Restructure and Reorganize project

.github/workflows/test.yml

@@ -45,5 +45,4 @@ jobs:
       - name: Check that the docs build (linux only)
         if: matrix.config.doc == 1
         run: |
-          pip install sphinx
           make -j 4 -C doc SPHINXOPTS="-W --keep-going" html

.gitignore

@@ -60,3 +60,5 @@ venv.bak/
 .idea
 *.swp
 *.bak
+
+test-files/

.pre-commit-config.yaml

@@ -9,7 +9,6 @@ repos:
         args: [--allow-multiple-documents]
       # - id: end-of-file-fixer
       # - id: trailing-whitespace
-
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.6.9
     hooks:

Makefile

@@ -13,3 +13,18 @@ lint: ## Run ruff linting
 .PHONY: format
 format: ## Run ruff formatting
 	@ruff format refl1d/ tests/ setup.py
+
+.PHONY: clean
+clean: ## Delete some cruft from builds/testing/etc.
+	rm -f `find . -type f -name '*.py[co]'`
+	rm -rf `find . -name __pycache__ -o -name "*.egg-info"` \
+		`find . -name 'output-*'` \
+		.coverage build dist \
+		doc/_build doc/api doc/tutorial \
+		.pytest_cache \
+		.ruff_cache 
+
+.PHONY: test
+test: ## Run pytest and doc tests
+	pytest -v
+	python check_examples.py --chisq

compareopt/slabs.py

@@ -1,17 +1,19 @@
-from __future__ import print_function
-
+import sys
 from random import getrandbits
-from numpy.random import uniform
-from refl1d.names import *
+
+import numpy as np
 from bumps.parameter import summarize
+from numpy.random import uniform
+
+from refl1d.models import SLD, Experiment, FitProblem, NeutronProbe, air, silicon
 
 num_layers = int(sys.argv[1])
 init_file = sys.argv[2] if len(sys.argv) > 2 else "/tmp/problem"
 
 out = open(init_file, "w")
 seed = getrandbits(16)
 print("seed", seed, file=out)
-numpy.random.seed(int(seed))
+np.random.seed(int(seed))
 
 
 # CONSTRAINTS="unknown"
@@ -48,7 +50,7 @@ def genlayer(name):
 
 sample = silicon(0, 5) | layers | air
 
-T = numpy.linspace(0, 5, 100)
+T = np.linspace(0, 5, 100)
 probe = NeutronProbe(T=T, dT=0.01, L=4.75, dL=0.0475)
 
 M = Experiment(probe=probe, sample=sample)

conftest.py

@@ -1,5 +1,6 @@
 collect_ignore = [
     "doc/guide/toffset.py",
+    "refl1d/wx_gui/",
     "tests/refl1d/Q_probe_oversample.py",
     # "tests/refl1d/snsdata_test.py",
 ]

doc/conf.py

@@ -11,7 +11,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
+import os
+import sys
 
 print("python %s" % sys.executable)
 
@@ -36,10 +37,11 @@
 print("== end path ==")
 
 # Register the refl1d model loader
-import refl1d.fitplugin
 import bumps.cli
 
-bumps.cli.install_plugin(refl1d.fitplugin)
+from refl1d.models.bumps_interface import fitplugin
+
+bumps.cli.install_plugin(fitplugin)
 
 # -- General configuration -----------------------------------------------------
 

doc/examples/TOF/du53.py

@@ -1,4 +1,4 @@
-from refl1d.names import *
+from refl1d.models import *
 
 instrument = SNS.Liquids(Tlo=0.3, slits_at_Tlo=0.2, TOF_range=(12000, 40000))
 probes = [

doc/examples/distribution/dist-example.py

@@ -1,8 +1,11 @@
-import sys, os
+import os
+import sys
+
+import numpy
 
 sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
-from refl1d.names import *
-from refl1d.dist import Weights, DistributionExperiment
+from refl1d.models import *
+from refl1d.models.dist import Weights, DistributionExperiment
 
 # Materials
 nickel = Material("Ni", fitby="relative_density")

doc/examples/eiv/model.py

@@ -9,7 +9,9 @@
 an error-in-variables fit.
 """
 
-from refl1d.names import *
+import numpy as np
+
+from refl1d.models import *
 
 # ********** model setup **********
 
@@ -26,7 +28,7 @@
 # n = 20
 n = 400
 dT, L, dL = 0.02, 4.75, 0.0475
-T = numpy.linspace(0, 5, n)
+T = np.linspace(0, 5, n)
 
