diff --git a/.travis.yml b/.travis.yml
index ba98443157a..084b8c95852 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -18,6 +18,7 @@ env:
- GIT_CI_USER=TravisCI
- GIT_CI_EMAIL=TravisCI@mdanalysis.org
- MDA_DOCDIR=${TRAVIS_BUILD_DIR}/package/doc/html/html
+ - MAINTAIN_DIR=${TRAVIS_BUILD_DIR}/maintainer
# Set default python version to avoid repetition later
- PYTHON_VERSION=3.6
- BUILD_DOCS=false
@@ -54,7 +55,7 @@ matrix:
BUILD_DOCS=true
BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace"
INSTALL_HOLE="false"
- PIP_DEPENDENCIES="${PIP_DEPENDENCIES} sphinx==1.8.5 sphinx-sitemap sphinx_rtd_theme"
+ PIP_DEPENDENCIES="${PIP_DEPENDENCIES} sphinx==1.8.5 sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0"
- env: NAME="Lint"
PYLINTRC="${TRAVIS_BUILD_DIR}/package/.pylintrc"
@@ -130,6 +131,14 @@ after_success:
codecov; \
fi
# can't use test here since this leads to travis fails even though the build passes
- - if [[ ${TRAVIS_PULL_REQUEST} == "false" ]] && [[ ${BUILD_DOCS} == "true" ]] && [[ ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} ]]; then
- bash ${TRAVIS_BUILD_DIR}/maintainer/deploy_docs.sh;
+ # turn off blocking as it causes large writes to stdout to fail
+ # (see https://github.com/travis-ci/travis-ci/issues/4704)
+ - |
+ if [[ ${TRAVIS_PULL_REQUEST} == "false" ]] && [[ ${BUILD_DOCS} == "true" ]] && [[ ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} ]]; then
+ python -c 'import os,sys,fcntl; flags = fcntl.fcntl(sys.stdout, fcntl.F_GETFL); fcntl.fcntl(sys.stdout, fcntl.F_SETFL, flags&~os.O_NONBLOCK);'
+ cd ${TRAVIS_BUILD_DIR}/package/MDAnalysis
+ export VERSION=$(python -c "import version; print(version.__version__)")
+ cd -
+ bash ${TRAVIS_BUILD_DIR}/maintainer/deploy_docs_via_travis.sh;
fi
+
diff --git a/README.rst b/README.rst
index bd4cee395ef..cdabe47170f 100644
--- a/README.rst
+++ b/README.rst
@@ -128,7 +128,7 @@ to find uncovered code.
.. |devdocs| image:: https://img.shields.io/badge/docs-development-yellow.svg
:alt: Documentation (development version)
- :target: https://www.mdanalysis.org/mdanalysis/
+ :target: https://docs.mdanalysis.org/dev
.. |numfocus| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A
:alt: Powered by NumFOCUS
diff --git a/maintainer/deploy_docs.sh b/maintainer/deploy_docs_via_travis.sh
old mode 100755
new mode 100644
similarity index 75%
rename from maintainer/deploy_docs.sh
rename to maintainer/deploy_docs_via_travis.sh
index c49f357a69c..af503e56727
--- a/maintainer/deploy_docs.sh
+++ b/maintainer/deploy_docs_via_travis.sh
@@ -14,6 +14,8 @@
# GIT_CI_USER name of the user to push docs as
# GIT_CI_EMAIL email of the user to push docs as
# MDA_DOCDIR path to the docdir from top of repo
+# MAINTAIN_DIR path to maintainer/
+# VERSION version of MDAnalysis
#
# NOTE: If any of these environment variables are not set or
# empty then the script will exit with and error (-o nounset).
@@ -32,24 +34,40 @@ rev=$(git rev-parse --short HEAD)
test -n "${GH_TOKEN}" || die "GH_TOKEN is empty: need OAuth GitHub token to continue" 100
test -n "${GH_REPOSITORY}" || die "GH_REPOSITORY must be set in .travis.yml" 100
test -n "${MDA_DOCDIR}" || die "MDA_DOCDIR must be set in .travis.yml" 100
+test -n "${MAINTAIN_DIR}" || die "MAINTAIN_DIR must be set in .travis.yml" 100
+test -n "${VERSION}" || die "VERSION must be set in .travis.yml" 100
+
cd ${MDA_DOCDIR} || die "Failed to 'cd ${MDA_DOCDIR}'. Run from the top level of the repository"
+# move into $version subdirectory
+mkdir ../${VERSION} && mv * ../${VERSION}
+
git init
git config user.name "${GIT_CI_USER}"
git config user.email "${GIT_CI_EMAIL}"
+mv ../${VERSION} $VERSION
+
git remote add upstream "https://${GH_TOKEN}@${GH_REPOSITORY}"
git fetch --depth 50 upstream ${GH_DOC_BRANCH} gh-pages
git reset upstream/gh-pages
+# for dev, latest, home redirects
+mkdir dev latest
+export URL="https://docs.mdanalysis.org"
+python ${MAINTAIN_DIR}/update_json_stubs_sitemap.py
touch .
touch .nojekyll
-git add -A .
