RFE adding support for mybinder.org

README.md

@@ -4,6 +4,10 @@
 
 <img src="atomsci/ddm/docs/ATOM_wordmark_black_transparent.png" width="370" height="100" class="center"></img>
 
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/truatpasteurdotfr/AMPL/master)
+
+[![Binder](https://mybinder.org/badge_logo.svg) with notebook](https://mybinder.org/v2/gh/truatpasteurdotfr/AMPL/master?filepath=atomsci%2Fddm%2FDelaney_Example.ipynb)
+
 
 AMPL is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.
 

atomsci/ddm/Delaney_Example.ipynb

@@ -64,7 +64,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "working_dir = '/usr/local/data'"
+    "working_dir = '/home/jovyan/atomsci/ddm/data'"
    ]
   },
   {

build.sh

@@ -5,7 +5,7 @@ APP=ampl
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 cd $DIR
 
-TOPDIR=`readlink -f .`
+TOPDIR=`readlink -f .`/
 
 BUILD_DIR=${TOPDIR}.build/$APP
 DIST_DIR=${TOPDIR}.dist

environment.yml

@@ -0,0 +1,313 @@
+name: atomsci
+channels:
+  - pytorch
+  - omnia
+  - deepchem
+  - rdkit
+  - conda-forge
+  - defaults
+dependencies:
+  - _ipyw_jlab_nb_ext_conf=0.1.0=py36he11e457_0
+  - absl-py=0.4.1=py_0
+  - alabaster=0.7.10=py36h306e16b_0
+  - anaconda-client=1.6.14=py36_0
+  - anaconda-navigator=1.8.7=py36_0
+  - anaconda-project=0.8.2=py36h44fb852_0
+  - asn1crypto=0.24.0=py36_0
+  - astor=0.7.1=py_0
+  - astroid=1.6.3=py36_0
+  - astropy=3.0.2=py36h3010b51_1
+  - attrs=18.1.0=py36_0
+  - babel=2.5.3=py36_0
+  - backcall=0.1.0=py36_0
+  - backports=1.0=py36hfa02d7e_1
+  - backports.shutil_get_terminal_size=1.0.0=py36hfea85ff_2
+  - beautifulsoup4=4.6.0=py36h49b8c8c_1
+  - bitarray=0.8.1=py36h14c3975_1
+  - bkcharts=0.2=py36h735825a_0
+  - blas=1.0=mkl
+  - blaze=0.11.3=py36h4e06776_0
+  - bleach=1.5.0=py36_0
+  - blosc=1.14.3=hdbcaa40_0
+  - bokeh=0.12.16=py36_0
+  - boost=1.63.0=py36h415b752_1
+  - boto=2.48.0=py36h6e4cd66_1
+  - bottleneck=1.2.1=py36haac1ea0_0
+  - bzip2=1.0.6=h14c3975_5
+  - c-ares=1.14.0=h470a237_0
+  - ca-certificates=2019.1.23=0
+  - cairo=1.14.12=h7636065_2
+  - certifi=2019.3.9=py36_0
+  - cffi=1.11.5=py36h9745a5d_0
+  - chardet=3.0.4=py36h0f667ec_1
+  - click=6.7=py36h5253387_0
+  - cloudpickle=0.5.3=py36_0
+  - clyent=1.2.2=py36h7e57e65_1
+  - colorama=0.3.9=py36h489cec4_0
+  - conda=4.6.12=py36_1
+  - conda-build=3.10.5=py36_0
+  - conda-env=2.6.0=h36134e3_1
+  - conda-verify=2.0.0=py36h98955d8_0
+  - contextlib2=0.5.5=py36h6c84a62_0
+  - cryptography=2.2.2=py36h14c3975_0
+  - cudatoolkit=9.0=h13b8566_0
+  - curl=7.60.0=h84994c4_0
+  - cycler=0.10.0=py36h93f1223_0
+  - cython=0.28.2=py36h14c3975_0
+  - cytoolz=0.9.0.1=py36h14c3975_0
+  - dask=0.17.5=py36_0