 # Set the motor uncertainty and the measurement uncertainty.
 angle_uncertainty = 0.005
@@ -142,7 +144,7 @@ def residuals(self):
         if self.probe.polarized:
             have_data = not all(x is None or x.R is None for x in self.probe.xs)
         else:
-            have_data = not (self.probe.R is None)
+            have_data = self.probe.R is not None
         if not have_data:
             resid = np.zeros(0)
             self._cache["residuals"] = resid

doc/examples/ex1/gendata.py

@@ -4,14 +4,15 @@
 
 from numpy.random import seed
 from bumps.fitproblem import load_problem
-from refl1d.snsdata import write_file
+
+from refl1d.models import SNS
 
 
 def main():
     seed(1)
     problem = load_problem("nifilm-tof.py")
     for i, p in enumerate(problem.fitness.probe.probes):
-        write_file("nifilm-tof-%d.dat" % (i + 1), p, title="Simulated 100 A Ni film")
+        SNS.write_file("nifilm-tof-%d.dat" % (i + 1), p, title="Simulated 100 A Ni film")
 
 
 if __name__ == "__main__":

doc/examples/ex1/nifilm-back.py

@@ -7,7 +7,9 @@
 #
 # We set up the example as before.
 
-from refl1d.names import *
+import numpy
+
+from refl1d.models import *
 
 nickel = Material("Ni")
 sample = silicon(0, 25) | nickel(100, 5) | air

doc/examples/ex1/nifilm-data.py

@@ -11,25 +11,25 @@
 
 # The sample and instrument definition is the same as before:
 
-from refl1d.names import *
+from refl1d.models import *
 
 nickel = Material("Ni")
 sample = silicon(0, 5) | nickel(100, 5) | air
 
 instrument = SNS.Liquids()
 
 # In this case we are loading multiple data sets into the same
-# :class:`ProbeSet <refl1d.probe.ProbeSet>` object.  If your
+# :class:`ProbeSet <refl1d.models.probe.probe.ProbeSet>` object.  If your
 # reduction program stitches together the data for you, then you can simply
 # use ``probe=instrument.load('file')``.
 
 files = ["nifilm-tof-%d.dat" % d for d in (1, 2, 3, 4)]
 probe = ProbeSet(instrument.load(f) for f in files)
 
 # The data and sample are combined into an
-# :class:`Experiment <refl1d.experiment.Experiment>`,
+# :class:`Experiment <refl1d.models.experiment.Experiment>`,
 # which again is bundled as a
-# :class:`FitProblem <refl1d.fitter.FitProblem>`
+# :class:`FitProblem <refl1d.models.bumps_interface.fitproblem.FitProblem>`
 # for the fitting program.
 
 M = Experiment(probe=probe, sample=sample)

doc/examples/ex1/nifilm-fit.py

@@ -8,7 +8,7 @@
 # We use the usual sample definition, except we set the thickness of the
 # nickel layer to 125 |Ang| so that the model does not match the data:
 
-from refl1d.names import *
+from refl1d.models import *
 
 # Turn off resolution bars in plots.  Only do this after you have plotted the
 # data with resolution bars so you know it looks reasonable, and you are not

doc/examples/ex1/nifilm-mixture.py

@@ -7,7 +7,7 @@
 # it does demonstrate a way to form a mixture of two materials by volume
 # :download:`nifilm-mixture.py <nifilm-mixture.py>`:
 
-from refl1d.names import *
+from refl1d.models import *
 
 # Here is the mixture formula.  We are giving the mass density along with the
 # chemical formula for each part, followed by the percentage for that part.

doc/examples/ex1/nifilm-tof.py

@@ -13,7 +13,7 @@
 #
 # The sample definition is the same:
 
-from refl1d.names import *
+from refl1d.models import *
 
 nickel = Material("Ni")
 sample = silicon(0, 5) | nickel(100, 5) | air
@@ -39,7 +39,7 @@
 # so much for a time-of-flight measurement, the central points will be
 # measured with much better precision, and the end points will be measured
 # with lower precision.  See
-# :meth:`Pulsed.simulate <refl1d.instrument.Pulsed.simulate>` for details
+# :meth:`Pulsed.simulate <refl1d.models.probe.instrument.Pulsed.simulate>` for details
 # on all simulation parameters.
 
 # Finally, we bundle the simulated measurement as a fit problem which

doc/examples/ex1/nifilm.py

@@ -26,9 +26,15 @@
 #
 # The first step in any model is to load the names of the functions and
 # data that we are going to use.  These are defined in a module named
-# refl1d.names, and we import them all as follows:
+# refl1d.models, and we can import them as follows:
 
-from refl1d.names import *
+import numpy  # This is the numpy library, which is used for numerical operations
+from refl1d.models import Material, Experiment, NeutronProbe, FitProblem, silicon, air
+
+# Alternatively, you can import them all, using:
+from refl1d.models import *
+# but this is not recommended for anything but simple scripts,
+# and may cause linting issues in your IDE.
 
