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deprecate: deprecate the rest of the methods in recipeorganizer.py #169

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Merged
sbillinge merged 21 commits into from
Mar 13, 2026
Merged

deprecate: deprecate the rest of the methods in recipeorganizer.py #169

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3b9b257
constrain and unconstrain deprecation
cadenmyers13 Mar 9, 2026
9993779
change name to register_restraint
cadenmyers13 Mar 9, 2026
1f301a3
restrain deprecation
cadenmyers13 Mar 9, 2026
8184be4
unrestrain deprecation
cadenmyers13 Mar 9, 2026
5d958fb
clearRestraints deprecation
cadenmyers13 Mar 9, 2026
7a2e29d
equationFromString deprecation
cadenmyers13 Mar 9, 2026
a5fb23c
news
cadenmyers13 Mar 9, 2026
a79dbec
constrain_parameter --> add_constraint
cadenmyers13 Mar 12, 2026
80173b6
unconstrain_parameter --> remove_constraint
cadenmyers13 Mar 12, 2026
31a57fc
add_restraint --> add_penalty
cadenmyers13 Mar 12, 2026
f04475c
remove_restraint --> remove_penalty
cadenmyers13 Mar 12, 2026
a197c76
register_restraint --> register_penalty
cadenmyers13 Mar 12, 2026
d77c6ac
clear_all_restraints --> clear_all_penalties
cadenmyers13 Mar 12, 2026
0b9e9f7
change lb to lower_bound everywhere
cadenmyers13 Mar 13, 2026
273e63a
change ub to upper_bound everywhere
cadenmyers13 Mar 13, 2026
7032d6b
add_penalty --> add_soft_bounds
cadenmyers13 Mar 13, 2026
dab361f
remove_penalty --> remove_soft_bounds
cadenmyers13 Mar 13, 2026
e67595d
register_penalty --> register_soft_bounds
cadenmyers13 Mar 13, 2026
680fee4
clear_all_penalties --> clear_all_soft_bounds
cadenmyers13 Mar 13, 2026
8c3618c
add more to add_soft_bounds docstring
cadenmyers13 Mar 13, 2026
c115478
more to docstring
cadenmyers13 Mar 13, 2026
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10 changes: 5 additions & 5 deletions docs/examples/coreshellnp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -91,14 +91,14 @@ def makeRecipe(stru1, stru2, datname):
# diameter to twice the shell radius.
recipe.add_variable(contribution.radius, 15)
recipe.add_variable(contribution.thickness, 11)
recipe.constrain(contribution.psize, "2 * radius")
recipe.constrain_parameter(contribution.psize, "2 * radius")

# Configure the fit variables
# Start by configuring the scale factor and resolution factors.
# We want the sum of the phase scale factors to be 1.
recipe.create_new_variable("scale_CdS", 0.7)
recipe.constrain(generator_cds.scale, "scale_CdS")
recipe.constrain(generator_zns.scale, "1 - scale_CdS")
recipe.constrain_parameter(generator_cds.scale, "scale_CdS")
recipe.constrain_parameter(generator_zns.scale, "1 - scale_CdS")
# We also want the resolution factor to be the same on each.

# Vary the global scale as well.
Expand All @@ -117,7 +117,7 @@ def makeRecipe(stru1, stru2, datname):
)
# Since we know these have stacking disorder, constrain the B33 adps for
# each atom type.
recipe.constrain("B33_1_cds", "B33_0_cds")
recipe.constrain_parameter("B33_1_cds", "B33_0_cds")
recipe.add_variable(generator_cds.delta2, name="delta2_cds", value=5)

phase_zns = generator_zns.phase
Expand All @@ -128,7 +128,7 @@ def makeRecipe(stru1, stru2, datname):
recipe.add_variable(
phase_zns.sgpars.xyzpars.z_1, name="z_1_zns", tag="xyz"
)
recipe.constrain("B33_1_zns", "B33_0_zns")
recipe.constrain_parameter("B33_1_zns", "B33_0_zns")
recipe.add_variable(generator_zns.delta2, name="delta2_zns", value=2.5)

