Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Pull request #37: Added documentation. Added RandomFields data sets. Fixed R CMD issues #51

Merged
merged 2 commits into from
Feb 9, 2024
Merged

Pull request #37: Added documentation. Added RandomFields data sets. Fixed R CMD issues #51

merged 2 commits into from
Feb 9, 2024

Conversation

sciome-bot
Copy link
Collaborator

No description provided.

@shail-choksi
Pull request #37: Added documentation. Added RandomFields data sets. …
076c0a1 
…Fixed R CMD issues

Merge in STAT/prestogp from master to to-git

Squashed commit of the following:

commit 7e330f30a659c579a3f291bc65c7918b9859c619
Merge: 13a6f44 f49d076
Author: sciome-bot <software.tools@sciome.com>
Date:   Wed Feb 7 23:25:05 2024 -0500

    Merge branch 'master' of ssh://sciome-bot/stat/prestogp

commit f49d0769a892df5dd711a2f8ebe08a3f9ca7af7b
Merge: 439790c 59baf72
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Feb 7 23:19:54 2024 -0500

    Pull request #35: Eb dev

    Merge in STAT/prestogp from eb-dev to master

    * commit '59baf720737abe59a04c98705c950ef1c7b63321':
      Fixed some documentation issues
      Removed C++11 compiler flag
      Added RandomFields data sets to PrestoGP
      Added knitr to Suggests in DESCRIPTION
      Documentation, R-cmd-check fixes, binomial regression

commit 59baf720737abe59a04c98705c950ef1c7b63321
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Feb 6 17:49:48 2024 -0500

    Fixed some documentation issues

commit d857d8b367e3b46581677c4925ba8617f462c4d5
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 1 02:16:44 2024 -0500

    Removed C++11 compiler flag

commit 662907d9e98a20ad06602c0dfe7e81b6390e3485
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 15:36:37 2024 -0500

    Added RandomFields data sets to PrestoGP

commit cf2aadb50ecebd9e2f4401493da6901f10ee993a
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 13:40:24 2024 -0500

    Added knitr to Suggests in DESCRIPTION

commit ef5f2c9145d481e4e24a98792913830d449cba86
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 01:31:53 2024 -0500

    Documentation, R-cmd-check fixes, binomial regression

commit 13a6f449d324e19f61d7e29797fc23c65ec020b8
Merge: 439790c 8ffb20b
Author: sciome-bot <software.tools@sciome.com>
Date:   Sun Jan 14 11:46:17 2024 -0500

    Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP

commit 439790cb0d96d85e80a3782ad533eee78afe41dc
Merge: f4af0d1 56f881f
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sun Jan 14 10:58:49 2024 -0500

    Pull request #32: Fixed some testthat issues

    Merge in STAT/prestogp from eb-dev to master

    * commit '56f881f96a0e55e60bca3c8a840ec31291665594':
      Fixed some testthat issues

commit 56f881f96a0e55e60bca3c8a840ec31291665594
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 14:05:12 2024 -0500

    Fixed some testthat issues

commit f4af0d1be3490dd2edd4f4fd0ae97bf729464748
Merge: db6cd4f ee193de
Author: sciome-bot <software.tools@sciome.com>
Date:   Sat Jan 13 12:37:28 2024 -0500

    Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP

commit db6cd4f6f86e760ee8393adf224cd0231ccde8cf
Merge: 55607e2 7da2588
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 12:11:56 2024 -0500

    Pull request #29: Fixed some bugs caused by the linter

    Merge in STAT/prestogp from eb-dev to master

    * commit '7da2588abba4491c1ff490de95e834d00f5df88e':
      Fixed some bugs caused by the linter

commit 7da2588abba4491c1ff490de95e834d00f5df88e
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 01:37:58 2024 -0500

    Fixed some bugs caused by the linter

commit 55607e291477d174b8323bf258a8e9aa5c4db84c
Merge: c7ed481 81b675d
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Fri Jan 12 19:37:55 2024 -0500

    Pull request #28: Final linting fixes

    Merge in STAT/prestogp from build-workflow to master

    * commit '81b675dda9b57f2a362c34876364adf5bcf45560':
      Fix remaining linting issues
      Fix all indentation errors
      Add indentation_linter configuration to lintr config file

commit 81b675d
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 19:36:05 2024 -0500

    Fix remaining linting issues

commit 06673a4
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 19:23:11 2024 -0500

    Fix all indentation errors

commit c7ed481479c2ca5a4fc111f429affd01b6c3ce53
Merge: 723c3eb 7bcfa1a
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Fri Jan 12 19:02:59 2024 -0500

