Make ipython a requirement

[acellera]

Make ipython a requirement

[stefdoerr]

I would prefer not to for a few reasons:

1. ipython does not come installed by default. You probably installed it yourself in the base environment.
2. moleculekit's main purpose is not meant to be used interactively like HTMD. It's a library to be used inside other projects. For people who want to program interactively HTMD comes with everything preinstalled.
3. It's also not a "dependency" of the code in any sense. Adding it in pulls lots of other stuff* which is not needed, potentially causing dependency issues, increasing install times etc, etc.

* Stuff

    package                    |            build
    ---------------------------|-----------------
    decorator-4.4.1            |             py_0          13 KB
    ipython-7.9.0              |   py37h39e3cac_0         1.1 MB
    jedi-0.15.1                |           py37_0         704 KB
    parso-0.5.1                |             py_0          68 KB
    pexpect-4.7.0              |           py37_0          80 KB
    prompt_toolkit-2.0.10      |             py_0         227 KB
    pygments-2.4.2             |             py_0         664 KB
    traitlets-4.3.3            |           py37_0         138 KB
    ------------------------------------------------------------

[giadefa]

it's 2MB of stuff

…

On Mon, 4 Nov 2019 at 09:45, Stefan Doerr ***@***.***> wrote: I would prefer not to for a few reasons: 1. ipython does not come installed by default. You probably installed it yourself in the base environment. 2. moleculekit's main purpose is not meant to be used interactively like HTMD. It's a library to be used inside other projects. For people who want to program interactively HTMD comes with everything preinstalled. 3. It's also not a "dependency" of the code in any sense. Adding it in pulls lots of other stuff* which is not needed, potentially causing dependency issues, increasing install times etc, etc. * Stuff package | build ---------------------------|----------------- decorator-4.4.1 | py_0 13 KB ipython-7.9.0 | py37h39e3cac_0 1.1 MB jedi-0.15.1 | py37_0 704 KB parso-0.5.1 | py_0 68 KB pexpect-4.7.0 | py37_0 80 KB prompt_toolkit-2.0.10 | py_0 227 KB pygments-2.4.2 | py_0 664 KB traitlets-4.3.3 | py37_0 138 KB ------------------------------------------------------------ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=AB3KUOSR7RLEM6YQMYCRCCTQSBNSJA5CNFSM4JIJGY72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDADNQQ#issuecomment-549467842>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB3KUOT4H2HSQPYGHBZ7FULQSBNSJANCNFSM4JIJGY7Q> .

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[stefdoerr]

The size is just a minor issue. As I said: a) ipython not installed by default. The problem is specific to your own setup b) it's not a real dep c) HTMD takes care of having an interactive installation.

[giadefa]

realistically you are going to use it via ipython, so I don't really see the issue

…

On Mon, 4 Nov 2019 at 10:36, Stefan Doerr ***@***.***> wrote: The size is just a minor issue. As I said: a) ipython not installed by default. The problem is specific to your own setup b) it's not a real dep c) HTMD takes care of having an interactive installation. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=AB3KUORESRYJZ4JBMIAVCQDQSBTT3A5CNFSM4JIJGY72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDAITHQ#issuecomment-549489054>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB3KUOWR6O2MX5S64IW4V4TQSBTT3ANCNFSM4JIJGY7Q> .

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[stefdoerr]

All apps built on top of moleculekit (i.e. all PM apps) don't need ipython. It's a python library, not an interactive environment like HTMD On Mon, Nov 4, 2019 at 8:55 PM Gianni De Fabritiis <[email protected]> wrote:

…

realistically you are going to use it via ipython, so I don't really see the issue On Mon, 4 Nov 2019 at 10:36, Stefan Doerr ***@***.***> wrote: > The size is just a minor issue. As I said: a) ipython not installed by > default. The problem is specific to your own setup b) it's not a real dep > c) HTMD takes care of having an interactive installation. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > < #38?email_source=notifications&email_token=AB3KUORESRYJZ4JBMIAVCQDQSBTT3A5CNFSM4JIJGY72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDAITHQ#issuecomment-549489054 >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AB3KUOWR6O2MX5S64IW4V4TQSBTT3ANCNFSM4JIJGY7Q > > . > -- <http://www.acellera.com> <https://twitter.com/acellera> <https://www.youtube.com/user/acelleracom> < https://www.linkedin.com/company/2133167?trk=tyah&trkInfo=clickedVertical%3Acompany%2CclickedEntityId%3A2133167%2Cidx%3A2-1-2%2CtarId%3A1448018583204%2Ctas%3Aacellera > <https://www.acellera.com/md-simulation-blog-news/> <http://is.gd/1eXkbS> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=AB4RLAROE2MSK7LKPMULMQLQSBV2JA5CNFSM4JIJGY72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDAKMWA#issuecomment-549496408>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4RLATRW4U6JCP76HFISX3QSBV2JANCNFSM4JIJGY7Q> .