+  - dask-core=0.17.5=py36_0
+  - datashape=0.5.4=py36h3ad6b5c_0
+  - dbus=1.13.2=h714fa37_1
+  - decorator=4.3.0=py36_0
+  - deepchem=2.1.0=py36_0
+  - distributed=1.21.8=py36_0
+  - docutils=0.14=py36hb0f60f5_0
+  - entrypoints=0.2.3=py36h1aec115_2
+  - et_xmlfile=1.0.1=py36hd6bccc3_0
+  - expat=2.2.5=he0dffb1_0
+  - fastcache=1.0.2=py36h14c3975_2
+  - fftw3f=3.3.4=2
+  - filelock=3.0.4=py36_0
+  - flask=1.0.2=py36_1
+  - flask-cors=3.0.4=py36_0
+  - fontconfig=2.12.6=h49f89f6_0
+  - freetype=2.8=hab7d2ae_1
+  - gast=0.2.0=py_0
+  - get_terminal_size=1.0.0=haa9412d_0
+  - gevent=1.3.0=py36h14c3975_0
+  - glib=2.56.1=h000015b_0
+  - glob2=0.6=py36he249c77_0
+  - gmp=6.1.2=h6c8ec71_1
+  - gmpy2=2.0.8=py36hc8893dd_2
+  - graphite2=1.3.11=h16798f4_2
+  - greenlet=0.4.13=py36h14c3975_0
+  - grpcio=1.14.1=py36hd60e7a3_0
+  - gst-plugins-base=1.14.0=hbbd80ab_1
+  - gstreamer=1.14.0=hb453b48_1
+  - h5py=2.7.1=py36ha1f6525_2
+  - harfbuzz=1.7.6=h5f0a787_1
+  - hdf5=1.10.2=hba1933b_1
+  - heapdict=1.0.0=py36_2
+  - html5lib=0.9999999=py36_0
+  - icu=58.2=h9c2bf20_1
+  - idna=2.6=py36h82fb2a8_1
+  - imageio=2.3.0=py36_0
+  - imagesize=1.0.0=py36_0
+  - intel-openmp=2018.0.0=8
+  - ipykernel=4.8.2=py36_0
+  - ipython=6.4.0=py36_0
+  - ipython_genutils=0.2.0=py36hb52b0d5_0
+  - ipywidgets=7.2.1=py36_0
+  - isort=4.3.4=py36_0
+  - itsdangerous=0.24=py36h93cc618_1
+  - jbig=2.1=hdba287a_0
+  - jdcal=1.4=py36_0
+  - jedi=0.12.0=py36_1
+  - jinja2=2.10=py36ha16c418_0
+  - joblib=0.11=py36_0
+  - jpeg=9b=h024ee3a_2
+  - jsonschema=2.6.0=py36h006f8b5_0
+  - jupyter=1.0.0=py36_4
+  - jupyter_client=5.2.3=py36_0
+  - jupyter_console=5.2.0=py36he59e554_1
+  - jupyter_core=4.4.0=py36h7c827e3_0
+  - jupyterlab=0.32.1=py36_0
+  - jupyterlab_launcher=0.10.5=py36_0
+  - kiwisolver=1.0.1=py36h764f252_0
+  - lazy-object-proxy=1.3.1=py36h10fcdad_0
+  - libcurl=7.60.0=h1ad7b7a_0
+  - libedit=3.1.20170329=h6b74fdf_2
+  - libffi=3.2.1=hd88cf55_4
+  - libgcc-ng=8.2.0=hdf63c60_1
+  - libgfortran-ng=7.2.0=hdf63c60_3
+  - libpng=1.6.34=hb9fc6fc_0
+  - libprotobuf=3.6.0=hd28b015_0
+  - libsodium=1.0.16=h1bed415_0
+  - libssh2=1.8.0=h9cfc8f7_4
+  - libstdcxx-ng=7.2.0=hdf63c60_3
+  - libtiff=4.0.9=he85c1e1_1
+  - libtool=2.4.6=h544aabb_3
+  - libxcb=1.13=h1bed415_1
+  - libxml2=2.9.8=h26e45fe_1
+  - libxslt=1.1.32=h1312cb7_0
+  - llvmlite=0.23.1=py36hdbcaa40_0
+  - locket=0.2.0=py36h787c0ad_1
+  - lxml=4.2.1=py36h23eabaa_0
+  - lzo=2.10=h49e0be7_2
+  - markdown=2.6.11=py_0
+  - markupsafe=1.0=py36hd9260cd_1
+  - matplotlib=2.2.2=py36h0e671d2_1
+  - mccabe=0.6.1=py36h5ad9710_1
+  - mdtraj=1.9.1=py36_1
+  - mistune=0.8.3=py36h14c3975_1
+  - mkl=2018.0.3=1