+git add -A ${VERSION}/
+git add .nojekyll versions.json
+git add index.html dev latest
+git add *.xml
+
# check for anything to commit
# https://stackoverflow.com/questions/3878624/how-do-i-programmatically-determine-if-there-are-uncommited-changes
-git diff-index --quiet HEAD -- || git commit -m "rebuilt html docs from branch ${GH_DOC_BRANCH} with sphinx at ${rev}"
+git diff-index --quiet HEAD -- || git commit -m "rebuilt html docs for version ${VERSION} from branch ${GH_DOC_BRANCH} with sphinx at ${rev}"
git push -q upstream HEAD:gh-pages
diff --git a/maintainer/deploy_master_docs.sh b/maintainer/deploy_master_docs.sh
deleted file mode 100755
index 2c9d5b8e03a..00000000000
--- a/maintainer/deploy_master_docs.sh
+++ /dev/null
@@ -1,91 +0,0 @@
-#!/bin/bash
-# Deploying docs from travis-ci.
-# See https://github.com/MDAnalysis/mdanalysis/issues/386
-# Script based on https://github.com/steveklabnik/automatically_update_github_pages_with_travis_example
-
-# Run this script from the top-level of the checked out git
-# repository. A github OAuth token must be available in the evironment
-# variable GH_TOKEN and is set up through the .travis.yml
-# env:global:secure parameter (encrypted with travis-ci's public key)/
-#
-# Additional environment variables set in .travis.yml
-# GH_REPOSITORY repo to full from and push to
-# GH_DOC_BRANCH branch from which the docs are built
-# GIT_CI_USER name of the user to push docs as
-# GIT_CI_EMAIL email of the user to push docs as
-# MDA_DOCDIR path to the docdir from top of repo
-#
-# NOTE: If any of these environment variables are not set or
-# empty then the script will exit with and error (-o nounset).
-
-# TESTING TO PUSH TO THE docs repo
-# Assume that this is MANUALLY run from top level of repo
-# and the docs were built with
-#
-# (cd package && python setup.py build_sphinx)
-#
-
-# The release sitemap.xml is generated from the development
-# sitemap.xml by changing MDA_DEVELOPMENT_DOCS_URL --> MDA_RELEASE_DOCS_URL
-#
-# See comment in package/doc/sphinx/source/conf.py for site_url.
-#
-MDA_RELEASE_DOCS_URL="https://www.mdanalysis.org/docs/"
-MDA_DEVELOPMENT_DOCS_URL="https://www.mdanalysis.org/mdanalysis/"
-
-GH_REPOSITORY=github.com/MDAnalysis/docs.git
-#MDA_DOCDIR=${TRAVIS_BUILD_DIR}/package/doc/html/html
-MDA_DOCDIR=package/doc/html/html
-GIT_CI_USER="TravisCI"
-GIT_CI_EMAIL="TravisCI@mdanalysis.org"
-
-# for informational purposes at the moment
-GH_DOC_BRANCH=$(git rev-parse --abbrev-ref HEAD)
-
-
-set -o errexit -o nounset
-
-function die () {
- local msg="$1" err=${2:-1}
- echo "ERROR: $msg [$err]"
- exit $err
-}
-
-rev=$(git rev-parse --short HEAD)
-rootdir="$(git rev-parse --show-toplevel)"
-
-maintainer_dir="${rootdir}/maintainer"
-
-# the following tests should be superfluous because of -o nounset
-test -n "${GH_TOKEN}" || die "GH_TOKEN is empty: need OAuth GitHub token to continue" 100
-test -n "${GH_REPOSITORY}" || die "GH_REPOSITORY must be set in .travis.yml" 100
-test -n "${MDA_DOCDIR}" || die "MDA_DOCDIR must be set in .travis.yml" 100
-
-cd ${MDA_DOCDIR} || die "Failed to 'cd ${MDA_DOCDIR}'. Run from the top level of the repository"
-
-# for local testing
-test -d .git && rm -rf .git
-
-git init
-git config user.name "${GIT_CI_USER}"
-git config user.email "${GIT_CI_EMAIL}"
-
-git remote add docs "https://${GH_TOKEN}@${GH_REPOSITORY}"
-git fetch --depth 10 docs master
-git reset docs/master
-
-touch .
