Merge pull request #7 from ufo-kit/python3

Python3

.readthedocs.yml

@@ -1 +1,25 @@
-requirements_file: docs_requirements.txt
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.8
+  install:
+    - requirements: requirements.txt
+    - requirements: requirements-examples.txt

.travis.yml

@@ -1,22 +1,23 @@
+dist: bionic
 language: python
 
 python:
-    - 2.7
-
-virtualenv:
-    system_site_packages: true
+    - 3.6
+    - 3.7
+    - 3.8
 
 before_install:
-    - sudo apt-get install -qq python-coverage
-    - sudo apt-get install -qq python-pyopencl
+    - sudo apt-get install -qq python3-pyopencl
 
 install:
-    - pip install python-coveralls
+    - pip install flake8
+    - pip install codecov
     - pip install -r requirements.txt
     - pip install .
 
 script:
-    - nosetests -a '!opencl' --with-coverage --cover-package=syris syris
+    - coverage run -m --source=syris unittest discover
+    - flake8 syris
 
 after_success:
-    - coveralls
+    - codecov

README.rst

@@ -1,13 +1,19 @@
 Syris
 =====
 
+.. image:: https://img.shields.io/badge/Python-3.6+-blue
+    :target: https://www.python.org/downloads/release/python-360
+
 .. image:: https://travis-ci.org/ufo-kit/syris.svg?branch=master
     :target: https://travis-ci.org/ufo-kit/syris
 
 .. image:: https://readthedocs.org/projects/syris/badge/?version=latest
     :target: http://syris.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
+.. image:: https://codecov.io/gh/ufo-kit/syris/branch/master/graph/badge.svg
+  :target: https://codecov.io/gh/ufo-kit/syris
+
 *Syris* (**sy**\ nchrotron **r**\ adiation **i**\ maging **s**\ imulation) is a
 framework for simulations of X-ray absorption and phase contrast dynamic imaging
 experiments, like time-resolved radiography, tomography or laminography. It
@@ -57,6 +63,15 @@ A simple white beam propagation example looks like this:
 For more detailed information please see the `reference <https://syris.readthedocs.io/en/latest>`_.
 
 
+Examples
+********
+
+Are stored in the **examples** directory. Make sure you install their
+dependencies by ``pip install -r requirements-examples.txt`` and then you can
+run them from the top-level directory of syris repository by e.g. ``python -m
+examples.simple``.
+
+
 Citation
 --------
 

docs/Makefile

@@ -1,153 +1,19 @@
-# Makefile for Sphinx documentation
+# Minimal makefile for Sphinx documentation
 #
 
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-PAPER         =
+SOURCEDIR     = source
 BUILDDIR      = build
 
-# Internal variables.
-PAPEROPT_a4     = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
-
+# Put it first so that "make" without argument is like "make help".
 help:
-	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       to make standalone HTML files"
-	@echo "  dirhtml    to make HTML files named index.html in directories"
-	@echo "  singlehtml to make a single large HTML file"
-	@echo "  pickle     to make pickle files"
-	@echo "  json       to make JSON files"
-	@echo "  htmlhelp   to make HTML files and a HTML help project"
-	@echo "  qthelp     to make HTML files and a qthelp project"
-	@echo "  devhelp    to make HTML files and a Devhelp project"
-	@echo "  epub       to make an epub"
-	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
-	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
-	@echo "  text       to make text files"
-	@echo "  man        to make manual pages"
-	@echo "  texinfo    to make Texinfo files"
-	@echo "  info       to make Texinfo files and run them through makeinfo"
-	@echo "  gettext    to make PO message catalogs"
-	@echo "  changes    to make an overview of all changed/added/deprecated items"
-	@echo "  linkcheck  to check all external links for integrity"
-	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
-
-clean:
-	-rm -rf $(BUILDDIR)/*
-
-html:
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml:
-	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml:
-	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
-	@echo
-	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle:
-	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
-	@echo
-	@echo "Build finished; now you can process the pickle files."
-
-json:
-	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
-	@echo
-	@echo "Build finished; now you can process the JSON files."
-
-htmlhelp:
-	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
-	@echo
-	@echo "Build finished; now you can run HTML Help Workshop with the" \
-	      ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp:
-	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
-	@echo
-	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
-	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Syris.qhcp"
-	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Syris.qhc"
-
-devhelp:
-	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
-	@echo
-	@echo "Build finished."
-	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/Syris"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Syris"
-	@echo "# devhelp"
-
-epub:
-	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
-	@echo
-	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-latex:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo
-	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
-	@echo "Run \`make' in that directory to run these through (pdf)latex" \
-	      "(use \`make latexpdf' here to do that automatically)."
-
-latexpdf:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo "Running LaTeX files through pdflatex..."
-	$(MAKE) -C $(BUILDDIR)/latex all-pdf
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-text:
-	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
-	@echo
-	@echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-man:
-	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
-	@echo
-	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-texinfo:
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo
-	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
-	@echo "Run \`make' in that directory to run these through makeinfo" \
-	      "(use \`make info' here to do that automatically)."
-
-info:
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo "Running Texinfo files through makeinfo..."
-	make -C $(BUILDDIR)/texinfo info
-	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-gettext:
-	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
-	@echo
-	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-changes:
-	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
-	@echo
-	@echo "The overview file is in $(BUILDDIR)/changes."
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-linkcheck:
-	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
-	@echo
-	@echo "Link check complete; look for any errors in the above output " \
-	      "or in $(BUILDDIR)/linkcheck/output.txt."
+.PHONY: help Makefile
 
-doctest:
-	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
-	@echo "Testing of doctests in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/doctest/output.txt."
+# 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)