install trouble - conflicting ipython requirements

[cssmillie]

I'm trying to install americangut, but I run into this error:

$ sudo python setup.py install --prefix=/home/directory ... Processing dependencies for americangut==0.0.1 error: ipython 3.2.3 is installed but ipython>=4.0.0 is required by set(['ipykernel'])

But when I install ipython 4.1.1 and re-run the same command, the americangut installer replaces it with ipython 3.2.3. I think this might be because IPython<4.0.0 is listed in the conda requirements.

Any ideas on how to get this installed? Thanks!

[jwdebelius]

The requirement has to do with ipymd, which lets your machine parse the markdown files as notebooks. Keep in mind this also requires modifying your ipython config file. Until we sort out how to get ipymd in Jupyter 4.0, the earlier version is required.

I'd recommend using miniconda as an environment manager. It's surprisingly easy to use, and lets you have as many versions of files as you want.

[cssmillie]

Thanks for the quick response! Sorry, I'm still a little confused. To solve this problem, what exactly should I do? Thanks again

Chris On Sun, Feb 7, 2016 at 14:37 J W Debelius notifications@github.com wrote:

The requirement has to do with ipymd, which lets your machine parse the markdown files as notebooks. Keep in mind this also requires modifying your ipython config file. Until we sort out how to get ipymd in Jupyter 4.0, the earlier version is required.

I'd recommend using miniconda http://conda.pydata.org/miniconda.html as an environment manager. It's surprisingly easy to use, and lets you have as many versions of files as you want.

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/issues/199#issuecomment-181090990 .

[jwdebelius]

Hi Chris,

1. Go to http://conda.pydata.org/miniconda.html and install the Python 2.7 version most appropriate for your system. Install it on your system.
2. Navigate to the american gut repository directory.
3. Create a new conda environment with the command conda create, i.e. conda create --name americangut --file conda_requirements.txt
4. Activate the conda environment (source activate americangut)
5. Install the required pip files (pip install -r pip_requirements.txt)
6. Install the repository (pip install . -e --no-deps)
7. Configure your system for ipymd using the installation instruction. You will only need to do this once.

[cssmillie]

Wow thanks!! Super helpful, I really appreciate it

Chris

On Sun, Feb 7, 2016 at 14:52 J W Debelius notifications@github.com wrote:

Hi Chris,

1. Go to http://conda.pydata.org/miniconda.html and install the Python 2.7 version most appropriate for your system. Install it on your system.
2. Navigate to the american gut repository directory.
3. Create a new conda environment with the command conda create, i.e. conda create --name americangut --file conda_requirements.txt
4. Activate the conda environment (source activate americangut)
5. Install the required pip files (pip install -r pip_requirements.txt)
6. Install the repository (pip install . -e --no-deps)
7. Configure your system for ipymd using the installation instruction https://github.com/rossant/ipymd#installation. You will only need to do this once.

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/issues/199#issuecomment-181093975 .

[cssmillie]

I'm trying to download the American Gut data from EBI, but it looks like it's missing. Do you know how I can get it? QIITA is a good option, but it doesn't work for me because I am downloading to a cluster, which is difficult in QIITA. Thanks!

Chris

On Sun, Feb 7, 2016 at 3:06 PM, Christopher Smillie csmillie@mit.edu wrote:

Wow thanks!! Super helpful, I really appreciate it

Chris

On Sun, Feb 7, 2016 at 14:52 J W Debelius notifications@github.com wrote:

Hi Chris,

1. Go to http://conda.pydata.org/miniconda.html and install the Python 2.7 version most appropriate for your system. Install it on your system.
2. Navigate to the american gut repository directory.
3. Create a new conda environment with the command conda create, i.e. conda create --name americangut --file conda_requirements.txt
4. Activate the conda environment (source activate americangut)
5. Install the required pip files (pip install -r pip_requirements.txt )
6. Install the repository (pip install . -e --no-deps)
7. Configure your system for ipymd using the installation instruction https://github.com/rossant/ipymd#installation. You will only need to do this once.

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/issues/199#issuecomment-181093975 .

[wasade]

What accession are you using? The full data are here:

http://www.ebi.ac.uk/ena/data/view/ERP012803

On Mon, Feb 8, 2016 at 5:28 PM, cssmillie notifications@github.com wrote:

I'm trying to download the American Gut data from EBI, but it looks like it's missing. Do you know how I can get it? QIITA is a good option, but it doesn't work for me because I am downloading to a cluster, which is difficult in QIITA. Thanks!

Chris

On Sun, Feb 7, 2016 at 3:06 PM, Christopher Smillie csmillie@mit.edu wrote:

Wow thanks!! Super helpful, I really appreciate it

Chris

On Sun, Feb 7, 2016 at 14:52 J W Debelius notifications@github.com wrote:

Hi Chris,

1. Go to http://conda.pydata.org/miniconda.html and install the Python 2.7 version most appropriate for your system. Install it on your system.
2. Navigate to the american gut repository directory.
3. Create a new conda environment with the command conda create, i.e. conda create --name americangut --file conda_requirements.txt
4. Activate the conda environment (source activate americangut)
5. Install the required pip files (pip install -r pip_requirements.txt )
6. Install the repository (pip install . -e --no-deps)
7. Configure your system for ipymd using the installation instruction https://github.com/rossant/ipymd#installation. You will only need to do this once.

— Reply to this email directly or view it on GitHub < https://github.com/biocore/American-Gut/issues/199#issuecomment-181093975> .

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/issues/199#issuecomment-181659700 .

[iugrina]

pip install -r pip_requirements.txt installs ipython==4.1.2 with the current version of pip_requirements.txt. Since you have <4.0.0 in conda_req could you please add to pip_req the exact version needed for the current AG repo (e.g. IPython>=3.2.1 or IPython==3.2.1)

[wasade]

Good catch, thanks. Will issue a PR shortly

[wasade]

Actually, Im a bit confused, ipython is not specified in directly pip_requirements.txt? I do recommend using conda as it does simplify the environment management.

@JWDebelius, you're primarily using Jupyter > 4.0.0, right?

[iugrina]

Yes, I've noticed the differences between conda_req and pip_req (https://github.com/biocore/American-Gut/issues/203).

As for the conda that is not an option for me :( (Python from source + pip + virtualenv)

[iugrina]

My questions/comments were resolved with #211