Add information about nest_vars.sh and update Linux installation instructions #1515

sarakonradi · 2020-04-15T09:53:11Z

This PR adds information on setting the module loading path correctly.

More specifically, it:

Adds a Setting the module loading path section below Installation from source
Removes the duplicate information in the IMPORTANT! admonition
Turns these instructions into numbered steps for a better user experience

It fixes #1222.

sarakonradi · 2020-04-15T09:58:49Z

@jougs Does this address your concern? Or do you suggest adding a section about nest_vars.sh in general, explaining all the paths that it entails?

terhorstd

added a little suggestion, but mostly fine with me. I would accept this with the changes.

I also like the idea of @sarakonradi to have a separate page explaining nest_vars.sh, that could be about general environment handling containing also the cases where nest_vars.sh is not needed when installing into a $CONDA_PREFIX or when it is replaced by a module load type of setup, etc. That should be a separate PR, however.

doc/installation/linux_install.rst

clinssen · 2020-04-22T08:42:53Z

@sarakonradi: could you set this PR to draft mode?

Waiting for my PR on @sarakonradi's fork to be merged (see https://github.com/sarakonradi/nest-simulator/pull/2/files) following updates in #1513.

Please feel free to leave any comments/suggestions there!

sarakonradi · 2020-04-22T09:22:55Z

@clinssen Sure! Just set it to draft mode.

It seems that your PR still includes the old information. For example, Python has been changed to Python 3.X and NEST requires at least version v2.8.12 of cmake has been updated to NEST requires CMake 3.12 or higher: https://github.com/nest/nest-simulator/blob/master/doc/installation/linux_install.rst

Could you perhaps merge master again and then let me know?

sarakonradi · 2020-04-22T10:28:40Z

@clinssen Thanks for rebasing. Just merged your PR and will keep an eye on #1513.

doc/installation/linux_install.rst

…stall.rst Co-Authored-By: Jochen Martin Eppler <[email protected]>

…all.rst Co-Authored-By: Jochen Martin Eppler <[email protected]>

Co-Authored-By: Jochen Martin Eppler <[email protected]>

…r into fix_issue_1222

sarakonradi · 2020-04-28T10:21:25Z

Very nice, thanks! I still have some suggestions for you to consider.

Thanks for your suggestions! Just applied them. I also fixed the merge conflict. doc/installation/linux_install.rst now includes the note on python bindings being enabled by default (#1507).

@jougs @terhorstd Please check!

jougs

LGTM!

clinssen

Many thanks!

jougs · 2020-05-07T00:52:40Z

@terhorstd are you also happy? If yes, please also click the button. Thanks!

doc/installation/linux_install.rst

sarakonradi · 2020-05-20T10:28:26Z

@terhorstd I created a separate issue (#1612) to address your concern regarding the dependencies file.

terhorstd

This PR does a lot more changes than adding information about nest_vars.sh, it basically reworks the Linux install instructions.

doc/installation/linux_install.rst

Co-authored-by: terhorstd <[email protected]>

sarakonradi · 2020-05-20T11:07:49Z

Added the information on Boost, as suggested by @terhorstd.

This PR does a lot more changes than adding information about nest_vars.sh, it basically reworks the Linux install instructions.

This is a classic instance of a PR evolving (more than it should) over time. As discussed in the doc meeting, it is best to keep future PRs small! Should we rename it or keep the title?

clinssen · 2020-06-15T10:42:53Z

Would propose to update the title and merge this so we can move on.

sarakonradi · 2020-06-15T14:17:57Z

Would propose to update the title and merge this so we can move on.

Done.

jougs · 2020-06-15T20:17:03Z

I totally agree that we should merge this one now and suggest to mark up the remarks in a next step, which should probably also check if they are still valid, some of them seem quite outdated...

