From 4b1beaaccfe161b684527f00db6fc835e77013b1 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Fri, 6 Feb 2026 12:09:21 -0500 Subject: [PATCH 1/6] deprecate addProfileGenerator --- docs/examples/coreshellnp.py | 4 ++-- docs/examples/crystalpdf.py | 2 +- docs/examples/crystalpdfall.py | 4 ++-- docs/examples/crystalpdfobjcryst.py | 2 +- docs/examples/crystalpdftwodata.py | 4 ++-- docs/examples/crystalpdftwophase.py | 4 ++-- docs/examples/ellipsoidsas.py | 2 +- docs/examples/gaussiangenerator.py | 2 +- docs/examples/npintensity.py | 2 +- docs/examples/npintensityII.py | 4 ++-- docs/examples/nppdfcrystal.py | 2 +- docs/examples/nppdfobjcryst.py | 2 +- docs/examples/nppdfsas.py | 4 ++-- src/diffpy/srfit/fitbase/fitcontribution.py | 21 ++++++++++++++++++++- src/diffpy/srfit/pdf/pdfcontribution.py | 2 +- tests/test_contribution.py | 18 +++++++++++++++--- 16 files changed, 55 insertions(+), 24 deletions(-) diff --git a/docs/examples/coreshellnp.py b/docs/examples/coreshellnp.py index 5b8c6eb2..deef927f 100644 --- a/docs/examples/coreshellnp.py +++ b/docs/examples/coreshellnp.py @@ -66,8 +66,8 @@ def makeRecipe(stru1, stru2, datname): # The FitContribution # Add both generators and the profile to the FitContribution. contribution = FitContribution("cdszns") - contribution.addProfileGenerator(generator_cds) - contribution.addProfileGenerator(generator_zns) + contribution.add_profile_generator(generator_cds) + contribution.add_profile_generator(generator_zns) contribution.set_profile(profile, xname="r") # Set up the characteristic functions. We use a spherical CF for the core diff --git a/docs/examples/crystalpdf.py b/docs/examples/crystalpdf.py index 835eb977..c3f1122c 100644 --- a/docs/examples/crystalpdf.py +++ b/docs/examples/crystalpdf.py @@ -74,7 +74,7 @@ def makeRecipe(ciffile, datname): # Here we associate the Profile and ProfileGenerator, as has been done # before. contribution = FitContribution("nickel") - contribution.addProfileGenerator(generator) + contribution.add_profile_generator(generator) contribution.set_profile(profile, xname="r") # Make the FitRecipe and add the FitContribution. diff --git a/docs/examples/crystalpdfall.py b/docs/examples/crystalpdfall.py index 8926952a..365e6f34 100644 --- a/docs/examples/crystalpdfall.py +++ b/docs/examples/crystalpdfall.py @@ -47,7 +47,7 @@ def makeProfile(datafile): def makeContribution(name, generator, profile): """Make a FitContribution and add a generator and profile.""" contribution = FitContribution(name) - contribution.addProfileGenerator(generator) + contribution.add_profile_generator(generator) contribution.set_profile(profile, xname="r") return contribution @@ -93,7 +93,7 @@ def makeRecipe( xcontribution_sini = makeContribution( "xsini", xgenerator_sini_ni, xprofile_sini ) - xcontribution_sini.addProfileGenerator(xgenerator_sini_si) + xcontribution_sini.add_profile_generator(xgenerator_sini_si) xcontribution_sini.setEquation("scale * (xG_sini_ni + xG_sini_si)") # As explained in another example, we want to minimize using Rw^2. diff --git a/docs/examples/crystalpdfobjcryst.py b/docs/examples/crystalpdfobjcryst.py index d28af6a3..f7236bcc 100644 --- a/docs/examples/crystalpdfobjcryst.py +++ b/docs/examples/crystalpdfobjcryst.py @@ -62,7 +62,7 @@ def makeRecipe(ciffile, datname): # The FitContribution contribution = FitContribution("nickel") - contribution.addProfileGenerator(generator) + contribution.add_profile_generator(generator) contribution.set_profile(profile, xname="r") # Make the FitRecipe and add the FitContribution. diff --git a/docs/examples/crystalpdftwodata.py b/docs/examples/crystalpdftwodata.py index b13da27f..fda20258 100644 --- a/docs/examples/crystalpdftwodata.py +++ b/docs/examples/crystalpdftwodata.py @@ -84,11 +84,11 @@ def makeRecipe(ciffile, xdatname, ndatname): # The FitContributions # We associate the x-ray PDFGenerator and Profile in one FitContribution... xcontribution = FitContribution("xnickel") - xcontribution.addProfileGenerator(xgenerator) + xcontribution.add_profile_generator(xgenerator) xcontribution.set_profile(xprofile, xname="r") # and the neutron objects in another. ncontribution = FitContribution("nnickel") - ncontribution.addProfileGenerator(ngenerator) + ncontribution.add_profile_generator(ngenerator) ncontribution.set_profile(nprofile, xname="r") # This example is different than the previous ones in that we are composing diff --git a/docs/examples/crystalpdftwophase.py b/docs/examples/crystalpdftwophase.py index 95e659b7..a47ff46e 100644 --- a/docs/examples/crystalpdftwophase.py +++ b/docs/examples/crystalpdftwophase.py @@ -72,8 +72,8 @@ def makeRecipe(niciffile, siciffile, datname): # Add both generators to the FitContribution. Add the Profile. This will # send the metadata to the generators. contribution = FitContribution("nisi") - contribution.addProfileGenerator(generator_ni) - contribution.addProfileGenerator(generator_si) + contribution.add_profile_generator(generator_ni) + contribution.add_profile_generator(generator_si) contribution.set_profile(profile, xname="r") # Write the fitting equation. We want to sum the PDFs from each phase and diff --git a/docs/examples/ellipsoidsas.py b/docs/examples/ellipsoidsas.py index 5c0826ec..35d8abd7 100644 --- a/docs/examples/ellipsoidsas.py +++ b/docs/examples/ellipsoidsas.py @@ -57,7 +57,7 @@ def makeRecipe(datname): # Here we associate the Profile and ProfileGenerator, as has been done # before. contribution = FitContribution("ellipsoid") - contribution.addProfileGenerator(generator) + contribution.add_profile_generator(generator) contribution.set_profile(profile, xname="q") # We want to fit the log of the signal to the log of the data so that the diff --git a/docs/examples/gaussiangenerator.py b/docs/examples/gaussiangenerator.py index f806e4a2..4f24b73c 100644 --- a/docs/examples/gaussiangenerator.py +++ b/docs/examples/gaussiangenerator.py @@ -144,7 +144,7 @@ def makeRecipe(): # attribute of the FitContribution by its name ("g"). Note that this will # set the fitting equation to "g", which calls the GaussianGenerator. contribution = FitContribution("g1") - contribution.addProfileGenerator(generator) + contribution.add_profile_generator(generator) contribution.set_profile(profile) # The FitRecipe diff --git a/docs/examples/npintensity.py b/docs/examples/npintensity.py index c193922e..5793d318 100644 --- a/docs/examples/npintensity.py +++ b/docs/examples/npintensity.py @@ -203,7 +203,7 @@ def makeRecipe(strufile, datname): # the FitContribution to name the x-variable of the profile "q", so we can # use it in equations with this name. contribution = FitContribution("bucky") - contribution.addProfileGenerator(generator) + contribution.add_profile_generator(generator) contribution.set_profile(profile, xname="q") # Now we're ready to define the fitting equation for the FitContribution. diff --git a/docs/examples/npintensityII.py b/docs/examples/npintensityII.py index 552eba96..44716cab 100644 --- a/docs/examples/npintensityII.py +++ b/docs/examples/npintensityII.py @@ -88,10 +88,10 @@ def makeRecipe(strufile, datname1, datname2): # The FitContributions # Create