[pre-commit.ci] auto fixes from pre-commit hooks

Author: pre-commit-ci[bot]

.codecov.yml

@@ -10,7 +10,7 @@ coverage:
   status:
     patch:
       default:
-        target: '80'
+        target: "80"
         if_no_uploads: error
         if_not_found: success
         if_ci_failed: failure
@@ -21,11 +21,11 @@ coverage:
         if_no_uploads: error
         if_not_found: success
         if_ci_failed: failure
-        paths: '!*/tests/.*'
+        paths: "!*/tests/.*"
 
       tests:
         target: 97.9%
-        paths: '*/tests/.*'
+        paths: "*/tests/.*"
 
 flags:
   tests:

.travis.yml

@@ -19,7 +19,6 @@ branches:
   except:
     - /^v[0-9]/
 
-
 before_install:
   - MYNAME=diffpy.srfit
   - MYCOMMIT="$(git rev-parse HEAD)"
@@ -28,25 +27,25 @@ before_install:
   - MYPYTHON=python; MYPIP=pip
   - NOSYS=true; NOAPT=true; NOBREW=true; NOMC=true
   - if ${MYUSEMC}; then
-        NOMC=false;
+    NOMC=false;
     elif [[ ${TRAVIS_OS_NAME} == linux ]]; then
-        NOAPT=false; NOSYS=false;
-        MYPIPFLAGS="--user";
+    NOAPT=false; NOSYS=false;
+    MYPIPFLAGS="--user";
     elif [[ ${TRAVIS_OS_NAME} == osx ]]; then
-        NOBREW=false; NOSYS=false;
-        MYPYTHON=python3;
-        MYPIP=pip3;
-        MYPIPFLAGS="--user";
+    NOBREW=false; NOSYS=false;
+    MYPYTHON=python3;
+    MYPIP=pip3;
+    MYPIPFLAGS="--user";
     fi
   - MYMCREPO=https://repo.anaconda.com/miniconda
   - case ${TRAVIS_OS_NAME} in
     linux)
-        MYMCBUNDLE=Miniconda3-latest-Linux-x86_64.sh ;;
+    MYMCBUNDLE=Miniconda3-latest-Linux-x86_64.sh ;;
     osx)
-        MYMCBUNDLE=Miniconda3-latest-MacOSX-x86_64.sh ;;
+    MYMCBUNDLE=Miniconda3-latest-MacOSX-x86_64.sh ;;
     *)
-        echo "Unsupported operating system." >&2;
-        exit 2 ;;
+    echo "Unsupported operating system." >&2;
+    exit 2 ;;
     esac
   - MYRUNDIR=${PWD}/build/rundir
 
@@ -67,11 +66,11 @@ before_install:
   - $NOAPT || test "${TRAVIS_OS_NAME}" = "linux" || exit $?
   - $NOAPT || PATH="$(echo "$PATH" | sed 's,:/opt/pyenv/[^:]*,,g')"
   - $NOAPT || test "$(which python)" = "/usr/bin/python" || (
-                  which python; exit 1)
+    which python; exit 1)
   - $NOAPT || sudo apt-get update -qq
   - $NOAPT || sudo apt-get install -y
-                  python-dev python-setuptools python-numpy
-                  build-essential
+    python-dev python-setuptools python-numpy
+    build-essential
 
   - $NOBREW || test "${TRAVIS_OS_NAME}" = "osx" || exit $?
   - $NOBREW || brew update
@@ -81,18 +80,17 @@ before_install:
   - $NOSYS || devutils/makesdist
   - $NOSYS || MYTARBUNDLE="$(ls -t "${PWD}"/dist/*.tar.gz | head -1)"
 
-
 install:
   - $NOMC || conda build --python=${MYPYTHON_VERSION} conda-recipe
   - $NOMC || conda render --python=${MYPYTHON_VERSION} --output conda-recipe |
-                sed 's,.*/,,; s/[.]tar[.]bz2$//; s/-/=/g' > /tmp/mypackage.txt
+    sed 's,.*/,,; s/[.]tar[.]bz2$//; s/-/=/g' > /tmp/mypackage.txt
   - $NOMC || source activate testenv
   - $NOMC || conda install --yes --use-local --file=/tmp/mypackage.txt
   - $NOMC || conda install --yes
-                diffpy.structure pyobjcryst "diffpy.srreal>=1.3.0"
+    diffpy.structure pyobjcryst "diffpy.srreal>=1.3.0"
   # TODO - always install srfit-sasview when ready for Python 3.
   - if $MYUSEMC && [[ "$MYPYTHON_VERSION" == 2.7 ]]; then
-        conda install --yes srfit-sasview;
+    conda install --yes srfit-sasview;
     fi
 
