From 50d31b6d923df8bd96c3fd0d79eaa5bd46cd9735 Mon Sep 17 00:00:00 2001
From: "K. Shankari" <shankari@eecs.berkeley.edu>
Date: Mon, 11 Feb 2019 20:50:49 -0800
Subject: [PATCH 01/11] Vastly simplify the set of dependencies for the main
 e-mission server

Significant decrease even on OSX, need to see what it is on docker...

1.6G	/Users/shankari/OSS/anaconda/envs/emission
627M	/Users/shankari/OSS/anaconda/envs/minimal_emission

Testing done:
- Started the server
- Connected the iOS emulator with location simulation
- Manually ended a couple of trips so that the data was pushed to the server
- Ran the pipeline

Bonus fix: Removed the reference to the tour model from the output generator because:
- it has a dependency on matplotlib
- we don't actually use it right now
---
 .../usercache/builtin_usercache_handler.py    |   2 +-
 setup/environment36.yml                       | 208 +-----------------
 2 files changed, 10 insertions(+), 200 deletions(-)

diff --git a/emission/net/usercache/builtin_usercache_handler.py b/emission/net/usercache/builtin_usercache_handler.py
index 73c1c0467..94d49916a 100644
--- a/emission/net/usercache/builtin_usercache_handler.py
+++ b/emission/net/usercache/builtin_usercache_handler.py
@@ -22,7 +22,7 @@
 
 import emission.net.usercache.formatters.formatter as enuf
 import emission.storage.pipeline_queries as esp
-import emission.storage.decorations.tour_model_queries as esdtmpq
+# import emission.storage.decorations.tour_model_queries as esdtmpq
 
