Updated docs and tests

Author: kcleal

docs/assets/images/splash.png

@@ -203,13 +203,10 @@ Draw the visualization to the raster surface. Caches state for using with intera
 **Returns:**
 - `Gw`: Self for method chaining
 
-### `draw_image(stream=True)`
+### `draw_image()`
 
 Draw the visualization and return it as a PIL Image.
 
-**Parameters:**
-- `stream` (bool, optional): Whether to use streaming mode for drawing
-
 **Returns:**
 - `PIL.Image`: The visualization as a PIL Image
 

docs/assets/images/splash1.png

@@ -13,20 +13,26 @@ nav_order: 2
 pip install gwplot
 ```
 
-### Building from Source (macOS)
+### Building from Source 
 
+#### MacOS
+
+Install dependencies using homebrew (shown), or conda.
 ```bash
-# Install dependencies with Homebrew
 brew install fontconfig freetype glfw htslib jpeg-turbo libpng xz
+```
 
-# Clone repository with submodules
+Clone repository with GW submodule, install using pip
+```bash
 git clone --recursive https://github.com/kcleal/gwplot
 cd gwplot
+pip install -e . -v  # Use editable mode for development
 
-# Install development version
-pip install -r requirements.txt
-pip install -e . -v
-
-# Run tests
+# Run tests, need -e option when using pip install
 python -m unittest discover -s ./tests
 ```
+
+#### Linux
+
+For linux users, building is more convoluted. You will need to install htslib, glfw and freetype. An
+example build script can be found in `ci/manylinux-build-deps`

docs/docs/API.md

@@ -9,16 +9,22 @@ description: "gwplot: a python library for plotting genomic sequencing data"
 
 `gwplot` is a plotting library for genomics data and a Python interface to GW, a high-performance interactive genome browser.
 
+Install using:
+
+```bash
+pip install gwplot
+```
+
 <br>
 
-![Alt text](/assets/images/splash.png "Gwplot")
+![Alt text](/assets/images/splash1.png "Gwplot")
 
 
 ## Features
 
 - **High-performance visualization** of genomic data including BAM files, VCF, BED, and other formats
-- **Customizable themes and colors** for creating publication-quality visualizations
-- **Multi-region support** for comparative genomics
+- **Customizable themes and colors** for creating high-quality visualizations
+- **Multi-regions and data tracks** for comparative genomics
 - **Interactive mode** for dynamic exploration of genomic regions
 - **Flexible output formats** including PNG, JPEG, and NumPy arrays for further processing
 - **Built-in access** to common reference genomes
@@ -36,5 +42,5 @@ gw.add_bam("sample.bam")
 gw.add_region("chr1", 1000000, 1100000)
 
 # Draw and save an image
-gw.draw().save_png("visualization.png")
+gw.draw().save_png("region.png")
 ```

docs/docs/Install.md

@@ -1673,27 +1673,19 @@ cdef class Gw:
         self.thisptr.runDrawNoBuffer()
         return self
 
-    def draw_image(self, stream=True):
+    def draw_image(self):
         """
         Draw the visualization and return it as a PIL Image.
 
-        Parameters
-        ----------
-        stream : bool, optional
-            Whether to use streaming mode for drawing
-
         Returns
         -------
         PIL.Image
             The visualization as a PIL Image
         """
-        if stream:
-            self.draw_stream()
-        else:
-            if not self.raster_surface_created:
-                self.make_raster_surface()
-            self.thisptr.processed = False
-            self.runDraw()
+        if not self.raster_surface_created:
+            self.make_raster_surface()
+        self.thisptr.processed = False
+        self.thisptr.runDrawNoBuffer()
         return Image.fromarray(self.array())
 
     def view_region(self, chrom, start, end):

docs/index.md

@@ -1,7 +1,7 @@
 
 import unittest
 import os
-from gwplot import Gw, GwPaint
+from gwplot import Gw, GwPalette
 import numpy as np
 import matplotlib.pyplot as plt
 from PIL import Image
@@ -62,7 +62,7 @@ def test_remove_region(self):
 
     def test_run_save_png(self):
         gw.draw()
-        gw.raster_to_png("out.png")
+        gw.save_png("out.png")
         print("test_run_save_png done")
 
     def test_to_ndarray(self):
@@ -72,7 +72,8 @@ def test_to_ndarray(self):
 
     def test_run_draw_no_buffer(self):
         gw.apply_command("ylim 30")
-        gw.draw_stream()
+        gw.set_low_memory(1)
+        gw.draw()
         img = Image.fromarray(gw.array())
         plt.figure()
         plt.imshow(img)
@@ -87,31 +88,31 @@ def test_run_draw_image(self):
         print("test_run_draw_image done")
 
     def test_set_paint(self):
-        gw.set_paint_ARBG(GwPaint.fcNormal, 255, 0, 0, 255)
+        gw.set_paint_ARBG(GwPalette.NORMAL_READ, 255, 0, 0, 255)
         print("test_set_paint done")
 
     def test_set_repaint(self):
-        gw.set_paint_ARBG(GwPaint.bgPaint, 55, 255, 0, 0)
+        gw.set_paint_ARBG(GwPalette.BACKGROUND, 55, 255, 0, 0)
         gw.draw()
-        gw.raster_to_png("out2.png")
+        gw.save_png("out2.png")
         print("test_set_repaint done")
 
-    def test_pysam(self):
-        if not have_pysam:
-            return
-        af = pysam.AlignmentFile(root + "/small.bam")
-        region = ("chr1", 1, 20000)
-        bam_itr = af.fetch(*region)
-
-        gw.clear_alignments()
-        gw.clear_regions()
-        gw.add_region(*region)
-
-        gw.add_pysam_alignments(bam_itr)
-
-        print(dir(bam_itr))
-        print(bam_itr)
-        print("test_pysam done")
+    # def test_pysam(self):
+    #     if not have_pysam:
+    #         return
+    #     af = pysam.AlignmentFile(root + "/small.bam")
+    #     region = ("chr1", 1, 20000)
+    #     bam_itr = af.fetch(*region)
+    #
+    #     gw.clear_alignments()
+    #     gw.clear_regions()
+    #     gw.add_region(*region)
+    #
+    #     gw.add_pysam_alignments(bam_itr)
+    #
+    #     print(dir(bam_itr))
+    #     print(bam_itr)
+    #     print("test_pysam done")
 
 def main():
     unittest.main()