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add conda_environment and setup description
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MaximilianFranz committed Sep 4, 2019
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15 changes: 15 additions & 0 deletions README.md
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Expand Up @@ -43,6 +43,14 @@ Configure the Observer in `experiment.py` to connect to your local host
Install and run Omniboard with the default settings and it will connect to your running `mongod` instance.
After that, the dashboard is available at `localhost:9000`.

## Alternative
When running on a cluster, or when you don't want to setup MongoDB, you can use the `FileStorageObserver` instead of
the `MongoObserver`.
Simply create directory `my_runs` and run the experiment via
```bash
python causaleval/experiment.py -F my_runs
```

# On logging
Results are stored row wise in a csv with fields:
`Metric, Method, Dataset, Size, Sample, Time, Score`. Meaning
Expand All @@ -56,6 +64,13 @@ Results are stored row wise in a csv with fields:


# Setting up the environment
## In Conda
Using the conda environment specification file `conda_env.txt` you can setup a conda environment with Python and R
installed:
```bash
conda create --name new_env --file conda_env.txt
```

## R - 3.6
You might have to install a few R packages from GitHub sources manually. Namely,
- https://github.com/saberpowers/causalLearning
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303 changes: 303 additions & 0 deletions conda_env.txt
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# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
_libgcc_mutex=0.1=main
_r-mutex=1.0.0=anacondar_1
absl-py=0.7.1=pypi_0
astor=0.8.0=pypi_0
atomicwrites=1.3.0=pypi_0
attrs=19.1.0=py37_1
backcall=0.1.0=py37_0
bartpy=0.0.2=pypi_0
binutils_impl_linux-64=2.31.1=h6176602_1
binutils_linux-64=2.31.1=h6176602_8
bleach=3.1.0=py37_0
bwidget=1.9.11=1
bzip2=1.0.8=h7b6447c_0
ca-certificates=2019.5.15=1
cairo=1.14.12=h8948797_3
certifi=2019.6.16=py37_1
cffi=1.12.3=pypi_0
colorama=0.4.1=pypi_0
curl=7.65.3=hbc83047_0
cycler=0.10.0=pypi_0
decorator=4.4.0=py37_1
defusedxml=0.6.0=py_0
docopt=0.6.2=pypi_0
entrypoints=0.3=py37_0
fontconfig=2.13.0=h9420a91_0
freetype=2.9.1=h8a8886c_1
fribidi=1.0.5=h7b6447c_0
gast=0.2.2=pypi_0
gcc_impl_linux-64=7.3.0=habb00fd_1
gcc_linux-64=7.3.0=h553295d_8
gfortran_impl_linux-64=7.3.0=hdf63c60_1
gfortran_linux-64=7.3.0=h553295d_8
glib=2.56.2=hd408876_0
gmp=6.1.2=h6c8ec71_1
google-pasta=0.1.7=pypi_0
graphite2=1.3.13=h23475e2_0
grpcio=1.22.0=pypi_0
gsl=2.4=h14c3975_4
gxx_impl_linux-64=7.3.0=hdf63c60_1
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jpeg=9b=h024ee3a_2
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