 import emission.core.wrapper.trip as ecwt
 import emission.core.wrapper.entry as ecwe
diff --git a/setup/environment36.yml b/setup/environment36.yml
index ad0a513be..e5f3954d1 100644
--- a/setup/environment36.yml
+++ b/setup/environment36.yml
@@ -3,219 +3,29 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- altair=1.2.1=py_0
-- branca=0.2.0=py_1
-- folium=0.5.0=py_0
-- vega=0.4.4=py36_1
-- vincent=0.4.4=py36_0
-- _license=1.1=py36_1
-- alabaster=0.7.10=py36_0
-- anaconda=4.4.0=np112py36_0
-- anaconda-client=1.6.3=py36_0
-- anaconda-navigator=1.6.2=py36_0
-- anaconda-project=0.6.0=py36_0
-- asn1crypto=0.22.0=py36_0
-- astroid=1.4.9=py36_0
-- astropy=1.3.2=np112py36_0
-- babel=2.4.0=py36_0
-- backports=1.0=py36_0
-- beautifulsoup4=4.6.0=py36_0
-- bitarray=0.8.1
-- blaze=0.10.1=py36_0
-- bleach=1.5.0=py36_0
-- bokeh=0.12.5=py36_1
-- boto=2.46.1=py36_0
-- bottleneck=1.2.1=np112py36_0
-- cffi=1.10.0=py36_0
-- chardet=3.0.3=py36_0
-- click=6.7=py36_0
-- cloudpickle=0.2.2=py36_0
-- clyent=1.2.2=py36_0
-- colorama=0.3.9=py36_0
-- contextlib2=0.5.5=py36_0
-- cryptography=1.8.1=py36_0
-- curl=7.52.1
-- cycler=0.10.0=py36_0
-- cython=0.25.2=py36_0
-- cytoolz=0.8.2=py36_0
-- dask=0.14.3=py36_1
-- datashape=0.5.4=py36_0
-- decorator=4.0.11=py36_0
-- distributed=1.16.3=py36_0
-- docutils=0.13.1=py36_0
-- entrypoints=0.2.2=py36_1
-- et_xmlfile=1.0.1=py36_0
-- fastcache=1.0.2=py36_1
-- flask=0.12.2=py36_0
-- flask-cors=3.0.2=py36_0
-- freetype=2.5.5
-- get_terminal_size=1.0.0=py36_0
-- gevent=1.2.1=py36_0
-- greenlet=0.4.12=py36_0
-- h5py=2.7.0=np112py36_0
-- heapdict=1.0.0=py36_1
-- html5lib=0.999=py36_0
-- idna=2.5=py36_0
-- imagesize=0.7.1=py36_0
-- ipykernel=4.6.1=py36_0
-- ipython=5.3.0=py36_0
-- ipython_genutils=0.2.0=py36_0
-- ipywidgets=6.0.0=py36_0
-- isort=4.2.5=py36_0
-- itsdangerous=0.24=py36_0
-- jdcal=1.3=py36_0
-- jedi=0.10.2=py36_2
-- jinja2=2.9.6=py36_0
-- jpeg=9b
-- jsonschema=2.6.0=py36_0
-- jupyter=1.0.0=py36_3
-- jupyter_client=5.0.1=py36_0
-- jupyter_console=5.1.0=py36_0
-- jupyter_core=4.3.0=py36_0
-- lazy-object-proxy=1.2.2=py36_0
-- libiconv=1.14
-- libpng=1.6.27
-- libtiff=4.0.6
-- libxml2=2.9.4
-- libxslt=1.1.29
-- llvmlite=0.18.0=py36_0
-- locket=0.2.0=py36_1
-- lxml=3.7.3=py36_0
-- markupsafe=0.23=py36_2
-- matplotlib=2.0.2=np112py36_0
-- mistune=0.7.4=py36_0
-- mkl=2017.0.1=0
-- mkl-service=1.1.2=py36_3
-- mpmath=0.19=py36_1
-- msgpack-python=0.4.8=py36_0
-- multipledispatch=0.4.9=py36_0
-- navigator-updater=0.1.0=py36_0
-- nbconvert=5.1.1=py36_0
-- nbformat=4.3.0=py36_0
-- networkx=1.11=py36_0
-- nltk=3.2.3=py36_0
-- nose=1.3.7=py36_1
-- notebook=5.0.0=py36_0
-- numba=0.33.0=np112py36_0
-- numexpr=2.6.2=np112py36_0
+- arrow=0.12.1
+- attrdict=2.0.0
+- cheroot=6.2.*=py36_0
+- future=0.16.0
+- geojson=2.3.0
+- google-auth=1.2.1
+- jsonpickle=0.9.6
 - numpy=1.12.1=py36_0
-- numpydoc=0.6.0=py36_0
-- odo=0.5.0=py36_1
-- olefile=0.44=py36_0
-- openpyxl=2.4.7=py36_0
-- openssl=1.0.2l
-- packaging=16.8=py36_0
 - pandas=0.20.1=np112py36_0
-- pandocfilters=1.4.1=py36_0
-- partd=0.3.8=py36_0
-- path.py=10.3.1=py36_0
-- pathlib2=2.2.1=py36_0
-- patsy=0.4.1=py36_0
-- pep8=1.7.0=py36_0
-- pexpect=4.2.1=py36_0
-- pickleshare=0.7.4=py36_0
-- pillow=4.1.1=py36_0
 - pip=9.0.1=py36_1
-- ply=3.10=py36_0
-- prompt_toolkit=1.0.14=py36_0
-- psutil=5.2.2=py36_0
-- py=1.4.33=py36_0
-- pycosat=0.6.2=py36_0
-- pycparser=2.17=py36_0
-- pycrypto=2.6.1=py36_6
-- pycurl=7.43.0=py36_2
-- pyflakes=1.5.0=py36_0
-- pygments=2.2.0=py36_0
-- pylint=1.6.4=py36_1
-- pyodbc=4.0.16=py36_0
-- pyopenssl=17.0.0=py36_0
-- pyparsing=2.1.4=py36_0
-- pyqt=5.6.0
-- pytest=3.0.7=py36_0
 - python=3.6.1=2
 - python-dateutil=2.6.0=py36_0
 - pytz=2017.2=py36_0
-- pywavelets=0.5.2=np112py36_0
-- pyyaml=3.12=py36_0
-- pyzmq=16.0.2=py36_0
-- qt=5.6.2
-- qtawesome=0.4.4=py36_0
-- qtconsole=4.3.0=py36_0
-- qtpy=1.2.1=py36_0
 - requests=2.14.2=py36_0
-- rope=0.9.4=py36_1
-- ruamel_yaml=0.11.14=py36_1
-- scikit-image=0.13.0=np112py36_0
 - scikit-learn=0.18.1=np112py36_1
 - scipy=0.19.0=np112py36_0
-- seaborn=0.7.1=py36_0
-- setuptools=27.2.0
-- simplegeneric=0.8.1=py36_1
-- singledispatch=3.4.0.3=py36_0
-- sip=4.18=py36_0
-- six=1.10.0=py36_0
-- snowballstemmer=1.2.1=py36_0
-- sortedcollections=0.5.3=py36_0
-- sortedcontainers=1.5.7=py36_0
-- sphinx=1.5.6=py36_0
-- spyder=3.1.4=py36_0
-- sqlalchemy=1.1.9=py36_0
 - sqlite=3.13.0
-- statsmodels=0.8.0=np112py36_0
-- sympy=1.0=py36_0
-- tblib=1.3.2=py36_0
-- testpath=0.3=py36_0
-- tk=8.5.18
-- toolz=0.8.2=py36_0
-- tornado=4.5.1=py36_0
-- traitlets=4.3.2=py36_0
-- unicodecsv=0.14.1=py36_0
-- wcwidth=0.1.7=py36_0
-- werkzeug=0.12.2=py36_0
-- wheel=0.29.0=py36_0
-- widgetsnbextension=2.0.0=py36_0
-- wrapt=1.10.10=py36_0
-- xlrd=1.0.0=py36_0
-- xlsxwriter=0.9.6=py36_0
-- xlwt=1.2.0=py36_0
-- xz=5.2.2
-- yaml=0.1.6=0
-- zict=0.1.2=py36_0
-- zlib=1.2.8
+- utm=0.4.2
+- xmltodict=0.11.0
 - pip:
-  - arrow==0.12.0
-  - attrdict==2.0.0
-  - backports.shutil-get-terminal-size==1.0.0
-  - cachetools==2.0.1
-  - certifi==2017.11.5
-  - cheroot==5.10.0
-  - enum34==1.1.6
-  - et-xmlfile==1.0.1
-  - future==0.16.0
-  - geojson==2.3.0
-  - google-auth==1.2.1
-  - ipython-genutils==0.2.0
-  - jaraco.classes==1.4.3
-  - jsonpickle==0.9.5
-  - jupyter-client==5.0.1
-  - jupyter-console==5.1.0
-  - jupyter-core==4.3.0
   - jwcrypto==0.4.2
-  - portend==2.2
-  - prompt-toolkit==1.0.14
-  - pyasn1==0.4.2
-  - pyasn1-modules==0.2.1
   - pyfcm==1.4.3
   - pygeocoder==1.2.5
   - pykml==0.1.3
   - pymongo==3.5.1
-  - python-crontab==2.2.7
-  - requests-toolbelt==0.8.0
-  - rope-py3k==0.9.4.post1
-  - rsa==3.4.2
-  - tables==3.3.0
-  - tempora==1.9
-  - urllib3==1.22
-  - utm==0.4.2
-  - xmltodict==0.11.0
 prefix: /Users/shankari/OSS/anaconda/envs/emission

