Restructure and Reorganize project

.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: v0.6.1
     hooks:

Makefile

@@ -13,3 +13,12 @@ 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 \
+		.pytest_cache \
+		.ruff_cache 

doc/examples/distribution/dist-example.py

@@ -2,7 +2,7 @@
 
 sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
 from refl1d.names import *
-from refl1d.dist import Weights, DistributionExperiment
+from refl1d.models.dist import Weights, DistributionExperiment
 
 # Materials
 nickel = Material("Ni", fitby="relative_density")

doc/examples/four_column/model.py

@@ -7,7 +7,9 @@
 
 # The following is copied directly from the spin value example
 
-from refl1d.names import *
+from refl1d.models.experiment import FitProblem
+from refl1d.names import air, SLD, Magnetism, MagnetismTwist, Experiment
+from refl1d.readers import load4
 
 Si = SLD(name="Si", rho=2.0737, irho=2.376e-5)
 Cu = SLD(name="Cu", rho=6.5535, irho=8.925e-4)
@@ -43,7 +45,7 @@
 # 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.readers.load4` function allow you to override things during
 # load, such as the sample broadening of the resolution.
 
 probe = load4("refl.txt")

doc/examples/profile/model.py

@@ -14,8 +14,8 @@
 # FunctionalProfile and FunctionalMagnetism are already available from
 # refl1d.names, but a couple of aliases make them a little easier to access.
 
-from refl1d.flayer import FunctionalProfile as FP
-from refl1d.flayer import FunctionalMagnetism as FM
+from refl1d.models.sample.flayer import FunctionalProfile as FP
+from refl1d.models.sample.flayer import FunctionalMagnetism as FM
 
 # Define the nuclear profile function.
 #

doc/examples/staj/De2_VATR.py

@@ -1,5 +1,5 @@
 from refl1d.names import *
-from refl1d.stajconvert import load_mlayer
+from refl1d.readers.stajconvert import load_mlayer
 
 # Load neutron model and data from staj file
 # Layer names are ordered from substrate to surface, and defaults to

doc/genmods.py

@@ -19,8 +19,6 @@
 MODULE_TEMPLATE is the template for each api module.
 """
 
-from __future__ import with_statement, print_function
-
 OPTIONS = {
     "absolute": False,  # True if package.module in table of contents
     "dir": "api",  # Destination directory for the api docs
@@ -32,42 +30,37 @@
 MODULES = [
     # ('__init__', 'Top level namespace'),
     # ('interface', 'Interface'),
-    ("abeles", "Pure python reflectivity calculator"),
-    ("anstodata", "Reader for ANSTO data format"),
-    ("cheby", "Freeform - Chebyshev model"),
-    # ('composition', 'Composition space model'),
-    # ('corrtest', 'Test for residual structure'),
-    ("dist", "Non-uniform samples"),
-    ("errors", "Plot sample profile uncertainty"),
-    ("experiment", "Reflectivity fitness function"),
+    # ('deprecated.magnetic', 'Magnetic Models'),
+    ("deprecated.freeform", "Freeform - Parametric B-Spline"),
     ("fitplugin", "Bumps plugin definition for reflectivity models"),
-    ("flayer", "Functional layers"),
-    ("freeform", "Freeform - Parametric B-Spline"),
-    ("fresnel", "Pure python Fresnel reflectivity calculator"),
-    ("garefl", "Adaptor for garefl models"),
-    ("instrument", "Reflectivity instrument definition"),
-    # ('interface', 'Models of interfacial roughness'),
-    # ('magnetic', 'Magnetic Models'),
-    ("magnetism", "Magnetic Models"),
-    ("material", "Material"),
-    ("materialdb", "Materials Database"),
-    ("model", "Reflectivity Models"),
-    ("mono", "Freeform - Monotonic Spline"),
+    ("fitting.abeles", "Pure python reflectivity calculator"),
+    ("fitting.backends", "Backends for low level reflectivity calculations"),
+    ("fitting.fresnel", "Pure python Fresnel reflectivity calculator"),
+    ("fitting.profile", "Model profile"),
+    ("fitting.reflectivity", "Basic reflectivity calculations"),
+    ("fitting.resolution", "Beam resolution calculations"),
+    ("fitting.uncertainty", "Plot sample profile uncertainty"),
+    ("models.dist", "Non-uniform samples"),
+    ("models.experiment", "Reflectivity fitness function"),
+    ("models.instrument", "Reflectivity instrument definition"),
+    ("models.probe", "Instrument probe"),
+    ("models.sample.cheby", "Freeform - Chebyshev model"),
+    ("models.sample.flayer", "Functional layers"),
+    ("models.sample.layers", "Models of Reflectivity Layer Structure"),
+    ("models.sample.magnetism", "Magnetic Models"),
+    ("models.sample.material", "Material"),
+    ("models.sample.materialdb", "Materials Database"),
+    ("models.sample.mono", "Freeform - Monotonic Spline"),
+    ("models.sample.polymer", "Polymer models"),
     ("names", "Public API"),
-    ("ncnrdata", "NCNR Data"),
-    # ('plottable', 'Style-based plot definitions'),
-    ("polymer", "Polymer models"),
-    ("probe", "Instrument probe"),
-    ("profile", "Model profile"),
-    ("refllib", "Low level reflectivity calculations"),
-    ("reflectivity", "Reflectivity"),
-    ("resolution", "Resolution"),
-    ("snsdata", "SNS Data"),
-    ("staj", "Staj File"),
-    ("stajconvert", "Staj File Converter"),
-    ("stitch", "Overlapping reflectivity curve stitching"),
-    ("support", "Environment support"),
-    ("util", "Miscellaneous functions"),
+    ("readers.anstodata", "Reader for ANSTO data format"),
+    ("readers.ncnrdata", "NCNR Data"),
+    ("readers.snsdata", "SNS Data"),
+    ("readers.staj", "Staj File"),
+    ("readers.stajconvert", "Staj File Converter"),
+    ("readers.stitch", "Overlapping reflectivity curve stitching"),
+    ("utils.support", "Environment support"),
+    ("utils.util", "Miscellaneous functions"),
 ]
 
