Add changelog and other minor documentation changes

.github/pull_request_template.md

@@ -0,0 +1,6 @@
+
+
+#### For reviewers
+<!-- Don't remove the checklist below. -->
+- [ ] New features, API changes, and deprecations are mentioned in the unreleased
+      section in `CHANGELOG.rst`.

CHANGELOG.rst

@@ -0,0 +1,19 @@
+=========
+Changelog
+=========
+
+Morphops implements common operations and algorithms for Geometric
+Morphometrics, in Python 3.
+
+All notable changes to this project will be documented in this file. The format is based
+on `Keep a Changelog <https://keepachangelog.com/en/1.1.0>`_.
+
+Contributors to each release are listed in alphabetical order by first name. List
+entries are sorted in descending chronological order.
+
+Unreleased
+==========
+
+Added
+-----
+- This project now keeps a changelog.

README.rst

@@ -1,21 +1,33 @@
-.. image:: https://travis-ci.com/vaipatel/morphops.svg?branch=master
-    :target: https://travis-ci.com/vaipatel/morphops
-
 Welcome to Morphops!
 ====================
 
 Morphops implements common operations and algorithms for Geometric
 Morphometrics, in Python 3.
 
+.. GitHub Actions
+.. image:: https://github.com/vaipatel/morphops/actions/workflows/build.yml/badge.svg
+    :target: https://github.com/vaipatel/morphops/actions/workflows/build.yml
+    :alt: Build status
+
+.. Read the Docs
+.. image:: https://readthedocs.org/projects/morphops/badge/?version=latest
+    :target: https://morphops.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+.. PyPI version
+.. image:: https://img.shields.io/pypi/v/morphops
+    :target: https://pypi.org/project/morphops
+    :alt: PyPI version
+
 Features
 ========
 
 Some high-level operations in the current version are
 
-* Centering, rescaling data: \
-* Rigid Rotation, Ordinary and Generalized Procrustes alignment: \
-* Thin-plate spline warping: \
-* Reading from and writing to \*.dta files: \
+* Centering, rescaling data:
+* Rigid Rotation, Ordinary and Generalized Procrustes alignment:
+* Thin-plate spline warping:
+* Reading from and writing to \*.dta files:
 
 Dependencies
 ------------
@@ -106,5 +118,4 @@ they can now be submitted to various commonly used statistical procedures like
 Principal Components Analysis and various kinds of regression for further
 analysis.
 
-
-**(This file was autogenerated from README_for_docs.rst by running `make README_for_gh html` in the docs directory)**
+**(This file was autogenerated from README_for_docs.rst by running `make README_for_gh` in the docs directory)**

README_for_docs.rst

@@ -1,36 +1,39 @@
-.. GitHub Actions
-.. image:: https://github.com/hakonanes/morphops/workflows/build/badge.svg
-    :target: https://github.com/hakonanes/morphops/actions
-    :alt: Build status
-
-|
-
-.. contents::
-    :local:
-
-|
-
 Welcome to Morphops!
 ====================
 
 Morphops implements common operations and algorithms for Geometric
 Morphometrics, in Python 3.
 
+.. GitHub Actions
+.. image:: https://github.com/vaipatel/morphops/actions/workflows/build.yml/badge.svg
+    :target: https://github.com/vaipatel/morphops/actions/workflows/build.yml
+    :alt: Build status
+
+.. Read the Docs
+.. image:: https://readthedocs.org/projects/morphops/badge/?version=latest
+    :target: https://morphops.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+.. PyPI version
+.. image:: https://img.shields.io/pypi/v/morphops
+    :target: https://pypi.org/project/morphops
+    :alt: PyPI version
+
 Features
 ========
 