From a327423014a5ea4cb442d57fa378c5867a4003b7 Mon Sep 17 00:00:00 2001
From: "K. Shankari" <shankari@eecs.berkeley.edu>
Date: Mon, 11 Feb 2019 22:44:19 -0800
Subject: [PATCH 02/11] Move the tour model tests into the tour model folder

So that they are not loitering around outside
---
 .../analysisTests/{ => tourModelTests}/TestClusterPipeline.py     | 0
 .../tests/analysisTests/{ => tourModelTests}/TestFeaturization.py | 0
 .../analysisTests/{ => tourModelTests}/TestRepresentatives.py     | 0
 3 files changed, 0 insertions(+), 0 deletions(-)
 rename emission/tests/analysisTests/{ => tourModelTests}/TestClusterPipeline.py (100%)
 rename emission/tests/analysisTests/{ => tourModelTests}/TestFeaturization.py (100%)
 rename emission/tests/analysisTests/{ => tourModelTests}/TestRepresentatives.py (100%)

diff --git a/emission/tests/analysisTests/TestClusterPipeline.py b/emission/tests/analysisTests/tourModelTests/TestClusterPipeline.py
similarity index 100%
rename from emission/tests/analysisTests/TestClusterPipeline.py
rename to emission/tests/analysisTests/tourModelTests/TestClusterPipeline.py
diff --git a/emission/tests/analysisTests/TestFeaturization.py b/emission/tests/analysisTests/tourModelTests/TestFeaturization.py
similarity index 100%
rename from emission/tests/analysisTests/TestFeaturization.py
rename to emission/tests/analysisTests/tourModelTests/TestFeaturization.py
diff --git a/emission/tests/analysisTests/TestRepresentatives.py b/emission/tests/analysisTests/tourModelTests/TestRepresentatives.py
similarity index 100%
rename from emission/tests/analysisTests/TestRepresentatives.py
rename to emission/tests/analysisTests/tourModelTests/TestRepresentatives.py

From 9b99263212875b2c2d9630782bdc57c503c7078b Mon Sep 17 00:00:00 2001
From: "K. Shankari" <shankari@eecs.berkeley.edu>
Date: Mon, 11 Feb 2019 22:44:57 -0800
Subject: [PATCH 03/11] Change the python version slightly + move tour model
 tests out

Since they all import matplotlib, which we have now removed from the production
environment
---
 .../tourModelTests/TestClusterPipeline.py                       | 0
 .../tourModelTests/TestFeaturization.py                         | 0
 .../tourModelTests/TestRepresentatives.py                       | 0
 .../tourModelTests/__init__.py                                  | 0
 .../analysisTests => incomplete_tests}/tourModelTests/common.py | 0
 setup/environment36.yml                                         | 2 +-
 6 files changed, 1 insertion(+), 1 deletion(-)
 rename emission/{tests/analysisTests => incomplete_tests}/tourModelTests/TestClusterPipeline.py (100%)
 rename emission/{tests/analysisTests => incomplete_tests}/tourModelTests/TestFeaturization.py (100%)
 rename emission/{tests/analysisTests => incomplete_tests}/tourModelTests/TestRepresentatives.py (100%)
 rename emission/{tests/analysisTests => incomplete_tests}/tourModelTests/__init__.py (100%)
 rename emission/{tests/analysisTests => incomplete_tests}/tourModelTests/common.py (100%)

diff --git a/emission/tests/analysisTests/tourModelTests/TestClusterPipeline.py b/emission/incomplete_tests/tourModelTests/TestClusterPipeline.py
similarity index 100%
rename from emission/tests/analysisTests/tourModelTests/TestClusterPipeline.py
rename to emission/incomplete_tests/tourModelTests/TestClusterPipeline.py
diff --git a/emission/tests/analysisTests/tourModelTests/TestFeaturization.py b/emission/incomplete_tests/tourModelTests/TestFeaturization.py
similarity index 100%
rename from emission/tests/analysisTests/tourModelTests/TestFeaturization.py
rename to emission/incomplete_tests/tourModelTests/TestFeaturization.py
diff --git a/emission/tests/analysisTests/tourModelTests/TestRepresentatives.py b/emission/incomplete_tests/tourModelTests/TestRepresentatives.py
similarity index 100%
rename from emission/tests/analysisTests/tourModelTests/TestRepresentatives.py
rename to emission/incomplete_tests/tourModelTests/TestRepresentatives.py
diff --git a/emission/tests/analysisTests/tourModelTests/__init__.py b/emission/incomplete_tests/tourModelTests/__init__.py
similarity index 100%
rename from emission/tests/analysisTests/tourModelTests/__init__.py
rename to emission/incomplete_tests/tourModelTests/__init__.py
diff --git a/emission/tests/analysisTests/tourModelTests/common.py b/emission/incomplete_tests/tourModelTests/common.py
similarity index 100%
rename from emission/tests/analysisTests/tourModelTests/common.py
rename to emission/incomplete_tests/tourModelTests/common.py
diff --git a/setup/environment36.yml b/setup/environment36.yml
index e5f3954d1..d5290fa33 100644
--- a/setup/environment36.yml
+++ b/setup/environment36.yml
@@ -13,7 +13,7 @@ dependencies:
 - numpy=1.12.1=py36_0
 - pandas=0.20.1=np112py36_0
 - pip=9.0.1=py36_1
-- python=3.6.1=2
+- python=3.6.*
 - python-dateutil=2.6.0=py36_0
 - pytz=2017.2=py36_0
 - requests=2.14.2=py36_0

From 249010d1ed2ed16978bcdd01999eba8305085b7c Mon Sep 17 00:00:00 2001
From: "K. Shankari" <shankari@eecs.berkeley.edu>
Date: Tue, 12 Feb 2019 07:43:42 -0800
Subject: [PATCH 04/11] Set a particular python version again

