Restructure helpers directory (#341)

* Restructure helpers directory --------- Co-authored-by: Harvey Devereux <[email protected]> Co-authored-by: Jacob Wilkins <[email protected]>
stfc · Nov 1, 2024 · 15a6b49 · 15a6b49
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diff --git a/docs/source/apidoc/janus_core.rst b/docs/source/apidoc/janus_core.rst
@@ -14,70 +14,72 @@ Module contents
 Submodules
 ----------
 
-janus\_core.cli.janus module
-----------------------------
+janus\_core.calculations.base module
+------------------------------------
 
-.. automodule:: janus_core.cli.janus
+.. automodule:: janus_core.calculations.base
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.cli.singlepoint module
-----------------------------------
+janus\_core.calculations.descriptors module
+-------------------------------------------
 
-.. automodule:: janus_core.cli.singlepoint
+.. automodule:: janus_core.calculations.descriptors
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.cli.geomopt module
-------------------------------
+janus\_core.calculations.eos module
+-----------------------------------
 
-.. automodule:: janus_core.cli.geomopt
+.. automodule:: janus_core.calculations.eos
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.cli.md module
--------------------------
+janus\_core.calculations.geom\_opt module
+-----------------------------------------
 
-.. automodule:: janus_core.cli.md
+.. automodule:: janus_core.calculations.geom_opt
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.cli.train module
-----------------------------
+janus\_core.calculations.md module
+----------------------------------
 
-.. automodule:: janus_core.cli.train
+.. automodule:: janus_core.calculations.md
    :members:
    :special-members:
    :private-members:
+   :inherited-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.cli.phonons module
-------------------------------
+janus\_core.calculations.phonons module
+---------------------------------------
 
-.. automodule:: janus_core.cli.phonons
+.. automodule:: janus_core.calculations.phonons
    :members:
    :special-members:
    :private-members:
+   :inherited-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.cli.eos module
---------------------------
+janus\_core.calculations.single\_point module
+---------------------------------------------
 
-.. automodule:: janus_core.cli.eos
+.. automodule:: janus_core.calculations.single_point
    :members:
    :special-members:
    :private-members:
@@ -94,107 +96,106 @@ janus\_core.cli.descriptors module
    :undoc-members:
    :show-inheritance:
 
-janus\_core.cli.types module
-----------------------------
+janus\_core.cli.eos module
+--------------------------
 
-.. automodule:: janus_core.cli.types
+.. automodule:: janus_core.cli.eos
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.cli.utils module
-----------------------------
+janus\_core.cli.geomopt module
+------------------------------
 
-.. automodule:: janus_core.cli.utils
+.. automodule:: janus_core.cli.geomopt
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.calculations.base module
-------------------------------------
+janus\_core.cli.janus module
+----------------------------
 
-.. automodule:: janus_core.calculations.base
+.. automodule:: janus_core.cli.janus
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.calculations.single\_point module
----------------------------------------------
+janus\_core.cli.md module
+-------------------------
 
-.. automodule:: janus_core.calculations.single_point
+.. automodule:: janus_core.cli.md
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.calculations.geom\_opt module
------------------------------------------
+janus\_core.cli.phonons module
+------------------------------
 
-.. automodule:: janus_core.calculations.geom_opt
+.. automodule:: janus_core.cli.phonons
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.calculations.md module
+janus\_core.cli.singlepoint module
 ----------------------------------
 
-.. automodule:: janus_core.calculations.md
+.. automodule:: janus_core.cli.singlepoint
    :members:
    :special-members:
    :private-members:
-   :inherited-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.calculations.phonons module
----------------------------------------
+janus\_core.cli.train module
+----------------------------
 
-.. automodule:: janus_core.calculations.phonons
+.. automodule:: janus_core.cli.train
    :members:
    :special-members:
    :private-members:
-   :inherited-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.calculations.eos module
------------------------------------
+janus\_core.cli.types module
+----------------------------
 
-.. automodule:: janus_core.calculations.eos
+.. automodule:: janus_core.cli.types
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.calculations.descriptors module
--------------------------------------------
+janus\_core.cli.utils module
+----------------------------
 
-.. automodule:: janus_core.calculations.descriptors
+.. automodule:: janus_core.cli.utils
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.helpers.mlip\_calculators module
---------------------------------------------
+janus\_core.helpers.janus\_types module
+---------------------------------------
 
-.. automodule:: janus_core.helpers.mlip_calculators
+.. automodule:: janus_core.helpers.janus_types
    :members:
-   :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
+   :exclude-members: clear,copy,setdefault,items,keys,get,pop,popitem,fromkeys,update,values
+   :special-members:
 
 janus\_core.helpers.log module
 ------------------------------
@@ -206,16 +207,15 @@ janus\_core.helpers.log module
    :undoc-members:
    :show-inheritance:
 
-janus\_core.helpers.janus\_types module
----------------------------------------
+janus\_core.helpers.mlip\_calculators module
+--------------------------------------------
 
-.. automodule:: janus_core.helpers.janus_types
+.. automodule:: janus_core.helpers.mlip_calculators
    :members:
+   :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
-   :exclude-members: clear,copy,setdefault,items,keys,get,pop,popitem,fromkeys,update,values
-   :special-members:
 
 janus\_core.helpers.utils module
 --------------------------------
@@ -227,51 +227,72 @@ janus\_core.helpers.utils module
    :undoc-members:
    :show-inheritance:
 
