Update for 2019-09-12

README.md

@@ -56,10 +56,12 @@ pandas
 pip
 pivottablejs
 pyparsing
+pyscaffold
 qgrid
 scikit-learn
 scipy
 seaborn
+sphinx
 statsmodels
 vaex
 vega
@@ -92,9 +94,9 @@ python -m ipykernel install --user --name $envname --display-name "$envname"
 # jupyterlab widgets
 # conda install -c conda-forge nodejs  
 jupyter labextension install @jupyter-widgets/jupyterlab-manager
-jupyter labextension install ipyvolume
-jupyter labextension install jupyter-threejs
-jupyter labextension install bqplot
+jupyter labextension install ipyvolume jupyter-threejs
+jupyter labextension install @jupyterlab/toc
+jupyter labextension install jupyter-threejs bqplot nbgather qgrid
 ```
 
 ### Troubleshooting
@@ -111,3 +113,14 @@ jupyter lab --NotebookApp.iopub_data_rate_limit=10000000
 ```
 
 ### Extra ideas
+
+```bash
+
+conda env export -n dspy3 -f environment.lock.yaml
+conda env update --file environment.yaml
+
+# to create new python package I did this from root directory of this repo
+putup insight
+cd insight/
+python setup.py develop
+```

environment.lock.yaml

@@ -0,0 +1,209 @@
+name: dspy3
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - alabaster=0.7.12=py_0
+  - altair=3.2.0=py36_0
+  - anaconda-client=1.7.2=py_0
+  - aplus=0.11.0=py_1
+  - appdirs=1.4.3=py_1
+  - appnope=0.1.0=py36_1000
+  - astropy=3.2.1=py36h01d97ff_0
+  - atomicwrites=1.3.0=py_0
+  - attrs=19.1.0=py_0
+  - babel=2.7.0=py_0
+  - backcall=0.1.0=py_0
+  - black=19.3b0=py_0
+  - bleach=3.1.0=py_0
+  - bqplot=0.11.8=py_0
+  - ca-certificates=2019.9.11=hecc5488_0
+  - cachetools=3.1.1=py_0
+  - certifi=2016.9.26=py36_0
+  - click=7.0=py_0
+  - cloudpickle=1.2.2=py_0
+  - clyent=1.2.2=py_1
+  - cycler=0.10.0=py_1
+  - cytoolz=0.10.0=py36h01d97ff_0
+  - dask-core=2.3.0=py_0
+  - dbus=1.13.6=h2f22bb5_0
+  - decorator=4.4.0=py_0
+  - defusedxml=0.5.0=py_1
+  - docutils=0.15.2=py36_0
+  - entrypoints=0.3=py36_1000
+  - expat=2.2.5=h6de7cb9_1003
+  - freetype=2.10.0=h24853df_1
+  - future=0.17.1=py36_1000
+  - gettext=0.19.8.1=h46ab8bc_1002
+  - glib=2.58.3=h9d45998_1002
+  - h5py=2.10.0=nompi_py36h6248fd5_100
+  - hdf5=1.10.5=nompi_h15a436c_1103
+  - icu=64.2=h6de7cb9_1
+  - imageio=2.5.0=py36_0
+  - imagesize=1.1.0=py_0
+  - importlib_metadata=0.22=py36_0
+  - intel-openmp=2019.4=233
+  - ipydatawidgets=4.0.1=py_0
+  - ipykernel=5.1.2=py36h5ca1d4c_0
+  - ipyscales=0.3.0=py_0
+  - ipython=7.8.0=py36h5ca1d4c_0
+  - ipython_genutils=0.2.0=py_1
+  - ipyvolume=0.5.2=py36_0
+  - ipywebrtc=0.5.0=py36_0
+  - ipywidgets=7.5.1=py_0
+  - jedi=0.15.1=py36_0
+  - jinja2=2.10.1=py_0
+  - joblib=0.13.2=py_0
