Merge branch 'package_prep'

.gitignore

@@ -8,3 +8,5 @@ __pycache__/
 /example_data/adc_041_7Nb
 /tutorial notebooks/working_copy.ipynb
 /tutorial notebooks/experiment.dump
+
+/docs/html

README.md

@@ -0,0 +1,13 @@
+Installation
+-------------
+
+To install as a Python module, type
+
+`python -m pip install .`
+
+from the root directory. 
+For developers, you should install in linked .egg mode using
+
+`python -m pip install . develop`
+
+If you are using a Python virtual environment, you should activate this first before using the above commands.

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/README.md

@@ -0,0 +1,26 @@
+Docs README
+-------------
+
+The documentation for xrdfit is generated using the Sphinx Python package and built and hosted at Read The Docs.
+
+Documentation is written in reStructuredText format and compiled by the Sphinx package into a HTML source. At compilation time Sphinx also scrapes docstrings from the Python scripts and adds these to the documentation.
+
+
+Requrements to compile documentation
+======================================
+
+Install: Sphinx (http://www.sphinx-doc.org/en/master/) - (conda install sphinx/pip install sphinx)
+
+
+Compiling documentation
+=========================
+
+To recompile the documentation after a change, from the docs folder use the commands::
+
+sphinx-build -b html ./source ./html
+
+If the structure of the Python scripts is significantly changed, api-doc can autogenerate the API documentation with the command::
+
+sphinx-apidoc -o ./source ../xrdfit
+
+The HTML output should not be committed to the repository, this is just a local preview version. Each time the repository is pushed to GitHub the docs are rebuilt from source at: https://xrdfit.readthedocs.io/en/latest/

docs/index.html

@@ -0,0 +1 @@
+<meta http-equiv="refresh" content="0; url=./html/index.html" />

docs/source/conf.py

@@ -0,0 +1,69 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'xrdfit'
+copyright = '2019, Peter Crowther'
+author = 'Peter Crowther'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# The master toctree document.
+master_doc = 'index'
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+html_theme_options = {"body_max_width": "100%"}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/source/index.rst

@@ -0,0 +1,20 @@
+.. xrdfit documentation master file, created by
+   sphinx-quickstart on Mon Dec 16 15:47:29 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to xrdfit's documentation!
+==================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/modules.rst

@@ -0,0 +1,7 @@
+xrdfit
+======
+
+.. toctree::
+   :maxdepth: 4
+
+   xrdfit

docs/source/xrdfit.rst

@@ -0,0 +1,46 @@
+xrdfit package
+==============
+
+Submodules
+----------
+
+xrdfit.fit\_analysis module
+---------------------------
+
+.. automodule:: xrdfit.fit_analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+xrdfit.plotting module
+----------------------
+
+.. automodule:: xrdfit.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+xrdfit.pv\_fit module
+---------------------
+
+.. automodule:: xrdfit.pv_fit
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+xrdfit.spectrum\_fitting module
+-------------------------------
+
+.. automodule:: xrdfit.spectrum_fitting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: xrdfit
+   :members:
+   :undoc-members:
+   :show-inheritance:

paper/paper.bib

@@ -0,0 +1,12 @@
+% Encoding: UTF-8
+
+@Misc{Newville2014,
+  author    = {Newville, Matthew and Stensitzki, Till and Allen, Daniel B. and Ingargiola, Antonino},
+  title     = {LMFIT: Non-Linear Least-Square Minimization and Curve-Fitting for Python},
+  year      = {2014},
+  doi       = {10.5281/ZENODO.11813},
+  keywords  = {python, non-linear least-squares optimization, curve-fitting},
+  publisher = {Zenodo},
+}
+
+@Comment{jabref-meta: databaseType:bibtex;}