-janus\_core.helpers.train module
---------------------------------
+janus\_core.helpers.stats
+-------------------------
 
-.. automodule:: janus_core.helpers.train
+.. automodule:: janus_core.helpers.stats
    :members:
    :special-members:
    :private-members:
+   :inherited-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.helpers.stats
--------------------------
+janus\_core.helpers.struct\_io
+------------------------------
 
-.. automodule:: janus_core.helpers.stats
+.. automodule:: janus_core.helpers.struct_io
    :members:
    :special-members:
    :private-members:
    :inherited-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.helpers.post_process module
----------------------------------------
+janus\_core.processing.correlator module
+----------------------------------------
 
-.. automodule:: janus_core.helpers.post_process
+.. automodule:: janus_core.processing.correlator
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.helpers.correlator module
--------------------------------------
+janus\_core.processing.observables module
+-----------------------------------------
 
-.. automodule:: janus_core.helpers.correlator
+.. automodule:: janus_core.processing.observables
    :members:
    :special-members:
    :private-members:
    :undoc-members:
    :show-inheritance:
 
-janus\_core.helpers.observables module
+janus\_core.processing.post\_process module
+-------------------------------------------
+
+.. automodule:: janus_core.processing.post_process
+   :members:
+   :special-members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
+
+janus\_core.processing.symmetry module
 --------------------------------------
 
-.. automodule:: janus_core.helpers.observables
+.. automodule:: janus_core.processing.symmetry
+   :members:
+   :special-members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
+
+janus\_core.training.train module
+---------------------------------
+
+.. automodule:: janus_core.training.train
    :members:
    :special-members:
    :private-members:

diff --git a/docs/source/developer_guide/tutorial.rst b/docs/source/developer_guide/tutorial.rst
@@ -187,9 +187,9 @@ Alternatively, using ``tox``::
 Adding a new Observable
 =======================
 
-Additional built-in observable quantities may be added for use by the ``janus_core.helpers.correlator.Correlation`` class. These should conform to the ``__call__`` signature of ``janus_core.helpers.janus_types.Observable``. For a user this can be accomplished by writing a function, or class also implementing a commensurate ``__call__``.
+Additional built-in observable quantities may be added for use by the ``janus_core.processing.correlator.Correlation`` class. These should conform to the ``__call__`` signature of ``janus_core.helpers.janus_types.Observable``. For a user this can be accomplished by writing a function, or class also implementing a commensurate ``__call__``.
 
-Built-in observables are collected within the ``janus_core.helpers.observables`` module. For example the ``janus_core.helpers.observables.Stress`` observable allows a user to quickly setup a given correlation of stress tensor components (with and without the ideal gas contribution). An observable for the ``xy`` component is obtained without the ideal gas contribution as:
+Built-in observables are collected within the ``janus_core.processing.observables`` module. For example the ``janus_core.processing.observables.Stress`` observable allows a user to quickly setup a given correlation of stress tensor components (with and without the ideal gas contribution). An observable for the ``xy`` component is obtained without the ideal gas contribution as:
 
 .. code-block:: python
 
@@ -203,4 +203,4 @@ A new built-in observables can be implemented by a class with the method:
 
 The ``__call__`` should contain all the logic for obtaining some ``float`` value from an ``Atoms`` object, alongside optional positional arguments and kwargs. The args and kwargs are set by a user when specifying correlations for a ``janus_core.calculations.md.MolecularDynamics`` run. See also ``janus_core.helpers.janus_types.CorrelationKwargs``. These are set at the instantiation of the ``janus_core.calculations.md.MolecularDynamics`` object and are not modified. These could be used e.g. to specify an observable calculated only from one atom's data.
 
-``janus_core.helpers.observables.Stress`` includes a constructor to take a symbolic component, e.g. ``"xx"`` or ``"yz"``, and determine the index required from ``ase.Atoms.get_stress`` on instantiation for ease of use.
+``janus_core.processing.observables.Stress`` includes a constructor to take a symbolic component, e.g. ``"xx"`` or ``"yz"``, and determine the index required from ``ase.Atoms.get_stress`` on instantiation for ease of use.
diff --git a/janus_core/calculations/base.py b/janus_core/calculations/base.py
@@ -12,7 +12,8 @@
     PathLike,
 )
 from janus_core.helpers.log import config_logger, config_tracker
-from janus_core.helpers.utils import FileNameMixin, input_structs, none_to_dict
+from janus_core.helpers.struct_io import input_structs
+from janus_core.helpers.utils import FileNameMixin, none_to_dict
 
 
 class BaseCalculation(FileNameMixin):

diff --git a/janus_core/calculations/descriptors.py b/janus_core/calculations/descriptors.py
@@ -15,7 +15,9 @@
     MaybeSequence,
     PathLike,
 )
-from janus_core.helpers.utils import check_calculator, none_to_dict, output_structs
+from janus_core.helpers.mlip_calculators import check_calculator
+from janus_core.helpers.struct_io import output_structs
+from janus_core.helpers.utils import none_to_dict
 
 
 class Descriptors(BaseCalculation):

diff --git a/janus_core/calculations/eos.py b/janus_core/calculations/eos.py
@@ -19,7 +19,8 @@
     OutputKwargs,
     PathLike,
 )
-from janus_core.helpers.utils import none_to_dict, output_structs
+from janus_core.helpers.struct_io import output_structs
+from janus_core.helpers.utils import none_to_dict
 
 
 class EoS(BaseCalculation):