# Give the recipe away so it can be used!
Expand Down
14 changes: 7 additions & 7 deletions docs/examples/crystalpdfall.py
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Expand Up @@ -113,24 +113,24 @@ def makeRecipe(
for par in phase_ni.sgpars:
recipe.add_variable(par, name=par.name + "_ni")
delta2_ni = recipe.create_new_variable("delta2_ni", 2.5)
recipe.constrain(xgenerator_ni.delta2, delta2_ni)
recipe.constrain(ngenerator_ni.delta2, delta2_ni)
recipe.constrain(xgenerator_sini_ni.delta2, delta2_ni)
recipe.constrain_parameter(xgenerator_ni.delta2, delta2_ni)
recipe.constrain_parameter(ngenerator_ni.delta2, delta2_ni)
recipe.constrain_parameter(xgenerator_sini_ni.delta2, delta2_ni)

for par in phase_si.sgpars:
recipe.add_variable(par, name=par.name + "_si")
delta2_si = recipe.create_new_variable("delta2_si", 2.5)
recipe.constrain(xgenerator_si.delta2, delta2_si)
recipe.constrain(xgenerator_sini_si.delta2, delta2_si)
recipe.constrain_parameter(xgenerator_si.delta2, delta2_si)
recipe.constrain_parameter(xgenerator_sini_si.delta2, delta2_si)

# Now the experimental parameters
recipe.add_variable(xgenerator_ni.scale, name="xscale_ni")
recipe.add_variable(xgenerator_si.scale, name="xscale_si")
recipe.add_variable(ngenerator_ni.scale, name="nscale_ni")
recipe.add_variable(xcontribution_sini.scale, 1.0, "xscale_sini")
recipe.create_new_variable("pscale_sini_ni", 0.8)
recipe.constrain(xgenerator_sini_ni.scale, "pscale_sini_ni")
recipe.constrain(xgenerator_sini_si.scale, "1 - pscale_sini_ni")
recipe.constrain_parameter(xgenerator_sini_ni.scale, "pscale_sini_ni")
recipe.constrain_parameter(xgenerator_sini_si.scale, "1 - pscale_sini_ni")

# The qdamp parameters are too correlated to vary so we fix them based on
# previous measurements.
Expand Down
4 changes: 2 additions & 2 deletions docs/examples/crystalpdftwodata.py
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Expand Up @@ -121,8 +121,8 @@ def makeRecipe(ciffile, xdatname, ndatname):
# delta2 is a non-structual material property. Thus, we constrain together
# delta2 Parameter from each PDFGenerator.
delta2 = recipe.create_new_variable("delta2", 2)
recipe.constrain(xgenerator.delta2, delta2)
recipe.constrain(ngenerator.delta2, delta2)
recipe.constrain_parameter(xgenerator.delta2, delta2)
recipe.constrain_parameter(ngenerator.delta2, delta2)

# We only need to constrain phase properties once since there is a single
# ObjCrystCrystalParSet for the Crystal.
Expand Down
20 changes: 10 additions & 10 deletions docs/examples/crystalpdftwophase.py
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Expand Up @@ -90,12 +90,12 @@ def makeRecipe(niciffile, siciffile, datname):
# Start by configuring the scale factor and resolution factors.
# We want the sum of the phase scale factors to be 1.
recipe.create_new_variable("scale_ni", 0.1)
recipe.constrain(generator_ni.scale, "scale_ni")
recipe.constrain(generator_si.scale, "1 - scale_ni")
recipe.constrain_parameter(generator_ni.scale, "scale_ni")
recipe.constrain_parameter(generator_si.scale, "1 - scale_ni")
# We also want the resolution factor to be the same on each.
recipe.create_new_variable("qdamp", 0.03)
recipe.constrain(generator_ni.qdamp, "qdamp")
recipe.constrain(generator_si.qdamp, "qdamp")
recipe.constrain_parameter(generator_ni.qdamp, "qdamp")
recipe.constrain_parameter(generator_si.qdamp, "qdamp")

# Vary the global scale as well.
recipe.add_variable(contribution.scale, 1)
Expand Down Expand Up @@ -123,18 +123,18 @@ def makeRecipe(niciffile, siciffile, datname):
# derived has no uncertainty. Thus, we will tell the recipe to scale the
# residual, which means that it will be weighted as much as the average
# data point during the fit.
recipe.restrain("a_ni", lb=3.527, ub=3.527, scaled=True)
recipe.add_restraint("a_ni", lb=3.527, ub=3.527, scaled=True)
# Now we do the same with the delta2 and Biso parameters (remember that
# Biso = 8*pi**2*Uiso)
recipe.restrain("delta2_ni", lb=2.22, ub=2.22, scaled=True)
recipe.restrain("Biso_0_ni", lb=0.454, ub=0.454, scaled=True)
recipe.add_restraint("delta2_ni", lb=2.22, ub=2.22, scaled=True)
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@sbillinge sbillinge Mar 11, 2026

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I think I like add_restraint better than constrain_parameter. It is not completely clear to me whether we are constraining parameters or variables or what is happening. Actually, I think that the constraint maps parameters to variables somehow. In that case, to avoid awkwardness, does it make sense to call it add_constraint. I am open to discussion on this, but I since we are deprecating everything, it is really our opportunity to think about this and get it right this time....