+  - jpeg=9c=h1de35cc_1001
+  - json5=0.8.5=py_0
+  - jsonschema=3.0.2=py36_0
+  - jupyter_client=5.3.1=py_0
+  - jupyter_console=6.0.0=py_0
+  - jupyter_contrib_core=0.3.3=py_2
+  - jupyter_contrib_nbextensions=0.5.1=py36_0
+  - jupyter_core=4.4.0=py_0
+  - jupyter_highlight_selected_word=0.2.0=py36_1000
+  - jupyter_latex_envs=1.4.4=py36_1000
+  - jupyter_nbextensions_configurator=0.4.1=py36_0
+  - jupyterlab=1.1.3=py_0
+  - jupyterlab_server=1.0.6=py_0
+  - kapteyn=2.3=py36hb7221d7_1003
+  - kiwisolver=1.1.0=py36h770b8ee_0
+  - libblas=3.8.0=12_openblas
+  - libcblas=3.8.0=12_openblas
+  - libcxx=8.0.1=0
+  - libcxxabi=8.0.1=0
+  - libffi=3.2.1=h6de7cb9_1006
+  - libgfortran=4.0.0=2
+  - libiconv=1.15=h01d97ff_1005
+  - liblapack=3.8.0=12_openblas
+  - libopenblas=0.3.7=h4bb4525_1
+  - libpng=1.6.37=h2573ce8_0
+  - libsodium=1.0.17=h01d97ff_0
+  - libtiff=4.0.10=hd08fb8f_1003
+  - libxml2=2.9.9=h12c6b28_5
+  - libxslt=1.1.33=h320ff13_0
+  - llvm-openmp=8.0.1=h770b8ee_0
+  - lxml=4.4.1=py36h08abf6f_0
+  - lz4-c=1.8.3=h6de7cb9_1001
+  - markupsafe=1.1.1=py36h1de35cc_0
+  - matplotlib=3.1.1=py36_1
+  - matplotlib-base=3.1.1=py36h3a684a6_1
+  - mistune=0.8.4=py36h1de35cc_1000
+  - mkl=2019.4=233
+  - more-itertools=7.2.0=py_0
+  - mpld3=0.3=py_1
+  - nbconvert=5.6.0=py36_1
+  - nbformat=4.4.0=py_1
+  - ncurses=6.1=h0a44026_1002
+  - networkx=2.3=py_0
+  - notebook=6.0.1=py36_0
+  - numexpr=2.7.0=py36h86efe34_0
+  - numpy=1.17.2=py36h6b0580a_0
+  - olefile=0.46=py_0
+  - openssl=1.1.1c=h01d97ff_0
+  - packaging=19.0=py_0
+  - pandas=0.25.1=py36h86efe34_0
+  - pandoc=2.7.3=0
+  - pandocfilters=1.4.2=py_1
+  - parso=0.5.1=py_0
+  - patsy=0.5.1=py_0
+  - pcre=8.41=h0a44026_1003
+  - pexpect=4.7.0=py36_0
+  - pickleshare=0.7.5=py36_1000
+  - pillow=6.1.0=py36h75ffe9a_1
+  - pip=19.2.3=py36_0
+  - pivottablejs=0.9.0=py36_0
+  - pluggy=0.12.0=py_0
+  - progressbar2=3.43.1=py_0
+  - prometheus_client=0.7.1=py_0
+  - prompt_toolkit=2.0.9=py_0
+  - psutil=5.6.3=py36h01d97ff_0
+  - ptyprocess=0.6.0=py_1001
+  - py=1.8.0=py_0
+  - pygments=2.4.2=py_0
+  - pyopengl=3.1.3b2=py_1
+  - pyparsing=2.4.2=py_0
+  - pyqt=5.9.2=py36h2a560b1_4
+  - pyrsistent=0.15.4=py36h01d97ff_0
+  - pyscaffold=3.2.2=py_0
+  - pytest=5.1.2=py36_0
+  - pytest-arraydiff=0.3=py_0
+  - pytest-astropy=0.5.0=py_0
+  - pytest-doctestplus=0.3.0=py_1
+  - pytest-openfiles=0.4.0=py_0
+  - pytest-remotedata=0.3.1=py_0
+  - pytest-runner=5.1=py_0
+  - python=3.6.7=h94afb7f_1005
+  - python-dateutil=2.8.0=py_0
+  - python-utils=2.3.0=py_1
+  - python.app=1.2=py36h1de35cc_1200
+  - pythreejs=2.1.1=py_0
+  - pytz=2019.2=py_0
