feat: Moved some core modules to top level (where they were imported …

…anyway)

changelog.d/20230503_133701_william.krekelberg_module_utilities.md

@@ -0,0 +1,46 @@
+<!-- markdownlint-disable MD041 -->
+<!--
+A new scriv changelog fragment.
+
+Uncomment the section that is right (remove the HTML comment wrapper).
+-->
+
+<!--
+### Removed
+
+- A bullet item for the Removed category.
+
+-->
+<!--
+### Added
+
+- A bullet item for the Added category.
+
+-->
+
+### Changed
+
+- Moved `modesl, data, idealgas` from `thermoextrap.core` to `thermoextrap`.
+  These were imported at top level anyway. This fixes issues with doing things
+  like `from thermoextrap.data import ...`, etc.
+- Moved `core._docstrings_` to `docstrings`.
+- Now using `cmomy.docstrings` instead of repeating them here.
+
+<!--
+### Deprecated
+
+- A bullet item for the Deprecated category.
+
+-->
+<!--
+### Fixed
+
+- A bullet item for the Fixed category.
+
+-->
+<!--
+### Security
+
+- A bullet item for the Security category.
+
+-->

docs/conf.py

@@ -211,7 +211,7 @@
     "Symbol": "~sympy.core.symbol.Symbol",
     "symFunction": "~sympy.core.function.Function",
     "ExtrapModel": "~thermoextrap.models.ExtrapModel",
-    # "DataCentralMoments": "~cmomy.core.data.DataCentralMoments"
+    # "DataCentralMoments": "~cmomy.DataCentralMoments"
 }
 
 

docs/reference/api-baseclasses.rst

@@ -7,37 +7,37 @@ Base classes
    :inherited-members:
    :members:
 
-.. autoclass:: thermoextrap.core.models.PiecewiseMixin
+.. autoclass:: thermoextrap.models.PiecewiseMixin
    :autosummary:
    :show-inheritance:
    :inherited-members:
    :members:
 
-.. autoclass:: thermoextrap.core.models.SymDerivBase
+.. autoclass:: thermoextrap.models.SymDerivBase
    :autosummary:
    :show-inheritance:
    :inherited-members:
    :members:
 
-.. autoclass:: thermoextrap.core.models.SymFuncBase
+.. autoclass:: thermoextrap.models.SymFuncBase
    :autosummary:
    :show-inheritance:
    :members:
 
 
-.. autoclass:: thermoextrap.core.data.AbstractData
+.. autoclass:: thermoextrap.data.AbstractData
    :autosummary:
    :show-inheritance:
    :inherited-members:
    :members:
 
-.. autoclass:: thermoextrap.core.data.DataCentralMomentsBase
+.. autoclass:: thermoextrap.data.DataCentralMomentsBase
    :autosummary:
    :show-inheritance:
    :inherited-members:
    :members:
 
-.. autoclass:: thermoextrap.core.data.DataValuesBase
+.. autoclass:: thermoextrap.data.DataValuesBase
    :autosummary:
    :show-inheritance:
    :inherited-members:

src/thermoextrap/__init__.py

@@ -1,10 +1,9 @@
 """Classes/routines to deal with thermodynamic extrapolation."""
 
-from . import beta, lnpi, volume, volume_idealgas
-
 # TODO: move data, idealgas, models to top level.
-from .core import data, idealgas, models
-from .core.data import (
+from . import beta, data, idealgas, lnpi, models, volume, volume_idealgas
+from .core.xrutils import xrwrap_alpha, xrwrap_uv, xrwrap_xv
+from .data import (
     DataCentralMoments,
     DataCentralMomentsVals,
     DataValues,
@@ -14,7 +13,7 @@
 )
 
 # expose some data/models
-from .core.models import (
+from .models import (
     Derivatives,
     ExtrapModel,
     ExtrapWeightedModel,
@@ -24,7 +23,6 @@
     PerturbModel,
     StateCollection,
 )
-from .core.xrutils import xrwrap_alpha, xrwrap_uv, xrwrap_xv
 
 # updated versioning scheme
 try:

src/thermoextrap/adaptive_interp.py

@@ -536,8 +536,8 @@ def factory_state_idealgas(
     """
 
     from . import beta as xpan_beta
-    from .core import idealgas
-    from .core.data import DataCentralMomentsVals
+    from . import idealgas
+    from .data import DataCentralMomentsVals
 