---
 setup/environment36.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup/environment36.yml b/setup/environment36.yml
index d5290fa33..e5f3954d1 100644
--- a/setup/environment36.yml
+++ b/setup/environment36.yml
@@ -13,7 +13,7 @@ dependencies:
 - numpy=1.12.1=py36_0
 - pandas=0.20.1=np112py36_0
 - pip=9.0.1=py36_1
-- python=3.6.*
+- python=3.6.1=2
 - python-dateutil=2.6.0=py36_0
 - pytz=2017.2=py36_0
 - requests=2.14.2=py36_0

From e3e4795e97b19662fa9e0f5f0b55ef1b97bb8732 Mon Sep 17 00:00:00 2001
From: "K. Shankari" <shankari@eecs.berkeley.edu>
Date: Tue, 12 Feb 2019 07:44:12 -0800
Subject: [PATCH 05/11] Add a new environment file for the nomkl version

So that we can make this more minimal
---
 setup/environment36.nomkl.yml | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 setup/environment36.nomkl.yml

diff --git a/setup/environment36.nomkl.yml b/setup/environment36.nomkl.yml
new file mode 100644
index 000000000..7a1bfe8f1
--- /dev/null
+++ b/setup/environment36.nomkl.yml
@@ -0,0 +1,32 @@
+name: emission
+channels:
+- conda-forge
+- defaults
+dependencies:
+- arrow=0.12.1
+- attrdict=2.0.0
+- cheroot=6.2.*=py36_0
+- future=0.16.0
+- geojson=2.3.0
+- google-auth=1.2.1
+- jsonpickle=0.9.6
+- nomkl
+- numpy=1.12.1
+- pandas=0.20.1
+- pip=9.0.1=py36_1
+- python=3.6.1=2
+- python-dateutil=2.6.0=py36_0
+- pytz=2017.2=py36_0
+- requests=2.14.2=py36_0
+- scikit-learn=0.18.1
+- scipy=0.19.0
+- sqlite=3.13.0
+- utm=0.4.2
+- xmltodict=0.11.0
+- pip:
+  - jwcrypto==0.4.2
+  - pyfcm==1.4.3
+  - pygeocoder==1.2.5
+  - pykml==0.1.3
+  - pymongo==3.5.1
+prefix: /Users/shankari/OSS/anaconda/envs/emission

From 465ee9562fd6693eff5812577bafb3744a9c3244 Mon Sep 17 00:00:00 2001
From: "K. Shankari" <shankari@eecs.berkeley.edu>
Date: Tue, 12 Feb 2019 07:45:53 -0800
Subject: [PATCH 06/11] Move out a couple of other common * queries

To not have to import matplotlib
---
 .../storageTests => incomplete_tests}/TestCommonPlaceQueries.py   | 0
 .../storageTests => incomplete_tests}/TestCommonTripQueries.py    | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename emission/{tests/storageTests => incomplete_tests}/TestCommonPlaceQueries.py (100%)
 rename emission/{tests/storageTests => incomplete_tests}/TestCommonTripQueries.py (100%)

diff --git a/emission/tests/storageTests/TestCommonPlaceQueries.py b/emission/incomplete_tests/TestCommonPlaceQueries.py
similarity index 100%
rename from emission/tests/storageTests/TestCommonPlaceQueries.py
rename to emission/incomplete_tests/TestCommonPlaceQueries.py
diff --git a/emission/tests/storageTests/TestCommonTripQueries.py b/emission/incomplete_tests/TestCommonTripQueries.py
similarity index 100%
rename from emission/tests/storageTests/TestCommonTripQueries.py
rename to emission/incomplete_tests/TestCommonTripQueries.py

From abe21dc54b06e9b15dca289f4a95d227a20bd62b Mon Sep 17 00:00:00 2001
From: "K. Shankari" <shankari@eecs.berkeley.edu>
Date: Tue, 12 Feb 2019 08:10:16 -0800
Subject: [PATCH 07/11] Move one more tour model file out

---
 .../storageTests => incomplete_tests}/TestTourModelQueries.py     | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename emission/{tests/storageTests => incomplete_tests}/TestTourModelQueries.py (100%)

diff --git a/emission/tests/storageTests/TestTourModelQueries.py b/emission/incomplete_tests/TestTourModelQueries.py
similarity index 100%
rename from emission/tests/storageTests/TestTourModelQueries.py
rename to emission/incomplete_tests/TestTourModelQueries.py

From 4616433c1e0446cc6328af6a76c5133a65cf364c Mon Sep 17 00:00:00 2001
From: "K. Shankari" <shankari@eecs.berkeley.edu>
Date: Tue, 12 Feb 2019 08:25:49 -0800
Subject: [PATCH 08/11] Add the exported versions of the environment