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@cadenmyers13 cadenmyers13 Mar 11, 2026 •
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@sbillinge Yeah lets go with add_. I think the words constrain and restrain can also get mixed up in the heads of users (and mine lol). What if we did change,

  • constrain --> add_constraint
  • restrain --> add_penalty or add_bounds or add_soft_bounds

what do you think?

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We actually have a Restraint class that manages all the restraints as well as _restraints attributes, so this could get confusing if we change... I still am not much of a fan of how similar those two words are

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There is a Restraint.penalty method though that calculates the penalty, so add_penalty might be okay

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Let's go with add_penalty, I like that.

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@sbillinge okay i made the change, see the commit messages and the news items for whats changed

recipe.add_restraint("Biso_0_ni", lb=0.454, ub=0.454, scaled=True)
#
# We can do the same with the silicon values. We haven't done a thorough
# job of measuring the uncertainties in the results, so we'll scale these
# as well.
recipe.restrain("a_si", lb=5.430, ub=5.430, scaled=True)
recipe.restrain("delta2_si", lb=3.54, ub=3.54, scaled=True)
recipe.restrain("Biso_0_si", lb=0.645, ub=0.645, scaled=True)
recipe.add_restraint("a_si", lb=5.430, ub=5.430, scaled=True)
recipe.add_restraint("delta2_si", lb=3.54, ub=3.54, scaled=True)
recipe.add_restraint("Biso_0_si", lb=0.645, ub=0.645, scaled=True)

# Give the recipe away so it can be used!
return recipe
Expand Down
2 changes: 1 addition & 1 deletion docs/examples/debyemodel.py
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Expand Up @@ -152,7 +152,7 @@ def makeRecipe():
# breaking the restraint by the point-average chi^2 value so that the
# restraint is roughly as significant as any other data point throughout
# the fit.
recipe.restrain(recipe.offset, lb=0, scaled=True)
recipe.add_restraint(recipe.offset, lb=0, scaled=True)

# We're done setting up the recipe. We can now do other things with it.
return recipe
Expand Down
4 changes: 2 additions & 2 deletions docs/examples/debyemodelII.py
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Expand Up @@ -89,8 +89,8 @@ def makeRecipeII():
# We create a new Variable and use the recipe's "constrain" method to
# associate the Debye temperature parameters with that variable.
recipe.create_new_variable("thetaD", 100)
recipe.constrain(recipe.lowT.thetaD, "thetaD")
recipe.constrain(recipe.highT.thetaD, "thetaD")
recipe.constrain_parameter(recipe.lowT.thetaD, "thetaD")
recipe.constrain_parameter(recipe.highT.thetaD, "thetaD")
return recipe


Expand Down
6 changes: 3 additions & 3 deletions docs/examples/npintensity.py
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Expand Up @@ -290,15 +290,15 @@ def gaussian(q, q0, width):
lattice = phase.getLattice()
a = lattice.a
recipe.add_variable(a)
recipe.constrain(lattice.b, a)
recipe.constrain(lattice.c, a)
recipe.constrain_parameter(lattice.b, a)
recipe.constrain_parameter(lattice.c, a)
# We want to refine the thermal parameters as well. We will add a new
# Variable that we call "Uiso" and constrain the atomic Uiso values to
# this. Note that we don't give Uiso an initial value. The initial value
# will be inferred from the following constraints.
Uiso = recipe.create_new_variable("Uiso")
for atom in phase.getScatterers():
recipe.constrain(atom.Uiso, Uiso)
recipe.constrain_parameter(atom.Uiso, Uiso)

# Give the recipe away so it can be used!
return recipe
Expand Down
6 changes: 3 additions & 3 deletions docs/examples/npintensityII.py
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Expand Up @@ -173,15 +173,15 @@ def gaussian(q, q0, width):
a = recipe.add_variable(lattice.a)
# We want to allow for isotropic expansion, so we'll make constraints for
# that.
recipe.constrain(lattice.b, a)
recipe.constrain(lattice.c, a)
recipe.constrain_parameter(lattice.b, a)
recipe.constrain_parameter(lattice.c, a)
# We want to refine the thermal parameters as well. We will add a new
# variable that we call "Uiso" and constrain the atomic Uiso values to
# this. Note that we don't give Uiso an initial value. The initial value
# will be inferred from the subsequent constraints.
Uiso = recipe.create_new_variable("Uiso")
for atom in phase.getScatterers():
recipe.constrain(atom.Uiso, Uiso)
recipe.constrain_parameter(atom.Uiso, Uiso)

