Merge pull request #3 from rs-station/refactor

Refactor
rs-station · Jul 21, 2024 · c0d2f5c · c0d2f5c
2 parents cbf623a + e682c54
commit c0d2f5c
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Showing 17 changed files with 42 additions and 42 deletions.
diff --git a/abismal/command_line/__init__.py b/abismal/command_line/__init__.py
diff --git a/abismal/abismal.py → abismal/command_line/abismal.py b/abismal/abismal.py → abismal/command_line/abismal.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 def main():
-    from abismal.parser import parser
+    from abismal.command_line.parser import parser
     parser = parser.parse_args()
 
     from abismal.io.tf_settings import set_log_level, set_gpu

diff --git a/abismal/command_line/parser/__init__.py b/abismal/command_line/parser/__init__.py
@@ -0,0 +1,38 @@
+"""
+ABISMAL - merge serial diffraction data using neural networks and variational inference.
+"""
+
+import abismal.command_line.parser.io as io
+import abismal.command_line.parser.architecture as architecture
+import abismal.command_line.parser.likelihood as likelihood
+import abismal.command_line.parser.optimizer as optimizer
+import abismal.command_line.parser.phenix as phenix
+import abismal.command_line.parser.priors as priors
+import abismal.command_line.parser.ray as ray
+import abismal.command_line.parser.surrogate_posterior as surrogate_posterior
+import abismal.command_line.parser.tf as tf
+import abismal.command_line.parser.training as training
+
+groups = [
+    architecture,
+    io,
+    likelihood,
+    optimizer,
+    phenix,
+    priors,
+    ray,
+    surrogate_posterior,
+    tf,
+    training,
+]
+
+from argparse import ArgumentParser
+parser = ArgumentParser(description=__doc__)
+for group in groups:
+    g = parser.add_argument_group(group.title, group.description)
+    for args,kwargs in group.args_and_kwargs:
+        g.add_argument(*args, **kwargs)
+
+all = [
+    parser,
+]
diff --git a/abismal/parser/architecture.py → abismal/command_line/parser/architecture.py b/abismal/parser/architecture.py → abismal/command_line/parser/architecture.py
diff --git a/abismal/parser/custom_types.py → abismal/command_line/parser/custom_types.py b/abismal/parser/custom_types.py → abismal/command_line/parser/custom_types.py
diff --git a/abismal/parser/io.py → abismal/command_line/parser/io.py b/abismal/parser/io.py → abismal/command_line/parser/io.py
diff --git a/abismal/parser/likelihood.py → abismal/command_line/parser/likelihood.py b/abismal/parser/likelihood.py → abismal/command_line/parser/likelihood.py
diff --git a/abismal/parser/optimizer.py → abismal/command_line/parser/optimizer.py b/abismal/parser/optimizer.py → abismal/command_line/parser/optimizer.py
diff --git a/abismal/parser/phenix.py → abismal/command_line/parser/phenix.py b/abismal/parser/phenix.py → abismal/command_line/parser/phenix.py
diff --git a/abismal/parser/priors.py → abismal/command_line/parser/priors.py b/abismal/parser/priors.py → abismal/command_line/parser/priors.py
@@ -1,7 +1,7 @@
 title = "Priors"
 description = "Arguments governing the prior distributions"
 
-from abismal.parser.custom_types import list_of_ints,list_of_ops,list_of_floats
+from abismal.command_line.parser.custom_types import list_of_ints,list_of_ops,list_of_floats
 
 args_and_kwargs = (
     (

diff --git a/abismal/parser/ray.py → abismal/command_line/parser/ray.py b/abismal/parser/ray.py → abismal/command_line/parser/ray.py
diff --git a/abismal/parser/surrogate_posterior.py → ...ommand_line/parser/surrogate_posterior.py b/abismal/parser/surrogate_posterior.py → ...ommand_line/parser/surrogate_posterior.py
diff --git a/abismal/parser/tf.py → abismal/command_line/parser/tf.py b/abismal/parser/tf.py → abismal/command_line/parser/tf.py
diff --git a/abismal/parser/training.py → abismal/command_line/parser/training.py b/abismal/parser/training.py → abismal/command_line/parser/training.py
diff --git a/abismal/io/stream.py b/abismal/io/stream.py
@@ -97,7 +97,7 @@ def get_dataset(self, peak_list_columns=None, **ray_kwargs):
                 'ewald_offset_x', 'ewald_offset_y', 'ewald_offset_z',
             ]
 
-        chunks = self.parallel_read_crystfel(
+        chunks = self.read_crystfel(
             wavelength=self.wavelength,
             peak_list_columns=peak_list_columns,
             **ray_kwargs,

diff --git a/abismal/parser/__init__.py b/abismal/parser/__init__.py
diff --git a/setup.py b/setup.py
@@ -41,7 +41,7 @@ def getVersionNumber():
     tests_require=['pytest', 'pytest-cov', 'pytest-xdist'],
     entry_points={
         "console_scripts": [
-            "abismal=abismal.abismal:main",
+            "abismal=abismal.command_line.abismal:main",
         ]
     },
 )