So that we know exactly which versions were used
---
 setup/environment36.exported.yml       | 57 +++++++++++++++++++++++++
 setup/environment36.nomkl.exported.yml | 58 ++++++++++++++++++++++++++
 2 files changed, 115 insertions(+)
 create mode 100644 setup/environment36.exported.yml
 create mode 100644 setup/environment36.nomkl.exported.yml

diff --git a/setup/environment36.exported.yml b/setup/environment36.exported.yml
new file mode 100644
index 000000000..04797fc90
--- /dev/null
+++ b/setup/environment36.exported.yml
@@ -0,0 +1,57 @@
+name: minimal_emission
+channels:
+- conda-forge
+- defaults
+dependencies:
+- arrow=0.12.1=py36_1002
+- attrdict=2.0.0=py_1
+- ca-certificates=2018.11.29=ha4d7672_0
+- cachetools=2.1.0=py_0
+- certifi=2018.11.29=py36_1000
+- cheroot=6.2.4=py36_0
+- future=0.16.0=py36_1002
+- geojson=2.3.0=py_0
+- google-auth=1.2.1=py_0
+- jsonpickle=0.9.6=py_1
+- more-itertools=4.3.0=py36_1000
+- ncurses=5.9=10
+- openssl=1.0.2p=h1de35cc_1002
+- pandas=0.20.1=np112py36_0
+- pip=9.0.1=py36_1
+- pyasn1=0.4.4=py_1
+- pyasn1-modules=0.2.3=py_0
+- python=3.6.1=2
+- python-dateutil=2.6.0=py36_0
+- pytz=2017.2=py36_0
+- readline=6.2=0
+- rsa=3.4.2=py_1
+- setuptools=40.8.0=py36_0
+- six=1.12.0=py36_1000
+- sqlite=3.13.0=1
+- tk=8.5.19=2
+- utm=0.4.2=py36_0
+- wheel=0.33.0=py36_0
+- xmltodict=0.11.0=py_1
+- xz=5.2.4=h1de35cc_1001
+- zlib=1.2.11=h1de35cc_1004
+- blas=1.0=mkl
+- intel-openmp=2019.1=144
+- mkl=2017.0.4=h1fae6ae_0
+- numpy=1.12.1=py36_0
+- requests=2.14.2=py36_0
+- scikit-learn=0.18.1=np112py36_1
+- scipy=0.19.0=np112py36_0
+- pip:
+  - asn1crypto==0.24.0
+  - cffi==1.11.5
+  - cryptography==2.5
+  - jwcrypto==0.4.2
+  - lxml==4.3.1
+  - pycparser==2.19
+  - pyfcm==1.4.3
+  - pygeocoder==1.2.5
+  - pykml==0.1.3
+  - pymongo==3.5.1
+  - requests-toolbelt==0.9.1
+prefix: /Users/shankari/OSS/anaconda/envs/minimal_emission
+
diff --git a/setup/environment36.nomkl.exported.yml b/setup/environment36.nomkl.exported.yml
new file mode 100644
index 000000000..88ac20fbe
--- /dev/null
+++ b/setup/environment36.nomkl.exported.yml
@@ -0,0 +1,58 @@
+name: minimal_emission_nomkl
+channels:
+- conda-forge
+- defaults
+dependencies:
+- arrow=0.12.1=py36_1002
+- attrdict=2.0.0=py_1
+- blas=1.1=openblas
+- ca-certificates=2018.11.29=ha4d7672_0
+- cachetools=2.1.0=py_0
+- certifi=2018.11.29=py36_1000
+- cheroot=6.2.4=py36_0
+- future=0.16.0=py36_1002
+- geojson=2.3.0=py_0
+- google-auth=1.2.1=py_0
+- jsonpickle=0.9.6=py_1
+- more-itertools=4.3.0=py36_1000
+- ncurses=5.9=10
+- numpy=1.12.1=py36_blas_openblas_200
+- openblas=0.2.19=2
+- openssl=1.0.2p=h1de35cc_1002
+- pandas=0.20.1=np112py36_0
+- pip=9.0.1=py36_1
+- pyasn1=0.4.4=py_1
+- pyasn1-modules=0.2.3=py_0
+- python=3.6.1=2
+- python-dateutil=2.6.0=py36_0
+- pytz=2017.2=py36_0
+- readline=6.2=0
+- rsa=3.4.2=py_1
+- scikit-learn=0.18.1=np112py36_blas_openblas_200
+- scipy=0.19.0=np112py36_blas_openblas_202
+- setuptools=40.8.0=py36_0
+- six=1.12.0=py36_1000
+- sqlite=3.13.0=1
+- tk=8.5.19=2
+- utm=0.4.2=py36_0
+- wheel=0.33.0=py36_0
+- xmltodict=0.11.0=py_1
+- xz=5.2.4=h1de35cc_1001
+- zlib=1.2.11=h1de35cc_1004
+- libgfortran=3.0.1=h93005f0_2
+- nomkl=3.0=0
+- requests=2.14.2=py36_0
+- pip:
+  - asn1crypto==0.24.0
+  - cffi==1.11.5
+  - cryptography==2.5
+  - jwcrypto==0.4.2
+  - lxml==4.3.1
+  - pycparser==2.19
+  - pyfcm==1.4.3
+  - pygeocoder==1.2.5
+  - pykml==0.1.3
+  - pymongo==3.5.1
+  - requests-toolbelt==0.9.1
+prefix: /Users/shankari/OSS/anaconda/envs/minimal_emission_nomkl
+

From d93cfd2a9bdcf31f86ec68acaf5bbcda73a8e43b Mon Sep 17 00:00:00 2001
From: "K. Shankari" <shankari@eecs.berkeley.edu>
Date: Tue, 12 Feb 2019 10:33:29 -0800
Subject: [PATCH 09/11] Add support for ipython notebook