# Give the recipe away so it can be used!
return recipe
Expand Down
4 changes: 2 additions & 2 deletions docs/examples/nppdfobjcryst.py
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Expand Up @@ -73,7 +73,7 @@ def makeRecipe(molecule, datname):
# has no scattering power. It is only used as a reference point for
# our bond length. We don't want to constrain it.
if not atom.isDummy():
recipe.constrain(atom.Biso, Biso)
recipe.constrain_parameter(atom.Biso, Biso)

# We need to let the molecule expand. If we were modeling it as a crystal,
# we could let the unit cell expand. For instruction purposes, we use a
Expand All @@ -97,7 +97,7 @@ def makeRecipe(molecule, datname):
# This creates a Parameter that moves the second atom according to the
# bond length. Note that each Parameter needs a unique name.
par = c60.addBondLengthParameter("rad%i" % i, center, atom)
recipe.constrain(par, radius)
recipe.constrain_parameter(par, radius)

# Add the correlation term, scale. The scale is too short to effectively
# determine qdamp.
Expand Down
8 changes: 4 additions & 4 deletions docs/examples/nppdfsas.py
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Expand Up @@ -113,8 +113,8 @@ def makeRecipe(ciffile, grdata, iqdata):
# Even though the cfcalculator and sasgenerator depend on the same sas
# model, we must still constrain the cfcalculator Parameters so that it is
# informed of changes in the refined parameters.
recipe.constrain(cfcalculator.radius_a, "radius_a")
recipe.constrain(cfcalculator.radius_b, "radius_b")
recipe.constrain_parameter(cfcalculator.radius_a, "radius_a")
recipe.constrain_parameter(cfcalculator.radius_b, "radius_b")

return recipe

Expand All @@ -126,9 +126,9 @@ def fitRecipe(recipe):
recipe.set_weight(recipe.pdf, 0)
recipe.fix("all")
recipe.free("radius_a", "radius_b", iqscale=1e8)
recipe.constrain("radius_b", "radius_a")
recipe.constrain_parameter("radius_b", "radius_a")
scipyOptimize(recipe)
recipe.unconstrain("radius_b")
recipe.unconstrain_parameter("radius_b")

# Tune PDF
recipe.set_weight(recipe.pdf, 1)
Expand Down
16 changes: 8 additions & 8 deletions docs/examples/simplepdftwophase.py
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Expand Up @@ -47,8 +47,8 @@ def makeRecipe(niciffile, siciffile, datname):
# Start by configuring the scale factor and resolution factors.
# We want the sum of the phase scale factors to be 1.
recipe.create_new_variable("scale_ni", 0.1)
recipe.constrain(contribution.ni.scale, "scale_ni")
recipe.constrain(contribution.si.scale, "1 - scale_ni")
recipe.constrain_parameter(contribution.ni.scale, "scale_ni")
recipe.constrain_parameter(contribution.si.scale, "1 - scale_ni")
# We also want the resolution factor to be the same on each. This is done
# for free by the PDFContribution. We simply need to add it to the recipe.
recipe.add_variable(contribution.qdamp, 0.03)
Expand Down Expand Up @@ -82,18 +82,18 @@ def makeRecipe(niciffile, siciffile, datname):
# derived has no uncertainty. Thus, we will tell the recipe to scale the
# residual, which means that it will be weighted as much as the average
# data point during the fit.
recipe.restrain("a_ni", lb=3.527, ub=3.527, scaled=True)
recipe.add_restraint("a_ni", lb=3.527, ub=3.527, scaled=True)
# Now we do the same with the delta2 and Biso parameters (remember that
# Biso = 8*pi**2*Uiso)
recipe.restrain("delta2_ni", lb=2.22, ub=2.22, scaled=True)
recipe.restrain("Biso_0_ni", lb=0.454, ub=0.454, scaled=True)
recipe.add_restraint("delta2_ni", lb=2.22, ub=2.22, scaled=True)
recipe.add_restraint("Biso_0_ni", lb=0.454, ub=0.454, scaled=True)
#
# We can do the same with the silicon values. We haven't done a thorough
# job of measuring the uncertainties in the results, so we'll scale these
# as well.
recipe.restrain("a_si", lb=5.430, ub=5.430, scaled=True)
recipe.restrain("delta2_si", lb=3.54, ub=3.54, scaled=True)
recipe.restrain("Biso_0_si", lb=0.645, ub=0.645, scaled=True)
recipe.add_restraint("a_si", lb=5.430, ub=5.430, scaled=True)
recipe.add_restraint("delta2_si", lb=3.54, ub=3.54, scaled=True)
recipe.add_restraint("Biso_0_si", lb=0.645, ub=0.645, scaled=True)

