diff --git a/.gitignore b/.gitignore
index da2e098..bd05c81 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,6 @@ node_modules
VERSION
VERSION.json
tests/nb/gif
+codeship.aes
+deployment/tokens
+
diff --git a/Dockerfile b/Dockerfile
index bd4dd2d..762f64d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -3,10 +3,10 @@ FROM continuumio/miniconda3:4.3.14
# Install requirements
RUN conda install -c openbabel openbabel
RUN conda install -c omnia biopython parmed
-RUN conda install jupyter
-RUN pip install "moldesign==0.8.0b3"
+RUN conda install jupyter git
ADD requirements.txt /opt/requirements.txt
+RUN pip install --pre moldesign # probably need to invalidate cache at this level
RUN pip install -r /opt/requirements.txt
# This disables notebook security until we can figure out a way to pass runtime tokens
@@ -26,3 +26,5 @@ RUN jupyter nbextension install --sys-prefix --py widgetsnbextension \
&& jupyter nbextension enable --sys-prefix --py nbmolviz
EXPOSE 8888
+
+ENTRYPOINT deployment/run_notebook.sh
diff --git a/NOTICE b/NOTICE
deleted file mode 100644
index fb86c4b..0000000
--- a/NOTICE
+++ /dev/null
@@ -1,53 +0,0 @@
-NBMolViz incorporates code from 3DMol.js, d3.js and PyQuante2
-
- 3DMol.js
----------------------
-3DMol.js is copyright (c) 2014, University of Pittsburgh and contributors
-Source file: nbmolviz/static/3Dmol.js
-Description: this is modified version of the 3DMol.js library.
- It has been modified to add the "forceRedraw" function.
-License file: nbmolviz/static/3dmol/LICENSE
-
- D3.js
----------------------
-D3.js is copyright (c) 2010-2016 Mike Bostock
-Source file: js/node_modules/nbmolviz2d/node_modules/d3/build/d3.node.js
-Description: This is the official version distributed via npm.
-Project: https://github.com/d3/d3
-License file: js/node_modules/nbmolviz2d/node_modules/d3/LICENSE
-
- PyQuante2
----------------------
-PyQuante2 is copyright (c) 2013 PyQuante Development Team
-Source file: nbmolviz/utils.py
-Description: The CCLibBasis class contains modified code from PyQuante2
-License:
-
-Copyright (c) 2013 PyQuante Development Team
-
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
- a. Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimer.
- b. Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- c. Neither the name of SymPy nor the names of its contributors
- may be used to endorse or promote products derived from this software
- without specific prior written permission.
-
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-DAMAGE.
diff --git a/NOTICES b/NOTICES
new file mode 100644
index 0000000..60327a0
--- /dev/null
+++ b/NOTICES
@@ -0,0 +1,305 @@
+NBMolViz incorporates code from PyQuante2 and the cPython standard library
+
+ PyQuante2
+---------------------
+PyQuante2 is copyright (c) 2013 PyQuante Development Team
+Source file: nbmolviz/utils.py
+Description: The CCLibBasis class contains modified code from PyQuante2
+License:
+
+Copyright (c) 2013 PyQuante Development Team
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+ a. Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ b. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ c. Neither the name of SymPy nor the names of its contributors
+ may be used to endorse or promote products derived from this software
+ without specific prior written permission.
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+
+
+ Python
+--------------------------------
+Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
+2011, 2012, 2013, 2014, 2015, 2016 Python Software Foundation; All Rights
+Reserved
+SOURCE CODE: nbmolviz/utils.py (`indent` function)
+DESCRIPTION: backports of Python 3 functions
+WEBSITE: https://www.python.org
+LICENSE:
+
+A. HISTORY OF THE SOFTWARE
+==========================
+
+Python was created in the early 1990s by Guido van Rossum at Stichting
+Mathematisch Centrum (CWI, see http://www.cwi.nl) in the Netherlands
+as a successor of a language called ABC. Guido remains Python's
+principal author, although it includes many contributions from others.