     # NOTE: this is for reproducible results.
     if seed_from_beta:
@@ -574,7 +574,7 @@ def callback_plot_progress(  # noqa: D417
 
     import matplotlib.pyplot as plt
 
-    from .core import idealgas
+    from . import idealgas
 
     if verbose:
         print("depth:", info_dict["depth"])

src/thermoextrap/beta.py

@@ -7,8 +7,8 @@
 from functools import lru_cache
 from typing import Literal
 
-from .core._docstrings import DOCFILLER_SHARED
-from .core.models import (
+from .docstrings import DOCFILLER_SHARED
+from .models import (
     Derivatives,
     ExtrapModel,
     PerturbModel,
@@ -692,7 +692,7 @@ def factory_perturbmodel(beta, uv, xv, alpha_name="beta", **kws):
     --------
     ~thermoextrap.models.PerturbModel
     """
-    from .core.data import factory_data_values
+    from .data import factory_data_values
 
     data = factory_data_values(uv=uv, xv=xv, order=0, central=False, **kws)
     return PerturbModel(alpha0=beta, data=data, alpha_name=alpha_name)

src/thermoextrap/core/__init__.py

@@ -1,9 +1 @@
 """Core modules."""
-from . import data, idealgas, models, stack
-
-__all__ = [
-    "data",
-    "models",
-    "idealgas",
-    "stack",
-]

src/thermoextrap/core/data.py → src/thermoextrap/data.py

@@ -26,14 +26,14 @@
 from custom_inherit import DocInheritMeta
 from module_utilities import cached
 
-from ._attrs_utils import (
+from .core._attrs_utils import (
     MyAttrsMixin,
     _cache_field,
     convert_dims_to_tuple,
     kw_only_field,
 )
-from ._docstrings import DOCFILLER_SHARED
-from .xrutils import xrwrap_uv, xrwrap_xv
+from .core.xrutils import xrwrap_uv, xrwrap_xv
+from .docstrings import DOCFILLER_SHARED
 
 try:
     from cmomy import xCentralMoments
@@ -51,7 +51,6 @@
     "DataValues",
     "DataValuesCentral",
     "DataCallbackABC",
-    "AbstractData",
     "factory_data_values",
     "resample_indices",
 ]

src/thermoextrap/gpr_active/active_utils.py

@@ -16,8 +16,9 @@
 from pymbar import timeseries
 from scipy import integrate, linalg, special
 
-from .. import DataCentralMomentsVals, ExtrapModel
 from .. import beta as xpan_beta
+from ..data import DataCentralMomentsVals
+from ..models import ExtrapModel
 from .gp_models import (
     ConstantMeanWithDerivs,
     DerivativeKernel,

src/thermoextrap/gpr_active/ig_active.py

@@ -11,8 +11,8 @@
 import xarray as xr
 
 from .. import beta as xpan_beta
-from ..core import idealgas
-from ..core.data import DataCentralMomentsVals
+from .. import idealgas
+from ..data import DataCentralMomentsVals
 from .active_utils import DataWrapper
 
 

src/thermoextrap/core/idealgas.py → src/thermoextrap/idealgas.py

@@ -14,7 +14,7 @@
 import numpy as np
 import sympy as sp
 
-from ._docstrings import DocFiller
+from .docstrings import DocFiller
 
 __all__ = [
     "x_ave",

src/thermoextrap/legacy/gpr.py

@@ -10,7 +10,7 @@
 import xarray as xr
 from gpflow.ci_utils import ci_niter
 
-from .core.models import StateCollection
+from .models import StateCollection
 
 
 # First define classes needed for a GPR model

src/thermoextrap/legacy/gpr_stack.py

@@ -11,7 +11,8 @@
 from gpflow.ci_utils import ci_niter
 from module_utilities import cached
 
-from .core.stack import GPRData, StackedDerivatives, multiindex_to_array
+
+from ..stack import GPRData, StackedDerivatives, multiindex_to_array
 
 __all__ = ("GPRData", "GPRModel", "StackedDerivatives", "factory_gprmodel")
 

src/thermoextrap/lnpi.py

@@ -25,10 +25,10 @@
 
 from . import beta as beta_xpan
 from .core._attrs_utils import _cache_field, convert_dims_to_tuple
-from .core._docstrings import DOCFILLER_SHARED
-from .core.data import DataCallbackABC
-from .core.models import Derivatives, ExtrapModel, SymFuncBase, SymSubs
 from .core.sputils import get_default_indexed, get_default_symbol
+from .data import DataCallbackABC
+from .docstrings import DOCFILLER_SHARED
+from .models import Derivatives, ExtrapModel, SymFuncBase, SymSubs
 
 docfiller_shared = DOCFILLER_SHARED.levels_to_top("cmomy", "xtrap", "beta").decorate
 

src/thermoextrap/core/models.py → src/thermoextrap/models.py

@@ -19,12 +19,11 @@
 from module_utilities import cached
 from scipy.special import factorial as sp_factorial
 
