add post about isolated environments #47

kain88-de · 2017-03-25T19:57:58Z

Since the new release might break some existing scripts for users I though it was a good idea to write a post about managing different software versions. This doesn't just touch python packages anymore though.

I would appreciate some help with the virtual env because I haven't used them in ages.

kain88-de · 2017-03-27T21:00:46Z

@MDAnalysis/coredevs Anyone using virtual envs?

jbarnoud · 2017-03-27T21:07:52Z

On 03/27/2017 11:00 PM, Max Linke wrote: @MDAnalysis/coredevs <https://github.com/orgs/MDAnalysis/teams/coredevs> Anyone using virtual envs? — You are receiving this because you are on a team that was mentioned. Reply to this email directly, view it on GitHub <#47 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABUWuukCsBxODqwmvfszaV8CAtGfCZ-Kks5rqCN-gaJpZM4MpMZf>.

I do. I'll have a look at soon as I find some time. I am quite busy at the moment, though.

richardjgowers · 2017-03-28T10:52:39Z

_posts/2017-11-11-environments.md

+More information about conda environments can be found in
+the [official documentation]().
+
+# Python Virtual Environments


Can't we just leave it at conda environments?

We could. I thought it might be nice though for people who don't use conda yet. Most scientists I know go with never change a running system and are rather slow to change to anything new.

richardjgowers · 2017-03-28T10:52:56Z

_posts/2017-11-11-environments.md

+
+Virtual environments will only work for python packages.
+
+# Automatically Change Environment Based On Folder


This sounds a bit hacky and weird and probably a bad idea?

There are some packages for bash and zsh that do that. I wanted to look for them again. If I don't find them I'll remove it again

If we don't currently use them, it's probably a bad idea to advocate that people use them. I'd rather we stuck to recommending things that we know work.

orbeckst · 2017-03-29T01:01:50Z

I'd generally echo @richardjgowers advice

"I'd rather we stuck to recommending things that we know work."

You could have a See Also section at the end with links to other approaches and tools. But I would keep the main post straight and to the point.

kain88-de · 2017-04-01T08:31:05Z

@orbeckst can you have a look over it. I added a small paragraph for virtual environments now.

jbarnoud · 2017-04-01T08:42:00Z

I'll extend on the virtual envs later today. I will especially add a word on virtualenvwrapper. I may also add a word on how to load a given version of gromacs with a virtual env.

kain88-de · 2017-04-01T09:31:37Z

Thanks. I forgot about the wrapper package.

orbeckst

Generally good, nothing major. See inline for suggestions.

orbeckst · 2017-04-02T03:13:11Z

_posts/2017-11-11-environments.md

+title: Managing software versioning using Conda environments
+---
+
+Research projects can often take months to years to complete, however the


, however --> but

orbeckst · 2017-04-02T03:14:10Z

_posts/2017-11-11-environments.md

+this.  These new versions of software will often include new features which
+might be of great use, but they might also introduce changes which break
+your existing work and introduce compatibility issues with other pieces
+of software.  So whilst for existing projects we might wish to freeze


Maybe tie this to the upcoming 0.16.0 – otherwise it's not really clear why this appears in the MDAnalysis blog.

orbeckst · 2017-04-02T03:15:10Z

_posts/2017-11-11-environments.md

+use the most up-to-date versions, leaving us needing to install multiple
+versions of multiple different pieces of software.
+
+In this post we will try to explain how conda and Python virtual environments


Highlight (and omit 'try'):

In this post we will explain how conda and Python virtual environments can be

Or even better: make these links to the sections below. With the new AnchorJS extension all headings will get anchors so you just have to run locally to find the anchor name and put in a link, something like

[conda](#conda-environments)

It's not clear from here if one should use either conda or virtualenvs or both.

OK I added the link to the descriptions.

orbeckst · 2017-04-02T03:18:38Z

_posts/2017-11-11-environments.md

+{% endhighlight %}
+
+For each research project, it is advised that you create a new environment so that
+the software used in each project does interfere across different projects.


does not interfere

(omission of the crucial word "not")

orbeckst · 2017-04-02T03:20:05Z

_posts/2017-11-11-environments.md

+versions.
+
+In this guide we will concentrate only on creating and managing environments
+with conda. For more information on general installation of package please refer


For more information on installing packages please ...

orbeckst · 2017-04-02T03:22:52Z

_posts/2017-11-11-environments.md

+scientific applications. It is mostly used for Python packages but the system
+can be used with any programs. The [conda-forge](https://conda-forge.github.io/)
+community also provides a large collection of scientific software for Python, R
+and perl. Conda should be your first choice to manage different software


I don't like the "Conda should be your first choice". It seems very paternalistic. Rather something like "Conda has shown itself to be an excellent tool to manage different software versions." or "Conda is now widely used to manage different software versions." Let your readers decide for themselves if they want to use it.

richardjgowers · 2017-04-02T08:33:09Z

Ok I addressed @orbeckst 's comments, all that is left is for the virtualenv to be written to a similar spec to conda.

kain88-de · 2017-04-02T10:41:11Z

Anything else that should be done for this post?

kain88-de · 2017-04-07T15:04:53Z

If we want to release on the weekend. Everyone OK if this goes live in the evening? I would still have to change the filename for the post date.

jbarnoud · 2017-04-07T15:21:12Z

On 04/07/2017 05:04 PM, Max Linke wrote: If we want to release on the weekend. Everyone OK if this goes live in the evening? I would still have to change the filename for the post date. — You are receiving this because you are on a team that was mentioned. Reply to this email directly, view it on GitHub <#47 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABUWuppkTPWIhpb2WB4avzFjkf8UPfM1ks5rtlCWgaJpZM4MpMZf>.

I am all for it.

To complicated for our purpose

kain88-de · 2017-04-07T16:22:58Z

OK this now ok to go. I changed the date

orbeckst · 2017-04-07T18:05:18Z

@kain88-de all merged (and added missing .md suffix to file name).

Do you want to do a tweet that links to the blog post?

kain88-de · 2017-04-07T18:36:27Z

Sure I can try a first tweet.

richardjgowers reviewed Mar 28, 2017

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orbeckst mentioned this pull request Mar 29, 2017

Update 2017-11-11-environments.md #48

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orbeckst approved these changes Apr 2, 2017

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orbeckst mentioned this pull request Apr 2, 2017

Blog Post for release 0.16.0 #26

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6 tasks

kain88-de force-pushed the python-envs branch from a87e10f to 54c1d37 Compare April 4, 2017 12:32

kain88-de and others added 11 commits April 7, 2017 18:19

add post about isolated environments

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remove linux modules

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To complicated for our purpose

Update 2017-11-11-environments.md (#48)

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add virtual env description

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Update 2017-11-11-environments.md

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Update 2017-11-11-environments.md

2cf1412

expand on virtualenv (#51)

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fix up links and minor formatting

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switch language to conda OR venvs

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use conda-forge channel

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use correct blog post date

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kain88-de force-pushed the python-envs branch from 54c1d37 to 5040540 Compare April 7, 2017 16:20

add authors

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orbeckst self-assigned this Apr 7, 2017

orbeckst merged commit 3977ab4 into master Apr 7, 2017

orbeckst deleted the python-envs branch April 7, 2017 17:58

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add post about isolated environments #47

add post about isolated environments #47

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		Virtual environments will only work for python packages.

		# Automatically Change Environment Based On Folder

add post about isolated environments #47

add post about isolated environments #47

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