 

doc/getting_started/install.rst

@@ -9,10 +9,10 @@ Installing the application
 | Windows installer: :slink:`%(winexe)s`
 | Source: :slink:`%(srczip)s`
 
-Recent versions of the Refl1D application are available for windows
+Recent versions of the Refl1D application are available for Windows
 from `github <https://github.com/reflectometry/refl1d/releases/latest>`_.
 The file `Refl1D-VERSION-exe.zip` contains python, the application, the
-supporting libraries and everything else needed to run the application.
+supporting libraries, and everything else needed to run the application.
 
 To install, download and extract the zip file. Go to the extracted directory
 and click on `refl1d_gui.bat`. This will open a dialog saying that the
@@ -79,7 +79,7 @@ You will need a C/C++ compiler.  If you already have Microsoft Visual C
 installed you are done. If not, you can use the MinGW compiler that is supplied
 with your python environment or download your own.  You can set MinGW
 as the default compiler by creating the file *Lib\distutils\\distutils.cfg*
-in your python directory (e.g., *C:\\Python3.8*) with the following content::
+in your python directory (e.g., *C:\\Python3.9*) with the following content::
 
     [build]
     compiler=mingw32

doc/guide/experiment.rst

@@ -40,8 +40,8 @@ function to yield reflectivities at intervals of 0.01.
 ::
 
     >>> from numpy import arange
-    >>> from refl1d.reflectivity import reflectivity_amplitude as reflamp
-    >>> from refl1d.reflectivity import convolve
+    >>> from refl1d.fitting.reflectivity import reflectivity_amplitude as reflamp
+    >>> from refl1d.fitting.reflectivity import convolve
     >>> Qin = arange(0,0.21,0.001)
     >>> w,rho,irho,sigma = zip((0,2.07,0,5),(0,0,0,0))
     >>> # the last layer has no interface

doc/guide/fitting.rst

@@ -410,7 +410,7 @@ Next we can reload the the error sample data from the DREAM MCMC sequence::
 
     from bumps.dream.state import load_state
     from bumps.errplot import calc_errors_from_state
-    from refl1d.errors import align_profiles
+    from refl1d.uncertainty import align_profiles
 
     state = load_state(os.path.join(store, model[:-3]))
     state.mark_outliers()
@@ -419,7 +419,7 @@ Next we can reload the the error sample data from the DREAM MCMC sequence::
     aligned_profiles = align_profiles(profiles, slabs, 2.5)
     # ... insert profile and residuals uncertainty plots here ...
 