   - $NOSYS || $MYPIP install $MYPIPFLAGS coverage
@@ -103,20 +101,17 @@ install:
   - cd ${MYRUNDIR}
   - MYGIT_REV=$($MYPYTHON -c "import ${MYNAME}.version as v; print(v.__git_commit__)")
   - if [[ "${MYCOMMIT}" != "${MYGIT_REV}" ]]; then
-        echo "Version mismatch ${MYCOMMIT} vs ${MYGIT_REV}.";
-        exit 1;
+    echo "Version mismatch ${MYCOMMIT} vs ${MYGIT_REV}.";
+    exit 1;
     fi
 
-
 before_script:
   - $NOBREW || USER_BASE="$(python3 -c 'import site; print(site.USER_BASE)')"
   - $NOBREW || PATH="${USER_BASE}/bin:${PATH}"
 
-
 script:
   - coverage run --source ${MYNAME} -m ${MYNAME}.tests.run
 
-
 after_success:
   # do not post coverage reports when testing with system Python.
   - $NOMC || $MYPIP install $MYPIPFLAGS codecov

doc/Makefile

@@ -31,4 +31,3 @@ clean:
 	rm -rf diffpy.srfitapi
 	rm -f srfit_examples.zip
 	$(MAKE) -C devmanual $@
-

doc/examples/README

@@ -1,26 +1,23 @@
-Purpose
-----------
+## Purpose
 
 These example scripts are intended to help a developer get acquainted with the
 SrFit programming interface. Although one can write scripts like these to drive
 optimization, these scripts do not represent the SrFit user interface. That
 interface will be made available in a future release.
 
-A secondary purpose of these tutorials is to generate interest in SrFit.  By
+A secondary purpose of these tutorials is to generate interest in SrFit. By
 reading through the examples we hope that you are inspired to think of exciting
 new ways to get the most out of your scientific data. If you think SrFit can
 help you with that, please feel free to contact us through the DiffPy website.
 
 http://www.diffpy.org
 
-
-Overview
-----------
+## Overview
 
 Three things are required for optimization: a function that generates a
 quantity to be minimized, variables that can be used to manipulate that
 function and an algorithm that can drive the function output to a smaller value
-by steering the variables.  For scientific purposes, the quantity to be
+by steering the variables. For scientific purposes, the quantity to be
 minimized is the disagreement between a measured profile and a theoretical
 profile. The scientific understanding of the system under consideration partly
 determines the suitability of the theoretical profile generator and the
@@ -30,38 +27,36 @@ The purpose of SrFit is to give users the means to combine known information
 about a system of interest in order to extract scientifically relevant
 quantities, and thus understanding from it. Various experimental procedures and
 theoretical calculations may be needed to gain the desired understanding of the
-system.  SrFit helps users combine these views of the system in a coherent and
+system. SrFit helps users combine these views of the system in a coherent and
 consistent manner.
 
 To achieve this purpose, SrFit provides:
 
-1) a function to be optimized (the residual) given one or more measured
+1. a function to be optimized (the residual) given one or more measured
    profiles, one or more profile generators and variables to be steered by an
    optimizer.
-2) constraints and restraints that encapsulate known information about the
+2. constraints and restraints that encapsulate known information about the
    system.
-3) a clearly defined programming interface that developers can use to add their
+3. a clearly defined programming interface that developers can use to add their
    own profile generators, thereby enabling the combination of more views of a
    system.
-4) an equation building interface that allows users to tweak profile generators
+4. an equation building interface that allows users to tweak profile generators
    when scientific understanding of a system is more advanced than the existing
    software.
 
 The examples described below will go into detail about each of these points.
 
+## Examples
 
-Examples
-----------
-
-The following examples are contained in the *doc/examples/* directory of the
-SrFit source distribution.  They can be downloaded from
+The following examples are contained in the _doc/examples/_ directory of the
+SrFit source distribution. They can be downloaded from
 http://dev.danse.us/packages/srfit_examples-alpha9.zip
 
 For each example, start by running the example by typing in the command line ::
 
     python example.py
 
-where *example.py* represents the example file. The output will show on screen
+where _example.py_ represents the example file. The output will show on screen
 and a plot window will display. Once you've studied the output and plot, close
 the plot window and open the example file. In the file there will be a
 description of what the script is doing and the purpose of the example. By
@@ -73,97 +68,94 @@ them in the order listed below.
 
 Basic:
 
-* gaussianrecipe.py_
-    Introductory recipe building and configuration. This introduces the
-    fundamental classes in SrFit.
+- gaussianrecipe.py\_
+  Introductory recipe building and configuration. This introduces the
+  fundamental classes in SrFit.
 
-* debyemodel.py_
-    Introductory recipe building and configuration. This shows how to use a
-    function created by someone else in a refinement. This example also
-    introduces restraints.
+- debyemodel.py\_
+  Introductory recipe building and configuration. This shows how to use a
+  function created by someone else in a refinement. This example also
+  introduces restraints.
 
-* debyemodelII.py_
-    Refine two different values of a variable from two different regions of a
-    profile. This example introduces constraints and working with multiple
-    contributions to a fit.
+- debyemodelII.py\_
+  Refine two different values of a variable from two different regions of a
+  profile. This example introduces constraints and working with multiple
+  contributions to a fit.
 