the FitContributions. contribution1 = FitContribution("bucky1") - contribution1.addProfileGenerator(generator1) + contribution1.add_profile_generator(generator1) contribution1.set_profile(profile1, xname="q") contribution2 = FitContribution("bucky2") - contribution2.addProfileGenerator(generator2) + contribution2.add_profile_generator(generator2) contribution2.set_profile(profile2, xname="q") # Now we're ready to define the fitting equation for each FitContribution. diff --git a/docs/examples/nppdfcrystal.py b/docs/examples/nppdfcrystal.py index 49ed32e6..fdaa3a8f 100644 --- a/docs/examples/nppdfcrystal.py +++ b/docs/examples/nppdfcrystal.py @@ -54,7 +54,7 @@ def makeRecipe(ciffile, grdata): pdfgenerator.setQmax(30.0) stru = loadCrystal(ciffile) pdfgenerator.setStructure(stru) - pdfcontribution.addProfileGenerator(pdfgenerator) + pdfcontribution.add_profile_generator(pdfgenerator) # Register the nanoparticle shape factor. from diffpy.srfit.pdf.characteristicfunctions import sphericalCF diff --git a/docs/examples/nppdfobjcryst.py b/docs/examples/nppdfobjcryst.py index 70c0bf83..25a9444d 100644 --- a/docs/examples/nppdfobjcryst.py +++ b/docs/examples/nppdfobjcryst.py @@ -52,7 +52,7 @@ def makeRecipe(molecule, datname): # The FitContribution contribution = FitContribution("bucky") - contribution.addProfileGenerator(generator) + contribution.add_profile_generator(generator) contribution.set_profile(profile, xname="r") # Make a FitRecipe. diff --git a/docs/examples/nppdfsas.py b/docs/examples/nppdfsas.py index 665e2377..08619722 100644 --- a/docs/examples/nppdfsas.py +++ b/docs/examples/nppdfsas.py @@ -58,7 +58,7 @@ def makeRecipe(ciffile, grdata, iqdata): pdfgenerator.setQmax(30.0) stru = loadCrystal(ciffile) pdfgenerator.setStructure(stru) - pdfcontribution.addProfileGenerator(pdfgenerator) + pdfcontribution.add_profile_generator(pdfgenerator) pdfcontribution.setResidualEquation("resv") # Create a SAS contribution as well. We assume the nanoparticle is roughly @@ -77,7 +77,7 @@ def makeRecipe(ciffile, grdata, iqdata): model = EllipsoidModel() sasgenerator = SASGenerator("generator", model) - sascontribution.addProfileGenerator(sasgenerator) + sascontribution.add_profile_generator(sasgenerator) sascontribution.setResidualEquation("resv") # Now we set up a characteristic function calculator that depends on the diff --git a/src/diffpy/srfit/fitbase/fitcontribution.py b/src/diffpy/srfit/fitbase/fitcontribution.py index 71048092..bbb23fb3 100644 --- a/src/diffpy/srfit/fitbase/fitcontribution.py +++ b/src/diffpy/srfit/fitbase/fitcontribution.py @@ -41,6 +41,13 @@ removal_version, ) +addprofilegenerator_dep_msg = build_deprecation_message( + base, + "addProfileGenerator", + "add_profile_generator", + removal_version, +) + class FitContribution(ParameterSet): """FitContribution class. @@ -179,7 +186,7 @@ def setProfile(self, profile, xname=None, yname=None, dyname=None): profile, xname=xname, yname=yname, dyname=dyname ) - def addProfileGenerator(self, gen, name=None): + def add_profile_generator(self, gen, name=None): """Add a ProfileGenerator to be used by this FitContribution. The ProfileGenerator is given a name so that it can be used as part of @@ -223,6 +230,18 @@ def addProfileGenerator(self, gen, name=None): return + @deprecated(addprofilegenerator_dep_msg) + def addProfileGenerator(self, gen, name=None): + """This function has been deprecated and will be removed in version + 4.0.0. + + Please use + diffpy.srfit.fitbase.FitContribution.add_profile_generator + instead. + """ + self.add_profile_generator(gen, name=name) + return + def setEquation(self, eqstr, ns={}): """Set the profile equation for the FitContribution. diff --git a/src/diffpy/srfit/pdf/pdfcontribution.py b/src/diffpy/srfit/pdf/pdfcontribution.py index bcd694ff..4809676c 100644 --- a/src/diffpy/srfit/pdf/pdfcontribution.py +++ b/src/diffpy/srfit/pdf/pdfcontribution.py @@ -273,7 +273,7 @@ def _setup_generator(self, gen): with setStructure or setPhase. """ # Add the generator to this FitContribution - self.addProfileGenerator(gen) + self.add_profile_generator(gen) # Set the proper equation for the fit, depending on the number of # phases we have. diff --git a/tests/test_contribution.py b/tests/test_contribution.py index 1332de33..37eae01b 100644 --- a/tests/test_contribution.py +++ b/tests/test_contribution.py @@ -67,6 +67,18 @@ def testAddProfileGenerator(self): self.assertTrue(fc._eq is not None) return + def test_add_profile_generator(self): + fc = self.fitcontribution + gen = self.gen + fc.add_profile_generator(gen, "gen") + + xobs = arange(0, 10, 0.5) + self.assertTrue(array_equal(xobs, gen(xobs))) + + self.assertTrue(gen.profile is None) + self.assertTrue(fc._eq is not None) + return + def testInteraction(self): """Test the interaction between the profile and profile generator.""" fc = self.fitcontribution @@ -75,7 +87,7 @@ def testInteraction(self): # Add the calculator and profile fc.set_profile(profile) - fc.addProfileGenerator(gen, "I") + fc.add_profile_generator(gen, "I") # Check attributes are created self.assertTrue(fc.profile is profile) @@ -120,7 +132,7 @@ def testReplacements(self): # Validate equations fc.set_profile(profile) - fc.addProfileGenerator(gen, "I") + fc.add_profile_generator(gen, "I") self.assertTrue(array_equal(gen.value, xobs)) self.assertTrue(array_equal(fc._eq(), xobs)) self.assertAlmostEqual(0, sum(fc._reseq())) @@ -196,7 +208,7 @@ def testResidual(noObserversInGlobalBuilders): # Add the calculator and profile fc.set_profile(profile) assert fc.profile is profile - fc.addProfileGenerator(gen, "I") + fc.add_profile_generator(gen, "I") assert fc._eq._value is None assert fc._reseq._value is None assert 1 == len(fc._generators) From 64b1ae92b8e170d3edcba5c9fc6c99f383e8b59c Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Fri, 6 Feb 2026 12:10:10 -0500 Subject: [PATCH 2/6] update api docs --- .../api/diffpy.srfit.equation.literals.rst | 32 +++--- docs/source/api/diffpy.srfit.equation.rst | 23 ++-- .../api/diffpy.srfit.equation.visitors.rst | 36 +++---- docs/source/api/diffpy.srfit.fitbase.rst | 102 +++++++++--------- docs/source/api/diffpy.srfit.interface.rst | 18 ++-- docs/source/api/diffpy.srfit.pdf.rst | 44 ++++---- docs/source/api/diffpy.srfit.rst | 35 +++--- docs/source/api/diffpy.srfit.sas.rst | 44 ++++---- docs/source/api/diffpy.srfit.structure.rst | 54 +++++----- docs/source/api/diffpy.srfit.util.rst | 40 ++++--- 10 files changed, 222 insertions(+), 206 deletions(-) diff --git a/docs/source/api/diffpy.srfit.equation.literals.rst b/docs/source/api/diffpy.srfit.equation.literals.rst index 35b905b1..20679c3e 100644 --- a/docs/source/api/diffpy.srfit.equation.literals.rst +++ b/docs/source/api/diffpy.srfit.equation.literals.rst @@ -1,27 +1,34 @@ +:tocdepth: -1 + diffpy.srfit.equation.literals package ====================================== +.. automodule:: diffpy.srfit.equation.literals + :members: + :undoc-members: + :show-inheritance: + Submodules ---------- -diffpy.srfit.equation.literals.abcs module ------------------------------------------- +diffpy.srfit.equation.literals.argument