+
+In 1995, Guido continued his work on Python at the Corporation for
+National Research Initiatives (CNRI, see http://www.cnri.reston.va.us)
+in Reston, Virginia where he released several versions of the
+software.
+
+In May 2000, Guido and the Python core development team moved to
+BeOpen.com to form the BeOpen PythonLabs team. In October of the same
+year, the PythonLabs team moved to Digital Creations, which became
+Zope Corporation. In 2001, the Python Software Foundation (PSF, see
+https://www.python.org/psf/) was formed, a non-profit organization
+created specifically to own Python-related Intellectual Property.
+Zope Corporation was a sponsoring member of the PSF.
+
+All Python releases are Open Source (see http://www.opensource.org for
+the Open Source Definition). Historically, most, but not all, Python
+releases have also been GPL-compatible; the table below summarizes
+the various releases.
+
+ Release Derived Year Owner GPL-
+ from compatible? (1)
+
+ 0.9.0 thru 1.2 1991-1995 CWI yes
+ 1.3 thru 1.5.2 1.2 1995-1999 CNRI yes
+ 1.6 1.5.2 2000 CNRI no
+ 2.0 1.6 2000 BeOpen.com no
+ 1.6.1 1.6 2001 CNRI yes (2)
+ 2.1 2.0+1.6.1 2001 PSF no
+ 2.0.1 2.0+1.6.1 2001 PSF yes
+ 2.1.1 2.1+2.0.1 2001 PSF yes
+ 2.1.2 2.1.1 2002 PSF yes
+ 2.1.3 2.1.2 2002 PSF yes
+ 2.2 and above 2.1.1 2001-now PSF yes
+
+Footnotes:
+
+(1) GPL-compatible doesn't mean that we're distributing Python under
+ the GPL. All Python licenses, unlike the GPL, let you distribute
+ a modified version without making your changes open source. The
+ GPL-compatible licenses make it possible to combine Python with
+ other software that is released under the GPL; the others don't.
+
+(2) According to Richard Stallman, 1.6.1 is not GPL-compatible,
+ because its license has a choice of law clause. According to
+ CNRI, however, Stallman's lawyer has told CNRI's lawyer that 1.6.1
+ is "not incompatible" with the GPL.
+
+Thanks to the many outside volunteers who have worked under Guido's
+direction to make these releases possible.
+
+
+B. TERMS AND CONDITIONS FOR ACCESSING OR OTHERWISE USING PYTHON
+===============================================================
+
+PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2
+--------------------------------------------
+
+1. This LICENSE AGREEMENT is between the Python Software Foundation
+("PSF"), and the Individual or Organization ("Licensee") accessing and
+otherwise using this software ("Python") in source or binary form and
+its associated documentation.
+
+2. Subject to the terms and conditions of this License Agreement, PSF hereby
+grants Licensee a nonexclusive, royalty-free, world-wide license to reproduce,
+analyze, test, perform and/or display publicly, prepare derivative works,
+distribute, and otherwise use Python alone or in any derivative version,
+provided, however, that PSF's License Agreement and PSF's notice of copyright,
+i.e., "Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
+2011, 2012, 2013, 2014, 2015, 2016, 2017 Python Software Foundation; All Rights
+Reserved" are retained in Python alone or in any derivative version prepared by
+Licensee.
+
+3. In the event Licensee prepares a derivative work that is based on
+or incorporates Python or any part thereof, and wants to make
+the derivative work available to others as provided herein, then
+Licensee hereby agrees to include in any such work a brief summary of
+the changes made to Python.
+
+4. PSF is making Python available to Licensee on an "AS IS"
+basis. PSF MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
+IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, PSF MAKES NO AND
+DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
+FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON WILL NOT
+INFRINGE ANY THIRD PARTY RIGHTS.
+
+5. PSF SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON
+FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS
+A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON,
+OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
+
+6. This License Agreement will automatically terminate upon a material
+breach of its terms and conditions.
