add docs

.gitignore

@@ -1,3 +1,7 @@
+Pipfile
+Pipfile.lock
+docs/_build
+
 __pycache__
 /dtwalign.egg-info/
 /build/

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/conf.py

@@ -0,0 +1,55 @@
+# 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:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- 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 = 'dtwalign'
+copyright = '2019, Takehiro Suzuki'
+author = 'Takehiro Suzuki'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1.0'
+
+
+# -- 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 = [
+]
+
+# 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 = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- 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'
+
+# 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/index.rst

@@ -0,0 +1,20 @@
+.. dtwalign documentation master file, created by
+   sphinx-quickstart on Mon Jul  8 20:47:17 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to dtwalign's documentation!
+====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

dtwalign/backtrack.py

@@ -7,55 +7,55 @@
 
 @jit(nopython=True)
 def _backtrack_jit(D, p_ar, last_idx=-1):
-        """Fast implementation by numba.jit.
+    """Fast implementation by numba.jit.
 
-        D : 2D array
-            cumsum cost matrix
-        p_ar : 3D array
-            step pattern array (see step_pattern.py)
-        """
-        # number of patterns
-        num_pattern = p_ar.shape[0]
-        # initialize index
-        i, j = D.shape
-        i -= 1
-        if last_idx == -1:
-            j -= 1
-        else:
-            j = last_idx
-        # alignment path
-        path = np.array(((i, j),), dtype=np.int64)
-        # cache to memorize D
-        D_cache = np.ones(num_pattern, dtype=np.float64) * np.inf
+    D : 2D array
+        cumsum cost matrix
+    p_ar : 3D array
+        step pattern array (see step_pattern.py)
+    """
+    # number of patterns
+    num_pattern = p_ar.shape[0]
+    # initialize index
+    i, j = D.shape
+    i -= 1
+    if last_idx == -1:
+        j -= 1
+    else:
+        j = last_idx
+    # alignment path
+    path = np.array(((i, j),), dtype=np.int64)
+    # cache to memorize D
+    D_cache = np.ones(num_pattern, dtype=np.float64) * np.inf
 
-        while True:
-            if i == 0 and j == 0:
-                break
-            for pidx in range(num_pattern):
-                # get D value corresponds to end of pattern node
-                pattern_index = p_ar[pidx, 0, 0:2]
-                ii = int(i + pattern_index[0])
-                jj = int(j + pattern_index[1])
-                if ii < 0 or jj < 0:
-                    D_cache[pidx] = np.inf
-                else:
-                    D_cache[pidx] = D[ii, jj]
+    while True:
+        if i == 0 and j == 0:
+            break
+        for pidx in range(num_pattern):
+            # get D value corresponds to end of pattern node
+            pattern_index = p_ar[pidx, 0, 0:2]
+            ii = int(i + pattern_index[0])
+            jj = int(j + pattern_index[1])
+            if ii < 0 or jj < 0:
+                D_cache[pidx] = np.inf
+            else:
+                D_cache[pidx] = D[ii, jj]
 
-            if (D_cache == np.inf).all():
-                # break if there is no direction can be taken
-                break
+        if (D_cache == np.inf).all():
+            # break if there is no direction can be taken
+            break
 
-            # find path minimize D_chache
-            min_pattern_idx = np.argmin(D_cache)
-            # get where pattern passed
-            path_to_add = _get_local_path(D, p_ar[min_pattern_idx, :, :], i, j)
-            # concatenate
-            path = np.vstack((path, path_to_add))
+        # find path minimize D_chache
+        min_pattern_idx = np.argmin(D_cache)
+        # get where pattern passed
+        path_to_add = _get_local_path(D, p_ar[min_pattern_idx, :, :], i, j)
+        # concatenate
+        path = np.vstack((path, path_to_add))
 
-            i += p_ar[min_pattern_idx, 0, 0]
-            j += p_ar[min_pattern_idx, 0, 1]
+        i += p_ar[min_pattern_idx, 0, 0]
+        j += p_ar[min_pattern_idx, 0, 1]
 
-        return path[::-1]
+    return path[::-1]
 
 
 @jit(nopython=True)

setup.py

@@ -17,7 +17,6 @@
 LONG_DESCRIPTION = open('README.txt').read()
 
 def main():
-
     setup(
         name=NAME,
         version=VERSION,