 Some high-level operations in the current version are
 
-* Centering, rescaling data: \
+* Centering, rescaling data:
   :meth:`remove_position(lmk_sets) <morphops.procrustes.remove_position>`,
   :meth:`remove_scale(lmk_sets) <morphops.procrustes.remove_scale>`
-* Rigid Rotation, Ordinary and Generalized Procrustes alignment: \
+* Rigid Rotation, Ordinary and Generalized Procrustes alignment:
   :meth:`rotate(src_sets,tar_sets) <morphops.procrustes.rotate>`,
   :meth:`opa(src_set,tar_set) <morphops.procrustes.opa>`,
   :meth:`gpa(all_sets) <morphops.procrustes.gpa>`
-* Thin-plate spline warping: \
+* Thin-plate spline warping:
   :meth:`tps_warp(X, Y, pts) <morphops.tps.tps_warp>`
-* Reading from and writing to \*.dta files: \
+* Reading from and writing to \*.dta files:
   :meth:`read_dta(fn) <morphops.io.read_dta>`,
   :meth:`write_dta(fn,lmk_sets,names) <morphops.io.write_dta>`
 

docs/Makefile

@@ -17,9 +17,8 @@ help:
 README_for_gh:
 	@echo "Building docs for GitHub"
 	@cp ../README_for_docs.rst ../$(README_FOR_GH)
-	sed -i '' -e '4,10d' ../$(README_FOR_GH)
+	echo "\n**(This file was autogenerated from README_for_docs.rst by running \`make README_for_gh\` in the docs directory)**" >> ../$(README_FOR_GH)
 	sed -i '' -e '/^  :meth:/ d' ../$(README_FOR_GH)
-	echo "\n\n**(This file was autogenerated from README_for_docs.rst by running \`make README_for_gh html\` in the docs directory)**" >> ../$(README_FOR_GH)
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

docs/source/changelog.rst

@@ -0,0 +1,2 @@
+.. This is a stub, see the top level CHANGELOG.rst file for the changelog.
+.. include:: ../../CHANGELOG.rst

docs/source/conf.py

@@ -12,23 +12,27 @@
 # 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.
 #
+from datetime import datetime
 import os
 import sys
 
+from morphops._version import __version__ as full_version
+
+
 sys.path.insert(0, os.path.abspath('../..'))
 sys.path.insert(0, os.path.abspath('../../morphops'))
 sys.setrecursionlimit(1500)
 
 # -- Project information -----------------------------------------------------
 
 project = 'Morphops'
-copyright = '2018-2020, Vaibhav Patel'
+copyright = f"2018-{datetime.now().year}, Vaibhav Patel"
 author = 'Vaibhav Patel'
 
 # The short X.Y version
 version = '0.1'
 # The full version, including alpha/beta/rc tags
-release = '0.1.11'
+release = full_version
 
 # -- General configuration ---------------------------------------------------
 
@@ -105,7 +109,7 @@
 # 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']
+#html_static_path = ['_static']
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -207,4 +211,4 @@
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3', None),
     'numpy': ('https://docs.scipy.org/doc/numpy/', None)
-}
+}

docs/source/index.rst

@@ -13,6 +13,11 @@ morphops module
 .. Members
 .. =======
 
+.. toctree::
+   :hidden:
+
+   changelog.rst
+
 Indices and tables
 ==================
 

morphops/io.py

@@ -15,7 +15,7 @@ class MopsFileWriteError(Exception):
 
 
 def read_dta(filename):
-    r"""Reads *.dta files, as written by the IDAV Landmark Editor.
+    r"""Reads \*.dta files, as written by the IDAV Landmark Editor.
 
     dta files typically have the following structure.
 
@@ -92,11 +92,11 @@ def read_dta(filename):
 
 
 def write_dta(filename, lmk_sets, names=[]):
-    r"""Writes *.dta files, as written by the IDAV Landmark Editor.
+    r"""Writes \*.dta files, as written by the IDAV Landmark Editor.
 
     See also
     --------
-    read_dta: For an explanation of the *.dta format.
+    read_dta: For an explanation of the \*.dta format.
 
     Todo
     ----

setup.py

@@ -1,5 +1,7 @@
+from itertools import chain
 from setuptools import setup, find_packages
 
+
 with open('README.rst') as readme_file:
     readme = readme_file.read()
 
@@ -8,8 +10,12 @@
     exec(version_file.read(), version)
 
 extra_feature_requirements = {
-    "tests": ["coverage >= 5.0", "pytest >= 5.4", "pytest-cov >= 2.8.1"],
+    "tests": ["coverage >= 5.0", "pytest >= 5.4", "pytest-cov >= 2.8.1", "tox"],
+    "docs": ["sphinx < 2", "sphinx-rtd-theme"],
 }
+extra_feature_requirements["dev"] = list(
+    chain(*list(extra_feature_requirements.values()))
+)
 
 setup(
     name='morphops',