+  - mkl-service=1.1.2=py36h17a0993_4
+  - mkl_fft=1.0.4=py36h4414c95_1
+  - mkl_random=1.0.1=py36h629b387_0
+  - more-itertools=4.1.0=py36_0
+  - mpc=1.0.3=hec55b23_5
+  - mpfr=3.1.5=h11a74b3_2
+  - mpmath=1.0.0=py36hfeacd6b_2
+  - msgpack-python=0.5.6=py36h6bb024c_0
+  - multipledispatch=0.5.0=py36_0
+  - navigator-updater=0.2.1=py36_0
+  - nbconvert=5.3.1=py36hb41ffb7_0
+  - nbformat=4.4.0=py36h31c9010_0
+  - ncurses=6.1=hf484d3e_0
+  - networkx=2.1=py36_0
+  - ninja=1.8.2=py36h6bb024c_1
+  - nltk=3.3.0=py36_0
+  - nose=1.3.7=py36hcdf7029_2
+  - notebook=5.5.0=py36_0
+  - numba=0.38.0=py36h637b7d7_0
+  - numexpr=2.6.5=py36h7bf3b9c_0
+  - numpydoc=0.8.0=py36_0
+  - odo=0.5.1=py36h90ed295_0
+  - olefile=0.45.1=py36_0
+  - openmm=7.2.2=py36_1
+  - openpyxl=2.5.3=py36_0
+  - openssl=1.0.2r=h7b6447c_0
+  - packaging=17.1=py36_0
+  - pandas=0.22.0=py36_1
+  - pandoc=1.19.2.1=hea2e7c5_1
+  - pandocfilters=1.4.2=py36ha6701b7_1
+  - pango=1.41.0=hd475d92_0
+  - parso=0.2.0=py36_0
+  - partd=0.3.8=py36h36fd896_0
+  - patchelf=0.9=hf79760b_2
+  - path.py=11.0.1=py36_0
+  - pathlib2=2.3.2=py36_0
+  - patsy=0.5.0=py36_0
+  - pcre=8.42=h439df22_0
+  - pdbfixer=1.4=py36_0
+  - pep8=1.7.1=py36_0
+  - pexpect=4.5.0=py36_0
+  - pickleshare=0.7.4=py36h63277f8_0
+  - pillow=5.0.0=py36_0
+  - pixman=0.34.0=hceecf20_3
+  - pkginfo=1.4.2=py36_1
+  - pluggy=0.6.0=py36hb689045_0
+  - ply=3.11=py36_0
+  - prompt_toolkit=1.0.15=py36h17d85b1_0
+  - protobuf=3.6.0=py36hfc679d8_0
+  - psutil=5.4.5=py36h14c3975_0
+  - ptyprocess=0.5.2=py36h69acd42_0
+  - py=1.5.3=py36_0
+  - pycodestyle=2.4.0=py36_0
+  - pycosat=0.6.3=py36h0a5515d_0
+  - pycparser=2.18=py36hf9f622e_1
+  - pycrypto=2.6.1=py36h14c3975_8
+  - pycurl=7.43.0.1=py36hb7f436b_0
+  - pyflakes=1.6.0=py36h7bd6a15_0
+  - pygments=2.2.0=py36h0d3125c_0
+  - pylint=1.8.4=py36_0
+  - pyodbc=4.0.23=py36hf484d3e_0
+  - pyopenssl=18.0.0=py36_0
+  - pyparsing=2.2.0=py36hee85983_1
+  - pyqt=5.9.2=py36h751905a_0
+  - pysocks=1.6.8=py36_0
+  - pytables=3.4.3=py36h02b9ad4_2
+  - pytest=3.5.1=py36_0
+  - pytest-arraydiff=0.2=py36_0
+  - pytest-astropy=0.3.0=py36_0
+  - pytest-doctestplus=0.1.3=py36_0
+  - pytest-openfiles=0.3.0=py36_0
+  - pytest-remotedata=0.2.1=py36_0
+  - python=3.6.6=hc3d631a_0
+  - python-dateutil=2.7.3=py36_0
+  - pytorch=1.0.1=py3.6_cuda9.0.176_cudnn7.4.2_2
+  - pytz=2018.4=py36_0
+  - pywavelets=0.5.2=py36he602eb0_0
+  - pyyaml=3.12=py36hafb9ca4_1
+  - pyzmq=17.0.0=py36h14c3975_0
+  - qt=5.9.5=h7e424d6_0
+  - qtawesome=0.4.4=py36h609ed8c_0
+  - qtconsole=4.3.1=py36h8f73b5b_0
+  - qtpy=1.4.1=py36_0
+  - rdkit=2017.09.1=py36_1
+  - readline=7.0=ha6073c6_4
+  - requests=2.18.4=py36he2e5f8d_1