[giadefa]

But all the users do, who will notice more machines or humans for the missing 2Mb.

…

On Mon, 4 Nov 2019, 11:16 Stefan Doerr, ***@***.***> wrote: All apps built on top of moleculekit (i.e. all PM apps) don't need ipython. It's a python library, not an interactive environment like HTMD On Mon, Nov 4, 2019 at 8:55 PM Gianni De Fabritiis < ***@***.***> wrote: > realistically you are going to use it via ipython, so I don't really see > the issue > > On Mon, 4 Nov 2019 at 10:36, Stefan Doerr ***@***.***> > wrote: > > > The size is just a minor issue. As I said: a) ipython not installed by > > default. The problem is specific to your own setup b) it's not a real dep > > c) HTMD takes care of having an interactive installation. > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > < > #38?email_source=notifications&email_token=AB3KUORESRYJZ4JBMIAVCQDQSBTT3A5CNFSM4JIJGY72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDAITHQ#issuecomment-549489054 > >, > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AB3KUOWR6O2MX5S64IW4V4TQSBTT3ANCNFSM4JIJGY7Q > > > > . > > > > > -- > <http://www.acellera.com> > > <https://twitter.com/acellera> > <https://www.youtube.com/user/acelleracom> > < > https://www.linkedin.com/company/2133167?trk=tyah&trkInfo=clickedVertical%3Acompany%2CclickedEntityId%3A2133167%2Cidx%3A2-1-2%2CtarId%3A1448018583204%2Ctas%3Aacellera > > > <https://www.acellera.com/md-simulation-blog-news/> > <http://is.gd/1eXkbS> > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > < #38?email_source=notifications&email_token=AB4RLAROE2MSK7LKPMULMQLQSBV2JA5CNFSM4JIJGY72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDAKMWA#issuecomment-549496408 >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AB4RLATRW4U6JCP76HFISX3QSBV2JANCNFSM4JIJGY7Q > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=AB3KUOUH5BC5JMLATV6WO4LQSBYH3A5CNFSM4JIJGY72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDAMPFQ#issuecomment-549504918>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB3KUORO2C473RG3TVHYSFDQSBYH3ANCNFSM4JIJGY7Q> .

[stefdoerr]

No, I'm trying to point out that this only happened because of your specific conda setup

(base) stefan@spectre:~$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
(base) stefan@spectre:~$ bash Miniconda3-latest-Linux-x86_64.sh
(base) stefan@spectre:~$ ipython
Command 'ipython' not found, but can be installed with:
sudo apt install ipython
(base) stefan@spectre:~$ conda install moleculekit -c acellera
(base) stefan@spectre:~$ ipython
Command 'ipython' not found, but can be installed with:
sudo apt install ipython
(base) stefan@spectre:~$ conda install ipython

ipython doesn't come installed with Miniconda.
The issue you had only exists because you explicitly installed ipython in your base environment and then created a different environment with moleculekit.
This would not have happened if a) you installed moleculekit in your base environment b) you hadn't installed ipython in the main environment c) if you were using Jupyter (which many people use). Should we also install jupyter, or Spyder because some people use it?

Examples which don't put ipython in their deps:

• PyEmma: https://github.com/markovmodel/PyEMMA/blob/devel/setup.py#L291
• MDTraj: https://github.com/mdtraj/mdtraj/blob/master/setup.py#L258
• Biopython: https://github.com/biopython/biopython/blob/master/setup.py#L282
• OpenMM: https://github.com/openmm/openmm/blob/8fac83437cfb9a8f156eb9e1609b7be17b1a52e8/.travis.yml#L5
• MSMBuilder: https://github.com/msmbuilder/msmbuilder/blob/master/setup.py#L82

I'm totally up for writing a user guide or "Get started" tutorial which shows how to use moleculekit and suggesting to use ipython or jupyter.

[stefdoerr]

Updated the readme to include detailed info on installation as well as how to use with ipython
d19400a