    Pull request #27: Lintr fixes. Added release and sanitizer actions

    Merge in STAT/prestogp from build-workflow to master

    * commit '7bcfa1aca78cc6b994cc0227c083357c58d50ca0': (21 commits)
      Add R_LINTR_LINTER_FILE to lint action to point to global .lintr file
      More lintr fixes for 1:length, 1:nrow and line length. Disabled object_length_linter
      WIP: Fix linter warnings for 1:nrow, 1:ncol and 1:length. Increase line length to 160 chars
      Don't build vignettes during the release action
      Move release action file to correct directory
      Add release action
      Reorder imports in RcppExports file
      Add missing dependency in Namespace/Description
      Remove unneeded exports from NAMESPACE
      Add missing comma in Imports section of DESCRIPTION
      Add missing comma in imports section of DESCRIPTION
      Rerun auto-formatter
      WIP - linting
      Add ignore rules for .lintr and .github for R build
      remove linter options from lint action as we have added .lintr project file. Fix all vector_logic_linter warnings
      Remove line length linter to see the remaining errors/warnings
      workaround for lintr bug: REditorSupport/languageserver#89
      Run auto-lint on vscode
      enable linting on build-workflow
      Add missing imports in DESCRIPTION
      ...

commit 29d82cd
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 18:40:17 2024 -0500

    Add indentation_linter configuration to lintr config file

commit 7bcfa1a
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 18:16:01 2024 -0500

    Add R_LINTR_LINTER_FILE to lint action to point to global .lintr file

commit b6df473
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 17:54:50 2024 -0500

    More lintr fixes for 1:length, 1:nrow and line length. Disabled object_length_linter

... and 21 more commits
@codecov Codecov
Copy link

codecov bot commented Feb 8, 2024 •
edited
Loading

Codecov Report

Attention: 16 lines in your changes are missing coverage. Please review.

Comparison is base (8ffb20b) 78.98% compared to head (95fef8c) 82.14%.
Report is 6 commits behind head on main.

Files Patch % Lines
R/PrestoGP_Util_Functions.R 74.07% 7 Missing ⚠️
R/PrestoGP_Model.R 78.57% 6 Missing ⚠️
R/PrestoGP_Multivariate_Vecchia.R 66.66% 2 Missing ⚠️
R/PrestoGP_CreateU_Multivariate.R 85.71% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main      #51      +/-   ##
==========================================
+ Coverage   78.98%   82.14%   +3.15%     
==========================================
  Files           9        9              
  Lines        1280     1271       -9     
==========================================
+ Hits         1011     1044      +33     
+ Misses        269      227      -42

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

This was linked to issues Feb 8, 2024
Duplicated locs can cause numeric issues #47
Closed
Documentation needed for core PrestoGP functions #19
Closed
@ericbair-sciome
Copy link
Collaborator

It looks like our bot automatically created this pull request. The main three changes in this version are the following:

  1. Documentation now exists for all user-facing functions.
  2. R CMD check should be passing. (It looks like the vignette is causing it to fail on the GitHub server. I created an issue about that.)
  3. Binomial regression is now implemented.

There are a few other minor optimizations and bug fixes as well. It looks like I accidentally created a few lint issues while doing this. I will try to push a quick patch to fix those.

@kyle-messier kyle-messier self-requested a review February 8, 2024 14:00
kyle-messier
kyle-messier approved these changes Feb 8, 2024
View reviewed changes
Copy link
Collaborator

@kyle-messier kyle-messier left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@ericbair-sciome @shail-choksi Thanks for the pushes moving this closer to being ready for primetime! I would say go ahead and merge, then remove the vignette causing R-CMD build issues. Then I can add the R-CMD-build as a test requirement. Thanks for adding the logistic regression. In the near future I'll start reviewing documentation as I start the pesticide analysis.

@sciome-bot
Pull request #39: Removed test vignette, fixed lint issues
95fef8c 
Merge in STAT/prestogp from master to to-git

Squashed commit of the following:

commit bab8357d1f3cdc45ab38110355cc6d106dba8440
Merge: 55c0e8e 5394772
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:19:24 2024 -0500

    Pull request #38: Removed vignette, fixed lint issues

    Merge in STAT/prestogp from eb-dev to master

    * commit '53947729624b47fa1920ef39bd23d86f6e5cd7b7':
      Removed vignette, fixed lint issues

commit 55c0e8e5ed2e189876c39d9e2337b51020b6505b
Merge: 7e330f3 076c0a1
Author: sciome-bot <software.tools@sciome.com>
Date:   Thu Feb 8 14:18:48 2024 -0500

    Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP

commit 53947729624b47fa1920ef39bd23d86f6e5cd7b7
Merge: b431df4 7e330f3
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 14:07:54 2024 -0500

    Resolved merge conflict

commit b431df45c0f80a54451536033c355b47620f3077
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 8 13:56:38 2024 -0500

    Removed vignette, fixed lint issues

commit 7e330f30a659c579a3f291bc65c7918b9859c619
Merge: 13a6f44 f49d076
Author: sciome-bot <software.tools@sciome.com>
Date:   Wed Feb 7 23:25:05 2024 -0500