This is a new environment that adds the packages for using the notebook
- new complete notebook environment
- new incremental notebook environment
- new setup script that sets up the notebook environment (incrementally)
- remove the unnessary six update in both the existing setup scripts
---
 setup/environment36.notebook.additions.yml |  12 +++
 setup/environment36.notebook.exported.yml  | 118 +++++++++++++++++++++
 setup/environment36.notebook.yml           |  38 +++++++
 setup/setup.sh                             |   1 -
 setup/setup_notebook.sh                    |   9 ++
 setup/setup_tests.sh                       |   1 -
 6 files changed, 177 insertions(+), 2 deletions(-)
 create mode 100644 setup/environment36.notebook.additions.yml
 create mode 100644 setup/environment36.notebook.exported.yml
 create mode 100644 setup/environment36.notebook.yml
 create mode 100755 setup/setup_notebook.sh

diff --git a/setup/environment36.notebook.additions.yml b/setup/environment36.notebook.additions.yml
new file mode 100644
index 000000000..cae61b2bb
--- /dev/null
+++ b/setup/environment36.notebook.additions.yml
@@ -0,0 +1,12 @@
+name: emission
+channels:
+- conda-forge
+- defaults
+dependencies:
+- altair=1.2.1=py_0
+- branca=0.2.0=py_1
+- folium=0.5.0=py_0
+- vega=0.4.4=py36_1
+- vincent=0.4.4=py36_0
+- ipython=5.3.0=py36_0
+- jupyter=1.0.0=py36_3
diff --git a/setup/environment36.notebook.exported.yml b/setup/environment36.notebook.exported.yml
new file mode 100644
index 000000000..02bcd6010
--- /dev/null
+++ b/setup/environment36.notebook.exported.yml
@@ -0,0 +1,118 @@
+name: minimal_emission_notebook
+channels:
+- conda-forge
+- defaults
+dependencies:
+- altair=1.2.1=py_0
+- appnope=0.1.0=py36_1000
+- arrow=0.12.1=py36_1002
+- attrdict=2.0.0=py_1
+- attrs=18.2.0=py_0
+- bleach=3.1.0=py_0
+- branca=0.2.0=py_1
+- ca-certificates=2018.11.29=ha4d7672_0
+- cachetools=2.1.0=py_0
+- certifi=2018.11.29=py36_1000
+- cheroot=6.2.4=py36_0
+- decorator=4.3.2=py_0
+- entrypoints=0.3=py36_1000
+- folium=0.5.0=py_0
+- future=0.16.0=py36_1002
+- geojson=2.3.0=py_0
+- google-auth=1.2.1=py_0
+- icu=58.2=h0a44026_1000
+- ipykernel=5.1.0=py36h24bf2e0_1002
+- ipython=5.3.0=py36_0
+- ipython_genutils=0.2.0=py_1
+- ipywidgets=7.4.2=py_0
+- jinja2=2.10=py_1
+- jpeg=9c=h1de35cc_1001
+- jsonpickle=0.9.6=py_1
+- jsonschema=3.0.0a3=py36_1000
+- jupyter_client=5.2.4=py_1
+- jupyter_console=5.2.0=py36_1
+- jupyter_core=4.4.0=py_0
+- libcxx=7.0.0=h2d50403_2
+- libpng=1.6.36=ha441bb4_1000
+- libsodium=1.0.16=h1de35cc_1001
+- llvm-meta=7.0.0=0
+- markupsafe=1.1.0=py36h1de35cc_1000
+- mistune=0.8.4=py36h1de35cc_1000
+- more-itertools=4.3.0=py36_1000
+- nbconvert=5.3.1=py_1
+- nbformat=4.4.0=py_1
+- ncurses=5.9=10
+- notebook=5.7.4=py36_1000
+- openssl=1.0.2p=h1de35cc_1002
+- pandas=0.20.1=np112py36_0
+- pandoc=2.6=1
+- pandocfilters=1.4.2=py_1
+- pexpect=4.6.0=py36_1000
+- pickleshare=0.7.5=py36_1000
+- pip=9.0.1=py36_1
+- prometheus_client=0.5.0=py_0
+- prompt_toolkit=1.0.15=py_1
+- ptyprocess=0.6.0=py36_1000
+- pyasn1=0.4.4=py_1
+- pyasn1-modules=0.2.3=py_0
+- pygments=2.3.1=py_0
+- pyqt=5.6.0=py36hc26a216_1008
+- pyrsistent=0.14.10=py36h1de35cc_0
+- python=3.6.1=2
+- python-dateutil=2.6.0=py36_0
+- pytz=2017.2=py36_0
+- pyzmq=17.1.2=py36h111632d_1001
+- qt=5.6.2=h9e3eb04_4
+- qtconsole=4.4.3=py_0
+- readline=6.2=0
+- rsa=3.4.2=py_1
+- send2trash=1.5.0=py_0
+- setuptools=40.8.0=py36_0
+- simplegeneric=0.8.1=py_1
+- sip=4.18.1=py36h0a44026_1000
+- six=1.12.0=py36_1000
+- sqlite=3.13.0=1
+- terminado=0.8.1=py36_1001