+  - rope=0.10.7=py36h147e2ec_0
+  - ruamel_yaml=0.15.35=py36h14c3975_1
+  - scikit-image=0.13.1=py36h14c3975_1
+  - scikit-learn=0.19.1=py36h7aa7ec6_0
+  - scipy=1.1.0=py36hfc37229_0
+  - seaborn=0.9.0=py36_0
+  - send2trash=1.5.0=py36_0
+  - setuptools=39.1.0=py36_0
+  - simdna=0.4.2=py_0
+  - simplegeneric=0.8.1=py36_2
+  - singledispatch=3.4.0.3=py36h7a266c3_0
+  - sip=4.19.8=py36hf484d3e_0
+  - six=1.11.0=py36h372c433_1
+  - snappy=1.1.7=hbae5bb6_3
+  - snowballstemmer=1.2.1=py36h6febd40_0
+  - sortedcollections=0.6.1=py36_0
+  - sortedcontainers=1.5.10=py36_0
+  - sphinx=1.7.4=py36_0
+  - sphinxcontrib=1.0=py36h6d0f590_1
+  - sphinxcontrib-websupport=1.0.1=py36hb5cb234_1
+  - spyder=3.2.8=py36_0
+  - sqlalchemy=1.2.7=py36h6b74fdf_0
+  - sqlite=3.24.0=h84994c4_0
+  - statsmodels=0.9.0=py36h3010b51_0
+  - sympy=1.1.1=py36hc6d1c1c_0
+  - tblib=1.3.2=py36h34cf8b6_0
+  - tensorboard=1.6.0=py36_0
+  - tensorflow=1.6.0=py36_0
+  - termcolor=1.1.0=py_2
+  - terminado=0.8.1=py36_1
+  - testpath=0.3.1=py36h8cadb63_0
+  - tk=8.6.7=hc745277_3
+  - toolz=0.9.0=py36_0
+  - torchvision=0.2.2=py_3
+  - tornado=5.0.2=py36_0
+  - traitlets=4.3.2=py36h674d592_0
+  - typing=3.6.4=py36_0
+  - unicodecsv=0.14.1=py36ha668878_0
+  - unixodbc=2.3.6=h1bed415_0
+  - urllib3=1.22=py36hbe7ace6_0
+  - wcwidth=0.1.7=py36hdf4376a_0
+  - webencodings=0.5.1=py36h800622e_1
+  - werkzeug=0.14.1=py36_0
+  - wheel=0.31.1=py36_0
+  - widgetsnbextension=3.2.1=py36_0
+  - wrapt=1.10.11=py36h28b7045_0
+  - xgboost=0.6a2=py36_2
+  - xlrd=1.1.0=py36h1db9f0c_1
+  - xlsxwriter=1.0.4=py36_0
+  - xlwt=1.3.0=py36h7b00a1f_0
+  - xz=5.2.4=h14c3975_4
+  - yaml=0.1.7=had09818_2
+  - zeromq=4.2.5=h439df22_0
+  - zict=0.1.3=py36h3a3bf81_0
+  - zlib=1.2.11=ha838bed_2
+  - pip
+  - pip:
+    - anyconfig==0.9.7
+    - bravado==10.2.1
+    - bravado-core==5.10.0
+    - feather-format==0.4.0
+    - jsonref==0.2
+    - keras==2.2.4
+    - keras-applications==1.0.7
+    - keras-preprocessing==1.0.9
+    - libroadrunner==1.5.3
+    - molvs==0.1.1
+    - monotonic==1.5
+    - mordred==1.2.0
+    - msgpack==0.6.1
+    - numpy==1.16.2
+    - pip==19.3.1
+    - py4j==0.10.7
+    - pyaml==18.11.0
+    - pyarrow==0.12.0
+    - pyspark==2.4.0
+    - rfc3987==1.3.8
+    - simplejson==3.16.0
+    - strict-rfc3339==0.7
+    - swagger-spec-validator==2.4.1
+    - umap-learn==0.3.7
+    - webcolors==1.8.1
+prefix: /srv/conda/envs/notebook/envs/atomsci

install.sh

@@ -12,7 +12,7 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 echo "DIR: $DIR"
 cd $DIR
 
-TOPDIR=`readlink -f .`
+TOPDIR=`readlink -f .`/
 
 DIST_DIR=${TOPDIR}.dist
 

postBuild

@@ -0,0 +1,2 @@
+./build.sh && ./install.sh
+