-touch .nojekyll
-
-git add -A .
-git commit -m "rebuilt html docs from branch ${GH_DOC_BRANCH} with sphinx at MDAnalysis/mdanalysis@${rev}"
-
-# fix sitemap.xml for release docs
-${maintainer_dir}/adapt_sitemap.py --search ${MDA_DEVELOPMENT_DOCS_URL} --replace ${MDA_RELEASE_DOCS_URL} -o sitemap.xml sitemap.xml
-
-git add sitemap.xml
-git commit -m "adjusted sitemap.xml for release docs at ${MDA_RELEASE_DOCS_URL}"
-
-git push -q docs HEAD:master
-
-
diff --git a/maintainer/update_json_stubs_sitemap.py b/maintainer/update_json_stubs_sitemap.py
new file mode 100644
index 00000000000..a699a0729a5
--- /dev/null
+++ b/maintainer/update_json_stubs_sitemap.py
@@ -0,0 +1,140 @@
+# Adapted from mdtraj/devtools/travis-ci/update_versions_json.py,
+# by Robert T McGibbon, under the LGPLv2.1 license
+# Similarly by the terms of LGPL this is also in the public domain
+# Lily Wang, 2020
+#
+# This script is called by deploy_docs_via_travis.sh to:
+# 1. update versions.json
+# 2. Write some redirect stubs
+# 3. Write a sitemap.xml file for the root directory
+#
+
+import json
+import os
+import shutil
+import xml.etree.ElementTree as ET
+
+try:
+ from urllib.request import Request, urlopen
+except ImportError:
+ from urllib2 import Request, urlopen
+
+URL = os.environ['URL']
+VERSION = os.environ['VERSION']
+
+
+def get_web_file(filename, callback, default):
+ url = os.path.join(URL, filename)
+ try:
+ page = Request(url, headers={'User-Agent': 'Mozilla/5.0'})
+ data = urlopen(page).read().decode()
+ except Exception as e:
+ print(e)
+ try:
+ with open(filename, 'r') as f:
+ return callback(f)
+ except IOError as e:
+ print(e)
+ return default
+ else:
+ return callback(data)
+
+
+# ========= WRITE JSON =========
+# Update $root/versions.json with links to the right version
+versions = get_web_file('versions.json', json.loads, [])
+existing = [item['version'] for item in versions]
+already_exists = VERSION in existing
+
+if not already_exists:
+ latest = 'dev' not in VERSION
+ if latest:
+ for ver in versions:
+ ver['latest'] = False
+
+ versions.append({
+ 'version': VERSION,
+ 'display': VERSION,
+ 'url': os.path.join(URL, VERSION),
+ 'latest': latest
+ })
+
+with open("versions.json", 'w') as f:
+ json.dump(versions, f, indent=2)
+
+# ========= WRITE HTML STUBS =========
+# Add HTML files to redirect:
+# index.html -> latest release
+# latest/index.html -> latest release
+# dev/index.html -> dev docs
+
+REDIRECT = """
+
+
+Redirecting to {url}
+
+
+"""
+
+for ver in versions[::-1]:
+ if ver['latest']:
+ latest_url = ver['url']
+else:
+ try:
+ latest_url = versions[-1]['url']
+ except IndexError:
+ latest_url = None
+
+for ver in versions[::-1]:
+ if 'dev' in ver['version']:
+ dev_url = ver['url']
+ break
+else:
+ try:
+ dev_url = versions[-1]['url']
+ except IndexError:
+ dev_url = None
+
+if latest_url:
+ with open('index.html', 'w') as f:
+ f.write(REDIRECT.format(url=latest_url))
+
+ with open('latest/index.html', 'w') as f:
+ f.write(REDIRECT.format(url=latest_url))
+
+if dev_url:
+ with open('dev/index.html', 'w') as f:
+ f.write(REDIRECT.format(url=dev_url))
+
+# ========= WRITE SUPER SITEMAP.XML =========
+# make one big sitemap.xml
+ET.register_namespace('xhtml', "http://www.w3.org/1999/xhtml")
+
+# so we could make 1 big sitemap as commented
+# below, but they must be max 50 MB / 50k URL.
