Specify environment managed using conda #15
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I began with the environment used by https://github.com/cognoma/cancer-data/blob/02a306aae0018623e495ed043ae47f5fccf3c370/environment.yml which uses recent versions of all explicit dependencies, such as Python 3.5.2 and pandas 0.18.1. Then, I added explicit dependencies imported by `1.TCGA-MLexample.ipynb`.
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@cgreene @gwaygenomics -- Y/N? |
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Confirming that the environment installs and activates properly on OS X. |
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| This repository uses [conda](http://conda.pydata.org/docs/ "Conda package management system and environment management system documentation") to manage its environment and install packages. If you don't have conda installed on your system, you can [download it here](http://conda.pydata.org/miniconda.html "Miniconda Homepage"). You can install the Python 2 or 3 version of Miniconda (or Anaconda), which determines the Python version of your root environment. Since we create a dedicated environment for this project, named `cognoma-machine-learning` whose explicit dependencies are specified in [`environment.yml`](environment.yml), the version of your root environment will not be relevant. | ||
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| With conda, you can create the `cognoma-machine-learning` environment using: |
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Add note here about forking/cloning repository before creating the environment - at least something mentioning the specific environment.yml must be in directory
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I am trying to install the environment in cygwin on windows 10. I got this error: |
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Okay I think we can drop scipy to 0.17.1. This is sad becasue 0.18.0 did bring lot's of changes. Eventually, we can return to 0.18.0 once Anaconda creates a Windows build. See ContinuumIO/anaconda-issues#925 for more information on the missing package issue. Will try out the downgrade. |
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Confirming that the updated @gwaygenomics, can you test out Windows again? I used: to remove the existing |
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$ conda env create --quiet --force --file environment.yml
Fetching package metadata .........
Solving package specifications: ..........
1 file(s) copied.
No psutil available.
To proceed, please conda install psutil#
# To activate this environment, use:
# $ source activate cognoma-machine-learning
#
# To deactivate this environment, use:
# $ source deactivatewhich seems to have been an issue in the past. I was able to activate the environment with |
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I'm starting to wonder if it makes sense just to specify an entire anaconda release, e.g. What happens if you run I think we'll probably be fine without |
it installs without error! But for some reason I still get the |
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ok, @dhimmel and I just discussed this issue - since the |
I began with the environment used by cancer-data, which uses recent versions of all explicit dependencies, such as Python 3.5.2 and pandas 0.18.1. Then, I added explicit dependencies imported by
1.TCGA-MLexample.ipynb.For testing, it would be great if at least one OS X and one Windows reviewer can successfully install. I created the environment on a Linux platform.