Merge pull request #5 from BvB93/devel

Update documentation

.gitignore

@@ -103,3 +103,4 @@ venv.bak/
 # mypy
 .mypy_cache/
 .DS_Store
+docs_out/

FOX/functions/radial_distribution.py

@@ -8,19 +8,23 @@
 
 
 def get_all_radial(xyz_array, idx_dict, dr=0.05, r_max=12.0, atoms=None):
-    """ Return the radial distribution functions (RDF's) for all possible atom-pairs in *atoms*
-    as dataframe. Accepts both 2d and 3d arrays of cartesian coordinates.
-
-    xyz_array <np.ndarray>: A m*n*3 or n*3 numpy array of the cartesian coordinates of m molecules
-        (isomers) consisting of n atoms.
-    idx_dict <dict>[<list>]: A dictionary consisting of {atomic symbols: [atomic indices]}.
-    dr <float>: The integration step-size in Angstrom, i.e. the distance between concentric spheres.
-    r_max <float>: The maximum to be evaluated interatomic distance.
-    atoms <None> or <tuple>[<str>]: A tuple of atomic symbols. An RDF will be calculated for all
-        possible atom-pairs in *atoms*. If *atoms* = <None>, An RDF will be calculated for all
-        possible atom-pairs in *idx_dict*.keys() (i.e. the entire molecule).
-    return <pd.DataFrame>: A Pandas dataframe of radial distribution functions, averaged over all
-        conformations in *xyz_array*.
+    """ Return the radial distribution functions (RDFs) for all possible atom-pairs in **atoms**
+    as dataframe. Accepts both 2d and 3d arrays of cartesian coordinates as input.
+
+    :parameter xyz_array: A *m*n*3* or *n*3* numpy array with the cartesian coordinates of *m*
+        molecules consisting of *n* atoms.
+    :type xyz_array: np.ndarray_
+    :parameter dict idx_dict: A dictionary consisting with atomic symbols as keys and matching
+        atomic indices as values (|str|_: |list|_ [|int|_]).
+    :parameter float dr: The integration step-size in Angstrom, *i.e.* the distance between
+        concentric spheres.
+    :parameter float r_max: The maximum to be evaluated interatomic distance.
+    :parameter atoms: A tuple of atomic symbols. RDFs will be calculated for all
+        possible atom-pairs in **atoms**. If *None*, calculate RDFs for all possible atom-pairs in
+        the keys of **idx_dict** (*i.e.* all possible atoms pairs in the molecule).
+    :type atoms: None or tuple [str]
+    :return: A dataframe (|pd.DataFrame|_) of radial distribution functions, averaged over all
+        conformations in **xyz_array**.
     """
     # Make sure we're dealing with a 3d array
     if len(xyz_array.shape) == 2:

FOX/functions/read_xyz.py

@@ -6,14 +6,15 @@
 
 
 def read_multi_xyz(xyz_file, ret_idx_dict=True):
-    """ Return a m*n*3 array of cartesian coordinates extracted from an xyz or multi-xyz file.
+    """ Reads a (multi) .xyz file and return a *m*n*3* array with the cartesian coordinates of *m*
+    molecules consisting of *n* atoms.
 
-    file <str>: The path + filename of a xyz or multi-xyz file.
-    ret_idx_dict <bool>: Return a dictionary consisting of {atomic symbols: [atomic indices]} as
-        derived from the first molecule in *file*.
-    return <np.ndarray> (and <dict>): A m*n*3 numpy array with the cartesian coordinates of
-        m molecules (isomers) consisting of n atoms. Optionally, a dictionary can be returned
-        consisting of {atomic symbols: [atomic indices]}.
+    :parameter str file: The path + filename of a xyz or multi-xyz file.
+    :parameter bool ret_idx_dict: In addition to returning cartesian coordinates, return a
+        dictionary with atomic symbols and matching atomic indices.
+    :return: A *m*n*3* array (|np.ndarray|_) of cartesian coordinates and, optionally, a dictionary
+        (|dict|_) with atomic symbols as keys and atomic indices as
+        values (|str|_: |list|_ [|int|_]).
     """
     with open(xyz_file, 'r') as file:
         # Define constants and construct a dictionary: {atomic symbols: [atomic indices]}

docs/Makefile

@@ -1,20 +1,195 @@
-# Minimal makefile for Sphinx documentation
+# Makefile for Sphinx documentation
 #
 