+# Yes, this is 100+ releases, but who knows when
+# that'll happen and who'll look at this then?
+# bigroot = ET.Element("urlset")
+# bigroot.set("xmlns", "http://www.sitemaps.org/schemas/sitemap/0.9")
+# for ver in versions:
+# tree = get_web_file(ver['version']+'/sitemap.xml', ET.fromstring,
+# ET.fromstring(''))
+# root = tree.getroot()
+# bigroot.extend(root.getchildren())
+# ET.ElementTree(bigroot).write('sitemap.xml',
+# xml_declaration=True,
+# encoding='utf-8',
+# method="xml")
+
+# so instead we make a sitemap of sitemaps.
+bigroot = ET.Element("sitemapindex")
+bigroot.set("xmlns", "http://www.sitemaps.org/schemas/sitemap/0.9")
+for ver in versions:
+ path = os.path.join(URL, '{}/sitemap.xml'.format(ver['version']))
+ sitemap = ET.SubElement(bigroot, 'sitemap')
+ ET.SubElement(sitemap, 'loc').text = path
+
+ET.ElementTree(bigroot).write('sitemap_index.xml',
+ xml_declaration=True,
+ encoding='utf-8',
+ method="xml")
diff --git a/package/doc/README b/package/doc/README
index 13a0dff5efb..60b66f94ae4 100644
--- a/package/doc/README
+++ b/package/doc/README
@@ -34,12 +34,12 @@ Online html manual
The documentation for the latest stable release can always be found at
- https://docs.mdanalysis.org
+ https://www.mdanalysis.org/docs
The docs for the latest development version are also on the internet
at
- http://devdocs.mdanalysis.org
+ http://docs.mdanalysis.org/dev
The manual includes all the doc strings with some additional text; it
is a work in progress and suggestions to improve it are welcome. File
diff --git a/package/doc/sphinx/source/conf.py b/package/doc/sphinx/source/conf.py
index 4155a3868ee..72c1b7e471d 100644
--- a/package/doc/sphinx/source/conf.py
+++ b/package/doc/sphinx/source/conf.py
@@ -15,6 +15,7 @@
import os
import platform
import datetime
+import msmb_theme # for little versions pop-up
# https://sphinx-rtd-theme.readthedocs.io/en/stable/
import sphinx_rtd_theme
@@ -42,11 +43,13 @@
mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
# for sitemap with https://github.com/jdillard/sphinx-sitemap
-# NOTE: This sitemap is only correct for the DEVELOPMENT doccs. The RELEASE docs
-# are served from https://www.mdanalysis.org/docs/ and the sitemap.xml
-# is manually fixed when deploying the release docs with the
-# maintainer/deploy_master_docs.sh script
-site_url = "https://www.mdanalysis.org/mdanalysis/"
+# This sitemap is correct both for the development and release docs, which
+# are both served from docs.mdanalysis.org/$version .
+# The docs used to be available automatically at mdanalysis.org/mdanalysis;
+# they are now at docs.mdanalysis.org/, which requires a CNAME DNS record
+# pointing to mdanalysis.github.io. To change this URL you should change/delete
+# the CNAME record for "docs" and update the URL in GitHub settings
+site_url = "https://docs.mdanalysis.org/"
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -78,7 +81,8 @@
# Dynamically calculate the version
packageversion = __import__('MDAnalysis').__version__
# The short X.Y version.
-version = '.'.join(packageversion.split('.')[:2])
+# version = '.'.join(packageversion.split('.')[:2])
+version = packageversion # needed for right sitemap.xml URLs
# The full version, including alpha/beta/rc tags.
release = packageversion
@@ -116,14 +120,14 @@
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
-#to include decorated objects like __init__
+# to include decorated objects like __init__
autoclass_content = 'both'
# -- 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 = 'sphinx_rtd_theme'
+html_theme = 'msmb_theme'
# 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
@@ -139,7 +143,7 @@
color = {'orange': '#FF9200',
'gray': '#808080',
'white': '#FFFFFF',
- 'black': '#000000',}
+ 'black': '#000000', }
html_theme_options = {
'canonical_url': '',
@@ -156,8 +160,15 @@
'titles_only': False,
}
+html_context = {
+ 'versions_json_url': 'https://docs.mdanalysis.org/versions.json'
