Formatting changes, update imports, other minor changes

.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

@@ -24,6 +24,7 @@ refl1d-webview-client*.tgz
 /bumps-*
 /Refl1D.pdf
 /output-*
+test-files/
 
 # Build
 *.so

Makefile

@@ -5,6 +5,20 @@ ROOTDIR = $(shell pwd)
 help: ## Print this help message
 	@perl -nle'print $& if m{^[/a-zA-Z_-]+:.*?## .*$$}' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-25s\033[0m %s\n", $$1, $$2}'
 
+.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
 
 .PHONY: lint
 lint: ## Run ruff linting

compareopt/slabs.py

@@ -1,9 +1,9 @@
-from __future__ import print_function
-
 from random import getrandbits
+
+from bumps.parameter import summarize
 from numpy.random import uniform
+
 from refl1d.names import *
-from bumps.parameter import summarize
 
 num_layers = int(sys.argv[1])
 init_file = sys.argv[2] if len(sys.argv) > 2 else "/tmp/problem"

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/_extensions/wx_directive.py

@@ -15,10 +15,14 @@
 
 # Note: adapted from matplotlib.sphinxext.plot_directive by Paul Kienzle
 
-from six.moves import StringIO
-
-import sys, os, glob, shutil, hashlib, imp, warnings
+import imp
+import os
 import re
+import shutil
+import sys
+import warnings
+
+from six.moves import StringIO
 
 try:
     from hashlib import md5
@@ -34,16 +38,13 @@
     from docutils.parsers.rst.directives.images import Image
 
     align = Image.align
-from docutils import nodes
-import sphinx
-
-import wx
-
 # Matplotlib helper utilities
 import matplotlib.cbook as cbook
 import numpy
 import png
-
+import sphinx
+import wx
+from docutils import nodes
 
 sphinx_version = sphinx.__version__.split(".")
 # The split is necessary for sphinx beta versions where the string is

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)
 

doc/examples/distribution/dist-example.py

@@ -1,4 +1,5 @@
-import sys, os
+import os
+import sys
 
 sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
 from refl1d.names import *

doc/genmods.py

@@ -19,7 +19,11 @@
 MODULE_TEMPLATE is the template for each api module.
 """
 
-from __future__ import with_statement, print_function
+import inspect
+import sys
+from os import makedirs
+from os.path import abspath, dirname, exists, getmtime
+from os.path import join as joinpath
 
 OPTIONS = {
     "absolute": False,  # True if package.module in table of contents
@@ -119,11 +123,6 @@
 """
 # ===================== Documentation generator =====================
 
-from os import makedirs
-from os.path import exists, dirname, getmtime, join as joinpath, abspath
-import inspect
-import sys
-
 
 def newer(file1, file2):
     return not exists(file1) or (getmtime(file1) < getmtime(file2))

doc/getting_started/contributing.rst

@@ -6,6 +6,11 @@ Contributing Changes
 
 .. contents:: :local:
 
+
+The refl1d package is a community project, and we welcome contributions from anyone.  
+The package is developed collaboratively on `Github <https://github.com>`_ - if you don't have an account yet, you can sign up for free. For direct write access to the repository, it is required that your accout have `two-factor authentication enabled <https://docs.github.com/en/authentication/securing-your-account-with-two-factor-authentication-2fa>`_.
+You may also want to configure your account to use `SSH keys <https://docs.github.com/en/authentication/connecting-to-github-with-ssh>`_ for authentication.
+
 The best way to contribute to the reflectometry package is to work
 from a copy of the source tree in the revision control system.
 
@@ -18,27 +23,55 @@ be downloaded from the `git page <http://www.git-scm.com/>`_, or you can use
 an integrated development environment (IDE) such as Eclipse and PyCharm, which
 may have git built in.
 
-Simple patches
---------------
 
-If you want to make one or two tiny changes, it is easiest to clone the
-project, make the changes, document and test, then send a patch.
+Getting the Code
+================
+
+To get the code, you will need to clone the repository.  If you are planning
+on making only a few small changes, you can clone the repository directly,
+make the changes, document and test, then send a patch (see `Simple patches <#Simple-patches>`_ below).
+
+If you are planning on making larger changes, you should fork the repository
+on github, make the changes in your fork, then issue a pull request to the
+main repository (see `Larger changes <#Larger-changes>`_ below).
+
+.. note::
+
+    If you are working on a fork, the clone line is slightly different::
+
+        git clone https://github.com/YourGithubAccount/refl1d
+
+
+    You will also need to keep your fork up to date
+    with the main repository.  You can do this by adding the main repository
+    as a remote, fetching the changes, then merging them into your fork.
+
+    .. code-block:: bash
+
+        # Add the main repository as a remote
+        git remote add refl1d
 