+  - pywavelets=1.0.3=py36h1e5eb4f_1
+  - pyyaml=5.1.2=py36h01d97ff_0
+  - pyzmq=18.0.2=py36hee98d25_2
+  - qgrid=1.1.1=py36_1001
+  - qt=5.9.7=h8cf7e54_3
+  - qtconsole=4.5.5=py_0
+  - readline=8.0=hcfe32e1_0
+  - requests=2.12.5=py36_0
+  - scikit-image=0.15.0=py36h86efe34_2
+  - scikit-learn=0.21.3=py36hd4ffd6c_0
+  - scipy=1.3.1=py36h7e0e109_2
+  - seaborn=0.9.0=py_1
+  - send2trash=1.5.0=py_0
+  - setuptools=41.2.0=py36_0
+  - sip=4.19.8=py36h0a44026_1000
+  - six=1.12.0=py36_1000
+  - snowballstemmer=1.9.1=py_0
+  - sphinx=2.2.0=py_0
+  - sphinxcontrib-applehelp=1.0.1=py_0
+  - sphinxcontrib-devhelp=1.0.1=py_0
+  - sphinxcontrib-htmlhelp=1.0.2=py_0
+  - sphinxcontrib-jsmath=1.0.1=py_0
+  - sphinxcontrib-qthelp=1.0.2=py_0
+  - sphinxcontrib-serializinghtml=1.1.3=py_0
+  - sqlite=3.29.0=hb7d70f7_1
+  - statsmodels=0.10.1=py36heacc8b8_0
+  - terminado=0.8.2=py36_0
+  - testpath=0.4.2=py_1001
+  - tk=8.6.9=h2573ce8_1003
+  - toml=0.10.0=py_0
+  - toolz=0.10.0=py_0
+  - tornado=6.0.3=py36h01d97ff_0
+  - traitlets=4.3.2=py36_1000
+  - traittypes=0.2.1=py_1
+  - vaex=1.0.0b6=py36_0
+  - vega=2.6.0=py36_0
+  - vega_datasets=0.7.0=py_0
+  - wcwidth=0.1.7=py_1
+  - webencodings=0.5.1=py_1
+  - wheel=0.33.6=py36_0
+  - widgetsnbextension=3.5.1=py36_0
+  - xlrd=1.2.0=py_0
+  - xz=5.2.4=h1de35cc_1001
+  - yaml=0.1.7=h1de35cc_1001
+  - yapf=0.28.0=py_0
+  - zeromq=4.3.2=h6de7cb9_2
+  - zipp=0.6.0=py_0
+  - zlib=1.2.11=h01d97ff_1006
+  - zstd=1.4.0=ha9f0a20_0
+  - pip:
+    - ansiwrap==0.8.4
+    - colorama==0.4.1
+    - findspark==1.3.0
+    - gitdb2==2.0.5
+    - gitpython==3.0.2
+    - jupyter==1.0.0
+    - nbdime==1.1.0
+    - papermill==1.1.0
+    - pyhive==0.6.1
+    - smmap2==2.0.5
+    - sql-magic==0.0.4
+    - sqlalchemy==1.3.8
+    - sqlparse==0.3.0
+    - tenacity==5.1.1
+    - textwrap3==0.9.2
+    - tqdm==4.35.0
+prefix: /Users/jonathan/miniconda3/envs/dspy3

insight/AUTHORS.rst

@@ -0,0 +1,5 @@
+============
+Contributors
+============
+
+* jbwhit <[email protected]>

insight/CHANGELOG.rst

@@ -0,0 +1,10 @@
+=========
+Changelog
+=========
+
+Version 0.1
+===========
+
+- Feature A added
+- FIX: nasty bug #1729 fixed
+- add your changes here!

insight/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2019 jbwhit
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

insight/README.rst

@@ -0,0 +1,19 @@
+=======
+insight
+=======
+
+
+Add a short description here!
+
+
+Description
+===========
+
+A longer description of your project goes here...
+
+
+Note
+====
+
+This project has been set up using PyScaffold 3.2.2. For details and usage
+information on PyScaffold see https://pyscaffold.org/.