+}
+
# Add any paths that contain custom themes here, relative to this directory.
-# html_theme_path = ['_themes',]
+html_theme_path = [
+ msmb_theme.get_html_theme_path(),
+ sphinx_rtd_theme.get_html_theme_path()
+]
# The name for this set of Sphinx documents. If None, it defaults to
# " v documentation".
@@ -246,8 +257,8 @@
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
- ('MDAnalysis.tex', u'MDAnalysis Documentation',
- authors, 'manual'),
+ ('MDAnalysis.tex', u'MDAnalysis Documentation',
+ authors, 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
diff --git a/package/requirements.txt b/package/requirements.txt
new file mode 100644
index 00000000000..2c22157aa5b
--- /dev/null
+++ b/package/requirements.txt
@@ -0,0 +1,24 @@
+biopython
+codecov
+cython
+griddataformats
+gsd
+hypothesis
+joblib>=0.12
+matplotlib
+mmtf-python
+mock
+msmb_theme==1.2.0
+netcdf4
+networkx
+numpy
+parmed
+psutil
+pytest
+scikit-learn
+scipy
+seaborn>=0.7.0,<=0.9
+sphinx==1.8.5
+sphinx_rtd_theme
+sphinx_sitemap
+tqdm
diff --git a/package/setup.py b/package/setup.py
index b97524d0e85..65a355e8a90 100755
--- a/package/setup.py
+++ b/package/setup.py
@@ -103,6 +103,9 @@
sys.exit(1)
cython_linetrace = False
+def abspath(file):
+ return os.path.join(os.path.dirname(os.path.abspath(__file__)),
+ file)
class Config(object):
"""Config wrapper class to get build options
@@ -122,6 +125,7 @@ class Config(object):
"""
def __init__(self, fname='setup.cfg'):
+ fname = abspath(fname)
if os.path.exists(fname):
self.config = configparser.SafeConfigParser()
self.config.read(fname)
@@ -152,9 +156,10 @@ class MDAExtension(Extension, object):
# This is accomplished by passing the get_numpy_include function
# as one of the include_dirs. This derived Extension class takes
# care of calling it when needed.
- def __init__(self, *args, **kwargs):
+ def __init__(self, name, sources, *args, **kwargs):
self._mda_include_dirs = []
- super(MDAExtension, self).__init__(*args, **kwargs)
+ sources = [abspath(s) for s in sources]
+ super(MDAExtension, self).__init__(name, sources, *args, **kwargs)
@property
def include_dirs(self):
@@ -163,7 +168,8 @@ def include_dirs(self):
try:
self._mda_include_dirs.append(item()) #The numpy callable
except TypeError:
- self._mda_include_dirs.append(item)
+ item = abspath(item)
+ self._mda_include_dirs.append((item))
return self._mda_include_dirs
@include_dirs.setter
@@ -459,7 +465,7 @@ def dynamic_author_list():
"Chronological list of authors" title.
"""
authors = []
- with codecs.open('AUTHORS', encoding='utf-8') as infile:
+ with codecs.open(abspath('AUTHORS'), encoding='utf-8') as infile:
# An author is a bullet point under the title "Chronological list of
# authors". We first want move the cursor down to the title of
# interest.
@@ -498,7 +504,7 @@ def dynamic_author_list():
+ authors + ['Oliver Beckstein'])
# Write the authors.py file.
- out_path = 'MDAnalysis/authors.py'
+ out_path = abspath('MDAnalysis/authors.py')
with codecs.open(out_path, 'w', encoding='utf-8') as outfile:
# Write the header
header = '''\
@@ -522,7 +528,7 @@ def dynamic_author_list():
except (OSError, IOError):
warnings.warn('Cannot write the list of authors.')
- with open("SUMMARY.txt") as summary:
+ with open(abspath('SUMMARY.txt')) as summary:
LONG_DESCRIPTION = summary.read()
CLASSIFIERS = [
'Development Status :: 4 - Beta',
diff --git a/testsuite/README b/testsuite/README
index d1c116b7163..c61fb7f75c5 100644
--- a/testsuite/README
+++ b/testsuite/README
@@ -50,7 +50,7 @@ Help is also available through the mailing list at https://groups.google.com/gro
.. |devdocs| image:: https://img.shields.io/badge/docs-development-yellow.svg
:alt: Documentation (development version)
- :target: https://www.mdanalysis.org/mdanalysis/
+ :target: https://docs.mdanalysis.org/dev/
.. |developergroup| image:: https://img.shields.io/badge/Google%20Group-Developers-lightgrey.svg
:alt: Developer Google Group