+- testpath=0.4.2=py36_1000
+- tk=8.5.19=2
+- tornado=5.1.1=py36h1de35cc_1000
+- traitlets=4.3.2=py36_1000
+- utm=0.4.2=py36_0
+- vega=0.4.4=py36_1
+- vincent=0.4.4=py36_0
+- wcwidth=0.1.7=py_1
+- webencodings=0.5.1=py_1
+- wheel=0.33.0=py36_0
+- widgetsnbextension=3.4.2=py36_1000
+- xmltodict=0.11.0=py_1
+- xz=5.2.4=h1de35cc_1001
+- zeromq=4.2.5=h0a44026_1006
+- zlib=1.2.11=h1de35cc_1004
+- blas=1.0=mkl
+- intel-openmp=2019.1=144
+- jupyter=1.0.0=py36_3
+- mkl=2017.0.4=h1fae6ae_0
+- numpy=1.12.1=py36_0
+- requests=2.14.2=py36_0
+- scikit-learn=0.18.1=np112py36_1
+- scipy=0.19.0=np112py36_0
+- pip:
+  - asn1crypto==0.24.0
+  - cffi==1.11.5
+  - cryptography==2.5
+  - ipython-genutils==0.2.0
+  - jupyter-client==5.2.4
+  - jupyter-console==5.2.0
+  - jupyter-core==4.4.0
+  - jwcrypto==0.4.2
+  - lxml==4.3.1
+  - prometheus-client==0.5.0
+  - prompt-toolkit==1.0.15
+  - pycparser==2.19
+  - pyfcm==1.4.3
+  - pygeocoder==1.2.5
+  - pykml==0.1.3
+  - pymongo==3.5.1
+  - requests-toolbelt==0.9.1
+prefix: /Users/shankari/OSS/anaconda/envs/minimal_emission_notebook
+
diff --git a/setup/environment36.notebook.yml b/setup/environment36.notebook.yml
new file mode 100644
index 000000000..9beafa67e
--- /dev/null
+++ b/setup/environment36.notebook.yml
@@ -0,0 +1,38 @@
+name: emission
+channels:
+- conda-forge
+- defaults
+dependencies:
+- altair=1.2.1=py_0
+- branca=0.2.0=py_1
+- folium=0.5.0=py_0
+- vega=0.4.4=py36_1
+- vincent=0.4.4=py36_0
+- ipython=5.3.0=py36_0
+- jupyter=1.0.0=py36_3
+- arrow=0.12.1
+- attrdict=2.0.0
+- cheroot=6.2.*=py36_0
+- future=0.16.0
+- geojson=2.3.0
+- google-auth=1.2.1
+- jsonpickle=0.9.6
+- numpy=1.12.1=py36_0
+- pandas=0.20.1=np112py36_0
+- pip=9.0.1=py36_1
+- python=3.6.1=2
+- python-dateutil=2.6.0=py36_0
+- pytz=2017.2=py36_0
+- requests=2.14.2=py36_0
+- scikit-learn=0.18.1=np112py36_1
+- scipy=0.19.0=np112py36_0
+- sqlite=3.13.0
+- utm=0.4.2
+- xmltodict=0.11.0
+- pip:
+  - jwcrypto==0.4.2
+  - pyfcm==1.4.3
+  - pygeocoder==1.2.5
+  - pykml==0.1.3
+  - pymongo==3.5.1
+prefix: /Users/shankari/OSS/anaconda/envs/emission
diff --git a/setup/setup.sh b/setup/setup.sh
index fa1745927..eafcc66c9 100755
--- a/setup/setup.sh
+++ b/setup/setup.sh
@@ -6,4 +6,3 @@
 # - on Windows: C:/Users/<user>/Miniconda3/Scripts/conda
 conda env update --name emission --file setup/environment36.yml
 source activate emission
-pip install six --upgrade
diff --git a/setup/setup_notebook.sh b/setup/setup_notebook.sh
new file mode 100755
index 000000000..21f24619e
--- /dev/null
+++ b/setup/setup_notebook.sh
@@ -0,0 +1,9 @@
+# If the conda binary is not found, specify the full path to it
+# you can find it by searching for "conda" under the miniconda3 directory
+# typical paths are:
+# - on linux: /home/<user>/miniconda3/bin/conda
+# - on OSX: /Users/<user>/miniconda3/bin/conda
+# - on Windows: C:/Users/<user>/Miniconda3/Scripts/conda
+conda env update --name emission --file setup/environment36.yml
+conda env update --name emission --file setup/environment36.notebook.additions.yml
+source activate emission
diff --git a/setup/setup_tests.sh b/setup/setup_tests.sh
index 9d05e67e7..c46bc1e0f 100755
--- a/setup/setup_tests.sh
+++ b/setup/setup_tests.sh
@@ -7,7 +7,6 @@ echo "Check with 'conda -V'"
 echo "Upgrade with 'conda update conda' from the *root* environment"
 conda env create --prefix ${CONDA_TEMP_PREFIX} --file setup/environment36.yml
 source activate ${CONDA_TEMP_PREFIX}
-pip install six --upgrade
 python bin/deploy/habitica_conf.py
 python bin/deploy/push_conf.py
 python bin/deploy/model_copy.py

