edited conda.md file

[kvale]

This is a nicely written howto guide! But the module conflicts with my already-installed anaconda distribution so I have not tested any of the commands.

I did some copyediting and clarification (at least IMO).

Here are a few comments:

1. You all mention that an environment should be kept updated, but don't describe the update commands.

2. Why doesn't the command prompt show (base) while in the base environment?

3. I'd put a link to a Conda cheatsheet toward the end of the document, such as https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf

[HenrikBengtsson]

Thanks a bunch for this.

1. You all mention that an environment should be kept updated, but don't describe the update commands.
2. I'd put a link to a Conda cheatsheet toward the end of the document, ...

Both tracked in Issue #90.

2. Why doesn't the command prompt show (base) while in the base environment?

Good point

Turns out that the 'base' environment is activated by default. This is a good property, because having the 'base' environment always activated (which most users have when they install Conda themselves), causes a lot of silent and noisy conflicts with core and module software stacks.

The following shows that 'base' is not activated when the module is loaded:

[hb-test@dev2 ~]$ module purge
[hb-test@dev2 ~]$ module load CBI miniconda3-py39/.4.12.0
[hb-test@dev2 ~]$ [hb-test@dev2 ~]$ conda info

     active environment : None
            shell level : 0
       user config file : /wynton/home/bengtsson/hb-test/.condarc
 populated config files : /wynton/home/cbi/shared/software/CBI/miniconda3-py39-4.12.0/.condarc
                          /wynton/home/bengtsson/hb-test/.condarc
          conda version : 4.12.0
...

One needs to manually activate it, e.g.

[hb-test@dev2 ~]$ conda activate base
(base) [hb-test@dev2 ~]$

but, ideally, people will always work with one of their own custom environments.