chore: sync code with srfit 3.4.0

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -17,5 +17,8 @@ jobs:
       project: diffpy.cmipdf
       c_extension: false
       headless: false
+      run: |
+        set -Eeuo pipefail
+        python -m pip install --no-deps diffpy.srfit==3.4.0rc0
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/tests-on-pr.yml

@@ -11,5 +11,8 @@ jobs:
       project: diffpy.cmipdf
       c_extension: false
       headless: false
+      run: |
+        set -Eeuo pipefail
+        python -m pip install --no-deps diffpy.srfit==3.4.0rc0
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

docs/source/api/diffpy.cmipdf.rst

@@ -1,30 +1,60 @@
 :tocdepth: -1
 
-|title|
-=======
-
-.. |title| replace:: diffpy.cmipdf package
+diffpy.cmipdf package
+=====================
 
 .. automodule:: diffpy.cmipdf
     :members:
     :undoc-members:
     :show-inheritance:
 
-Subpackages
------------
-
-.. toctree::
-   diffpy.cmipdf.example_package
-
 Submodules
 ----------
 
-|module|
---------
+diffpy.cmipdf.pdfgenerator module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.cmipdf.pdfgenerator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.cmipdf.debyepdfgenerator module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.cmipdf.debyepdfgenerator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.cmipdf.basepdfgenerator module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.cmipdf.basepdfgenerator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.cmipdf.pdfcontribution module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.cmipdf.pdfcontribution
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.cmipdf.pdfparser module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.cmipdf.pdfparser
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
-.. |module| replace:: diffpy.cmipdf.example_submodule module
+diffpy.cmipdf.characteristicfunctions module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.cmipdf.example_submodule
+.. automodule:: diffpy.cmipdf.characteristicfunctions
     :members:
     :undoc-members:
     :show-inheritance:

docs/source/conf.py

@@ -50,7 +50,7 @@
     "sphinx.ext.intersphinx",
     "sphinx_rtd_theme",
     "sphinx_copybutton",
-    "m2r",
+    "m2r2",
 ]
 
 # Add any paths that contain templates here, relative to this directory.

news/sync-srfit-3.4.0.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news needed: syncing with srfit.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/test-standards.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: Restyle tests to the group standards; no user-facing change.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -49,11 +49,17 @@ exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 [project.scripts]
-diffpy-cmipdf = "diffpy.cmipdf.app:main"
+diffpy-cmipdf = "diffpy.cmipdf.cmipdf_app:main"
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}
 
+[tool.pytest.ini_options]
+# Fail when cmipdf source calls one of its own deprecated names.
+filterwarnings = [
+    "error:'diffpy\\.cmipdf\\.:DeprecationWarning:diffpy\\.cmipdf",
+]
+
 [tool.codespell]
 exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"

requirements/docs.txt

@@ -2,4 +2,4 @@ sphinx
 sphinx_rtd_theme
 sphinx-copybutton
 doctr
-m2r
+m2r2

src/diffpy/__init__.py

@@ -12,3 +12,7 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
+
+from pkgutil import extend_path
+
+__path__ = extend_path(__path__, __name__)

src/diffpy/cmipdf/basepdfgenerator.py

@@ -117,7 +117,7 @@ def _set_calculator(self, calc):
         """
         self._calc = calc
         for pname in self.__class__._parnames:
-            self.addParameter(ParameterAdapter(pname, self._calc, attr=pname))
+            self.add_parameter(ParameterAdapter(pname, self._calc, attr=pname))
         self._process_metadata()
         return
 
@@ -195,7 +195,7 @@ def set_scattering_type(self, stype="X"):
         ValueError
             If the scattering type is unknown.
         """
-        self._calc.setScatteringFactorTableByType(stype)
+        self._calc.scatteringfactortable = stype
         # update the meta dictionary only if there was no exception
         self.meta["stype"] = self.get_scattering_type()
         return

src/diffpy/cmipdf/characteristicfunctions.py

@@ -225,18 +225,20 @@ def lognormal_spherical_distribution(radial_dist, p_diameter, p_sigma):
     (not of the particle size), and s is the width of the distribution.
     This is
     the characteristic function for the lognormal distribution of particle
-    diameter:
+    diameter::
 
