Added numpy and pysam as hard dependencies

Author: kcleal

docs/docs/Install.md

@@ -16,11 +16,7 @@ Base installation:
 pip install gwplot
 ```
 
-`gwplot` also has a few optional runtime dependencies including `numpy`, `pillow` and `pysam`. Fetch them using:
-
-```bash
-pip install gwplot[all]
-```
+`gwplot` also has `pillow` as an optional runtime dependency.
 
 ### Building from Source 
 

docs/docs/api/gw-saving-images.md

@@ -194,9 +194,6 @@ Convert the pixel data to a numpy array using zero-copy interface.
 **Returns:**
 - `numpy.ndarray` or `None`: RGBA image data as a 3D numpy array (height × width × 4) or None if the raster surface hasn't been created
 
-**Raises:**
-- `ImportError`: If Numpy could not be imported
-
 **Example:**
 ```python
 # Get the visualization as a numpy array

gwplot/interface.pyx

@@ -2,36 +2,18 @@
 import os
 import json
 from typing import Any, Dict, List, Optional, Tuple
-from libcpp.string cimport string
-from libcpp.vector cimport vector
-
-cdef bint HAVE_NUMPY = False
+import numpy as np
 cdef bint HAVE_PILLOW = False
-cdef bint HAVE_PYSAM = False
-try:
-    import numpy as np
-    cimport numpy as np
-    np.import_array()
-    HAVE_NUMPY = True
-except (ImportError, ModuleNotFoundError):
-    pass
-
 try:
     from PIL import Image
     HAVE_PILLOW = True
 except (ImportError, ModuleNotFoundError):
     pass
 
-cdef class AlignedSegment:
-    pass
-
-try:
-    from pysam.libcalignedsegment cimport AlignedSegment
-    HAVE_PYSAM = True
-except (ImportError, ModuleNotFoundError):
-    pass
-
+from libcpp.string cimport string
+from libcpp.vector cimport vector
 from cpython.bytes cimport PyBytes_FromStringAndSize
+from pysam.libcalignedsegment cimport AlignedSegment
 
 __all__ = ["Gw", "GwPalette"]
 
@@ -1496,15 +1478,12 @@ cdef class Gw:
 
         Raises
         ------
-        ImportError
-            If pysam could not be imported
         IndexError
             If the region_index or bam_index are out of range
         UserWarning
             If any normal collections are already present in the Gw object
         """
-        if not HAVE_PYSAM:
-            raise ImportError("Pysam could not be imported")
+
         if not self.raster_surface_created:
             self.make_raster_surface()
         cdef bint needs_clearing = <bint>False
@@ -1974,8 +1953,6 @@ cdef class Gw:
             RGBA image data as a 3D numpy array (height × width × 4)
             or None if the raster surface hasn't been created
         """
-        if not HAVE_NUMPY:
-            raise ImportError("Numpy could not be imported")
         if not self.raster_surface_created:
             return None
         #return np.array(self).reshape(self.canvas_height, self.canvas_width, 4)

pyproject.toml

@@ -17,20 +17,12 @@ classifiers = [
     "Operating System :: POSIX :: Linux",
     "Operating System :: MacOS :: MacOS X",
 ]
-dependencies = [ "setuptools>=61.0" ]
+dependencies = [ "setuptools>=61.0", "numpy>=1.19.3", "pysam>=0.21.0" ]
 
 [project.optional-dependencies]
-test = ["matplotlib",
-    "Flask",
-    "pysam>=0.21.0",
-    "numpy>=1.19.3",
-    "pillow"]
-pysam = ["pysam>=0.21.0"]
-numpy = ["numpy>=1.19.3"]
+test = ["matplotlib", "Flask", "pillow"]
 pillow = ["pillow"]
-all = ["pysam>=0.21.0",
-    "numpy>=1.19.3",
-    "pillow"]
+all = ["matplotlib", "Flask", "pillow"]
 
 [tool.setuptools]
 packages = ["gwplot"]