Merge 117705c into 701c33a

.circleci/config.yml

@@ -0,0 +1,64 @@
+defaults: &defaults
+  working_directory: ~/markovmodel/PyEMMA
+  docker:
+    - image: continuumio/miniconda3
+
+inst_conda_bld: &inst_conda_bld
+  - run: conda config --add channels conda-forge
+  - run: conda config --set always_yes true
+  - run: conda config --set quiet true
+  - run: conda install conda-build
+
+version: 2
+
+jobs:
+  build:
+    <<: *defaults
+    parallelism: 1
+    steps:
+      - checkout
+      - run: git fetch --unshallow || true
+      - run: apt-get install -y cpp gcc
+      - run: apt-get install -y libx11-6 python-dev git build-essential
+      - run: apt-get install -y autoconf automake gcc g++ make gfortran
+      - run: apt-get install -y python-tables
+      - run: apt-get install -y libhdf5-serial-dev
+
+      - run: conda config --add channels conda-forge
+      - run: conda config --set always_yes true
+      - run: conda config --set quiet true
+      - run: conda install conda-build
+      - run: which pip
+      - run: conda install numpy;
+      - run: conda install numba;
+      - run: conda install dask;
+      - run: pip install tables
+      - run: pip install scipy==1.5.4
+      - run: pip install pip --upgrade;
+      #- run: python setup.py install
+      - run: pip install -e .
+
+      - run: pip install coverage
+      - run: git clone -b neuronunit https://github.com/russelljjarvis/jit_hub.git
+      - run: cd jit_hub; pip install -e .; cd ..;
+      - run: pip install cython
+      - run: pip install asciiplotlib;
+      - run: git clone -b master https://github.com/russelljjarvis/BluePyOpt.git
+      - run: cd BluePyOpt; pip install -e .
+      - run: pip install git+https://github.com/russelljjarvis/eFEL
+      - run: pip install ipfx
+      - run: pip install streamlit
+      - run: pip install sklearn
+      - run: pip install seaborn
+      - run: pip install frozendict
+      - run: pip install plotly
+      - run: pip install --upgrade colorama
+      - run: rm -rf /opt/conda/lib/python3.8/site-packages/sciunit
+      - run: git clone -b dev https://github.com/russelljjarvis/sciunit.git
+      - run: cd sciunit; pip install -e .; cd ..;
+      - run: pip install allensdk==0.16.3
+      - run: cd neuronunit/unit_test; python rheobase_dtc_test.py
+      - run: cd neuronunit/unit_test; python adexp_opt.py
+      - run: cd neuronunit/unit_test; coverage run adexp_opt.py
+      - run: cd neuronunit/unit_test; coverage run izhi_opt.py
+      - run: cd neuronunit/unit_test; coverage report

.travis.yml

@@ -21,13 +21,22 @@ install:
   - conda info -a
   - pip install -U pip
   - pip install .
+  - pip install sklearn
+  - pip install seaborn
   - pip install coveralls
   - pip install pylmeasure # required by morphology tests
+  - sh build.sh
+
 ######################################################
 
 script:
   - export NC_HOME='.' # NeuroConstruct isn't used but tests need this
                        # variable set to pass.
-  - sh test.sh
+  - cd neuronunit/unit_test; coverage run rheobase_dtc_test.py; cd -;
+  - cd neuronunit/unit_test; coverage run adexp_opt.py; cd -;
+  - cd neuronunit/unit_test; coverage run izhi_opt.py; cd -;
+  - cd neuronunit/unit_test; coverage report; cd -;
+
+  #- sh test.sh
 after_success:
   - coveralls

README.md

@@ -1,3 +1,7 @@
+### Circle CI russelljjarvis/optimization build:
+[![Build Status](https://circleci.com/gh/russelljjarvis/neuronunit/tree/optimization.svg?style=svg)](https://app.circleci.com/pipelines/github/russelljjarvis/neuronunit/)
+### Travis CI scidash/optimization build:
+[![Travis](https://travis-ci.org/scidash/neuronunit.svg?branch=optimization)](https://travis-ci.org/scidash/neuronunit)  
 | Master  | Dev |
 | ------------- | ------------- |
 | [![Travis](https://travis-ci.org/scidash/neuronunit.svg?branch=master)](https://travis-ci.org/scidash/neuronunit) | [![Travis](https://travis-ci.org/scidash/neuronunit.svg?branch=dev)](https://travis-ci.org/scidash/neuronunit)  |

build.sh

@@ -0,0 +1,31 @@
+apt-get install -y cpp gcc
+apt-get install -y libx11-6 python-dev git build-essential
+apt-get install -y autoconf automake gcc g++ make gfortran
+apt-get install -y python-tables
+apt-get install -y libhdf5-serial-dev
+conda install numpy;
+conda install numba;
+conda install dask;
+pip install pip --upgrade;
+pip install tables
+pip install scipy==1.5.4
+pip install -e .
+pip install coverage
+git clone -b neuronunit https://github.com/russelljjarvis/jit_hub.git
+cd jit_hub; pip install -e .; cd ..;
+pip install cython
+pip install asciiplotlib;
+git clone -b master https://github.com/russelljjarvis/BluePyOpt.git
+cd BluePyOpt; pip install -e .
+pip install git+https://github.com/russelljjarvis/eFEL
+pip install ipfx
+pip install streamlit
+pip install sklearn
+pip install seaborn
+pip install frozendict
+pip install plotly
+pip install --upgrade colorama
+rm -rf /opt/conda/lib/python3.8/site-packages/sciunit
+git clone -b dev https://github.com/russelljjarvis/sciunit.git
+cd sciunit; pip install -e .; cd ..;
+pip install allensdk==0.16.3

environment.yml

@@ -6,7 +6,15 @@ dependencies:
 - pip:
   - neo==0.4
   - elephant
-  - scoop
-  - git+http://github.com/scidash/sciunit@dev#egg=sciunit-1.5.6
-  - git+http://github.com/rgerkin/AllenSDK@python3.5#egg=allensdk-0.12.4.1
-  - git+http://github.com/rgerkin/pyNeuroML@master#egg=pyneuroml-0.2.3
+  - dask
+  - numba
+  - streamlit
+  - sklearn
+  - seaborn
+  - frozendict
+  - plotly
+  - asciiplotlib
+  - ipfx
+  - git+https://github.com/russelljjarvis/jit_jub@neuronunit
+  - git+https://github.com/russelljjarvis/BluePyOpt
+  - git+https://github.com/russelljjarvis/sciunit@dev

neuronunit/allenapi/__init__.py

@@ -0,0 +1,3 @@
+"""Allen API for NeuronUnit"""
+
+import warnings