module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.equation.literals.abcs +.. automodule:: diffpy.srfit.equation.literals.argument :members: :undoc-members: :show-inheritance: -diffpy.srfit.equation.literals.argument module ----------------------------------------------- +diffpy.srfit.equation.literals.abcs module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.equation.literals.argument +.. automodule:: diffpy.srfit.equation.literals.abcs :members: :undoc-members: :show-inheritance: diffpy.srfit.equation.literals.literal module ---------------------------------------------- +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.equation.literals.literal :members: @@ -29,18 +36,9 @@ diffpy.srfit.equation.literals.literal module :show-inheritance: diffpy.srfit.equation.literals.operators module ------------------------------------------------ +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.equation.literals.operators :members: :undoc-members: :show-inheritance: - - -Module contents ---------------- - -.. automodule:: diffpy.srfit.equation.literals - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.equation.rst b/docs/source/api/diffpy.srfit.equation.rst index f5642da1..ef74cf23 100644 --- a/docs/source/api/diffpy.srfit.equation.rst +++ b/docs/source/api/diffpy.srfit.equation.rst @@ -1,19 +1,27 @@ +:tocdepth: -1 + diffpy.srfit.equation package ============================= +.. automodule:: diffpy.srfit.equation + :members: + :undoc-members: + :show-inheritance: + Subpackages ----------- .. toctree:: + :titlesonly: - diffpy.srfit.equation.literals diffpy.srfit.equation.visitors + diffpy.srfit.equation.literals Submodules ---------- diffpy.srfit.equation.builder module ------------------------------------- +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.equation.builder :members: @@ -21,18 +29,9 @@ diffpy.srfit.equation.builder module :show-inheritance: diffpy.srfit.equation.equationmod module ----------------------------------------- +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.equation.equationmod :members: :undoc-members: :show-inheritance: - - -Module contents ---------------- - -.. automodule:: diffpy.srfit.equation - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.equation.visitors.rst b/docs/source/api/diffpy.srfit.equation.visitors.rst index de17f93d..88c35374 100644 --- a/docs/source/api/diffpy.srfit.equation.visitors.rst +++ b/docs/source/api/diffpy.srfit.equation.visitors.rst @@ -1,54 +1,52 @@ +:tocdepth: -1 + diffpy.srfit.equation.visitors package ====================================== -Submodules ----------- - -diffpy.srfit.equation.visitors.argfinder module ------------------------------------------------ - -.. automodule:: diffpy.srfit.equation.visitors.argfinder +.. automodule:: diffpy.srfit.equation.visitors :members: :undoc-members: :show-inheritance: -diffpy.srfit.equation.visitors.printer module ---------------------------------------------- +Submodules +---------- -.. automodule:: diffpy.srfit.equation.visitors.printer +diffpy.srfit.equation.visitors.validator module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.srfit.equation.visitors.validator :members: :undoc-members: :show-inheritance: diffpy.srfit.equation.visitors.swapper module ---------------------------------------------- +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.equation.visitors.swapper :members: :undoc-members: :show-inheritance: -diffpy.srfit.equation.visitors.validator module ------------------------------------------------ +diffpy.srfit.equation.visitors.argfinder module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.equation.visitors.validator +.. automodule:: diffpy.srfit.equation.visitors.argfinder :members: :undoc-members: :show-inheritance: diffpy.srfit.equation.visitors.visitor module ---------------------------------------------- +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.equation.visitors.visitor :members: :undoc-members: :show-inheritance: +diffpy.srfit.equation.visitors.printer module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Module contents ---------------- - -.. automodule:: diffpy.srfit.equation.visitors +.. automodule:: diffpy.srfit.equation.visitors.printer :members: :undoc-members: :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.fitbase.rst b/docs/source/api/diffpy.srfit.fitbase.rst index 44093442..19bc255e 100644 --- a/docs/source/api/diffpy.srfit.fitbase.rst +++ b/docs/source/api/diffpy.srfit.fitbase.rst @@ -1,142 +1,140 @@ +:tocdepth: -1 + diffpy.srfit.fitbase package ============================ -Submodules ----------- - -diffpy.srfit.fitbase.calculator module --------------------------------------- - -.. automodule:: diffpy.srfit.fitbase.calculator +.. automodule:: diffpy.srfit.fitbase :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.configurable module ----------------------------------------- +Submodules +---------- -.. automodule:: diffpy.srfit.fitbase.configurable +diffpy.srfit.fitbase.simplerecipe module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.srfit.fitbase.simplerecipe :members: :undoc-members: :show-inheritance: diffpy.srfit.fitbase.constraint module --------------------------------------- +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.fitbase.constraint :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.fitcontribution module -------------------------------------------- - -.. automodule:: diffpy.srfit.fitbase.fitcontribution - :members: - :undoc-members: - :show-inheritance: - diffpy.srfit.fitbase.fithook module ------------------------------------ +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.fitbase.fithook :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.fitrecipe module -------------------------------------- +diffpy.srfit.fitbase.fitresults module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.fitbase.fitrecipe +.. automodule:: diffpy.srfit.fitbase.fitresults :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.fitresults module --------------------------------------- +diffpy.srfit.fitbase.profilegenerator module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.fitbase.fitresults +.. automodule:: diffpy.srfit.fitbase.profilegenerator :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.parameter module -------------------------------------- +diffpy.srfit.fitbase.validatable module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.fitbase.parameter +.. automodule:: diffpy.srfit.fitbase.validatable :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.parameterset module ----------------------------------------- +diffpy.srfit.fitbase.configurable module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.fitbase.parameterset +.. automodule:: diffpy.srfit.fitbase.configurable :members: :undoc-members: :show-inheritance: diffpy.srfit.fitbase.profile module ------------------------------------ +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.fitbase.profile :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.profilegenerator module --------------------------------------------- +diffpy.srfit.fitbase.restraint