    Merge branch 'master' of ssh://sciome-bot/stat/prestogp

commit f49d0769a892df5dd711a2f8ebe08a3f9ca7af7b
Merge: 439790c 59baf72
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Feb 7 23:19:54 2024 -0500

    Pull request #35: Eb dev

    Merge in STAT/prestogp from eb-dev to master

    * commit '59baf720737abe59a04c98705c950ef1c7b63321':
      Fixed some documentation issues
      Removed C++11 compiler flag
      Added RandomFields data sets to PrestoGP
      Added knitr to Suggests in DESCRIPTION
      Documentation, R-cmd-check fixes, binomial regression

commit 59baf720737abe59a04c98705c950ef1c7b63321
Author: Eric Bair <eric.bair@sciome.com>
Date:   Tue Feb 6 17:49:48 2024 -0500

    Fixed some documentation issues

commit d857d8b367e3b46581677c4925ba8617f462c4d5
Author: Eric Bair <eric.bair@sciome.com>
Date:   Thu Feb 1 02:16:44 2024 -0500

    Removed C++11 compiler flag

commit 662907d9e98a20ad06602c0dfe7e81b6390e3485
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 15:36:37 2024 -0500

    Added RandomFields data sets to PrestoGP

commit cf2aadb50ecebd9e2f4401493da6901f10ee993a
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 13:40:24 2024 -0500

    Added knitr to Suggests in DESCRIPTION

commit ef5f2c9145d481e4e24a98792913830d449cba86
Author: Eric Bair <eric.bair@sciome.com>
Date:   Wed Jan 31 01:31:53 2024 -0500

    Documentation, R-cmd-check fixes, binomial regression

commit 13a6f449d324e19f61d7e29797fc23c65ec020b8
Merge: 439790c 8ffb20b
Author: sciome-bot <software.tools@sciome.com>
Date:   Sun Jan 14 11:46:17 2024 -0500

    Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP

commit 439790cb0d96d85e80a3782ad533eee78afe41dc
Merge: f4af0d1 56f881f
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sun Jan 14 10:58:49 2024 -0500

    Pull request #32: Fixed some testthat issues

    Merge in STAT/prestogp from eb-dev to master

    * commit '56f881f96a0e55e60bca3c8a840ec31291665594':
      Fixed some testthat issues

commit 56f881f96a0e55e60bca3c8a840ec31291665594
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 14:05:12 2024 -0500

    Fixed some testthat issues

commit f4af0d1be3490dd2edd4f4fd0ae97bf729464748
Merge: db6cd4f ee193de
Author: sciome-bot <software.tools@sciome.com>
Date:   Sat Jan 13 12:37:28 2024 -0500

    Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP

commit db6cd4f6f86e760ee8393adf224cd0231ccde8cf
Merge: 55607e2 7da2588
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 12:11:56 2024 -0500

    Pull request #29: Fixed some bugs caused by the linter

    Merge in STAT/prestogp from eb-dev to master

    * commit '7da2588abba4491c1ff490de95e834d00f5df88e':
      Fixed some bugs caused by the linter

commit 7da2588abba4491c1ff490de95e834d00f5df88e
Author: Eric Bair <eric.bair@sciome.com>
Date:   Sat Jan 13 01:37:58 2024 -0500

    Fixed some bugs caused by the linter

commit 55607e291477d174b8323bf258a8e9aa5c4db84c
Merge: c7ed481 81b675d
Author: Shail Choksi <shail.choksi@sciome.com>
Date:   Fri Jan 12 19:37:55 2024 -0500

    Pull request #28: Final linting fixes

    Merge in STAT/prestogp from build-workflow to master

    * commit '81b675dda9b57f2a362c34876364adf5bcf45560':
      Fix remaining linting issues
      Fix all indentation errors
      Add indentation_linter configuration to lintr config file

commit 81b675d
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 19:36:05 2024 -0500

    Fix remaining linting issues

commit 06673a4
Author: sciome-bot <software.tools@sciome.com>
Date:   Fri Jan 12 19:23:11 2024 -0500

    Fix all indentation errors

... and 25 more commits
@ericbair-sciome ericbair-sciome linked an issue Feb 8, 2024 that may be closed by this pull request
Vignette is causing R CMD check to fail #52
Closed
@ericbair-sciome
Copy link
Collaborator

I pushed a minor fix this morning that removed the vignette and fixed a couple linting issues that I overlooked. It looks like all of our tests are passing now. Hooray!

@kyle-messier
Copy link
Collaborator

@sciome-bot @ericbair-sciome @shail-choksi @sigmafelix @brian-bk22
image

@kyle-messier
Copy link
Collaborator

@shail-choksi @ericbair-sciome Y'all can merge!

@sciome-bot sciome-bot merged commit 07de767 into main Feb 9, 2024
7 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@kyle-messier kyle-messier kyle-messier approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
4 participants
@sciome-bot @ericbair-sciome @kyle-messier @shail-choksi