+
+7. Nothing in this License Agreement shall be deemed to create any
+relationship of agency, partnership, or joint venture between PSF and
+Licensee. This License Agreement does not grant permission to use PSF
+trademarks or trade name in a trademark sense to endorse or promote
+products or services of Licensee, or any third party.
+
+8. By copying, installing or otherwise using Python, Licensee
+agrees to be bound by the terms and conditions of this License
+Agreement.
+
+
+BEOPEN.COM LICENSE AGREEMENT FOR PYTHON 2.0
+-------------------------------------------
+
+BEOPEN PYTHON OPEN SOURCE LICENSE AGREEMENT VERSION 1
+
+1. This LICENSE AGREEMENT is between BeOpen.com ("BeOpen"), having an
+office at 160 Saratoga Avenue, Santa Clara, CA 95051, and the
+Individual or Organization ("Licensee") accessing and otherwise using
+this software in source or binary form and its associated
+documentation ("the Software").
+
+2. Subject to the terms and conditions of this BeOpen Python License
+Agreement, BeOpen hereby grants Licensee a non-exclusive,
+royalty-free, world-wide license to reproduce, analyze, test, perform
+and/or display publicly, prepare derivative works, distribute, and
+otherwise use the Software alone or in any derivative version,
+provided, however, that the BeOpen Python License is retained in the
+Software, alone or in any derivative version prepared by Licensee.
+
+3. BeOpen is making the Software available to Licensee on an "AS IS"
+basis. BEOPEN MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
+IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, BEOPEN MAKES NO AND
+DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
+FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF THE SOFTWARE WILL NOT
+INFRINGE ANY THIRD PARTY RIGHTS.
+
+4. BEOPEN SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF THE
+SOFTWARE FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS
+AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THE SOFTWARE, OR ANY
+DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
+
+5. This License Agreement will automatically terminate upon a material
+breach of its terms and conditions.
+
+6. This License Agreement shall be governed by and interpreted in all
+respects by the law of the State of California, excluding conflict of
+law provisions. Nothing in this License Agreement shall be deemed to
+create any relationship of agency, partnership, or joint venture
+between BeOpen and Licensee. This License Agreement does not grant
+permission to use BeOpen trademarks or trade names in a trademark
+sense to endorse or promote products or services of Licensee, or any
+third party. As an exception, the "BeOpen Python" logos available at
+http://www.pythonlabs.com/logos.html may be used according to the
+permissions granted on that web page.
+
+7. By copying, installing or otherwise using the software, Licensee
+agrees to be bound by the terms and conditions of this License
+Agreement.
+
+
+CNRI LICENSE AGREEMENT FOR PYTHON 1.6.1
+---------------------------------------
+
+1. This LICENSE AGREEMENT is between the Corporation for National
+Research Initiatives, having an office at 1895 Preston White Drive,
+Reston, VA 20191 ("CNRI"), and the Individual or Organization
+("Licensee") accessing and otherwise using Python 1.6.1 software in
+source or binary form and its associated documentation.
+
+2. Subject to the terms and conditions of this License Agreement, CNRI
+hereby grants Licensee a nonexclusive, royalty-free, world-wide
+license to reproduce, analyze, test, perform and/or display publicly,
+prepare derivative works, distribute, and otherwise use Python 1.6.1
+alone or in any derivative version, provided, however, that CNRI's
+License Agreement and CNRI's notice of copyright, i.e., "Copyright (c)
+1995-2001 Corporation for National Research Initiatives; All Rights
+Reserved" are retained in Python 1.6.1 alone or in any derivative
+version prepared by Licensee. Alternately, in lieu of CNRI's License
+Agreement, Licensee may substitute the following text (omitting the
+quotes): "Python 1.6.1 is made available subject to the terms and
+conditions in CNRI's License Agreement. This Agreement together with
+Python 1.6.1 may be located on the Internet using the following
+unique, persistent identifier (known as a handle): 1895.22/1013. This
+Agreement may also be obtained from a proxy server on the Internet
+using the following URL: http://hdl.handle.net/1895.22/1013".