# Give the recipe away so it can be used!
return recipe
Expand Down
18 changes: 9 additions & 9 deletions docs/examples/threedoublepeaks.py
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Expand Up @@ -121,9 +121,9 @@ def peakloc(mu):
return 180 / pi * arcsin(pi / 180 * l2 * sin(mu) / l1)

recipe.register_function(peakloc)
recipe.constrain(contribution.mu12, "peakloc(mu11)")
recipe.constrain(contribution.mu22, "peakloc(mu21)")
recipe.constrain(contribution.mu32, "peakloc(mu31)")
recipe.constrain_parameter(contribution.mu12, "peakloc(mu11)")
recipe.constrain_parameter(contribution.mu22, "peakloc(mu21)")
recipe.constrain_parameter(contribution.mu32, "peakloc(mu31)")

# Vary the width of the peaks. We know the functional form of the peak
# broadening.
Expand All @@ -139,20 +139,20 @@ def sig(sig0, dsig, mu):
# Now constrain the peak widths to this
recipe.sig0.value = 0.001
recipe.dsig.value = 4.0
recipe.constrain(contribution.sig11, "sig(sig0, dsig, mu11)")
recipe.constrain(
recipe.constrain_parameter(contribution.sig11, "sig(sig0, dsig, mu11)")
recipe.constrain_parameter(
contribution.sig12,
"sig(sig0, dsig, mu12)",
ns={"mu12": contribution.mu12},
)
recipe.constrain(contribution.sig21, "sig(sig0, dsig, mu21)")
recipe.constrain(
recipe.constrain_parameter(contribution.sig21, "sig(sig0, dsig, mu21)")
recipe.constrain_parameter(
contribution.sig22,
"sig(sig0, dsig, mu22)",
ns={"mu22": contribution.mu22},
)
recipe.constrain(contribution.sig31, "sig(sig0, dsig, mu31)")
recipe.constrain(
recipe.constrain_parameter(contribution.sig31, "sig(sig0, dsig, mu31)")
recipe.constrain_parameter(
contribution.sig32,
"sig(sig0, dsig, mu32)",
ns={"mu32": contribution.mu32},
Expand Down
35 changes: 35 additions & 0 deletions news/recipeorg-dep2.rst
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@@ -0,0 +1,35 @@
**Added:**

* Added ``constrain_parameter`` method to ``RecipeOrganizer``.
* Added ``unconstrain_parameter`` method to ``RecipeOrganizer``.
* Added ``add_restraint`` method to ``RecipeOrganizer``.
* Added ``remove_restraint`` method to ``RecipeOrganizer``.
* Added ``register_restraint`` method to ``RecipeOrganizer``.
* Added ``clear_all_restraints`` method to ``RecipeOrganizer``.
* Added ``get_equation_from_string`` method to ``RecipeOrganizer``.

**Changed:**

* <news item>

**Deprecated:**

* Deprecated ``constrain`` method of ``RecipeOrganizer``. Use ``constrain_parameter`` instead.
* Deprecated ``unconstrain`` method of ``RecipeOrganizer``. Use ``unconstrain_parameter`` instead.
* Deprecated ``restrain`` method of ``RecipeOrganizer``. Use ``add_restraint`` instead.
* Deprecated ``unrestrain`` methods of ``RecipeOrganizer``. Use ``remove_restraint`` instead.
* Deprecated ``addRestraint`` method of ``RecipeOrganizer``. Use ``register_restraint`` instead.
* Deprecate ``clearRestraints`` method of ``RecipeOrganizer``. Use ``clear_all_restraints`` instead.
* Deprecated ``equationFromString`` method of ``RecipeOrganizer``. Use ``get_equation_from_string`` instead.

**Removed:**

* <news item>

**Fixed:**

* <news item>

**Security:**

* <news item>
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