-The function :func:`refl1d.errors.calc_errors` provides details on the data
+The function :func:`refl1d.uncertainty.calc_errors` provides details on the data
 structures for *profiles*, *Q* and *residuals*.  Look at the source in
 refl1d/errors.py to see how this data is used to produce the error plots
 with _profiles_overplot, _profiles_contour, _residuals_overplot and

doc/guide/intro.rst

@@ -9,7 +9,7 @@ Using Refl1D
 The Refl1D library is organized into modules.  Specific functions and
 classes can be imported from a module, such as::
 
-    >>> from refl1d.model import Slab
+    >>> from refl1d.models.sample.layers import Slab
 
 The most common imports have been gathered together in refl1d.names.  This
 allows you to use names like :class:`Slab <refl1d.model.Slab>` directly::

doc/guide/toffset.py

@@ -21,7 +21,7 @@
 """
 
 from pylab import *
-from refl1d.reflectivity import reflectivity
+from ornl.refl1d.refl1d.fitting.reflectivity import reflectivity
 
 rho = 2.07  # silicon rho for neutrons
 L = 5  # Wavelength 5 angstroms

refl1d/refl_tr.py → explore/refl_tr.py

@@ -1,5 +1,4 @@
-# This program is public domain.
-r"""
+"""
 Optical matrix form of the reflectivity calculation.
 
 This is a pure python implementation of reflectometry which returns the
@@ -35,10 +34,8 @@
 [4] https://en.wikipedia.org/wiki/Prefix_sum
 """
 
-from __future__ import print_function, division
-
 import numpy as np
-from numpy import asarray, isscalar, empty, ones, ones_like
+from numpy import asarray, isscalar, ones, ones_like
 from numpy import sqrt, exp, pi
 
 
@@ -226,7 +223,7 @@ def check():
     rho *= 100  # show point below critical edge
     print("q", q)
     try:
-        from .abeles import refl
+        from refl1d.fitting.abeles import refl
 
         r_old = refl(q / 2, depth, rho, irho=irho, sigma=sigma)
         print("rold", r_old)

pyproject.toml

@@ -22,8 +22,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    # "bumps>=0.7.16",
-    "bumps@git+https://github.com/bumps/bumps.git#egg=master",
+    "bumps >= 1.0.0a0",
     "matplotlib",
     "numba",
     "numpy",
@@ -32,9 +31,9 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-dev = ["pre-commit", "ruff", "pytest", "pytest-cov"]
+dev = ["pre-commit", "ruff", "pytest", "pytest-cov", "sphinx"]
 full = ["wxpython", "ipython"]
-webview = ["bumps[webview]@git+https://github.com/bumps/bumps.git#egg=master"]
+webview = ["bumps[webview] >= 1.0.0a0"]
 
 [project.urls]
 documentation = "https://refl1d.github.io"
@@ -47,9 +46,7 @@ build-backend = "setuptools.build_meta"
 
 [tool.ruff]
 line-length = 120
-exclude = [
-    "*.txt",
-]
+exclude = ["*.txt"]
 
 # [tool.ruff.lint]
 # select = [
@@ -65,15 +62,11 @@ exclude = [
 version = { attr = "refl1d.__version__" }
 
 [tool.setuptools]
-packages = [
-    "refl1d",
-    "refl1d.view",
-    "refl1d.lib.python",
-    "refl1d.lib.numba",
-    "refl1d.webview.server",
-]
 script-files = ["bin/refl1d_cli.py", "bin/refl1d_gui.py"]
 
+[tool.setuptools.packages.find]
+include = ["refl1d"]
+
 [project.scripts]
 refl1d = "refl1d.main:main"
 refl1d-webview = "refl1d.webview.server.webserver:main"

refl1d/__init__.py

@@ -29,8 +29,8 @@
 def use(backend_name: BACKEND_NAMES):
     global BACKEND_NAME
     BACKEND_NAME = backend_name
-    if "refl1d.refllib" in sys.modules:
+    if "refl1d.fitting.backends" in sys.modules:
         # then it's already been imported:
-        import refl1d.refllib
+        import refl1d.fitting.backends as backends
 
-        refl1d.refllib.set_backend(backend_name)
+        backends.set_backend(backend_name)