Edits to User Guide documentation #995

atravitz · 2024-10-31T22:13:49Z

Edits just to the top level and Setup section. Further edits for other sections (and to update graphics) will follow in later PRs.

Developers certificate of origin

[x ] I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

codecov · 2024-10-31T22:22:20Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.84%. Comparing base (4c06370) to head (6e44bfb).
Report is 26 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #995      +/-   ##
==========================================
- Coverage   94.59%   92.84%   -1.76%     
==========================================
  Files         134      134              
  Lines        9940     9940              
==========================================
- Hits         9403     9229     -174     
- Misses        537      711     +174

Flag	Coverage Δ
fast-tests	`92.84% <ø> (?)`
slow-tests	`?`

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

IAlibay

I'm going to put a block here because it looks like some of the things here will need some discussion / will have differing views.

docs/guide/results/index.rst

docs/guide/setup/alchemical_network_model.rst

docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst

docs/guide/setup/creating_atom_mappings_and_scores.rst

docs/guide/setup/defining_protocols.rst

docs/guide/setup/index.rst

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

ijpulidos

Much clearer and concise, great work! I just added some comments.

docs/guide/introduction.rst

docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst

docs/guide/setup/creating_atom_mappings_and_scores.rst

docs/guide/setup/creating_ligand_networks.rst

docs/guide/setup/index.rst

hannahbaumann

Thank for you all your work on this @atravitz , this looks great overall! Just left a few suggestions!

docs/guide/setup/alchemical_network_model.rst

docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst

docs/guide/setup/defining_protocols.rst

Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>

atravitz

@IAlibay A couple items I addressed but you should take one more look at. I think we need to revisit the ligand network section as a whole. Maybe a follow-up PR?

docs/guide/introduction.rst

docs/guide/setup/index.rst

docs/guide/setup/creating_atom_mappings_and_scores.rst

atravitz · 2024-11-12T23:09:58Z

docs/guide/setup/creating_atom_mappings_and_scores.rst

+The :func:`default_lomap_score` function combines several criteria
+(such as the number of heavy atoms, if certain chemical changes are present,
+and if ring sizes are being mutated), into a single value.
+It is possible to combine scoring functions in this way because each scoring function returns a normalized value.


let me know if this is better.

docs/guide/setup/defining_protocols.rst

docs/guide/setup/alchemical_network_model.rst

docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst

docs/guide/setup/creating_atom_mappings_and_scores.rst

docs/guide/troubleshooting.rst

mikemhenry · 2024-11-13T19:06:23Z

+1 to removing see also from the TOC but keeping that section on the page

mikemhenry · 2024-11-13T19:07:14Z

same with references

mikemhenry · 2024-11-13T19:16:02Z

Also while we are at it, I think we should have a call to action on this page:
https://openfe--995.org.readthedocs.build/en/995/guide/introduction.html

In between the Introduction and Workflow overview section as a .. note:: that is something like "If you have used openfe, please use this citation xxx." I think some sentence about also sponsoring the project would be good as well.

Also also, feel free to just convert this comment into an issue if you think it warrants further discussion and/or is outside the scope of the PR.

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

hannahbaumann

Thanks, lgtm!

atravitz added 4 commits October 31, 2024 13:30

adding cross-page references

4b90b00

setup index edits

22d9751

edits to chemical systems docs

1cca068

edits to atom mappings and scores

5173b30

atravitz and others added 6 commits November 1, 2024 12:45

formatting fixes to atom mappings

4982c71

updating protocol user guide docs

4544d60

edits to ligand networks guide

52ff058

edits to alchemical network planners

fae1a9d

remove accidentally added .pngs

9fd6757

Merge branch 'main' into docs_user_guide_edits

2ae25f1

atravitz marked this pull request as ready for review November 1, 2024 21:38

atravitz requested a review from mikemhenry November 1, 2024 21:39

IAlibay requested changes Nov 5, 2024

View reviewed changes

atravitz and others added 2 commits November 5, 2024 14:33

Update docs/guide/setup/defining_protocols.rst

e192696

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

Update docs/guide/setup/index.rst

e2c6c4e

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

ijpulidos reviewed Nov 8, 2024

View reviewed changes

hannahbaumann requested changes Nov 11, 2024

View reviewed changes

atravitz and others added 10 commits November 12, 2024 11:07

adding links to introduction

0b2978d

Apply suggestions from code review

3895871

Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

Merge branch 'main' into docs_user_guide_edits

8ad09d1

Apply suggestions from code review

5a7737c

Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>

fixing bash rendering

83d1093

fixing typo

360e317

making language clearer

93eb486

making protocol description clearer

10e13e7

renaming to Results Gathering

96cb6f1

back to bold

6dcf884

atravitz commented Nov 13, 2024

View reviewed changes

mikemhenry reviewed Nov 13, 2024

View reviewed changes

docs/guide/setup/creating_atom_mappings_and_scores.rst Outdated Show resolved Hide resolved

mikemhenry reviewed Nov 13, 2024

View reviewed changes

docs/guide/troubleshooting.rst Outdated Show resolved Hide resolved

mikemhenry approved these changes Nov 13, 2024

View reviewed changes

atravitz and others added 2 commits November 14, 2024 12:53

making warning more visible

0c8f130

Apply suggestions from code review

4273a36

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

hannahbaumann approved these changes Nov 15, 2024

View reviewed changes

Merge branch 'main' into docs_user_guide_edits

6e44bfb

atravitz merged commit 9b0b4b2 into main Nov 15, 2024
11 checks passed

atravitz deleted the docs_user_guide_edits branch November 15, 2024 14:57

atravitz mentioned this pull request Nov 15, 2024

More user guide edits #1018

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Edits to User Guide documentation #995

Edits to User Guide documentation #995

atravitz commented Oct 31, 2024 •

edited

Loading

codecov bot commented Oct 31, 2024 •

edited

Loading

IAlibay left a comment

ijpulidos left a comment

hannahbaumann left a comment

atravitz left a comment

atravitz Nov 12, 2024

mikemhenry commented Nov 13, 2024

mikemhenry commented Nov 13, 2024

mikemhenry commented Nov 13, 2024

hannahbaumann left a comment

Edits to User Guide documentation #995

Edits to User Guide documentation #995

Conversation

atravitz commented Oct 31, 2024 • edited Loading

Developers certificate of origin

codecov bot commented Oct 31, 2024 • edited Loading

Codecov Report

IAlibay left a comment

Choose a reason for hiding this comment

ijpulidos left a comment

Choose a reason for hiding this comment

hannahbaumann left a comment

Choose a reason for hiding this comment

atravitz left a comment

Choose a reason for hiding this comment

atravitz Nov 12, 2024

Choose a reason for hiding this comment

mikemhenry commented Nov 13, 2024

mikemhenry commented Nov 13, 2024

mikemhenry commented Nov 13, 2024

hannahbaumann left a comment

Choose a reason for hiding this comment

atravitz commented Oct 31, 2024 •

edited

Loading

codecov bot commented Oct 31, 2024 •

edited

Loading