From 11ff18f7fea41fb7e12387dac41ecf7c0beb7b61 Mon Sep 17 00:00:00 2001
From: "K. Shankari" <shankari@eecs.berkeley.edu>
Date: Tue, 12 Feb 2019 11:18:20 -0800
Subject: [PATCH 10/11] Add a new non-mkl version

- Remove the 2.7 environment because it is obsolete
---
 setup/environment27.yml | 70 -----------------------------------------
 setup/setup_nomkl.sh    |  8 +++++
 2 files changed, 8 insertions(+), 70 deletions(-)
 delete mode 100644 setup/environment27.yml
 create mode 100755 setup/setup_nomkl.sh

diff --git a/setup/environment27.yml b/setup/environment27.yml
deleted file mode 100644
index a6a6da2b6..000000000
--- a/setup/environment27.yml
+++ /dev/null
@@ -1,70 +0,0 @@
-name: py27
-dependencies:
-- certifi=2016.2.28=py27_0
-- cycler=0.10.0=py27_0
-- freetype=2.5.5=2
-- functools32=3.2.3.2=py27_0
-- icu=54.1=0
-- libpng=1.6.30=1
-- matplotlib=2.0.2=np113py27_0
-- mkl=2017.0.3=0
-- numpy=1.13.1=py27_0
-- openssl=1.0.2l=0
-- pandas=0.20.3=py27_0
-- patsy=0.4.1=py27_0
-- pip=9.0.1=py27_1
-- pyparsing=2.2.0=py27_0
-- pyqt=5.6.0=py27_2
-- python=2.7.13=0
-- python-dateutil=2.6.1=py27_0
-- pytz=2017.2=py27_0
-- qt=5.6.2=2
-- readline=6.2=2
-- scikit-learn=0.19.0=np113py27_0
-- scipy=0.19.1=np113py27_0
-- seaborn=0.8=py27_0
-- setuptools=36.4.0=py27_1
-- sip=4.18=py27_0
-- six=1.10.0=py27_0
-- sqlite=3.13.0=0
-- statsmodels=0.8.0=np113py27_0
-- subprocess32=3.2.7=py27_0
-- tk=8.5.18=0
-- wheel=0.29.0=py27_0
-- zlib=1.2.11=0
-- pip:
-  - arrow==0.12.0
-  - asn1crypto==0.23.0
-  - attrdict==2.0.0
-  - backports.functools-lru-cache==1.4
-  - cachetools==2.0.1
-  - cffi==1.11.2
-  - chardet==3.0.4
-  - cheroot==5.10.0
-  - cherrypy==12.0.1
-  - cryptography==2.1.4
-  - enum34==1.1.6
-  - future==0.16.0
-  - geojson==2.3.0
-  - google-auth==1.2.1
-  - idna==2.6
-  - ipaddress==1.0.18
-  - jaraco.classes==1.4.3
-  - jwcrypto==0.4.2
-  - lxml==4.1.1
-  - portend==2.2
-  - pyasn1==0.4.2
-  - pyasn1-modules==0.2.1
-  - pycparser==2.18
-  - pyfcm==1.4.3
-  - pygeocoder==1.2.5
-  - pykml==0.1.3
-  - pymongo==3.5.1
-  - python-crontab==2.2.7
-  - requests==2.18.4
-  - requests-toolbelt==0.8.0
-  - rsa==3.4.2
-  - tempora==1.9
-  - urllib3==1.22
-  - utm==0.4.2
-  - xmltodict==0.11.0
diff --git a/setup/setup_nomkl.sh b/setup/setup_nomkl.sh
new file mode 100755
index 000000000..845e7a9ac
--- /dev/null
+++ b/setup/setup_nomkl.sh
@@ -0,0 +1,8 @@
+# If the conda binary is not found, specify the full path to it
+# you can find it by searching for "conda" under the miniconda3 directory
+# typical paths are:
+# - on linux: /home/<user>/miniconda3/bin/conda
+# - on OSX: /Users/<user>/miniconda3/bin/conda
+# - on Windows: C:/Users/<user>/Miniconda3/Scripts/conda
+conda env update --name emission --file setup/environment36.nomkl.yml
+source activate emission

From 07f4dc95a65fac2068d7db711a407a8efcf39e67 Mon Sep 17 00:00:00 2001
From: "K. Shankari" <shankari@eecs.berkeley.edu>
Date: Tue, 12 Feb 2019 13:27:52 -0800
Subject: [PATCH 11/11] Remove notebook packages we don't need

Turns out that altair and vincent are added back anyway by folium.
But at least I tried!
---
 setup/environment36.notebook.additions.yml |  3 ---
 setup/environment36.notebook.exported.yml  | 10 +++++-----
 setup/environment36.notebook.yml           |  3 ---
 3 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/setup/environment36.notebook.additions.yml b/setup/environment36.notebook.additions.yml
index cae61b2bb..bf7ca0a8d 100644
--- a/setup/environment36.notebook.additions.yml
+++ b/setup/environment36.notebook.additions.yml
@@ -3,10 +3,7 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- altair=1.2.1=py_0
 - branca=0.2.0=py_1
 - folium=0.5.0=py_0
-- vega=0.4.4=py36_1
-- vincent=0.4.4=py36_0
 - ipython=5.3.0=py36_0
 - jupyter=1.0.0=py36_3
diff --git a/setup/environment36.notebook.exported.yml b/setup/environment36.notebook.exported.yml
index 02bcd6010..56ba48e75 100644
--- a/setup/environment36.notebook.exported.yml
+++ b/setup/environment36.notebook.exported.yml
@@ -1,9 +1,9 @@
-name: minimal_emission_notebook
+name: emission-new
 channels:
 - conda-forge
 - defaults
 dependencies:
-- altair=1.2.1=py_0
+- altair=2.3.0=py36_1001
 - appnope=0.1.0=py36_1000
 - arrow=0.12.1=py36_1002
 - attrdict=2.0.0=py_1
@@ -75,11 +75,11 @@ dependencies:
 - terminado=0.8.1=py36_1001
 - testpath=0.4.2=py36_1000
 - tk=8.5.19=2
+- toolz=0.9.0=py_1
 - tornado=5.1.1=py36h1de35cc_1000
 - traitlets=4.3.2=py36_1000
 - utm=0.4.2=py36_0
-- vega=0.4.4=py36_1
-- vincent=0.4.4=py36_0
+- vincent=0.4.4=py_1
 - wcwidth=0.1.7=py_1
 - webencodings=0.5.1=py_1
 - wheel=0.33.0=py36_0
@@ -114,5 +114,5 @@ dependencies:
   - pykml==0.1.3
   - pymongo==3.5.1
   - requests-toolbelt==0.9.1
-prefix: /Users/shankari/OSS/anaconda/envs/minimal_emission_notebook
+prefix: /Users/shankari/OSS/anaconda/envs/emission-new
 
diff --git a/setup/environment36.notebook.yml b/setup/environment36.notebook.yml
index 9beafa67e..9bfa55f57 100644
--- a/setup/environment36.notebook.yml
+++ b/setup/environment36.notebook.yml
@@ -3,11 +3,8 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- altair=1.2.1=py_0
 - branca=0.2.0=py_1
 - folium=0.5.0=py_0
-- vega=0.4.4=py36_1
-- vincent=0.4.4=py36_0
 - ipython=5.3.0=py36_0
 - jupyter=1.0.0=py36_3
 - arrow=0.12.1