-Clone the project as follows::
+        # Fetch the changes from the main repository
+        git fetch refl1d
 
-    git clone https://github.com/reflectometry/refl1d.git
+        # Merge the changes into your fork
+        git merge refl1d/master
 
-You will need bumps and periodictable to run.  If you are fixing bugs in the
-scattering length density calculator or the fitting engine, you will want to
-clone the repositories as sister directories to the refl1d source tree::
+        # Push the changes to your fork
+        git push
 
-    git clone https://github.com/bumps/bumps.git
-    git clone https://github.com/pkienzle/periodictable.git
 
-If you are only working with the refl1d modeling code, then you can install
-bumps and periodictable using pip::
+Once you have the code, you will need to install Refl1D, including its dependencies.
+You can do this by following the instructions in the `Installation guide <install.html>`_.
 
-    pip install periodictable bumps
+.. simple-patches:
+
+Simple patches
+--------------
+
+If you want to make one or two tiny changes, it is easiest to clone the
+repository, make the changes, then send a patch.  This is the simplest way
+to contribute to the project.
 
 To run the package from the source tree use the following::
 
@@ -55,13 +88,13 @@ As you make changes to the package, you can see what you have done using git::
     git diff
 
 Please update the documentation and add tests for your changes.  We use
-doctests on all of our examples that we know our documentation is correct.
-More thorough tests are found in test directory.  With the nosetest package,
-you can run the tests using::
-
-    python tests.py
+doctests on all of our examples so that we know our documentation is correct.
+More thorough tests are found in test directory. You can run these tests via pytest, 
+or via the convenience Makefile target::
 
-Nose is available on linux form apt-get
+    pytest 
+    # or
+    make test
 
 When all the tests run, create a patch and send it to paul.kienzle@nist.gov::
 
@@ -73,14 +106,9 @@ Larger changes
 For a larger set of changes, you should fork refl1d on github, and issue pull
 requests for each part.
 
-Once you have create the fork, the clone line is slightly different::
-
-    git clone https://github.com/YourGithubAccount/refl1d
-
 After you have tested your changes, you will need to push them to your github
 fork::
 
-    git log
     git commit -a -m "short sentence describing what the change is for"
     git push
 
@@ -97,12 +125,14 @@ track updates to the original refl1d package using::
     git push
 
 When making changes, you need to take care that they work on different
-versions of python.   In particular, RHEL6, Centos6.5, Rocks and
-ScientificLinux all run python 2.6, most linux/windows/mac users run
-python 2.7, but some of the more bleeding edge distributions run 3.3/3.4.
-The anaconda distribution makes it convenient to maintain multiple independent
-environments
-Even better is to test against all python versions 2.6, 2.7, 3.3, 3.4::
+versions of python. Using conda makes it convenient to maintain multiple independent
+environments. You can create a new environment for testing with, for example::
+
+    conda create -n py312 python=3.12
+    conda activate py312
+    pip install -e .[dev]
+
+Even better is to test against all current python versions::
 
     pythonX.Y tests.py
     pythonX.Y run.py
@@ -113,7 +143,7 @@ Building Documentation
 ======================
 
 Building the package documentation requires a working Sphinx installation,
-and latex to build the pdf. As of this writing we are using sphinx 1.2.
+and latex to build the pdf. As of this writing we are using sphinx 8.0.2.
 
 The command line to build the docs is as follows::
 
@@ -124,8 +154,8 @@ You can see the result by pointing your browser to::
     doc/_build/html/index.html
     doc/_build/latex/Refl1d.pdf
 
-Note that this only works with a unix-like environment for now since we are
-using *make*.  On windows, you can run sphinx directly from python::
+On Windows, you may first need to install `mingw32-make` via conda, 
+or simply run sphinx directly from python::
 
     cd doc
     python -m sphinx.__init__ -b html -d _build/doctrees . _build/html
@@ -168,17 +198,17 @@ to a checkin on the master branch via GitHub Actions.
 OS/X Installer
 ==============
 
-Note: OS/X installer is no longer maintained.
+A Python script is available to build the OS/X installer::
 
-To build a Mac OS/X standalone executable you will need the py2app package.
-This should already be available in your mac python environment.
+    extra/build_dmg.py
 
-Build the executable using::
+This script builds a `.dmg` based on the contents of the `dist/<product version>.app` directory.
+It can be called with the name and version of the product as arguments, e.g.::
 
-    python setup_py2app
+    python extra/build_dmg.py Refl1D 0.8.17
 
-This creates a *.dmg* file in the *dist* directory with the Refl1D app
-inside.
+This script is also run automatically on github in response
+to a checkin on the master branch via GitHub Actions.
 
 Creating a new release
 ----------------------