+
+3. In the event Licensee prepares a derivative work that is based on
+or incorporates Python 1.6.1 or any part thereof, and wants to make
+the derivative work available to others as provided herein, then
+Licensee hereby agrees to include in any such work a brief summary of
+the changes made to Python 1.6.1.
+
+4. CNRI is making Python 1.6.1 available to Licensee on an "AS IS"
+basis. CNRI MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
+IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, CNRI MAKES NO AND
+DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
+FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON 1.6.1 WILL NOT
+INFRINGE ANY THIRD PARTY RIGHTS.
+
+5. CNRI SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON
+1.6.1 FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS
+A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON 1.6.1,
+OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
+
+6. This License Agreement will automatically terminate upon a material
+breach of its terms and conditions.
+
+7. This License Agreement shall be governed by the federal
+intellectual property law of the United States, including without
+limitation the federal copyright law, and, to the extent such
+U.S. federal law does not apply, by the law of the Commonwealth of
+Virginia, excluding Virginia's conflict of law provisions.
+Notwithstanding the foregoing, with regard to derivative works based
+on Python 1.6.1 that incorporate non-separable material that was
+previously distributed under the GNU General Public License (GPL), the
+law of the Commonwealth of Virginia shall govern this License
+Agreement only as to issues arising under or with respect to
+Paragraphs 4, 5, and 7 of this License Agreement. Nothing in this
+License Agreement shall be deemed to create any relationship of
+agency, partnership, or joint venture between CNRI and Licensee. This
+License Agreement does not grant permission to use CNRI trademarks or
+trade name in a trademark sense to endorse or promote products or
+services of Licensee, or any third party.
+
+8. By clicking on the "ACCEPT" button where indicated, or by copying,
+installing or otherwise using Python 1.6.1, Licensee agrees to be
+bound by the terms and conditions of this License Agreement.
+
+ ACCEPT
+
+
+CWI LICENSE AGREEMENT FOR PYTHON 0.9.0 THROUGH 1.2
+--------------------------------------------------
+
+Copyright (c) 1991 - 1995, Stichting Mathematisch Centrum Amsterdam,
+The Netherlands. All rights reserved.
+
+Permission to use, copy, modify, and distribute this software and its
+documentation for any purpose and without fee is hereby granted,
+provided that the above copyright notice appear in all copies and that
+both that copyright notice and this permission notice appear in
+supporting documentation, and that the name of Stichting Mathematisch
+Centrum or CWI not be used in advertising or publicity pertaining to
+distribution of the software without specific, written prior
+permission.
+
+STICHTING MATHEMATISCH CENTRUM DISCLAIMS ALL WARRANTIES WITH REGARD TO
+THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS, IN NO EVENT SHALL STICHTING MATHEMATISCH CENTRUM BE LIABLE
+FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT
+OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+
diff --git a/codeship-services.yml b/codeship-services.yml
index e69de29..fced88d 100644
