added environment.yml to ensure same python setup

README.md

@@ -2,3 +2,28 @@
 
 Interneurons in the subiculum  have a polar axonal cloud instead of a circular as found in other brain regions. Additionally, pyramidal neurons in the subiculum lack recurrent connections, but they connect via recurrent inhibition. Therefore, inhibition plays a major role in this circuitry and we pose the question, which function the extraordinary axon morphology serves in this setting.
 
+### How to run the scripts
+
+It is recommended to use Anaconda (https://www.continuum.io/downloads) to create a virtual environment with the necessary dependencies. With anaconda, it is a one button install. Af
+ter cloning the repository and changing into the root folder, type
+```
+conda env create -f environment.yml
+```
+
+This creates an environment called interneuron_polarity, which can be activated via
+```bash
+conda activate interneuron_polarity
+```
+
+If you need additional packages, install them via `conda install` and update the environment file via
+
+```bash
+conda env export > environment.yml
+```
+
+To update the existing enviroment
+```bash
+conda-env update -f environment.yml
+```
+
+

environment.yml

@@ -0,0 +1,190 @@
+name: interneuron_polarity
+channels:
+  - https://repo.continuum.io/pkgs/free
+  - defaults
+  - conda-forge
+  - ostrokach-forge
+  - pkgw-forge
+dependencies:
+  - at-spi2-atk=2.26.2=h9b4a0fc_1
+  - at-spi2-core=2.28.0=h9b4a0fc_1
+  - atk=2.25.90=hf2eb9ee_1001
+  - atomicwrites=1.3.0=py37_1
+  - attrs=19.1.0=py37_1
+  - backcall=0.1.0=py37_0
+  - binutils_impl_linux-64=2.31.1=h6176602_1
+  - binutils_linux-64=2.31.1=h6176602_7
+  - blas=1.0=mkl
+  - bleach=3.1.0=py37_0
+  - boost=1.69.0=py37h8619c78_1001
+  - boost-cpp=1.69.0=h11c811c_1000
+  - brian2=2.2.2.1=py37hc9558a2_1
+  - bzip2=1.0.6=h14c3975_5
+  - ca-certificates=2019.11.28=hecc5488_0
+  - cairo=1.14.12=h8948797_3
+  - cairomm=1.12.2=0
+  - certifi=2019.11.28=py37_0
+  - cgal=4.13=py37he1b5a44_1
+  - cgal-cpp=4.13=h4f13b39_1
+  - cycler=0.10.0=py37_0
+  - cython=0.29.13=py37he1b5a44_0
+  - dbus=1.13.6=h746ee38_0
+  - decorator=4.4.0=py37_1
+  - defusedxml=0.5.0=py37_1
+  - entrypoints=0.3=py37_0
+  - epoxy=1.5.2=h14c3975_1
+  - expat=2.2.6=he6710b0_0
+  - fastcache=1.0.2=py37h14c3975_2
+  - ffmpeg=4.1.3=h167e202_0
+  - fontconfig=2.13.1=he4413a7_1000
+  - freetype=2.9.1=h8a8886c_1
+  - gcc_impl_linux-64=7.3.0=habb00fd_1
+  - gcc_linux-64=7.3.0=h553295d_7
+  - gdk-pixbuf=2.36.9=1
+  - glib=2.56.2=hd408876_0
+  - glob2=0.6=py37_1
+  - gmp=6.1.2=h6c8ec71_1
+  - gmpy2=2.0.8=py37h10f8cd9_2
+  - gnutls=3.6.5=hd3a4fd2_1002
+  - gobject-introspection=1.56.1=py37hbc4ca2d_2
+  - graph-tool=2.28.dev0=py37h0dcec27_0
+  - graphite2=1.3.13=h23475e2_0
+  - gsl=2.4=h14c3975_4
+  - gst-plugins-base=1.14.0=hbbd80ab_1
+  - gstreamer=1.14.0=hb453b48_1
+  - gtk3=3.22.30=h2c0c718_1
+  - gxx_impl_linux-64=7.3.0=hdf63c60_1
+  - gxx_linux-64=7.3.0=h553295d_7
+  - harfbuzz=1.8.8=hffaf4a1_0
+  - icu=58.2=h9c2bf20_1
+  - intel-openmp=2019.3=199
+  - ipykernel=5.1.0=py37h39e3cac_0
+  - ipython=7.4.0=py37h39e3cac_0
+  - ipython_genutils=0.2.0=py37_0
+  - ipywidgets=7.4.2=py37_0
+  - jedi=0.13.3=py37_0
+  - jinja2=2.10.1=py37_0
+  - jpeg=9b=h024ee3a_2
+  - jsonschema=3.0.1=py37_0
+  - jupyter=1.0.0=py37_7
+  - jupyter_client=5.2.4=py37_0
+  - jupyter_console=6.0.0=py37_0
+  - jupyter_core=4.4.0=py37_0
+  - jupyterlab=0.33.11=py37_0
+  - jupyterlab_launcher=0.11.2=py37h28b3542_0
+  - kiwisolver=1.0.1=py37hf484d3e_0
