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Release 2.2.366 #1277

Merged
merged 121 commits into from
Sep 9, 2024
Merged

Release 2.2.366 #1277

merged 121 commits into from
Sep 9, 2024

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Yuri05
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@Yuri05 Yuri05 commented Sep 9, 2024

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pchelle and others added 30 commits March 24, 2023 13:19
* Fixes #949 add new symbols to dictionary

Note that the new method leads to smaller symbols that are scaled bigger in the RE theme

* Use filled symbols by default in the configuration

* Remove dot from dictionary
* Fixes #1011 Increment version 2.1=>2.2
Fixes #1012 Exclude PRs when installing packages from the latest AppVeyour build

* adjust linter

* adjust linter

* removed lint again (not working)

---------

Co-authored-by: Yuri05 <Yuri05@github.com>
For some reason, the properties defined in color and linetype of ribbons are actually used to create the legend key even if they are not used by the ribbon itself. Using a blank linetype remove the line from the legend key.
* Fixes #1024 set showtext dpi before saving plots

* Fixes #1024 identity line is added to obs-vs-pred plots

* Fix dpi side effect

* Increase shape size

* Add margin to have prettier x/y labels

* Remove 0-fold from legend
* Fixes #932 error and warning better handled in PK Ratio task

* Add tests assessing that ill formatted PK Ratios are caught

* Fix test and provide default for other PK parameters fixing #915
)

Note that the function `getFigurePathsFromReport` is export so that users can query their report and find all the figure paths it linked
* Fixes #189 check if unit is from dimension in PkParameterInfo

* Remove unused dimension check function that already exists in ospsuite

* Unit test use character for providing unit
* Fixes #977 pie chart displayed with appropriate size

- I used the occasion to include prettier time ticks performed in the other time profile plots
- The mass balance results are obtained the same way as in the Matlab version which is not accurate (total amount should be time-dependent)

* Install ospsuite new dependency (data.table package )
* Fixes #789 include delta parameter from guest et al formula

* Throw error if parameter defined in Guest but not PKParameters

* Fixes #1041 update naming from tlf update on axis limits (#1042)
* Fixes #1049 undefined delta does not crash qualification

* Fixes #1049 handle undefined guest values in measure and caption

* Update test to account for undefined guest values

* Test that undefined null delta has same results as defining delta = 1
…es (#1058)

* Fixes #1057 special/unicode characters removed/translated in file names

* Remove greek letter test as not translated consistently

On Linux, mu seems to be read correctly and translated into u
On Windows, mu seems to be read as ? and translated as I
Locally (Windows), it is

* Test if specifying file encoding works

* Delete removeForbiddenLetters test
Actually, this was not a pandoc issue but a missing `overwrite` parameter in `copyReport()`
* Fixes #478 indicate lloq in time profiles

* Fixes #478 lloq dotted lines appear on plots

* Enforce missing lloq as numeric class preventing ggplot scale issues

* Update documentation now that lloq is handled differently
Note that word document include page break when finding the reference tag (before the figure), so figure and its caption are within the same page
* Fixes #382 document word report template

* Fixes #382 update vignette and expose html feature for word

* Fix spelling

* Update LaTeX and GitHub naming
From local tests, the html is correctly displayed in md and translated by pandoc in the docx.
@Yuri05 Let me know if this works on your side
* Fixes #1071 auto-numbering does not mess up static images

The auto-numbering algorithm for Figures assumes that the caption is below the figure. In the qualification example, it was above.
The fix renders a more robust way of including the bookmarks before the figure without needing a placeholder for the md figure inclusion line

* Remove todo comment
pchelle and others added 27 commits April 26, 2024 20:32
* Fixes #1212 download the templates within the documentation site

* Remove duplicate line that used html link
* Fixes #1209 allow different outputs for pop PK parameter plots

* Fix skip logic checking reference set data is present

* Keep reference set as first in the PK parameter summaries

* Add test for different PK parameters and output paths
* Fixes #1227 Windows build: migrate from rClr to rSharp
Fixes #1226 Failing tests under Windows with rSharp instead of rClr

* Fix remaining issues with rClr

* fix typo and extend WORDLIST

---------

Co-authored-by: Yuri05 <Yuri05@github.com>
* Fixes #1230 time offset for multiple applications is appropriate

* Add test checking time offset for multiple applications

* Replace deprecated cinst by choco install in appveyor

* Add time offset checks when creating a simulation set

* Fix call of new method in ospsuite utils

* Fix application times function with outputs as list

* endTime accounts for user-defined minimumSimulationEndTime
* Fixes #1238 minimumSimulationEndTime use base unit

* Fixes #1237 timeOffset time points are added to schema
* Fixes #1247 include guest parameter in DDI plot captions

* Update roxygen documentation
* Fixes #1252 use <br> tag instead of \n for linebreak

* Centralize caption for residuals labelling
* Fixes #1258 install dependencies from Github

* Trigger appveyor build

* Add github pat in environment

* Revert "Add github pat in environment"

This reverts commit 38e68a5.

* Check if unsetting the PAT works in using install github

* Revert "Check if unsetting the PAT works in using install github"

This reverts commit ad87b95.

* Use pak instead of remotes

* Use release archives

* zip archives are directly packages

* Download and package name should match for installation

* Use develop version for utils

* Use develop version of tlf
* Fixes #1251 Outputs grouped by groupID in time profile and residuals

* Update tests to account for new outcomes

* Add Group column in qualification simulated data.frame
* Fixes #1271 remove blanks before anchors in titles

* Remove spaces from test TOC
* Fixes #1261 throw an error if data is not utf-8 encoded

* Test dictionaries had non utf-8 characters
* Fixes #1233 details installation procedures in readme

* Noticed there was orcid for everyone, adding mine to appear in readme

* Update installation procedures
* Fixes #1274 Prevent crash of 0 simulated values in log scale

Provides a warning for such a case

* Remove the curve and legend if values are all <=0

* Update message for <=0
@Yuri05 Yuri05 requested a review from pchelle September 9, 2024 08:20
@Yuri05 Yuri05 merged commit 881c212 into main Sep 9, 2024
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3 participants