chore: update cmomy and module-utilities

environment.yaml

@@ -9,10 +9,10 @@ dependencies:
   - scipy
   - xarray
   #  - openmm
-  - cmomy>=0.1.9
+  - cmomy>=0.4
   - custom-inherit
   - attrs
-  - module-utilities >= 0.1
+  - module-utilities>=0.2
   - pymbar<4.0
   - pip
   - pip:

environment/dev.yaml

@@ -3,12 +3,12 @@ channels:
   - wpk-nist
 dependencies:
   - attrs
-  - cmomy>=0.1.9
+  - cmomy>=0.4
   - custom-inherit
   - ipykernel
   - ipython
   - matplotlib
-  - module-utilities >= 0.1
+  - module-utilities>=0.2
   - nbconvert
   - numpy
   - pip

environment/docs.yaml

@@ -3,11 +3,11 @@ channels:
   - wpk-nist
 dependencies:
   - attrs
-  - cmomy>=0.1.9
+  - cmomy>=0.4
   - custom-inherit
   - ipython
   - matplotlib
-  - module-utilities >= 0.1
+  - module-utilities>=0.2
   - numpy
   - pip
   - pymbar<4.0

environment/lint.yaml

@@ -3,9 +3,9 @@ channels:
   - wpk-nist
 dependencies:
   - attrs
-  - cmomy>=0.1.9
+  - cmomy>=0.4
   - custom-inherit
-  - module-utilities >= 0.1
+  - module-utilities>=0.2
   - mypy
   - numpy
   - pandas

environment/test.yaml

@@ -3,9 +3,9 @@ channels:
   - wpk-nist
 dependencies:
   - attrs
-  - cmomy>=0.1.9
+  - cmomy>=0.4
   - custom-inherit
-  - module-utilities >= 0.1
+  - module-utilities>=0.2
   - numpy
   - pandas
   - pip

pyproject.toml

@@ -32,10 +32,10 @@ dependencies = [
     "xarray >= 0.16",
     "sympy",
     "scipy",
-    "cmomy >= 0.1.9",
+    "cmomy >= 0.4",
     "custom-inherit",
     "attrs",
-    "module-utilities >= 0.1",
+    "module-utilities >= 0.2",
 ]
 
 [project.urls]

src/thermoextrap/__init__.py

@@ -1,6 +1,8 @@
 """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 (
     DataCentralMoments,

src/thermoextrap/core/_docstrings.py

@@ -2,97 +2,11 @@
 
 from __future__ import annotations
 
+from cmomy.docstrings import docfiller as DOCFILLER_CMOMY
+
 # from .external.docfiller import DocFiller
 from module_utilities.docfiller import DocFiller
 
-# TODO: clean this up.
-# There's a better way to do all this
-# - import cmomy docstrings
-# - use namespaces
-
-_docstring_cmomy = """\
-Parameters
-----------
-copy : bool, optional
-    If True, copy the data.  If False, attempt to use view.
-copy_kws : mapping, optional
-    extra arguments to copy
-verify : bool, optional
-    If True, make sure data is c-contiguous
-check_shape : bool, optional
-    If True, check that shape of resulting object is correct.
-mom : int or tuple of int
-    Order or moments.  If integer or length one tuple, then moments are for
-    a single variable.  If length 2 tuple, then comoments of two variables
-mom_ndim : {1, 2}
-    Value indicates if moments (``mom_ndim = 1``) or comoments (``mom_ndim=2``).
-val_shape : tuple, optional
-    Shape of `values` part of data.  That is, the non-moment dimensions.
-shape : tuple, optional
-    Total shape.  ``shape = val_shape + tuple(m+1 for m in mom)``
-dtype : dtype, optional
-    Optional ``dtype`` for output data.
-zeros_kws : mapping, optional
-    Optional parameters to :func:`numpy.zeros`
-axis : int
-    Axis to reduce along.
-broadcast : bool, optional
-    If True, and ``x=(x0, x1)``, then perform 'smart' broadcasting.
-    In this case, if ``x1.ndim = 1`` and ``len(x1) == x0.shape[axis]``, then
-    broadcast `x1` to ``x0.shape``.
-freq : array of int, optional
-    Array of shape ``(nrep, size)`` where `nrep` is the number of replicates and
-    ``size = self.shape[axis]``.  `freq` is the weight that each sample contributes
-    to resamples values.  See :func:`~cmomy.resample.randsamp_freq`
-indices : array of int, optional
-    Array of shape ``(nrep, size)``.  If passed, create `freq` from indices.
-    See :func:`~cmomy.resample.randsamp_freq`.
-nrep : int, optional
-    Number of replicates.  Create `freq` with this many replicates.
-    See :func:`~cmomy.resample.randsamp_freq`
-pushed : same as object
-    Same as object, with new data pushed onto `self.data`
-resample_kws : mapping
-    Extra arguments to :func:`~cmomy.resample.resample_vals`
-full_output : bool, optional
-    If True, also return `freq` array
-convert_kws : mapping
-    Extra arguments to :func:`~cmomy.convert.to_central_moments` or :func:`~cmomy.convert.to_central_comoments`
-dims : hashable or sequence of hashable, optional
-    Dimension of resulting :class:`xarray.DataArray`.
-
-    * If ``len(dims) == self.ndim``, then dims specifies all dimensions.
-    * If ``len(dims) == self.val_ndim``, ``dims = dims + mom_dims``
-
-    Default to ``('dim_0', 'dim_1', ...)``
-mom_dims : hashable or tuple of hashable
-    Name of moment dimensions.  Defaults to ``('xmom', 'umom')``
-attrs : mapping
-    Attributes of output
-coords : mapping
-    Coordinates of output
-name : hashable
-    Name of output
-indexes : Any
-    indexes attribute.  This is ignored.
-template : DataArray
-    If present, output will have attributes of `template`.
-    Overrides other options.
-dim : hashable, optional
-    Dimension to reduce along.
-rep_dim : hashable, optional
-    Name of new 'replicated' dimension:
-rec_dim : hashable, optional
-    Name of dimension for 'records', i.e., multiple observations.
-"""
-
-DOCFILLER_CMOMY = DocFiller.from_docstring(
-    _docstring_cmomy, combine_keys="parameters"
-).assign_combined_key(
-    "xr_params", ["dims", "attrs", "coords", "name", "indexes", "template"]
-)
-
-
 # add uv_xv_array
 _docstring_xtrap = """\
 Parameters