module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.fitbase.profilegenerator +.. automodule:: diffpy.srfit.fitbase.restraint :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.profileparser module ------------------------------------------ +diffpy.srfit.fitbase.fitcontribution module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.fitbase.profileparser +.. automodule:: diffpy.srfit.fitbase.fitcontribution :members: :undoc-members: :show-inheritance: diffpy.srfit.fitbase.recipeorganizer module -------------------------------------------- +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.fitbase.recipeorganizer :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.restraint module -------------------------------------- +diffpy.srfit.fitbase.fitrecipe module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.fitbase.restraint +.. automodule:: diffpy.srfit.fitbase.fitrecipe :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.simplerecipe module ----------------------------------------- +diffpy.srfit.fitbase.parameterset module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.fitbase.simplerecipe +.. automodule:: diffpy.srfit.fitbase.parameterset :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.validatable module ---------------------------------------- +diffpy.srfit.fitbase.calculator module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.fitbase.validatable +.. automodule:: diffpy.srfit.fitbase.calculator :members: :undoc-members: :show-inheritance: +diffpy.srfit.fitbase.parameter module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.srfit.fitbase.parameter + :members: + :undoc-members: + :show-inheritance: -Module contents ---------------- +diffpy.srfit.fitbase.profileparser module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.fitbase +.. automodule:: diffpy.srfit.fitbase.profileparser :members: :undoc-members: :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.interface.rst b/docs/source/api/diffpy.srfit.interface.rst index 4b6296a8..92497fea 100644 --- a/docs/source/api/diffpy.srfit.interface.rst +++ b/docs/source/api/diffpy.srfit.interface.rst @@ -1,22 +1,20 @@ +:tocdepth: -1 + diffpy.srfit.interface package ============================== -Submodules ----------- - -diffpy.srfit.interface.interface module ---------------------------------------- - -.. automodule:: diffpy.srfit.interface.interface +.. automodule:: diffpy.srfit.interface :members: :undoc-members: :show-inheritance: +Submodules +---------- -Module contents ---------------- +diffpy.srfit.interface.interface module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.interface +.. automodule:: diffpy.srfit.interface.interface :members: :undoc-members: :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.pdf.rst b/docs/source/api/diffpy.srfit.pdf.rst index a336a375..424c7f16 100644 --- a/docs/source/api/diffpy.srfit.pdf.rst +++ b/docs/source/api/diffpy.srfit.pdf.rst @@ -1,62 +1,60 @@ +:tocdepth: -1 + diffpy.srfit.pdf package ======================== +.. automodule:: diffpy.srfit.pdf + :members: + :undoc-members: + :show-inheritance: + Submodules ---------- -diffpy.srfit.pdf.basepdfgenerator module ----------------------------------------- +diffpy.srfit.pdf.debyepdfgenerator module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.pdf.basepdfgenerator +.. automodule:: diffpy.srfit.pdf.debyepdfgenerator :members: :undoc-members: :show-inheritance: diffpy.srfit.pdf.characteristicfunctions module ------------------------------------------------ +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.pdf.characteristicfunctions :members: :undoc-members: :show-inheritance: -diffpy.srfit.pdf.debyepdfgenerator module ------------------------------------------ - -.. automodule:: diffpy.srfit.pdf.debyepdfgenerator - :members: - :undoc-members: - :show-inheritance: - -diffpy.srfit.pdf.pdfcontribution module ---------------------------------------- +diffpy.srfit.pdf.pdfparser module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.pdf.pdfcontribution +.. automodule:: diffpy.srfit.pdf.pdfparser :members: :undoc-members: :show-inheritance: diffpy.srfit.pdf.pdfgenerator module ------------------------------------- +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.pdf.pdfgenerator :members: :undoc-members: :show-inheritance: -diffpy.srfit.pdf.pdfparser module ---------------------------------- +diffpy.srfit.pdf.basepdfgenerator module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.pdf.pdfparser +.. automodule:: diffpy.srfit.pdf.basepdfgenerator :members: :undoc-members: :show-inheritance: +diffpy.srfit.pdf.pdfcontribution module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Module contents ---------------- - -.. automodule:: diffpy.srfit.pdf +.. automodule:: diffpy.srfit.pdf.pdfcontribution :members: :undoc-members: :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.rst b/docs/source/api/diffpy.srfit.rst index ebff42c6..8f840d0c 100644 --- a/docs/source/api/diffpy.srfit.rst +++ b/docs/source/api/diffpy.srfit.rst @@ -1,9 +1,7 @@ :tocdepth: -1 -|title| -======= - -.. |title| replace:: diffpy.srfit package +diffpy.srfit package +==================== .. automodule:: diffpy.srfit :members: @@ -14,12 +12,23 @@ Subpackages ----------- .. toctree:: - diffpy.srfit.equation - diffpy.srfit.equation.literals - diffpy.srfit.equation.visitors - diffpy.srfit.fitbase - diffpy.srfit.interface - diffpy.srfit.pdf - diffpy.srfit.sas - diffpy.srfit.structure - diffpy.srfit.util + :titlesonly: + + diffpy.srfit.interface + diffpy.srfit.equation + diffpy.srfit.util + diffpy.srfit.pdf + diffpy.srfit.sas + diffpy.srfit.fitbase + diffpy.srfit.structure + +Submodules +---------- + +diffpy.srfit.exceptions module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.srfit.exceptions + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.sas.rst b/docs/source/api/diffpy.srfit.sas.rst index 40f24b3d..8ad88d91 100644 --- a/docs/source/api/diffpy.srfit.sas.rst +++ b/docs/source/api/diffpy.srfit.sas.rst @@ -1,54 +1,60 @@ +:tocdepth: -1 + diffpy.srfit.sas package ======================== +.. automodule:: diffpy.srfit.sas + :members: + :undoc-members: + :show-inheritance: + Submodules ---------- -diffpy.srfit.sas.prcalculator module ------------------------------------- +diffpy.srfit.sas.sasparser module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.sas.prcalculator +.. automodule:: diffpy.srfit.sas.sasparser :members: :undoc-members: :show-inheritance: -diffpy.srfit.sas.sasgenerator module ------------------------------------- +diffpy.srfit.sas.prcalculator module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.sas.sasgenerator +.. automodule:: diffpy.srfit.sas.prcalculator :members: :undoc-members: :show-inheritance: -diffpy.srfit.sas.sasparameter module ------------------------------------- +diffpy.srfit.sas.sasprofile module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.sas.sasparameter +.. automodule:: diffpy.srfit.sas.sasprofile :members: :undoc-members: :show-inheritance: -diffpy.srfit.sas.sasparser module ---------------------------------- +diffpy.srfit.sas.sasparameter module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.sas.sasparser +.. automodule:: diffpy.srfit.sas.sasparameter :members: :undoc-members: :show-inheritance: -diffpy.srfit.sas.sasprofile module ----------------------------------- +diffpy.srfit.sas.sasimport module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.sas.sasprofile +.. automodule:: diffpy.srfit.sas.sasimport :members: :undoc-members: :show-inheritance: +diffpy.srfit.sas.sasgenerator module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Module contents ---------------- - -.. automodule:: diffpy.srfit.sas +.. automodule:: diffpy.srfit.sas.sasgenerator :members: :undoc-members: :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.structure.rst b/docs/source/api/diffpy.srfit.structure.rst index 1bb5dd22..59063abd 100644 --- a/docs/source/api/diffpy.srfit.structure.rst +++ b/docs/source/api/diffpy.srfit.structure.rst @@ -1,70 +1,68 @@ +:tocdepth: -1 + diffpy.srfit.structure package ============================== +.. automodule:: diffpy.srfit.structure + :members: + :undoc-members: + :show-inheritance: + Submodules ---------- -diffpy.srfit.structure.basestructureparset module -------------------------------------------------- +diffpy.srfit.structure.objcrystparset module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.structure.basestructureparset +.. automodule:: diffpy.srfit.structure.objcrystparset :members: :undoc-members: :show-inheritance: -diffpy.srfit.structure.bvsrestraint module ------------------------------------------- +diffpy.srfit.structure.basestructureparset module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.structure.bvsrestraint +.. automodule:: diffpy.srfit.structure.basestructureparset :members: :undoc-members: :show-inheritance: -diffpy.srfit.structure.cctbxparset module ------------------------------------------ +diffpy.srfit.structure.srrealparset module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.structure.cctbxparset +.. automodule:: diffpy.srfit.structure.srrealparset :members: :undoc-members: :show-inheritance: diffpy.srfit.structure.diffpyparset module ------------------------------------------- +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.structure.diffpyparset :members: :undoc-members: :show-inheritance: -diffpy.srfit.structure.objcrystparset module --------------------------------------------- - -.. automodule:: diffpy.srfit.structure.objcrystparset - :members: - :undoc-members: - :show-inheritance: - -diffpy.srfit.structure.sgconstraints module -------------------------------------------- +diffpy.srfit.structure.cctbxparset module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.structure.sgconstraints +.. automodule:: diffpy.srfit.structure.cctbxparset :members: :undoc-members: :show-inheritance: -diffpy.srfit.structure.srrealparset module ------------------------------------------- +diffpy.srfit.structure.bvsrestraint module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.structure.srrealparset +.. automodule:: diffpy.srfit.structure.bvsrestraint :members: :undoc-members: :show-inheritance: +diffpy.srfit.structure.sgconstraints module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Module contents ---------------- - -.. automodule:: diffpy.srfit.structure +.. automodule:: diffpy.srfit.structure.sgconstraints :members: :undoc-members: :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.util.rst b/docs/source/api/diffpy.srfit.util.rst index 64541ce6..2471e5ad 100644 --- a/docs/source/api/diffpy.srfit.util.rst +++ b/docs/source/api/diffpy.srfit.util.rst @@ -1,46 +1,60 @@ +:tocdepth: -1 + diffpy.srfit.util package ========================= +.. automodule:: diffpy.srfit.util + :members: + :undoc-members: + :show-inheritance: + Submodules ---------- diffpy.srfit.util.inpututils module ------------------------------------ +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: diffpy.srfit.util.inpututils :members: :undoc-members: :show-inheritance: -diffpy.srfit.util.nameutils module ----------------------------------- +diffpy.srfit.util.observable module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.util.nameutils +.. automodule:: diffpy.srfit.util.observable :members: :undoc-members: :show-inheritance: -diffpy.srfit.util.observable module ------------------------------------ +diffpy.srfit.util.tagmanager module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.util.observable +.. automodule:: diffpy.srfit.util.tagmanager :members: :undoc-members: :show-inheritance: -diffpy.srfit.util.tagmanager module ------------------------------------ +diffpy.srfit.util.argbinders module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.util.tagmanager +.. automodule:: diffpy.srfit.util.argbinders :members: :undoc-members: :show-inheritance: +diffpy.srfit.util.nameutils module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Module contents ---------------- +.. automodule:: diffpy.srfit.util.nameutils + :members: + :undoc-members: + :show-inheritance: -.. automodule:: diffpy.srfit.util +diffpy.srfit.util.weakrefcallable module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.srfit.util.weakrefcallable :members: :undoc-members: :show-inheritance: From 7a9a4626dc443980b888b55974a6e219754a19a9 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Fri, 6 Feb 2026 12:35:36 -0500 Subject: [PATCH 3/6] mock utils and pyobjcryst for doc rendering --- docs/source/conf.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/source/conf.py b/docs/source/conf.py index aa4fd14b..6f33a1b7 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -55,6 +55,11 @@ "m2r2", ] +autodoc_mock_imports = [ + "diffpy.utils", + "pyobjcryst", +] + # Add any paths that contain templates here, relative to this directory. templates_path = ["_templates"] From a9053e3e864e5b5aa23069304900d0d923494339 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Fri, 6 Feb 2026 12:36:40 -0500 Subject: [PATCH 4/6] news --- news/addprofilegenerator-dep.rst | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 news/addprofilegenerator-dep.rst diff --git a/news/addprofilegenerator-dep.rst b/news/addprofilegenerator-dep.rst new file mode 100644 index 00000000..3a281ff7 --- /dev/null +++ b/news/addprofilegenerator-dep.rst @@ -0,0 +1,23 @@ +**Added:** + +* Added ``add_profile_generator`` to replace deprecated function. + +**Changed:** + +* + +**Deprecated:** + +* Deprecated ``addProfileGenerator`` for removal in 4.0.0. + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* From 8663f1272a77981d83fd399d25a176fb28c471cd Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Fri, 6 Feb 2026 12:42:47 -0500 Subject: [PATCH 5/6] restore api docs --- .../api/diffpy.srfit.equation.literals.rst | 32 +++--- docs/source/api/diffpy.srfit.equation.rst | 23 ++-- .../api/diffpy.srfit.equation.visitors.rst | 36 ++++--- docs/source/api/diffpy.srfit.fitbase.rst | 102 +++++++++--------- docs/source/api/diffpy.srfit.interface.rst | 18 ++-- docs/source/api/diffpy.srfit.pdf.rst | 44 ++++---- docs/source/api/diffpy.srfit.rst | 35 +++--- docs/source/api/diffpy.srfit.sas.rst | 44 ++++---- docs/source/api/diffpy.srfit.structure.rst | 54 +++++----- docs/source/api/diffpy.srfit.util.rst | 40 +++---- 10 files changed, 206 insertions(+), 222 deletions(-) diff --git a/docs/source/api/diffpy.srfit.equation.literals.rst b/docs/source/api/diffpy.srfit.equation.literals.rst index 20679c3e..35b905b1 100644 --- a/docs/source/api/diffpy.srfit.equation.literals.rst +++ b/docs/source/api/diffpy.srfit.equation.literals.rst @@ -1,34 +1,27 @@ -:tocdepth: -1 - diffpy.srfit.equation.literals package ====================================== -.. automodule:: diffpy.srfit.equation.literals - :members: - :undoc-members: - :show-inheritance: - Submodules ---------- -diffpy.srfit.equation.literals.argument module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.equation.literals.abcs module +------------------------------------------ -.. automodule:: diffpy.srfit.equation.literals.argument +.. automodule:: diffpy.srfit.equation.literals.abcs :members: :undoc-members: :show-inheritance: -diffpy.srfit.equation.literals.abcs module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.equation.literals.argument module +---------------------------------------------- -.. automodule:: diffpy.srfit.equation.literals.abcs +.. automodule:: diffpy.srfit.equation.literals.argument :members: :undoc-members: :show-inheritance: diffpy.srfit.equation.literals.literal module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +--------------------------------------------- .. automodule:: diffpy.srfit.equation.literals.literal :members: @@ -36,9 +29,18 @@ diffpy.srfit.equation.literals.literal module :show-inheritance: diffpy.srfit.equation.literals.operators module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +----------------------------------------------- .. automodule:: diffpy.srfit.equation.literals.operators :members: :undoc-members: :show-inheritance: + + +Module contents +--------------- + +.. automodule:: diffpy.srfit.equation.literals + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.equation.rst b/docs/source/api/diffpy.srfit.equation.rst index ef74cf23..f5642da1 100644 --- a/docs/source/api/diffpy.srfit.equation.rst +++ b/docs/source/api/diffpy.srfit.equation.rst @@ -1,27 +1,19 @@ -:tocdepth: -1 - diffpy.srfit.equation package ============================= -.. automodule:: diffpy.srfit.equation - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- .. toctree:: - :titlesonly: - diffpy.srfit.equation.visitors diffpy.srfit.equation.literals + diffpy.srfit.equation.visitors Submodules ---------- diffpy.srfit.equation.builder module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +------------------------------------ .. automodule:: diffpy.srfit.equation.builder :members: @@ -29,9 +21,18 @@ diffpy.srfit.equation.builder module :show-inheritance: diffpy.srfit.equation.equationmod module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +---------------------------------------- .. automodule:: diffpy.srfit.equation.equationmod :members: :undoc-members: :show-inheritance: + + +Module contents +--------------- + +.. automodule:: diffpy.srfit.equation + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.equation.visitors.rst b/docs/source/api/diffpy.srfit.equation.visitors.rst index 88c35374..de17f93d 100644 --- a/docs/source/api/diffpy.srfit.equation.visitors.rst +++ b/docs/source/api/diffpy.srfit.equation.visitors.rst @@ -1,52 +1,54 @@ -:tocdepth: -1 - diffpy.srfit.equation.visitors package ====================================== -.. automodule:: diffpy.srfit.equation.visitors +Submodules +---------- + +diffpy.srfit.equation.visitors.argfinder module +----------------------------------------------- + +.. automodule:: diffpy.srfit.equation.visitors.argfinder :members: :undoc-members: :show-inheritance: -Submodules ----------- - -diffpy.srfit.equation.visitors.validator module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.equation.visitors.printer module +--------------------------------------------- -.. automodule:: diffpy.srfit.equation.visitors.validator +.. automodule:: diffpy.srfit.equation.visitors.printer :members: :undoc-members: :show-inheritance: diffpy.srfit.equation.visitors.swapper module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +--------------------------------------------- .. automodule:: diffpy.srfit.equation.visitors.swapper :members: :undoc-members: :show-inheritance: -diffpy.srfit.equation.visitors.argfinder module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.equation.visitors.validator module +----------------------------------------------- -.. automodule:: diffpy.srfit.equation.visitors.argfinder +.. automodule:: diffpy.srfit.equation.visitors.validator :members: :undoc-members: :show-inheritance: diffpy.srfit.equation.visitors.visitor module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +--------------------------------------------- .. automodule:: diffpy.srfit.equation.visitors.visitor :members: :undoc-members: :show-inheritance: -diffpy.srfit.equation.visitors.printer module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.equation.visitors.printer +Module contents +--------------- + +.. automodule:: diffpy.srfit.equation.visitors :members: :undoc-members: :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.fitbase.rst b/docs/source/api/diffpy.srfit.fitbase.rst index 19bc255e..44093442 100644 --- a/docs/source/api/diffpy.srfit.fitbase.rst +++ b/docs/source/api/diffpy.srfit.fitbase.rst @@ -1,140 +1,142 @@ -:tocdepth: -1 - diffpy.srfit.fitbase package ============================ -.. automodule:: diffpy.srfit.fitbase +Submodules +---------- + +diffpy.srfit.fitbase.calculator module +-------------------------------------- + +.. automodule:: diffpy.srfit.fitbase.calculator :members: :undoc-members: :show-inheritance: -Submodules ----------- - -diffpy.srfit.fitbase.simplerecipe module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.fitbase.configurable module +---------------------------------------- -.. automodule:: diffpy.srfit.fitbase.simplerecipe +.. automodule:: diffpy.srfit.fitbase.configurable :members: :undoc-members: :show-inheritance: diffpy.srfit.fitbase.constraint module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +-------------------------------------- .. automodule:: diffpy.srfit.fitbase.constraint :members: :undoc-members: :show-inheritance: +diffpy.srfit.fitbase.fitcontribution module +------------------------------------------- + +.. automodule:: diffpy.srfit.fitbase.fitcontribution + :members: + :undoc-members: + :show-inheritance: + diffpy.srfit.fitbase.fithook module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +----------------------------------- .. automodule:: diffpy.srfit.fitbase.fithook :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.fitresults module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.fitbase.fitrecipe module +------------------------------------- -.. automodule:: diffpy.srfit.fitbase.fitresults +.. automodule:: diffpy.srfit.fitbase.fitrecipe :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.profilegenerator module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.fitbase.fitresults module +-------------------------------------- -.. automodule:: diffpy.srfit.fitbase.profilegenerator +.. automodule:: diffpy.srfit.fitbase.fitresults :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.validatable module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.fitbase.parameter module +------------------------------------- -.. automodule:: diffpy.srfit.fitbase.validatable +.. automodule:: diffpy.srfit.fitbase.parameter :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.configurable module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.fitbase.parameterset module +---------------------------------------- -.. automodule:: diffpy.srfit.fitbase.configurable +.. automodule:: diffpy.srfit.fitbase.parameterset :members: :undoc-members: :show-inheritance: diffpy.srfit.fitbase.profile module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +----------------------------------- .. automodule:: diffpy.srfit.fitbase.profile :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.restraint module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.fitbase.profilegenerator module +-------------------------------------------- -.. automodule:: diffpy.srfit.fitbase.restraint +.. automodule:: diffpy.srfit.fitbase.profilegenerator :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.fitcontribution module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.fitbase.profileparser module +----------------------------------------- -.. automodule:: diffpy.srfit.fitbase.fitcontribution +.. automodule:: diffpy.srfit.fitbase.profileparser :members: :undoc-members: :show-inheritance: diffpy.srfit.fitbase.recipeorganizer module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +------------------------------------------- .. automodule:: diffpy.srfit.fitbase.recipeorganizer :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.fitrecipe module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.fitbase.restraint module +------------------------------------- -.. automodule:: diffpy.srfit.fitbase.fitrecipe +.. automodule:: diffpy.srfit.fitbase.restraint :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.parameterset module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.fitbase.simplerecipe module +---------------------------------------- -.. automodule:: diffpy.srfit.fitbase.parameterset +.. automodule:: diffpy.srfit.fitbase.simplerecipe :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.calculator module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.fitbase.validatable module +--------------------------------------- -.. automodule:: diffpy.srfit.fitbase.calculator +.. automodule:: diffpy.srfit.fitbase.validatable :members: :undoc-members: :show-inheritance: -diffpy.srfit.fitbase.parameter module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -.. automodule:: diffpy.srfit.fitbase.parameter - :members: - :undoc-members: - :show-inheritance: -diffpy.srfit.fitbase.profileparser module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Module contents +--------------- -.. automodule:: diffpy.srfit.fitbase.profileparser +.. automodule:: diffpy.srfit.fitbase :members: :undoc-members: :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.interface.rst b/docs/source/api/diffpy.srfit.interface.rst index 92497fea..4b6296a8 100644 --- a/docs/source/api/diffpy.srfit.interface.rst +++ b/docs/source/api/diffpy.srfit.interface.rst @@ -1,20 +1,22 @@ -:tocdepth: -1 - diffpy.srfit.interface package ============================== -.. automodule:: diffpy.srfit.interface - :members: - :undoc-members: - :show-inheritance: - Submodules ---------- diffpy.srfit.interface.interface module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +--------------------------------------- .. automodule:: diffpy.srfit.interface.interface :members: :undoc-members: :show-inheritance: + + +Module contents +--------------- + +.. automodule:: diffpy.srfit.interface + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.pdf.rst b/docs/source/api/diffpy.srfit.pdf.rst index 424c7f16..a336a375 100644 --- a/docs/source/api/diffpy.srfit.pdf.rst +++ b/docs/source/api/diffpy.srfit.pdf.rst @@ -1,60 +1,62 @@ -:tocdepth: -1 - diffpy.srfit.pdf package ======================== -.. automodule:: diffpy.srfit.pdf - :members: - :undoc-members: - :show-inheritance: - Submodules ---------- -diffpy.srfit.pdf.debyepdfgenerator module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.pdf.basepdfgenerator module +---------------------------------------- -.. automodule:: diffpy.srfit.pdf.debyepdfgenerator +.. automodule:: diffpy.srfit.pdf.basepdfgenerator :members: :undoc-members: :show-inheritance: diffpy.srfit.pdf.characteristicfunctions module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +----------------------------------------------- .. automodule:: diffpy.srfit.pdf.characteristicfunctions :members: :undoc-members: :show-inheritance: -diffpy.srfit.pdf.pdfparser module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.pdf.debyepdfgenerator module +----------------------------------------- -.. automodule:: diffpy.srfit.pdf.pdfparser +.. automodule:: diffpy.srfit.pdf.debyepdfgenerator + :members: + :undoc-members: + :show-inheritance: + +diffpy.srfit.pdf.pdfcontribution module +--------------------------------------- + +.. automodule:: diffpy.srfit.pdf.pdfcontribution :members: :undoc-members: :show-inheritance: diffpy.srfit.pdf.pdfgenerator module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +------------------------------------ .. automodule:: diffpy.srfit.pdf.pdfgenerator :members: :undoc-members: :show-inheritance: -diffpy.srfit.pdf.basepdfgenerator module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.pdf.pdfparser module +--------------------------------- -.. automodule:: diffpy.srfit.pdf.basepdfgenerator +.. automodule:: diffpy.srfit.pdf.pdfparser :members: :undoc-members: :show-inheritance: -diffpy.srfit.pdf.pdfcontribution module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.pdf.pdfcontribution +Module contents +--------------- + +.. automodule:: diffpy.srfit.pdf :members: :undoc-members: :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.rst b/docs/source/api/diffpy.srfit.rst index 8f840d0c..ebff42c6 100644 --- a/docs/source/api/diffpy.srfit.rst +++ b/docs/source/api/diffpy.srfit.rst @@ -1,7 +1,9 @@ :tocdepth: -1 -diffpy.srfit package -==================== +|title| +======= + +.. |title| replace:: diffpy.srfit package .. automodule:: diffpy.srfit :members: @@ -12,23 +14,12 @@ Subpackages ----------- .. toctree:: - :titlesonly: - - diffpy.srfit.interface - diffpy.srfit.equation - diffpy.srfit.util - diffpy.srfit.pdf - diffpy.srfit.sas - diffpy.srfit.fitbase - diffpy.srfit.structure - -Submodules ----------- - -diffpy.srfit.exceptions module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -.. automodule:: diffpy.srfit.exceptions - :members: - :undoc-members: - :show-inheritance: + diffpy.srfit.equation + diffpy.srfit.equation.literals + diffpy.srfit.equation.visitors + diffpy.srfit.fitbase + diffpy.srfit.interface + diffpy.srfit.pdf + diffpy.srfit.sas + diffpy.srfit.structure + diffpy.srfit.util diff --git a/docs/source/api/diffpy.srfit.sas.rst b/docs/source/api/diffpy.srfit.sas.rst