 # This statement imports functions like SLD and Material for defining
 # materials, Parameter, Slab and Stack for defining materials,

doc/examples/four_column/model.py

@@ -7,7 +7,7 @@
 
 # The following is copied directly from the spin value example
 
-from refl1d.names import *
+from refl1d.models import *
 
 Si = SLD(name="Si", rho=2.0737, irho=2.376e-5)
 Cu = SLD(name="Cu", rho=6.5535, irho=8.925e-4)
@@ -43,7 +43,7 @@
 # Here's the new loader.  Much simplified since the reduction computes the
 # appropriate $\Delta Q$ for the data points, and we don't need to specify
 # the slit openings and distances for the data set.  The options to the
-# :func:`refl1d.probe.load4` function allow you to override things during
+# :func:`refl1d.models.probe.data_loaders.load4.load4` function allow you to override things during
 # load, such as the sample broadening of the resolution.
 
 probe = load4("refl.txt")

doc/examples/freemag/pmf.py

@@ -1,5 +1,5 @@
-from refl1d.names import *
-from copy import copy
+import numpy
+from refl1d.models import *
 
 # FIT USING REFL1D 0.6.12
 # === Data files ===

doc/examples/ill_posed/anticor.py

@@ -15,7 +15,8 @@
 # Since silicon and air are defined, the only material we need to
 # define is nickel.
 
-from refl1d.names import *
+import numpy
+from refl1d.models import *
 
 nickel = Material("Ni")
 

doc/examples/ill_posed/tethered.py

@@ -1,7 +1,10 @@
-from refl1d.names import *
-import periodictable
 from copy import copy
 
+import numpy
+import periodictable
+
+from refl1d.models import *
+
 numpy.random.seed(1)
 
 # Start with an SiOx layer of pure silicon so there is no contrast match.

doc/examples/interface/model.py

@@ -1,4 +1,6 @@
-from refl1d.names import *
+import numpy
+
+from refl1d.models import *
 
 
 sharp = FreeInterface(below=silicon, above=gold, dz=[0.01, 1, 0.01], dp=[0.01, 1, 0.01])

doc/examples/magrough/model.py

@@ -1,4 +1,6 @@
-from refl1d.names import *
+import numpy
+
+from refl1d.models import *
 
 nickel = Material("Ni")
 copper = Material("Cu")

doc/examples/mixed/mixed.py

@@ -16,7 +16,9 @@
 # Since silicon and air are defined, the only material we need to
 # define is nickel.
 
-from refl1d.names import *
+import numpy
+
+from refl1d.models import *
 
 nickel = Material("Ni")
 

doc/examples/mixed/mixed_magnetic.py

@@ -1,4 +1,6 @@
-from refl1d.names import *
+import numpy
+
+from refl1d.models import *
 
 nickel = Material("Ni")
 

doc/examples/polymer/freeform.py

@@ -5,7 +5,7 @@
 # freeform interface which varies the density between layers using a
 # cubic spline interface.
 
-from refl1d.names import *
+from refl1d.models import *
 from copy import copy
 
 # Materials used

doc/examples/polymer/tethered.py

@@ -4,7 +4,7 @@
 #
 # We first need to define the materials
 
-from refl1d.names import *
+from refl1d.models import *
 from copy import copy
 
 # === Materials ===
@@ -17,15 +17,15 @@
 
 # In this case we are using the neutron scattering length density as is
 # standard practice in reflectivity experiments rather than the chemical
-# formula and mass density.  The :class:`SLD <refl1d.material.SLD>` class
+# formula and mass density.  The :class:`SLD <refl1d.models.sample.material.SLD>` class
 # allows us to name the material and define the real and imaginary components
 # of scattering length density $\rho$.  Note that we are using the imaginary
 # $\rho_i$ rather than the absorption coefficient $\mu = 2\lambda\rho_i$
 # since it removes the dependence on wavelength from the calculation of
 # the reflectivity.
 #
 # For the tethered polymer we don't use a simple slab model, but instead
-# define a :class:`PolymerBrush <refl1d.polymer.PolymerBrush>`
+# define a :class:`PolymerBrush <refl1d.models.sample.polymer.PolymerBrush>`
 # layer, which understands that the system is compose of polymer plus
 # solvent, and that the polymer chains tail off like:
 #