--- a/codeship-services.yml
+++ b/codeship-services.yml
@@ -0,0 +1,14 @@
+builder:
+ build:
+ dockerfile: ./deployment/Dockerfile.build
+ context: ./
+ volumes:
+ - ./nbmv-dist:/opt/nbmv-dist
+
+publisher:
+ encrypted_env_file: deployment/tokens.crypt
+ build:
+ dockerfile: ./deployment/Dockerfile.build
+ context: ./
+ volumes:
+ - ./nbmv-dist:/opt/nbmv-dist
diff --git a/codeship-steps.yml b/codeship-steps.yml
index e69de29..22e6e68 100644
--- a/codeship-steps.yml
+++ b/codeship-steps.yml
@@ -0,0 +1,9 @@
+- name: build
+ service: builder
+ command: bash -c "python setup.py sdist && cp -r dist /opt/nbmv-dist"
+
+- name: publish
+ service: publisher
+ # matches tags that are valid PEP440 versions
+ tag: '^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)((a|rc|b)(0|[1-9]\d*))?$'
+ command: deployment/publish.sh
diff --git a/deployment/Dockerfile.build b/deployment/Dockerfile.build
new file mode 100644
index 0000000..c57b6c2
--- /dev/null
+++ b/deployment/Dockerfile.build
@@ -0,0 +1,12 @@
+FROM continuumio/miniconda3:4.3.14
+
+RUN apt-get update \
+ && apt-get install -y build-essential
+
+# Install requirements
+RUN conda install git nodejs
+RUN pip install moldesign==0.8.0rc4 twine
+
+# Finally, install the actual package
+ADD . /opt/notebook-molecular-visualization
+WORKDIR /opt/notebook-molecular-visualization
diff --git a/deployment/publish.sh b/deployment/publish.sh
new file mode 100755
index 0000000..e077768
--- /dev/null
+++ b/deployment/publish.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+# Publish a new release (triggered by a git tag that conforms to a PEP440 release)
+# Exit 1 if there's a mismatch between the git tag and the package's version
+#
+# Expects to run in base directory of the repository
+
+# fail immediately if any command fails:
+set -e
+
+PKG='nbmolviz'
+
+if [[ -z ${CI_BRANCH} ]]; then
+ echo "Variable \"\$CI_BRANCH\" not set - cannot publish"
+ exit 2
+fi
+
+ARTIFACT=/opt/nbmv-dist/dist/${PKG}-${CI_BRANCH}.tar.gz
+
+if [ ! -f $ARTIFACT ]; then
+ echo "No build artifact found! Expected ${ARTIFACT}"
+ exit 3
+fi
+
+pip install ${ARTIFACT}
+pyversion=$(python -c "import ${PKG}; print(${PKG}.__version__)" | tail -n 1)
+
+if [ "${pyversion}" == "${CI_BRANCH}" ]; then
+ echo "Deploying version ${CI_BRANCH}"
+else
+ echo "Can't publish - ${PKG} package version '${pyversion}' differs from its Git tag '${CI_BRANCH}'"
+ exit 1
+fi
+
+echo "Uploading version ${CI_BRANCH} to PyPI:"
+twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} ${ARTIFACT}
diff --git a/deployment/run_notebook.sh b/deployment/run_notebook.sh
index 4b17a19..ea5b1f1 100755
--- a/deployment/run_notebook.sh
+++ b/deployment/run_notebook.sh
@@ -1,3 +1,3 @@
#!/bin/bash
-jupyter notebook --ip=127.0.0.1 --no-browser --port=8888 --allow-root $@
+jupyter notebook --ip=0.0.0.0 --no-browser --port=8888 --allow-root $@
diff --git a/deployment/tokens.crypt b/deployment/tokens.crypt
new file mode 100644
index 0000000..07e85df
--- /dev/null
+++ b/deployment/tokens.crypt
@@ -0,0 +1 @@
+Zqc9x7efhLyMK2hQyt83/wr4HTzv6Q0ZRwyPRuZAXtSRXHI0UmJpdvittQiWP/QmAuHO33zpO4pgjs9NoB5vseTk
\ No newline at end of file
diff --git a/js/package-lock.json b/js/package-lock.json
new file mode 100644
index 0000000..457583c
--- /dev/null
+++ b/js/package-lock.json
@@ -0,0 +1,4433 @@
+{
+ "name": "nbmolviz-js",
+ "requires": true,
+ "lockfileVersion": 1,
+ "dependencies": {
