Initial run of pre-commit

.pre-commit-config.yaml

@@ -5,8 +5,9 @@ exclude: |
   (?x)(
     ^scripts/disBatch/|
     ^tests/Mini_N64_L32/|
-    \.asdf$
-  )'
+    \.asdf$|
+    \.svg$
+  )
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks

CHANGES.rst

@@ -65,7 +65,7 @@ New Features
 - Add pack9 reader [#25]
 - Add light cone catalog reading to ``CompaSOHaloCatalog`` [#11]
 
-Enhancements 
+Enhancements
 ~~~~~~~~~~~~
 - Sped up RNG for reseeding [#24]
 
@@ -112,8 +112,8 @@ Changes
 
 Fixes
 ~~~~~
-- Fixed issue where satellite galaxy halo ID was incorrect. 
-  
+- Fixed issue where satellite galaxy halo ID was incorrect.
+
 New Features
 ~~~~~~~~~~~~
 - ``CompaSOHaloCatalog`` can read "cleaned" halo catalogs with ``cleaned=True`` (the default) [#6]
@@ -135,7 +135,7 @@ Deprecations
 ~~~~~~~~~~~~
 - Passing a string to the ``load_subsamples`` argument of ``CompaSOHaloCatalog`` is deprecated;
   use a dict instead, like: ``load_subsamples=dict(A=True, rv=True)``. [#6]
-  
+
 - ``cleaned_halos`` renamed to ``cleaned``
 
 0.4.0 (2021-02-03)
@@ -162,7 +162,7 @@ Fixes
 ~~~~~
 - Specify minimum Astropy version to avoid
   ``AttributeError: 'numpy.ndarray' object has no attribute 'info'``
-  
+
 0.2.0 (2020-07-08)
 ------------------
 

abacusnbody/__init__.py

@@ -1 +1,3 @@
 from .version import __version__
+
+__all__ = ['__version__']

abacusnbody/data/asdf.py

@@ -8,37 +8,38 @@
 handle Blosc compression.
 '''
 
-import time
 import struct
+import time
 
-import numpy as np
+import asdf
 import blosc
-from asdf.extension import Extension, Compressor
+import numpy as np
+from asdf.extension import Compressor, Extension
+
 
-import asdf
 def _monkey_patch(*args,**kwargs):
     raise Exception("Please use abacusnbody.data.asdf.set_nthreads(nthreads)")
-    
+
 asdf.compression.set_decompression_options = _monkey_patch
 
 def set_nthreads(nthreads):
     blosc.set_nthreads(nthreads)
-    
+
 
 class BloscCompressor(Compressor):
     '''
     An implementation of Blosc compression, as used by Abacus.
     '''
-        
+
     @property
     def label(self):
         '''
         The string labels in the binary block headers
         that indicate Blosc compression
         '''
         return b'blsc'
-    
-    
+
+
     def compress(self, data, **kwargs):
         '''Useful compression kwargs:
         nthreads
@@ -51,14 +52,14 @@ def compress(self, data, **kwargs):
         '''
         # Blosc code probably assumes contiguous buffer
         assert data.contiguous
-        
+
         nthreads = kwargs.pop('nthreads', 1)
         compression_block_size = kwargs.pop('compression_block_size',1<<22)
         blosc_block_size = kwargs.pop('blosc_block_size', 512*1024)
         typesize = kwargs.pop('typesize','auto')  # dtype size in bytes, e.g. 8 for int64
         clevel = kwargs.pop('clevel',1)  # compression level, usually only need lowest for zstd
         cname = kwargs.pop('cname','zstd')  # compressor name, default zstd, good performance/compression tradeoff
-        
+
         shuffle = kwargs.pop('shuffle', 'shuffle')
         if shuffle == 'shuffle':
             shuffle = blosc.SHUFFLE
@@ -68,58 +69,58 @@ def compress(self, data, **kwargs):
             shuffle = blosc.NOSHUFFLE
         else:
             raise ValueError(shuffle)
-        
+
         blosc.set_nthreads(nthreads)
         blosc.set_blocksize(blosc_block_size)
-        
+
         if typesize == 'auto':
             this_typesize = data.itemsize
         else:
             this_typesize = typesize
         #assert this_typesize != 1
-        
+
         nelem = compression_block_size // data.itemsize
         for i in range(0,len(data),nelem):
             compressed = blosc.compress(data[i:i+nelem], typesize=this_typesize, clevel=clevel, shuffle=shuffle, cname=cname,
                                     **kwargs)
             header = struct.pack('!I', len(compressed))
             # TODO: this probably triggers a data copy, feels inefficient. Probably have to add output array arg to blosc to fix
             yield header + compressed
-    
-    
+
+
     def decompress(self, blocks, out, **kwargs):
         '''Useful decompression kwargs:
         nthreads
         '''
         # TODO: controlled globally for now
         #nthreads = kwargs.pop('nthreads',1)
         #blosc.set_nthreads(nthreads)
-        
+
         _size = 0
         _pos = 0
         _buffer = None
         _partial_len = b''
-        
+
         decompression_time = 0.
         bytesout = 0
-        
+
         # Blosc code probably assumes contiguous buffer
         if not out.contiguous:
             raise ValueError(out.contiguous)
-        
+
         # get the out address
         out = np.frombuffer(out, dtype=np.uint8).ctypes.data
-        
+
         for block in blocks:
             block = memoryview(block).cast('c')
             try:
                 block = block.toreadonly()  # python>=3.8 only
             except AttributeError:
                 pass
-            
+
             if not block.contiguous:
                 raise ValueError(block.contiguous)
-                
+
             while len(block):
                 if not _size:
                     # Don't know the (compressed) length of this block yet
@@ -166,14 +167,14 @@ def decompress(self, blocks, out, **kwargs):
                     _size = 0
 
         return bytesout
-       
+
 
 class AbacusExtension(Extension):
     '''
     An ASDF Extension that deals with Abacus types and formats.
     Currently only implements Blosc compression.
     '''
-    
+
     @property
     def extension_uri(self):
         """
@@ -186,7 +187,7 @@ class itself.
         str
         """
         return "asdf://abacusnbody.org/extensions/abacus-0.0.1"
-    
+
     @property
     def compressors(self):
         '''