@terhorstd: can you have a final look and push the button if you're happy?

sarakonradi added 3 commits April 15, 2020 11:12

Add module loading path subheading

d4c52cb

Add module path information

8918bb8

Update nest_vars.sh section

c634598

sarakonradi requested a review from jougs April 15, 2020 09:53

sarakonradi mentioned this pull request Apr 15, 2020

Final checks of documentation #1445

Closed

24 tasks

sarakonradi self-assigned this Apr 15, 2020

sarakonradi changed the title ~~Add information on setting NEST_MODULE_PATH by sourcing nest_vars.sh~~ Add information about nest_vars.sh to documentation Apr 15, 2020

sarakonradi mentioned this pull request Apr 15, 2020

Avoid naming conflicts by installing shared objects to lib/nest instead of lib #1513

Merged

heplesser requested review from heplesser, clinssen and terhorstd and removed request for jougs and heplesser April 20, 2020 08:47

heplesser added I: No breaking change Previously written code will work as before, no one should note anything changing (aside the fix) S: Normal Handle this with default priority T: Enhancement New functionality, model or documentation labels Apr 20, 2020

heplesser added this to the NEST 3.0 milestone Apr 20, 2020

update documentation of nest_vars.sh

e317788

terhorstd requested changes Apr 22, 2020

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sarakonradi marked this pull request as draft April 22, 2020 09:14

clinssen and others added 2 commits April 22, 2020 11:43

manual rebase linux_install.rst on latest master branch

e139456

Merge pull request #2 from clinssen/update_nest_vars_doc

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clinssen reviewed Apr 22, 2020

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sarakonradi and others added 7 commits April 28, 2020 11:58

Update environment variables information in doc/installation/linux_in…

df499ae

…stall.rst Co-Authored-By: Jochen Martin Eppler <[email protected]>

Update "environment variables" section in doc/installation/linux_inst…

517debf

…all.rst Co-Authored-By: Jochen Martin Eppler <[email protected]>

Update shell script information in doc/installation/linux_install.rst

592f5c0

Co-Authored-By: Jochen Martin Eppler <[email protected]>

Apply remaining suggestions to doc/installation/linux_install.rst

e028e6d

Co-Authored-By: Jochen Martin Eppler <[email protected]>

Fix conflict in doc/installation/linux_install.rst

30a924a

Merge branch 'fix_issue_1222' of github.com:sarakonradi/nest-simulato…

636b03a

…r into fix_issue_1222

Update note format in doc/installation/linux_install.rst

fd1cb9c

jougs approved these changes Apr 29, 2020

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sarakonradi added 2 commits May 4, 2020 10:20

Refer to 'Environment variables' section, as suggested by @clinssen

7675fd6

Update install path, as suggested by @clinssen

16a9e5f

clinssen approved these changes May 6, 2020

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Merge branch 'master' into fix_issue_1222

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terhorstd reviewed May 20, 2020

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sarakonradi mentioned this pull request May 20, 2020

Collect dependencies in central file #1612

Closed

terhorstd requested changes May 20, 2020

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Add information on Boost

b8298ed

Co-authored-by: terhorstd <[email protected]>

sarakonradi changed the title ~~Add information about nest_vars.sh to documentation~~ Add information about nest_vars.sh and update Linux installation instructions Jun 15, 2020

sarakonradi requested a review from terhorstd June 15, 2020 14:18

jougs removed the request for review from terhorstd June 15, 2020 20:15

terhorstd approved these changes Jun 16, 2020

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terhorstd merged commit b284961 into nest:master Jun 16, 2020

sarakonradi deleted the fix_issue_1222 branch September 21, 2020 08:44

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Add information about nest_vars.sh and update Linux installation instructions #1515

Add information about nest_vars.sh and update Linux installation instructions #1515

sarakonradi commented Apr 15, 2020

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jougs commented Jun 15, 2020

Add information about nest_vars.sh and update Linux installation instructions #1515

Add information about nest_vars.sh and update Linux installation instructions #1515

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