paper/paper.md

@@ -0,0 +1,45 @@
+---
+title: 'xrdfit: A Python package for fitting SXRD diffraction spectra'
+tags:
+  - Python
+  - physics
+  - crystallography
+  - material structure
+authors:
+  - name: Peter Crowther
+    orcid: 0000-0002-5430-6924
+    affiliation:  1
+  - name: Christopher Daniel
+	orcid: 0000-0002-5574-6833
+    affiliation: 1
+affiliations:
+ - name: Univeristy of Manchester
+   index: 1
+date: 16 December 2019
+bibliography: paper.bib
+
+---
+
+# Summary
+
+100 words on xrd and material structure
+
+``xrdfit`` is an Python package for fitting the peaks found in shallow x-ray 
+diffraction spectra. It is designed to be an easy to use tool for quick analysis of
+spectra. Features are included for automating fitting over many spectra to enable
+tracking of peaks as they shift through the experiment. Some basic Materials anlysis
+algorithms are added which allow converstion of the peak positions to material properties
+like strain. ``xrdfit`` uses the Python package ``lmfit`` for the underlying fitting [@Newville2014].
+
+``xrdfit`` is designed to be used by experimental researchers who need to 
+process SXRD spectra but do not have a detailed knowledge of programming or
+fitting. It has been used for the analysis of data presented in [insert paper here].
+We hope that its public release will allow other researchers to benefit from 
+fast data fitting, reducing the effort required to do basic analysis of their
+experimental data.
+
+# Acknowledgements
+
+We acknowledge funding from 
+
+# References

readthedocs.yaml

@@ -0,0 +1,10 @@
+# This file provides configuration for building the documentation at: https://xrdfit.readthedocs.io/en/latest/index.html
+
+version: 2
+
+python:
+  version: 3.6
+  install:
+    - requirements: requirements.txt
+    - method: setuptools
+      path: .

requirements.txt

@@ -0,0 +1,7 @@
+numpy
+matplotlib
+pandas
+dill
+tqdm
+scipy
+lmfit

setup.py

@@ -0,0 +1,18 @@
+from setuptools import setup, find_packages
+
+setup(
+    name='xrdfit',
+    version='0.1',
+    description='Automated fitting of XRD peaks using Pseudo-Voight fits',
+    author='Peter Crowther',
+    packages=find_packages(),
+    install_requires=['numpy',
+                      'matplotlib',
+                      'pandas',
+                      'dill',
+                      'tqdm',
+                      'scipy',
+                      'lmfit'
+                      ],
+    extras_require={"documentation_compilation": "sphinx"}
+)

tests/Tests.ipynb

@@ -26,13 +26,9 @@
     "\n",
     "%autoreload 2\n",
     "\n",
-    "import sys\n",
-    "sys.path.append('./..')\n",
-    "\n",
     "from glob import glob\n",
     "\n",
-    "import spectrum_fitting\n",
-    "from spectrum_fitting import PeakParams"
+    "from xrdfit.spectrum_fitting import PeakParams, FitSpectrum"
    ]
   },
   {
@@ -68,7 +64,7 @@
    "outputs": [],
    "source": [
     "for file_path in test_files:\n",
-    "    spectral_data = spectrum_fitting.FitSpectrum(file_path, 90, verbose=False)\n",
+    "    spectral_data = FitSpectrum(file_path, 90, verbose=False)\n",
     "    spectral_data.plot(1, show_points=True)"
    ]
   },
@@ -86,7 +82,7 @@
    "outputs": [],
    "source": [
     "for file_path in test_files:\n",
-    "    spectral_data = spectrum_fitting.FitSpectrum(file_path, 90, verbose=False)\n",
+    "    spectral_data = FitSpectrum(file_path, 90, verbose=False)\n",
     "    peak_params = spectral_data.detect_peaks(1)\n",
     "    spectral_data.plot_peak_params(peak_params, 1, show_points=True)"
    ]
@@ -105,7 +101,7 @@
    "outputs": [],
    "source": [
     "for file_path in test_files:\n",
-    "    spectral_data = spectrum_fitting.FitSpectrum(file_path, 90, verbose=False)\n",
+    "    spectral_data = FitSpectrum(file_path, 90, verbose=False)\n",
     "    peak_params = spectral_data.detect_peaks(1)\n",
     "    spectral_data.fit_peaks(peak_params, 1)\n",
     "\n",
@@ -128,7 +124,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "spectral_data = spectrum_fitting.FitSpectrum(\"../tests/full_spectrum.txt\", 90, verbose=False)\n",
+    "spectral_data = FitSpectrum(\"../tests/full_spectrum.txt\", 90, verbose=False)\n",
     "peak_params = spectral_data.detect_peaks(1)\n",
     "spectral_data.plot_peak_params(peak_params, 1, show_points=True)\n",
     "spectral_data.fit_peaks(peak_params, 1)\n",