Add scikit-beam correlation code.

skbeam_copied/.coveragerc

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+[run]
+source=skbeam
+[report]
+omit =
+    */python?.?/*
+    */site-packages/nose/*
+    skbeam/__init__.py
+    # ignore _version.py and versioneer.py
+    .*version.*
+    *_version.py
+
+exclude_lines =
+    def set_default

skbeam_copied/.flake8

@@ -0,0 +1,11 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    versioneer.py,
+    pyxrf/_version.py,
+    doc/conf.py,
+    doc/sphinxext/*
+max-line-length = 115

skbeam_copied/.gitattributes

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+skbeam/_version.py export-subst

skbeam_copied/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+venv/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+doc/_build/
+doc/resource/api/core/_as_gen/
+
+# pytest
+.pytest_cache/
+
+# PyBuilder
+target/
+
+# Editor files
+#mac
+.DS_Store
+*~
+
+#vim
+*.swp
+*.swo
+
+#pycharm
+.idea/*
+
+
+#Ipython Notebook
+.ipynb_checkpoints
+
+# Project-specific ignores:
+skbeam/core/accumulators/histogram.c

skbeam_copied/.travis.yml

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+language: python
+sudo: false
+
+addons:
+  apt_packages:
+      - pandoc
+env:
+  global:
+    - SUBMIT_CODECOV: false
+    - BUILD_DOCS: false
+    - GH_REF: github.com/scikit-beam/scikit-beam.git
+    - secure: "KzntGlmLDUZlAB8ZiSRBtONJypv4atrnFxl+THCW8kg6YbiODcCxG9cez7mfmh63wpJ54+zeGvgGljeVvjb7bjB2p+4hZy+mLoP9xoE1w5qF4XaQ5YTOYaSQqCeWa5cEIi+854gFX7gOfW5qL+EJf7h3HtmndI15zaU5gOPjSDU="
+
+matrix:
+  include:
+    - python: 3.7
+      env: BUILD_DOCS=true SUBMIT_CODECOV=true NUMPY=1.17
+    - os: osx
+      language: generic
+      env: TRAVIS_PYTHON_VERSION=3.6 NUMPY=1.17
+    - os: osx
+      language: generic
+      env: TRAVIS_PYTHON_VERSION=3.7 NUMPY=1.17
+
+python:
+  - 3.6
+  - 3.7
+
+env:
+  - NUMPY=1.16
+  - NUMPY=1.17
+  - NUMPY=1.18
+
+before_install:
+  - |
+    set -e
+    if [ "$TRAVIS_OS_NAME" == "linux" ]; then
+        arch="Linux"
+    elif [ "$TRAVIS_OS_NAME" == "osx" ]; then
+        arch="MacOSX"
+    else
+        echo "Unknown arch $TRAVIS_OS_NAME"
+        exit 1
+    fi
+    wget https://repo.continuum.io/miniconda/Miniconda3-latest-${arch}-x86_64.sh -O miniconda.sh
+    chmod +x miniconda.sh
+    ./miniconda.sh -b -p ~/mc
+    source ~/mc/etc/profile.d/conda.sh
+    conda update conda --yes
+    export CONDARC=ci/condarc
+
+install:
+  - export GIT_FULL_HASH=`git rev-parse HEAD`
+  - conda create -n testenv python=$TRAVIS_PYTHON_VERSION numpy=$NUMPY
+  - conda activate testenv
+  - conda install xraylib  # this is the only package not available on PyPI
+  - pip install -r requirements.txt
+  - pip install -r requirements-dev.txt
+  # # need to build_ext -i for the tests so that the .so is local to the source
+  # # code.  We could also setup.py develop, but I'm not sure if that is any
+  # # better
+  - python setup.py install build_ext -i
+  - pip install codecov
+  - conda list
+  - pip list
+
+before_script:
+  # define a merge size check function that ensures no huge file was committed
+  # to the repo by accident
+  - |
+    size_check() {
+        GIT_TARGET_EXTRA="+refs/heads/${TRAVIS_BRANCH}"
+        GIT_SOURCE_EXTRA="+refs/pull/${TRAVIS_PULL_REQUEST}/merge"
+        echo TRAVIS_BRANCH=$TRAVIS_BRANCH
+        echo TRAVIS_PULL_REQUEST=$TRAVIS_PULL_REQUEST
+        echo TRAVIS_REPO_SLUG=$TRAVIS_REPO_SLUG
+        echo GIT_TARGET_EXTRA=$GIT_TARGET_EXTRA
+        echo GIT_SOURCE_EXTRA=$GIT_SOURCE_EXTRA
+        mkdir ~/repo-clone
+        pushd ~/repo-clone
+        git init && git remote add -t ${TRAVIS_BRANCH} origin git://github.com/${TRAVIS_REPO_SLUG}.git
+        git fetch origin ${GIT_TARGET_EXTRA}
+        git checkout -qf FETCH_HEAD
+        git tag travis-merge-target
+        git gc --aggressive
+        TARGET_SIZE=`du -s . | sed -e "s/\t.*//"`
+        echo TARGET_SIZE=$TARGET_SIZE
+        git pull origin ${GIT_SOURCE_EXTRA}
+        git gc --aggressive
+        MERGE_SIZE=`du -s . | sed -e "s/\t.*//"`
+        popd
+        echo MERGE_SIZE=$MERGE_SIZE
+        if [ "${MERGE_SIZE}" != "${TARGET_SIZE}" ]; then
+            SIZE_DIFF=`expr \( ${MERGE_SIZE} - ${TARGET_SIZE} \)`
+        else
+            SIZE_DIFF=0
+        fi
+
+        echo SIZE_DIFF=$SIZE_DIFF
+
+        echo -e "Estimated content size difference = ${SIZE_DIFF} kB"
+
+        if test ${SIZE_DIFF} -lt $1; then
+            echo "Size check passed"
+            return 0
+        else
+            echo "Size check failed"
+            return 1
+        fi
+      }
+
+script:
+  - flake8
+  - coverage run run_tests.py
+  - coverage report -m
+  # Check the merge size to make sure nothing huge was committed, but only do
+  # it on one of the branches
+  - if [ $BUILD_DOCS == 'true' ]; then
+        size_check 100;
+    fi;
+  - |
+    set -e
+    if [ $BUILD_DOCS == 'true' ]; then
+        pip install -r requirements-doc.txt
+        pushd ../
+        git clone https://github.com/scikit-beam/scikit-beam-examples.git
+        popd
+        cd doc
+        bash build_docs.sh
+        cd ..
+    fi
+
+after_success:
+  - if [ $SUBMIT_CODECOV == 'true' ]; then codecov; fi;
+  - |
+    set -e
+    if [ $TRAVIS_BRANCH == 'master' ] && [ $TRAVIS_PULL_REQUEST == 'false' ] && [ $BUILD_DOCS ]; then
+        openssl aes-256-cbc -K $encrypted_b4ed46da4197_key -iv $encrypted_b4ed46da4197_iv -in skbeam-docs-deploy.enc -out skbeam-docs-deploy -d
+        eval `ssh-agent -s`
+        chmod 600 skbeam-docs-deploy
+        ssh-add skbeam-docs-deploy
+        cd doc
+        bash push_docs.sh
+        cd ..
+    fi