-    F(r, mu, s) = 0.5*Erfc((-mu-3*s^2+Log(r))/(sqrt(2)*s))
-               + 0.25*r^3*Erfc((-mu+Log(r))/(sqrt(2)*s))*exp(-3*mu-4.5*s^2)
-               - 0.75*r*Erfc((-mu-2*s^2+Log(r))/(sqrt(2)*s))*exp(-mu-2.5*s^2)
+        F(r, mu, s) = (
+            0.5*Erfc((-mu-3*s^2+Log(r))/(sqrt(2)*s))
+            + 0.25*r^3*Erfc((-mu+Log(r))/(sqrt(2)*s))*exp(-3*mu-4.5*s^2)
+            - 0.75*r*Erfc((-mu-2*s^2+Log(r))/(sqrt(2)*s))*exp(-mu-2.5*s^2)
+        )
 
     The expectation value of the distribution gives the average particle
     diameter, p_diameter. The variance of the distribution gives p_sigma^2.
-    mu and s can be expressed in terms of these as:
+    mu and s can be expressed in terms of these as::
 
-    s^2 = log((p_sigma/p_diameter)^2 + 1)
-    mu = log(p_diameter) - s^2/2
+        s^2 = log((p_sigma/p_diameter)^2 + 1)
+        mu = log(p_diameter) - s^2/2
 
     Source unknown
     """
@@ -402,14 +404,14 @@ def __init__(self, name, model):
         # Wrap normal parameters
         for parname in model.params:
             par = SASParameter(parname, model)
-            self.addParameter(par)
+            self.add_parameter(par)
 
         # Wrap dispersion parameters
         for parname in model.dispersion:
             name = parname + "_width"
             parname += ".width"
             par = SASParameter(name, model, parname)
-            self.addParameter(par)
+            self.add_parameter(par)
 
         return
 

src/diffpy/cmipdf/pdfcontribution.py

@@ -100,10 +100,10 @@ def __init__(self, name):
 
         # Need a parameter for the overall scale, in the case that this is a
         # multi-phase fit.
-        self.newParameter("scale", 1.0)
+        self.new_parameter("scale", 1.0)
         # Profile-related parameters that will be shared between the generators
-        self.newParameter("qdamp", 0)
-        self.newParameter("qbroad", 0)
+        self.new_parameter("qdamp", 0)
+        self.new_parameter("qbroad", 0)
         return
 
     # Data methods

src/diffpy/cmipdf/pdfparser.py

@@ -52,6 +52,7 @@ class PDFParser(ProfileParser):
     _banks
         The data from each bank. Each bank contains a
         (x, y, dx, dy) tuple:
+
         x
             A numpy array containing the independent
             variable read from the file.

tests/conftest.py

@@ -1,12 +1,10 @@
 import importlib.resources
 import json
-import logging
-from functools import lru_cache
 from pathlib import Path
 
 import pytest
 
-logger = logging.getLogger(__name__)
+from diffpy.structure import PDFFitStructure
 
 
 @pytest.fixture
@@ -23,46 +21,6 @@ def user_filesystem(tmp_path):
     yield tmp_path
 
 
-# diffpy.structure
-@lru_cache()
-def has_diffpy_structure():
-    try:
-        import diffpy.structure as m
-
-        del m
-        return True
-    except ImportError:
-        logger.warning(
-            "Cannot import diffpy.structure, Structure tests skipped."
-        )
-        return False
-
-
-# diffpy.srreal
-
-
-@lru_cache()
-def has_diffpy_srreal():
-    try:
-        import diffpy.srreal.pdfcalculator as m
-
-        del m
-        return True
-    except ImportError:
-        logger.warning("Cannot import diffpy.srreal, PDF tests skipped.")
-        return False
-
-
-@pytest.fixture(scope="session")
-def diffpy_structure_available():
-    return has_diffpy_structure()
-
-
-@pytest.fixture(scope="session")
-def diffpy_srreal_available():
-    return has_diffpy_srreal()
-
-
 @pytest.fixture(scope="session")
 def datafile():
     """Fixture to load a test data file from the testdata package
@@ -81,3 +39,14 @@ def _as_list(values):
         return None if values is None else values.tolist()
 
     return _as_list
+
+
+@pytest.fixture
+def ni_pdffit_structure(datafile):
+    """Fixture for the Ni structure from ni.cif with Biso = 1 on every
+    atom."""
+    structure = PDFFitStructure()
+    structure.read(str(datafile("ni.cif")))
+    for atom in structure:
+        atom.Bisoequiv = 1
+    return structure