+ "@types/jquery": {
+ "version": "https://registry.npmjs.org/@types/jquery/-/jquery-2.0.41.tgz",
+ "integrity": "sha1-uHugUQEfme2+WG2Plygud4bgGm0="
+ },
+ "@types/underscore": {
+ "version": "https://registry.npmjs.org/@types/underscore/-/underscore-1.8.0.tgz",
+ "integrity": "sha1-eiLvWE1v5Zry5Ae64Hnit/ilEC8="
+ },
+ "3dmol": {
+ "version": "1.1.4",
+ "resolved": "https://registry.npmjs.org/3dmol/-/3dmol-1.1.4.tgz",
+ "integrity": "sha1-HdSXVZqMehUe163HSXbcBF0krvU="
+ },
+ "babel-core": {
+ "version": "6.26.0",
+ "resolved": "https://registry.npmjs.org/babel-core/-/babel-core-6.26.0.tgz",
+ "integrity": "sha1-rzL3izGm/O8RnIew/Y2XU/A6C7g=",
+ "dev": true,
+ "requires": {
+ "babel-code-frame": "6.26.0",
+ "babel-generator": "6.26.0",
+ "babel-helpers": "6.24.1",
+ "babel-messages": "6.23.0",
+ "babel-register": "6.26.0",
+ "babel-runtime": "6.26.0",
+ "babel-template": "6.26.0",
+ "babel-traverse": "6.26.0",
+ "babel-types": "6.26.0",
+ "babylon": "6.18.0",
+ "convert-source-map": "1.5.0",
+ "debug": "2.6.9",
+ "json5": "0.5.1",
+ "lodash": "4.17.4",
+ "minimatch": "3.0.4",
+ "path-is-absolute": "1.0.1",
+ "private": "0.1.7",
+ "slash": "1.0.0",
+ "source-map": "0.5.7"
+ },
+ "dependencies": {
+ "ansi-regex": {
+ "version": "2.1.1",
+ "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-2.1.1.tgz",
+ "integrity": "sha1-w7M6te42DYbg5ijwRorn7yfWVN8=",
+ "dev": true
+ },
+ "ansi-styles": {
+ "version": "2.2.1",
+ "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-2.2.1.tgz",
+ "integrity": "sha1-tDLdM1i2NM914eRmQ2gkBTPB3b4=",
+ "dev": true
+ },
+ "babel-code-frame": {
+ "version": "6.26.0",
+ "resolved": "https://registry.npmjs.org/babel-code-frame/-/babel-code-frame-6.26.0.tgz",
+ "integrity": "sha1-Y/1D99weO7fONZR9uP42mj9Yx0s=",
+ "dev": true,
+ "requires": {
+ "chalk": "1.1.3",
+ "esutils": "2.0.2",
+ "js-tokens": "3.0.2"
+ }
+ },
+ "babel-generator": {
+ "version": "6.26.0",
+ "resolved": "https://registry.npmjs.org/babel-generator/-/babel-generator-6.26.0.tgz",
+ "integrity": "sha1-rBriAHC3n248odMmlhMFN3TyDcU=",
+ "dev": true,
+ "requires": {
+ "babel-messages": "6.23.0",
+ "babel-runtime": "6.26.0",
+ "babel-types": "6.26.0",
+ "detect-indent": "4.0.0",
+ "jsesc": "1.3.0",
+ "lodash": "4.17.4",
+ "source-map": "0.5.7",
+ "trim-right": "1.0.1"
+ }
+ },
+ "babel-helpers": {
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diff --git a/js/package.json b/js/package.json
index d166e42..f85e8b1 100644
--- a/js/package.json
+++ b/js/package.json
@@ -23,9 +23,10 @@
"webpack": "^1.12.14"
},
"dependencies": {
+ "d3": "4.10.0",
"jupyter-js-widgets": "^2.1.4",
"molecule-2d-for-react": "^0.2.3",
- "molecule-3d-for-react": "^0.4.2",
+ "molecule-3d-for-react": "^0.4.5",
"react": "^15.3.2",
"react-dom": "^15.3.2",
"underscore": "^1.8.3"
diff --git a/nbmolviz/__main__.py b/nbmolviz/__main__.py
index 50bb547..08d416e 100644
--- a/nbmolviz/__main__.py
+++ b/nbmolviz/__main__.py
@@ -51,7 +51,7 @@ def main():
if args.command == 'check':
print('Expected version:', _version.get_versions()['version'])
- versions = install.get_installed_versions('nbmolviz-js', True)
+ versions = install.get_installed_versions('nbmolviz', True)
foundone = False
for key, vers in versions.items():
if vers.installed:
diff --git a/nbmolviz/install.py b/nbmolviz/install.py
index 56ffe58..c48014c 100644
--- a/nbmolviz/install.py
+++ b/nbmolviz/install.py
@@ -1,3 +1,7 @@