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = Auto-FOX
-SOURCEDIR     = .
-BUILDDIR      = _build
+PAPER         =
+BUILDDIR      = build
+PDFBUILDER    = /tmp
+PDF           = ../manual.pdf
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
 
-# Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@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 "  applehelp  to make an Apple Help Book"
+	@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 "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@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 "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  coverage   to run coverage check of 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/qmflows.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/qmflows.qhc"
+
+applehelp:
+	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+	@echo
+	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+	@echo "N.B. You won't be able to view it unless you put it in" \
+	      "~/Library/Documentation/Help or install it in your application" \
+	      "bundle."
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/qmflows"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/qmflows"
+	@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) $(PDFBUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(PDFBUILDDIR)/latex all-pdf
+	cp $(PDFBUILDDIR)/latex/*.pdf $(PDF)
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@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."
+
+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."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+coverage:
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/coverage/python.txt."
 
-.PHONY: help Makefile
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
 
-# 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)
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

docs/rdf.rst

@@ -1,10 +1,21 @@
 Radial Distribution Function Generator
 ======================================
 
-A radial distribution function (RDF) generator reader has been implemented in the FOX.functions.radial_distribution_ module.
+A radial distribution function (RDF) generator has been implemented in the FOX.functions.radial_distribution_ module.
 The radial distribution function, or pair correlation function, describes how the particale density in a system varies as a function of distance from a reference particle.
 The herein implemented get_all_radial() function is designed for constructing RDFs between all possible (user-defined) atom-pairs.
 
 .. autofunction:: FOX.functions.radial_distribution.get_all_radial
 
 .. _FOX.functions.radial_distribution: https://github.com/BvB93/auto-FOX/tree/master/FOX/functions
+
+.. _np.ndarray: https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html
+.. _pd.DataFrame: https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html
+.. _str: https://docs.python.org/3/library/stdtypes.html#str
+.. _list: https://docs.python.org/3/library/stdtypes.html#list
+.. _int: https://docs.python.org/3/library/functions.html#int
+
+.. |pd.DataFrame| replace:: *pd.DataFrame*
+.. |str| replace:: *str*
+.. |list| replace:: *list*
+.. |int| replace:: *int*

docs/xyz_reader.rst

@@ -8,3 +8,14 @@ The herein implemented read_multi_xyz() function allows for the fast, and memory
 .. autofunction:: FOX.functions.read_xyz.read_multi_xyz
 
 .. _FOX.functions.read_xyz: https://github.com/BvB93/auto-FOX/tree/master/FOX/functions
+.. _np.ndarray: https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html
+.. _dict: https://docs.python.org/3/library/stdtypes.html#dict
+.. _str: https://docs.python.org/3/library/stdtypes.html#str
+.. _list: https://docs.python.org/3/library/stdtypes.html#list
+.. _int: https://docs.python.org/3/library/functions.html#int
+
+.. |np.ndarray| replace:: *np.ndarray*
+.. |dict| replace:: *dict*
+.. |str| replace:: *str*
+.. |list| replace:: *list*
+.. |int| replace:: *int*

setup.py

@@ -21,7 +21,7 @@
     long_description=readme + '\n\n',
     author='Bas van Beek',
     author_email='b.f.van.beek@vu.nl',
-    url='https://github.com//Auto-FOX',
+    url='https://github.com/BvB93/Auto-FOX',
     packages=['FOX'],
     package_dir={'FOX': 'FOX'},
     include_package_data=True,