name: Install dependencies
+    - name: Install build dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
+        pip install build twine
+    - name: Build package
+      run: |
+        python -m build
+    - name: Publish to PyPI
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
       run: |
-        python setup.py sdist bdist_wheel
         twine upload dist/*

.gitignore

@@ -82,6 +82,15 @@ instance/
 
 # Sphinx documentation
 docs/build/
+# Sphinx generated HTML files in docs root (old structure)
+# These should now be built by CI/CD and not committed
+docs/*.html
+docs/*.js
+docs/_sources/
+docs/_static/
+docs/_images/
+docs/_gallery/
+docs/objects.inv
 
 # PyBuilder
 target/

coolbox/__init__.py

@@ -1 +1 @@
-__version__ = '0.3.9'
+__version__ = '0.4.0'

coolbox/__main__.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python
+
+from coolbox.cli import CLI
+import fire
+
+
+def main():
+    fire.Fire(CLI)
+
+
+if __name__ == "__main__":
+    main()

coolbox/core/browser/base.py

@@ -205,7 +205,9 @@ def preload_imgs(self, directions):
         Preloading images to self.fig_cache.
 
         Can load image in one of 4 directions:
-            left, right, zoom-in, zoom-out
+
+        - left, right, zoom-in, zoom-out
+
         or load all directions.
         """
 

coolbox/core/coverage/__init__.py

@@ -17,3 +17,10 @@
 HistCoverage = track_to_coverage(Hist)
 BigWigCoverage = track_to_coverage(BigWig)
 BedGraphCoverage = track_to_coverage(BedGraph)
+
+__all__ = [
+    "HighLights", "HighLightsFromFile", "Vlines", "VlinesFromFile", "HLines",
+    "TADCoverage", "ArcsCoverage", "PairsCoverage", "BEDPECoverage", "HiCPeaksCoverage",
+    "HistCoverage", "BigWigCoverage", "BedGraphCoverage",
+    "track_to_coverage", 
+]

coolbox/core/coverage/base.py

@@ -114,6 +114,9 @@ def check_track_type(self, allow):
             )
             raise ValueError(msg)
 
+    def fetch_data(self, gr: GenomeRange, **kwargs):
+        raise NotImplementedError
+
 
 class CoverageStack(object):
     """
@@ -189,14 +192,18 @@ def plot(self, ax, gr: GenomeRange, **kwargs):
             self.track_instance.properties['height'] = self.track.properties['height']
         self.track_instance.plot(ax, gr, **kwargs)
 
+    def fetch_data(self, gr: GenomeRange, **kwargs):
+        return self.track_instance.fetch_data(gr, **kwargs)
+
     # TODO , other track methods
     cov_class = type(
         track_class.__name__ + "Coverage",
         (Coverage,),
         {
             "__init__": init,
             "__doc__": track_class.__doc__,
-            "plot": plot
+            "plot": plot,
+            "fetch_data": fetch_data
         }
     )
 

coolbox/core/coverage/highlights.py

@@ -1,10 +1,9 @@
 from coolbox.utilities import (
-    opener, ReadBed,
-    Interval, IntervalTree,
     rgb2hex,
     get_logger, GenomeRange,
     to_gr
 )
+from coolbox.utilities.reader.tab import get_indexed_tab_reader
 from .base import Coverage
 
 log = get_logger(__name__)
@@ -13,24 +12,10 @@
 class _Highlights(object):
     DEFAULT_COLOR = '#ff5d0f'
 
-    def fetch_data(self, gr: GenomeRange, **kwargs):
-        gr = to_gr(gr)
-        if gr.chrom not in list(self.interval_tree):
-            gr.change_chrom_names()
-
-        return [
-            (region.begin, region.end, region.data)
-            for region in sorted(
-                self.interval_tree[gr.chrom][gr.start - 10000 : gr.end + 10000]
-            )
-        ]
-
     def plot(self, ax, gr: GenomeRange, **kwargs):
-
         regions = self.fetch_data(gr, **kwargs)
-
         for (start, end, color) in regions:
-            if self.properties['color'] != 'bed_rgb':
+            if self.properties['color'] != 'rgb':
                 color = self.properties['color']
             if type(color) is not str:
                 color = rgb2hex(*color)
@@ -55,10 +40,11 @@ class HighLightsFromFile(Coverage, _Highlights):
     ----------
     file_ : str
         Path to the file.
+        Contains columns: chrom, start, end, color
 
     color : str, optional
         High light region color,
-        use 'bed_rgb' for specify color from the file, default 'bed_rgb'.
+        use 'rgb' for specify color from the file, default 'rgb'.
 
     alpha : float, optional
         High light region alpha value, default 0.1.
@@ -81,11 +67,12 @@ class HighLightsFromFile(Coverage, _Highlights):
     name : str, optional
         The name of thr Coverage.
     """
+    FIELDS = ['chrom', 'start', 'end', 'color']
 
     def __init__(self, file_, **kwargs):
         properties_dict = {
             "file": file_,
-            "color": "bed_rgb",
+            "color": "rgb",
             "alpha": 0.1,
             "border_line": False,
             "border_line_style": "dashed",
@@ -95,30 +82,13 @@ def __init__(self, file_, **kwargs):
         }
         properties_dict.update(kwargs)
         super().__init__(properties_dict)
-        self.interval_tree = self.__process_bed()
-
-    def __process_bed(self):
-        bed = ReadBed(opener(self.properties['file']))
-
-        if self.properties['color'] == 'bed_rgb' and bed.file_type not in ['bed12', 'bed9']:
-            log.warning("*WARNING* Color set to 'bed_rgb', but bed file does not have the rgb field. The color has "
-                        "been set to {}".format(HighLights.DEFAULT_COLOR))
-            self.properties['color'] = HighLights.DEFAULT_COLOR
-
-        interval_tree = {}
-
-        for intval in bed:
+        self.reader = get_indexed_tab_reader(
+            self.properties['file'],
+            columns=HighLightsFromFile.FIELDS)
 
-            if intval.chromosome not in interval_tree:
-                interval_tree[intval.chromosome] = IntervalTree()
-
-            if self.properties['color'] == 'bed_rgb':
-                color = intval.rgb
-            else:
-                color = self.properties['color']
-            interval_tree[intval.chromosome].add(Interval(intval.start, intval.end, color))
-
-        return interval_tree
+    def fetch_data(self, gr: GenomeRange, **kwargs):
+        df = self.reader.query_var_chr(gr, **kwargs)
+        return df[['start', 'end', 'color']].values.tolist()
 
 
 class HighLights(Coverage, _Highlights):
@@ -195,3 +165,15 @@ def __intervaltree_from_list(self, region_list):
             itree.setdefault(chr_, IntervalTree())
             itree[chr_][grange.start:grange.end + 1] = grange
         return itree
+
+    def fetch_data(self, gr: GenomeRange, **kwargs):
+        gr = to_gr(gr)
+        if gr.chrom not in list(self.interval_tree):
+            gr = gr.change_chrom_names()
+
+        return [
+            (region.begin, region.end, region.data)
+            for region in sorted(
+                self.interval_tree[gr.chrom][gr.start - 10000 : gr.end + 10000]
+            )
+        ]