+from __future__ import print_function, absolute_import, division, unicode_literals
+from future.builtins import *
+from future import standard_library
+standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
@@ -57,13 +61,25 @@ def location_writable():
config_paths = jupyter_config_dirs()
ext_paths = nbextension_ordered_paths()
writable = {}
- for location in ext_paths:
- writable[location] = (
- os.access(config_paths[location], os.W_OK | os.X_OK) and
- os.access(ext_paths[location], os.W_OK | os.X_OK))
+ for pathname in ext_paths:
+ confpath = config_paths[pathname]
+ extpath = ext_paths[pathname]
+
+ confpath = _get_first_parent_directory(confpath)
+ extpath = _get_first_parent_directory(extpath)
+
+ writable[pathname] = (
+ os.access(confpath, os.W_OK | os.X_OK) and
+ os.access(extpath, os.W_OK | os.X_OK))
return writable
+def _get_first_parent_directory(path):
+ while not os.path.exists(path):
+ path = os.path.dirname(path)
+ return path
+
+
def preferred_install_location():
versions = get_installed_versions('nbmolviz', True)
for loc in 'environment user system'.split():
@@ -75,13 +91,19 @@ def preferred_install_location():
def autoinstall():
- """ Attempt to install and activate the notebook extensions
+ """ Attempt to install and activate the notebook extensions.
+
+ If a given extension is already installed, this will install the latest version into the
+ same location.
+
+ Otherwise, it will install into the first writable location in the following list:
+ 1. virtual environment extensions directory
+ 2. current user's extensions directory
+ 3. global extensions directory
Raises:
ValueError: if there are no writable install locations
"""
- from moldesign import compute
- from . import __version__ as nbv_version
from . import widget_utils as wu
preferred = preferred_install_location()
@@ -90,23 +112,10 @@ def autoinstall():
state = wu.extensions_install_check()
for dep in state:
- do_install = False
- if not state[dep]['installed'] or state[dep]['enabled'] != state[dep]['installed']:
- print("Activating '%s' extensions:" % dep)
- do_install = True
- elif (dep == 'nbmolviz' and
- not compute.config.get('skip_nbmolviz_version_check', False) and
- state[dep]['installed'] and
- state[dep]['version'] != nbv_version):
- print("Updating 'nbmolviz' extensions from %s to %s:" % (state[dep]['version'],
- nbv_version))
- do_install = True
- else:
- print("'%s' extensions already activated." % dep)
-
- if do_install:
- activate_extension(dep, FLAGS[preferred])
-
+ install_location = state[dep]['installed'] if state[dep]['installed'] else preferred
+ activate_extension(dep, FLAGS[install_location])
+ print()
+ lift_iopub_rate_limit()
def get_installed_versions(pyname, getversion):
@@ -160,6 +169,65 @@ def get_installed_versions(pyname, getversion):
writable[k])
for k in installed}
+IOPUB_LINES = """### MOLDESIGN modification
+c.NotebookApp.iopub_data_rate_limit = 100000000000
+### END MOLDESIGN MODIFICATION
+"""
+
+
+def lift_iopub_rate_limit():
+ from jupyter_core import paths as jupypaths
+ from .utils import indent
+
+ config_dir = jupypaths.jupyter_config_dir()
+ nbcfgfile = os.path.join(config_dir, 'jupyter_notebook_config.py')
+ backup_basepath = nbcfgfile+'.bak'
+ bakfile = backup_basepath
+
+ print("Disabling Jupyter rate limits to allow visualization "
+ "(see https://github.com/jupyter/notebook/issues/2287 )")
+
+ if not os.path.exists(nbcfgfile):
