adds script to import cctbx data to rs (#264)

Co-authored-by: kmdalton <[email protected]>

reciprocalspaceship/dtypes/internals.py

@@ -1359,7 +1359,7 @@ def round(self: T, decimals: int = 0, *args, **kwargs) -> T:
 
 @wraps(libmissing.is_numeric_na)
 def is_numeric_na(values):
-    allowed_dtypes = ("float32", "int32")
+    allowed_dtypes = ("float64", "float32", "int32")
     if isinstance(values, np.ndarray) and values.dtype in allowed_dtypes:
         return np.isnan(values)
     return libmissing.is_numeric_na(values)

reciprocalspaceship/io/__init__.py

@@ -1,6 +1,7 @@
 from reciprocalspaceship.io.ccp4map import write_ccp4_map
 from reciprocalspaceship.io.crystfel import read_crystfel
 from reciprocalspaceship.io.csv import read_csv
+from reciprocalspaceship.io.dials import print_refl_info, read_dials_stills
 from reciprocalspaceship.io.mtz import (
     from_gemmi,
     read_cif,

reciprocalspaceship/io/common.py

@@ -0,0 +1,48 @@
+import logging
+import warnings
+from contextlib import contextmanager
+from importlib.util import find_spec
+
+
+def set_ray_loglevel(level):
+    logger = logging.getLogger("ray")
+    logger.setLevel(level)
+    for handler in logger.handlers:
+        handler.setLevel(level)
+
+
+def check_for_ray():
+    has_ray = True
+    if find_spec("ray") is None:
+        has_ray = False
+
+        message = (
+            "ray (https://www.ray.io/) is not available..." "Falling back to serial."
+        )
+        warnings.warn(message, ImportWarning)
+    return has_ray
+
+
+def check_for_mpi():
+    try:
+        from mpi4py import MPI
+
+        return True
+    except Exception as err:
+        message = (
+            f"Failed `from mpi4py import MPI` with {err}. Falling back to serial mode."
+        )
+        warnings.warn(message, ImportWarning)
+        return False
+
+
+@contextmanager
+def ray_context(log_level="DEBUG", **ray_kwargs):
+    import ray
+
+    set_ray_loglevel(log_level)
+    ray.init(**ray_kwargs)
+    try:
+        yield ray
+    finally:
+        ray.shutdown()

reciprocalspaceship/io/crystfel.py

@@ -1,13 +1,12 @@
 import mmap
 import re
-from contextlib import contextmanager
-from importlib.util import find_spec
 from typing import Union
 
 import gemmi
 import numpy as np
 
 from reciprocalspaceship import DataSet, concat
+from reciprocalspaceship.io.common import check_for_ray, ray_context
 from reciprocalspaceship.utils import angle_between, eV2Angstroms
 
 # See Rupp Table 5-2
@@ -60,17 +59,6 @@
 }
 
 
-@contextmanager
-def ray_context(**ray_kwargs):
-    import ray
-
-    ray.init(**ray_kwargs)
-    try:
-        yield ray
-    finally:
-        ray.shutdown()
-
-
 class StreamLoader(object):
     """
     An object that loads stream files into rs.DataSet objects in parallel.
@@ -304,15 +292,7 @@ def read_crystfel(
 
         # Check whether ray is available
         if use_ray:
-            if find_spec("ray") is None:
-                use_ray = False
-                import warnings
-
-                message = (
-                    "ray (https://www.ray.io/) is not available..."
-                    "Falling back to serial stream file parser."
-                )
-                warnings.warn(message, ImportWarning)
+            use_ray = check_for_ray()
 
         with open(self.filename, "r") as f:
             memfile = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)