-from thermoextrap.core.data import AbstractData, kw_only_field
-
-from ._attrs_utils import MyAttrsMixin, _cache_field
-from ._docstrings import DOCFILLER_SHARED
-from .sputils import get_default_indexed, get_default_symbol
-from .xrutils import xrwrap_alpha
+from .core._attrs_utils import MyAttrsMixin, _cache_field
+from .core.sputils import get_default_indexed, get_default_symbol
+from .core.xrutils import xrwrap_alpha
+from .data import AbstractData, kw_only_field
+from .docstrings import DOCFILLER_SHARED
 
 try:
     from pymbar import mbar
@@ -59,7 +58,7 @@ class SymFuncBase(sp.Function):
 
     See Also
     --------
-    :class:`thermoextrap.core.models.SymDerivBase`
+    :class:`thermoextrap.models.SymDerivBase`
 
     """
 
@@ -77,7 +76,7 @@ def deriv_args(cls):
         raise NotImplementedError("must specify in sublcass")
 
     def fdiff(self, argindex=1):
-        """Derivative of function.  This will be used by :class:`thermoextrap.core.models.SymDerivBase`."""
+        """Derivative of function.  This will be used by :class:`thermoextrap.models.SymDerivBase`."""
         raise NotImplementedError("must specify in subclass")
 
     @classmethod
@@ -100,7 +99,7 @@ class SymDerivBase(metaclass=DocInheritMeta(style="numpy_with_merge")):
     ----------
     func : symFunction
         Function to differentiate.  This should (most likely) be an instance
-        of :class:`thermoextrap.core.models.SymFuncBase`
+        of :class:`thermoextrap.models.SymFuncBase`
     args : sequence of Symbol
         Arguments to func
     {expand}
@@ -145,7 +144,7 @@ def __getitem__(self, order):
 @attrs.define
 class SymSubs:
     """
-    Class to handle substitution on :class:`thermoextrap.core.models.SymDerivBase`.
+    Class to handle substitution on :class:`thermoextrap.models.SymDerivBase`.
 
     Parameters
     ----------

src/thermoextrap/recursive_interp.py

@@ -17,10 +17,10 @@
 # TODO: Change this to point to the "new" ideagas.py
 # TODO: rework this code to be cleaner
 # from ..legacy.ig import IGmodel
-from .core import idealgas
+from . import idealgas
 from .core._deprecate import deprecate, deprecate_kwarg
-from .core.data import factory_data_values
-from .core.models import ExtrapModel, InterpModel
+from .data import factory_data_values
+from .models import ExtrapModel, InterpModel
 
 try:
     import matplotlib.pyplot as plt

src/thermoextrap/core/stack.py → src/thermoextrap/stack.py

@@ -482,8 +482,6 @@ def from_states(
         `StackedDerivatives.from_derivs`
         """
 
-        from .models import StateCollection
-
         if not isinstance(states, StateCollection):
             states = StateCollection(states)
 

src/thermoextrap/volume.py

@@ -16,10 +16,10 @@
 from module_utilities import cached
 
 from .core._attrs_utils import _cache_field
-from .core._docstrings import DOCFILLER_SHARED
-from .core.data import DataCallbackABC, DataValues
-from .core.models import Derivatives, ExtrapModel
 from .core.xrutils import xrwrap_xv
+from .data import DataCallbackABC, DataValues
+from .docstrings import DOCFILLER_SHARED
+from .models import Derivatives, ExtrapModel
 
 docfiller_shared = DOCFILLER_SHARED.levels_to_top(
     "cmomy", "xtrap", "beta", "volume"

src/thermoextrap/volume_idealgas.py

@@ -6,8 +6,8 @@
 
 from functools import lru_cache
 
-from .core._docstrings import DOCFILLER_SHARED
-from .core.models import Derivatives, ExtrapModel
+from .docstrings import DOCFILLER_SHARED
+from .models import Derivatives, ExtrapModel
 
 docfiller_shared = DOCFILLER_SHARED.levels_to_top(
     "cmomy", "xtrap", "beta", "volume"
@@ -104,7 +104,7 @@ def factory_extrapmodel(volume, uv, xv, order=1, alpha_name="volume", **kws):
     if order != 1:
         raise ValueError("only first order supported")
 
-    from .core.data import factory_data_values
+    from .data import factory_data_values
 
     data = factory_data_values(
         uv=uv, xv=xv, order=order, central=False, xalpha=False, **kws

tests/test_stack.py

@@ -4,7 +4,7 @@
 import xarray as xr
 
 import thermoextrap as xtrap
-from thermoextrap.core import stack
+from thermoextrap import stack
 
 
 @pytest.fixture

tests/test_u_equations.py

@@ -15,7 +15,7 @@ def data(request):
 
     n = request.param
     data.n = n
-    data.u, data.x1 = xtrap.core.models.get_default_symbol("u", "x1")
+    data.u, data.x1 = xtrap.models.get_default_symbol("u", "x1")
     data.du, data.dxdu = get_default_indexed("du", "dxdu")
     data.xu, data.ui = get_default_indexed("xu", "u")