index 8ad88d91..40f24b3d 100644 --- a/docs/source/api/diffpy.srfit.sas.rst +++ b/docs/source/api/diffpy.srfit.sas.rst @@ -1,60 +1,54 @@ -:tocdepth: -1 - diffpy.srfit.sas package ======================== -.. automodule:: diffpy.srfit.sas - :members: - :undoc-members: - :show-inheritance: - Submodules ---------- -diffpy.srfit.sas.sasparser module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.sas.prcalculator module +------------------------------------ -.. automodule:: diffpy.srfit.sas.sasparser +.. automodule:: diffpy.srfit.sas.prcalculator :members: :undoc-members: :show-inheritance: -diffpy.srfit.sas.prcalculator module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.sas.sasgenerator module +------------------------------------ -.. automodule:: diffpy.srfit.sas.prcalculator +.. automodule:: diffpy.srfit.sas.sasgenerator :members: :undoc-members: :show-inheritance: -diffpy.srfit.sas.sasprofile module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.sas.sasparameter module +------------------------------------ -.. automodule:: diffpy.srfit.sas.sasprofile +.. automodule:: diffpy.srfit.sas.sasparameter :members: :undoc-members: :show-inheritance: -diffpy.srfit.sas.sasparameter module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.sas.sasparser module +--------------------------------- -.. automodule:: diffpy.srfit.sas.sasparameter +.. automodule:: diffpy.srfit.sas.sasparser :members: :undoc-members: :show-inheritance: -diffpy.srfit.sas.sasimport module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.sas.sasprofile module +---------------------------------- -.. automodule:: diffpy.srfit.sas.sasimport +.. automodule:: diffpy.srfit.sas.sasprofile :members: :undoc-members: :show-inheritance: -diffpy.srfit.sas.sasgenerator module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.sas.sasgenerator +Module contents +--------------- + +.. automodule:: diffpy.srfit.sas :members: :undoc-members: :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.structure.rst b/docs/source/api/diffpy.srfit.structure.rst index 59063abd..1bb5dd22 100644 --- a/docs/source/api/diffpy.srfit.structure.rst +++ b/docs/source/api/diffpy.srfit.structure.rst @@ -1,68 +1,70 @@ -:tocdepth: -1 - diffpy.srfit.structure package ============================== -.. automodule:: diffpy.srfit.structure - :members: - :undoc-members: - :show-inheritance: - Submodules ---------- -diffpy.srfit.structure.objcrystparset module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.structure.basestructureparset module +------------------------------------------------- -.. automodule:: diffpy.srfit.structure.objcrystparset +.. automodule:: diffpy.srfit.structure.basestructureparset :members: :undoc-members: :show-inheritance: -diffpy.srfit.structure.basestructureparset module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.structure.bvsrestraint module +------------------------------------------ -.. automodule:: diffpy.srfit.structure.basestructureparset +.. automodule:: diffpy.srfit.structure.bvsrestraint :members: :undoc-members: :show-inheritance: -diffpy.srfit.structure.srrealparset module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.structure.cctbxparset module +----------------------------------------- -.. automodule:: diffpy.srfit.structure.srrealparset +.. automodule:: diffpy.srfit.structure.cctbxparset :members: :undoc-members: :show-inheritance: diffpy.srfit.structure.diffpyparset module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +------------------------------------------ .. automodule:: diffpy.srfit.structure.diffpyparset :members: :undoc-members: :show-inheritance: -diffpy.srfit.structure.cctbxparset module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.structure.objcrystparset module +-------------------------------------------- -.. automodule:: diffpy.srfit.structure.cctbxparset +.. automodule:: diffpy.srfit.structure.objcrystparset :members: :undoc-members: :show-inheritance: -diffpy.srfit.structure.bvsrestraint module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.structure.sgconstraints module +------------------------------------------- -.. automodule:: diffpy.srfit.structure.bvsrestraint +.. automodule:: diffpy.srfit.structure.sgconstraints :members: :undoc-members: :show-inheritance: -diffpy.srfit.structure.sgconstraints module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.structure.srrealparset module +------------------------------------------ -.. automodule:: diffpy.srfit.structure.sgconstraints +.. automodule:: diffpy.srfit.structure.srrealparset + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: diffpy.srfit.structure :members: :undoc-members: :show-inheritance: diff --git a/docs/source/api/diffpy.srfit.util.rst b/docs/source/api/diffpy.srfit.util.rst index 2471e5ad..64541ce6 100644 --- a/docs/source/api/diffpy.srfit.util.rst +++ b/docs/source/api/diffpy.srfit.util.rst @@ -1,60 +1,46 @@ -:tocdepth: -1 - diffpy.srfit.util package ========================= -.. automodule:: diffpy.srfit.util - :members: - :undoc-members: - :show-inheritance: - Submodules ---------- diffpy.srfit.util.inpututils module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +----------------------------------- .. automodule:: diffpy.srfit.util.inpututils :members: :undoc-members: :show-inheritance: -diffpy.srfit.util.observable module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.util.nameutils module +---------------------------------- -.. automodule:: diffpy.srfit.util.observable +.. automodule:: diffpy.srfit.util.nameutils :members: :undoc-members: :show-inheritance: -diffpy.srfit.util.tagmanager module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.util.observable module +----------------------------------- -.. automodule:: diffpy.srfit.util.tagmanager +.. automodule:: diffpy.srfit.util.observable :members: :undoc-members: :show-inheritance: -diffpy.srfit.util.argbinders module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diffpy.srfit.util.tagmanager module +----------------------------------- -.. automodule:: diffpy.srfit.util.argbinders +.. automodule:: diffpy.srfit.util.tagmanager :members: :undoc-members: :show-inheritance: -diffpy.srfit.util.nameutils module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.srfit.util.nameutils - :members: - :undoc-members: - :show-inheritance: +Module contents +--------------- -diffpy.srfit.util.weakrefcallable module -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -.. automodule:: diffpy.srfit.util.weakrefcallable +.. automodule:: diffpy.srfit.util :members: :undoc-members: :show-inheritance: From 92e8158c8745c8d9f74b89bb449f730a96c6ae10 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Fri, 6 Feb 2026 13:23:49 -0500 Subject: [PATCH 6/6] revert conf.py commit --- docs/source/conf.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 6f33a1b7..aa4fd14b 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -55,11 +55,6 @@ "m2r2", ] -autodoc_mock_imports = [ - "diffpy.utils", - "pyobjcryst", -] - # Add any paths that contain templates here, relative to this directory. templates_path = ["_templates"]