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Updates to Docs#970

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dwhswenson merged 20 commits into
openpathsampling:masterfrom
dwhswenson:docs
Jun 11, 2021
Merged

Updates to Docs#970
dwhswenson merged 20 commits into
openpathsampling:masterfrom
dwhswenson:docs

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@dwhswenson

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Includes some new files:

  • A discussion of ways to contribute; trying to discourage people from just modifying existing things in a breaking way in their own forks; and encouraging development of plugins as well as direct contributions to core
  • A list of projects in the "OPS Ecosystem", i.e., various codes that have not been included in the core of OPS but which might be useful. Includes several completed E-CAM modules, as well as some of my own side projects.
  • A new "Getting Help" section. NOTE: New policy! Please post usage questions at http://mattermodeling.stackexchange.com, using the tag openpathsampling (and any other tags that are relevant). If you already have a StackOverflow account, its basically a click to join. This allows GitHub Issues to focus on bugs, etc., and hopefully solicits help from others, as well.

This PR also updates links to repos that have moved from E-CAM's GitLab to GitHub (and can now be launched with binder!)

Unfortunately, we don't have docs deployment in CI yet, after the switchover from Travis. I'll probably hold off on merge until I can deploy, but please do read over the additions and let me know what you think.

@codecov

codecov Bot commented Jan 30, 2021

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Codecov Report

Merging #970 (6770376) into master (4a12af0) will not change coverage.
The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #970   +/-   ##
=======================================
  Coverage   81.30%   81.30%           
=======================================
  Files         139      139           
  Lines       15150    15150           
=======================================
  Hits        12317    12317           
  Misses       2833     2833           
Impacted Files Coverage Δ
openpathsampling/__init__.py 100.00% <ø> (ø)
openpathsampling/pathmover.py 84.91% <ø> (ø)
openpathsampling/collectivevariables/__init__.py 100.00% <100.00%> (ø)
...pathsampling/collectivevariables/plumed_wrapper.py 100.00% <100.00%> (ø)

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@dwhswenson dwhswenson added docs issues/PRs related to documentation misc PR labels Jan 31, 2021

@sroet sroet left a comment

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Looks reasonable to me, a couple points:

  • all http should be changed to https
  • how are we (maintainers/devs/expercienced users) supposed to keep track of the new question channel on mattermodeling.stackexchange.com?
  • For the binder links it would be nice if they were uniform, either jupyter or jupyter-lab

Comment thread docs/developers/general_advice.rst Outdated
Comment thread docs/developers/general_advice.rst Outdated
Comment thread docs/examples/index.rst Outdated
Comment thread docs/examples/index.rst
Comment thread docs/getting_help.rst Outdated
Comment thread docs/getting_help.rst Outdated
Comment thread docs/examples/index.rst
Co-authored-by: Sander Roet <sanderroet@hotmail.com>
@dwhswenson

dwhswenson commented Feb 2, 2021

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From a review comment from @sroet (buried in a resolved conversation), regarding the OPS tag on http://mattermodeling.stackexchange.com:

Also, how can we (as experienced users) sign up for email updates on these tags?

A couple options for subscribing, from the current StackExchange UI:

  1. Create a custom filter notification. Filter on the openpathsampling tag to create a filter for all questions tagged with openpathsampling across the entire StackExchange network (obviously, there's only one site with that tag right now). Choose email notifications to get the email. You can narrow by site (if, for example, you wanted to see python-tagged questions on mattermodeling.SE without drowning in the firehose from SO).

  2. You can also subscribe to any tag with RSS: On any question that has a given tag, hover over the tag. At the top-right of the thing that appears on hover, you'll see the RSS icon. Click on that to get the URL for an RSS feed for that tag on that site (gives more flexibility in how to manage notifications than email).

(Note: the only question currently tagged with openpathsampling is a placeholder so the tag doesn't get auto-deleted -- it isn't related to OPS. Over the weekend I answered good questions from emails from a couple users and I've asked them to re-post there. So I hope we'll see a few real questions soon.)

@dwhswenson

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This is ready for review and comment. I will leave it open for at least 24 hours, merging no earlier than Thu 10 Jun 18:00 GMT (14:00 my local).

I've tested the new deploy_docs workflow within the docs_deploy branch -- it works, as can been seen at this actions link (for the next 90 days), or simply from the fact that openpathsampling.org is reporting OPS version 1.4.3.dev0 as the latest development version (as opposed to 1.4.1.dev0, as it was before).

Thanks to @jchodera for meeting this morning to get the AWS stuff set up!

@dwhswenson dwhswenson merged commit aaff2b8 into openpathsampling:master Jun 11, 2021
@dwhswenson dwhswenson deleted the docs branch June 11, 2021 02:51
@jchodera

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@dwhswenson Did it work?

@dwhswenson

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@jchodera : Yep -- everything went perfectly smoothly. Thanks again for your help!

I added a new workflow to handle building/deploying docs. This will replace our old after_success script, and will allow us to have better control over when we want to build/deploy docs. That's the only place the new env secrets need to be used. This also adds extra security: a breach like the CodeCov breach should not affect the AWS secrets, because they're not used in the same workflow step (or even the same workflow). The same was true of our PyPI secrets -- although I rotated them after the CodeCov breach anyway.

@dwhswenson dwhswenson mentioned this pull request Jul 5, 2021
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