+ print("Creating jupyter config file at %s" % nbcfgfile)
+ cmd = "jupyter notebook --generate-config"
+ print(" > %s" % cmd)
+ subprocess.check_call(cmd.split())
+ else:
+ for i in range(100):
+ # if "jupyter_notebook_config.py.bak.N" exists for N=0...99, we'll overwrite # 99
+ # Feel free to submit a PR if you're not OK with this :)
+ if os.path.exists(bakfile):
+ bakfile = backup_basepath+('.%d' % i)
+ else:
+ break
+ print('Previous configuration file saved to %s' % bakfile)
+
+ os.rename(nbcfgfile, bakfile)
+
+ with open(bakfile, 'r') as bakstream, open(nbcfgfile, 'w') as modstream:
+ found = False
+ lineiter = iter(bakstream)
+ while True:
+ try:
+ line = next(lineiter)
+ except StopIteration:
+ break
+
+ if line.strip() == "### MOLDESIGN modification":
+ found = True
+ modstream.write(IOPUB_LINES)
+ for i in range(2): # remove the next two lines
+ next(lineiter)
+ else:
+ modstream.write(line)
+
+ if not found:
+ modstream.write(IOPUB_LINES)
+
+ print('The following lines lines were added to the bottom of %s:' % nbcfgfile)
+ print(indent(IOPUB_LINES, ' > '), end='')
+ print("\nThese changes will take effect the next time Jupyter is launched.")
+
def activate(flags):
try:
@@ -168,7 +236,7 @@ def activate(flags):
if exc.returncode == 2:
raise PermissionError(
('ERROR - failed to enable the widget extensions with %s.' % flags) +
- ' Try rerunning the command with \"sudo\"!')
+ ' Try rerunning the command with \"sudo\"!')
else:
raise
diff --git a/nbmolviz/mdtconfig/compute.py b/nbmolviz/mdtconfig/compute.py
index 127929f..19e0f44 100644
--- a/nbmolviz/mdtconfig/compute.py
+++ b/nbmolviz/mdtconfig/compute.py
@@ -1,4 +1,4 @@
-from __future__ import print_function, absolute_import, division
+from __future__ import print_function, absolute_import, division, unicode_literals
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
@@ -29,7 +29,6 @@
from ..uielements.components import HBox, VBox
-
def configure():
from IPython.display import display
display(MDTConfig())
@@ -62,7 +61,8 @@ def __init__(self):
super().__init__(children=self.children)
def make_header(self):
- img = io.open(os.path.join(mdt.PACKAGEPATH, '_static_data/img/banner.png'), 'r+b').read()
+ with io.open(os.path.join(mdt.PACKAGEPATH, '_static_data/img/banner.png'), 'rb') as imfile:
+ img = imfile.read()
encoded = base64.b64encode(img).decode('ascii')
img = '
'%encoded)
links = [self._makelink(*args) for args in
@@ -85,32 +85,21 @@ def _makelink(url, text):
text=text)
-class ChangeLog(HBox):
+class ChangeLog(VBox):
def __init__(self):
- from pip._vendor.packaging import version
+ import markdown
super().__init__()
self.version = ipy.HTML('')
- self.textarea = ipy.Textarea(layout=ipy.Layout(width='700px', height='300px'))
+ self.textarea = ipy.HTML(layout=ipy.Layout(width='700px', height='300px'))
threading.Thread(target=self.version_check).start()
- p1 = os.path.join(mdt.PACKAGEPATH, "HISTORY.rst")
- p2 = os.path.join(mdt.PACKAGEPATH, "..", "HISTORY.rst")
- if os.path.exists(p1):
- path = p1
- elif os.path.exists(p2):
- path = p2
- else:
- path = None
-
- if path is not None:
- with open(path, 'r') as infile:
- self.textarea.value = infile.read()
- else:
- self.textarea.value = 'HISTORY.rst not found'
-
- self.textarea.disabled = True
+ path = os.path.join(mdt.PACKAGEPATH, "HISTORY.md")
+ with open(path, 'r') as infile:
+ html = markdown.markdown(infile.read())
+ self.textarea.value = '%s