 Advanced:
 
-* gaussiangenerator.py_
-    Create a custom ProfileGenerator and use it in a refinement. This is an
-    instructive extension to gaussianrecipe.py_.
-
-* npintensity.py_
-    Use diffpy.structure to build a nanoparticle intensity generator, and use
-    it to refine a structure to simulated data.
+- gaussiangenerator.py*
+  Create a custom ProfileGenerator and use it in a refinement. This is an
+  instructive extension to gaussianrecipe.py*.
 
-* npintensityII.py_
-    Use the calculator built in npintensity.py to simultaneously refine a
-    structure to two data sets.
+- npintensity.py\_
+  Use diffpy.structure to build a nanoparticle intensity generator, and use
+  it to refine a structure to simulated data.
 
+- npintensityII.py\_
+  Use the calculator built in npintensity.py to simultaneously refine a
+  structure to two data sets.
 
-Use Cases
------------
+## Use Cases
 
 There are several examples that demonstrate various SrFit use cases. These do
 not adopt the tutorial format of the previous examples. Regardless, developers
 should read through these use cases to gain an understanding of PDF and SAS
 refinement with SrFit.
 
-* crystalpdf.py_
-    Refine a diffpy.structure crystal to PDF data using automatic explicit
-    space group constraints.
+- crystalpdf.py\_
+  Refine a diffpy.structure crystal to PDF data using automatic explicit
+  space group constraints.
 
-* simplepdf.py_
-    As crystalpdf.py_, but with a simplified interface.
+- simplepdf.py*
+  As crystalpdf.py*, but with a simplified interface.
 
-* crystalpdfobjcryst.py_
-    Refine a pyobjcryst crystal to PDF data using automatic implicit space
-    group constraints.
+- crystalpdfobjcryst.py\_
+  Refine a pyobjcryst crystal to PDF data using automatic implicit space
+  group constraints.
 
-* crystalpdftwophase.py_
-    Refine a two-phase structure to PDF data using two profile generators.
+- crystalpdftwophase.py\_
+  Refine a two-phase structure to PDF data using two profile generators.
 
-* simplepdftwophase.py_
-    crystalpdftwophase.py_ using the simplified PDFContribution interface.
+- simplepdftwophase.py*
+  crystalpdftwophase.py* using the simplified PDFContribution interface.
 
-* crystalpdftwodata.py_
-    Refine a single structure to x-ray and neutron data simultaneously.
+- crystalpdftwodata.py\_
+  Refine a single structure to x-ray and neutron data simultaneously.
 
-* crystalpdfall.py_
-    Refine a two-phase structure using four data sets.
+- crystalpdfall.py\_
+  Refine a two-phase structure using four data sets.
 
-* nppdfobjcryst.py_
-    Refine the C60 structure to real data.
+- nppdfobjcryst.py\_
+  Refine the C60 structure to real data.
 
-* nppdfcrystal.py_
-    Fit a nanoparticle PDF as a crystal PDF attenuated by a nanoparticle form
-    factor.
+- nppdfcrystal.py\_
+  Fit a nanoparticle PDF as a crystal PDF attenuated by a nanoparticle form
+  factor.
 
-* coreshellnp.py_
-    As above, but fit the PDF from core-shell nanoparticles.
+- coreshellnp.py\_
+  As above, but fit the PDF from core-shell nanoparticles.
 
-* ellipsoidsas.py_
-    Refine an ellipsoid SAS model to ideal data.
+- ellipsoidsas.py\_
+  Refine an ellipsoid SAS model to ideal data.
 
-* nppdfsas.py_
-    Refine PDF from nanoparticle of assumed shape using a crystal model and SAS
-    data from the same system.
+- nppdfsas.py\_
+  Refine PDF from nanoparticle of assumed shape using a crystal model and SAS
+  data from the same system.
 
-Miscellaneous
---------------
+## Miscellaneous
 
 These demonstrate other SrFit features. These are in flux and may not be in
 future versions.
 
-* simplerecipe.py_
-    This introduces the SimpleRecipe class that is a FitRecipe with an embedded
-    Profile and FitContribution. SimpleRecipe exposes methods from the Profile
-    and FitContribution, and adds other methods so it is easy to set up a
-    simple fit.
-
-* interface.py_
-    This example introduces some interface enhancements that allow the SrFit
-    recipes to be written with less code. This is not the same as a
-    full-featured scripting interface, but rather somewhere in between a
-    scripting interface and the API.
+- simplerecipe.py\_
+  This introduces the SimpleRecipe class that is a FitRecipe with an embedded
+  Profile and FitContribution. SimpleRecipe exposes methods from the Profile
+  and FitContribution, and adds other methods so it is easy to set up a
+  simple fit.
+
+- interface.py\_
+  This example introduces some interface enhancements that allow the SrFit
+  recipes to be written with less code. This is not the same as a
+  full-featured scripting interface, but rather somewhere in between a
+  scripting interface and the API.