+  - lame=3.100=h14c3975_1001
+  - libcroco=0.6.12=h468c787_1001
+  - libedit=3.1.20181209=hc058e9b_0
+  - libffi=3.2.1=hd88cf55_4
+  - libgcc=7.2.0=h69d50b8_2
+  - libgcc-ng=8.2.0=hdf63c60_1
+  - libgfortran-ng=7.3.0=hdf63c60_0
+  - libiconv=1.15=h516909a_1005
+  - libpng=1.6.36=hbc83047_0
+  - librsvg=2.40.19=h84fa2a2_1000
+  - libsigcpp=2.10.0=hf484d3e_1001
+  - libsodium=1.0.16=h1bed415_0
+  - libstdcxx-ng=8.2.0=hdf63c60_1
+  - libtiff=4.0.10=h2733197_2
+  - libuuid=2.32.1=h14c3975_1000
+  - libxcb=1.13=h1bed415_1
+  - libxml2=2.9.9=he19cac6_0
+  - markupsafe=1.1.1=py37h7b6447c_0
+  - matplotlib=3.0.3=py37h5429711_0
+  - mistune=0.8.4=py37h7b6447c_0
+  - mkl=2019.3=199
+  - mkl_fft=1.0.10=py37ha843d7b_0
+  - mkl_random=1.0.2=py37hd81dba3_0
+  - more-itertools=7.0.0=py37_0
+  - mpc=1.1.0=h10f8cd9_1
+  - mpfr=4.0.1=hdf1c602_3
+  - mpmath=1.1.0=py37_0
+  - nbconvert=5.4.1=py37_3
+  - nbformat=4.4.0=py37_0
+  - ncurses=6.1=he6710b0_1
+  - nettle=3.4.1=h1bed415_1002
+  - nose=1.3.7=py37_2
+  - notebook=5.7.8=py37_0
+  - numpy=1.16.2=py37h7e9f1db_0
+  - numpy-base=1.16.2=py37hde5b4d6_0
+  - openh264=1.8.0=hdbcaa40_1000
+  - openssl=1.1.1d=h516909a_0
+  - pandas=0.24.2=py37he6710b0_0
+  - pandoc=2.2.3.2=0
+  - pandocfilters=1.4.2=py37_1
+  - pango=1.40.14=he752989_2
+  - parso=0.4.0=py_0
+  - patsy=0.5.1=py37_0
+  - pcre=8.43=he6710b0_0
+  - pexpect=4.7.0=py37_0
+  - pickleshare=0.7.5=py37_0
+  - pip=19.0.3=py37_0
+  - pixman=0.38.0=h7b6447c_0
+  - pluggy=0.11.0=py_0
+  - prometheus_client=0.6.0=py37_0
+  - prompt_toolkit=2.0.9=py37_0
+  - ptyprocess=0.6.0=py37_0
+  - py=1.8.0=py37_0
+  - pycairo=1.18.1=py37h2a1e443_0
+  - pygments=2.3.1=py37_0
+  - pygobject=3.28.3=py37h89f6ae1_1001
+  - pyparsing=2.4.0=py_0
+  - pyqt=5.9.2=py37h05f1152_2
+  - pyrsistent=0.14.11=py37h7b6447c_0
+  - pyscaffold=3.2.1=py_0
+  - pytest=4.5.0=py37_0
+  - python=3.7.3=h0371630_0
+  - python-dateutil=2.8.0=py37_0
+  - pytz=2019.1=py_0
+  - pyzmq=18.0.0=py37he6710b0_0
+  - qt=5.9.7=h5867ecd_1
+  - qtconsole=4.4.3=py37_0
+  - readline=7.0=h7b6447c_5
+  - scipy=1.2.1=py37h7c811a0_0
+  - seaborn=0.9.0=py37_0
+  - send2trash=1.5.0=py37_0
+  - setuptools=41.0.0=py37_0
+  - sip=4.19.8=py37hf484d3e_0
+  - six=1.12.0=py37_0
+  - sparsehash=2.0.3=hf484d3e_1000
+  - sqlite=3.27.2=h7b6447c_0
+  - statsmodels=0.9.0=py37h035aef0_0
+  - sympy=1.4=py37_0
+  - terminado=0.8.2=py37_0
+  - testpath=0.4.2=py37_0
+  - tk=8.6.8=hbc83047_0
+  - tornado=6.0.2=py37h7b6447c_0
+  - tqdm=4.42.1=py_0
+  - traitlets=4.3.2=py37_0
+  - wcwidth=0.1.7=py37_0
+  - webencodings=0.5.1=py37_1
+  - wheel=0.33.1=py37_0
+  - widgetsnbextension=3.4.2=py37_0
+  - x264=1!152.20180806=h14c3975_0
+  - xorg-fixesproto=5.0=h14c3975_1002
+  - xorg-inputproto=2.3.2=h14c3975_1002
+  - xorg-kbproto=1.0.7=h14c3975_1002
+  - xorg-libice=1.0.9=h516909a_1004
+  - xorg-libsm=1.2.3=h84519dc_1000
+  - xorg-libx11=1.6.7=h14c3975_1000
+  - xorg-libxext=1.3.4=h516909a_0
+  - xorg-libxfixes=5.0.3=h516909a_1004
+  - xorg-libxi=1.7.9=h516909a_1002
+  - xorg-libxrender=0.9.10=h516909a_1002
+  - xorg-libxtst=1.2.3=h14c3975_1002
+  - xorg-recordproto=1.14.2=h14c3975_1002
+  - xorg-renderproto=0.11.1=h14c3975_1002
+  - xorg-xextproto=7.3.0=h14c3975_1002
+  - xorg-xproto=7.0.31=h14c3975_1007
+  - xz=5.2.4=h14c3975_4
+  - zeromq=4.3.1=he6710b0_3
+  - zlib=1.2.11=h7b6447c_3
+  - zstd=1.3.7=h0b5b093_0
+  - pip:
+    - noise==1.2.2
+    - numexpr==2.7.1
+    - pypet==0.4.3
+    - tables==3.6.1
+prefix: /home/pfeiffer/Applications/miniconda2/envs/interneuron_polarity
+