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V6.3.3 dev #401

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StuartWheater merged 58 commits intodatashield:v6.3.4-devfrom
villegar:v6.3.3-dev
Jul 25, 2025
Merged

V6.3.3 dev #401
StuartWheater merged 58 commits intodatashield:v6.3.4-devfrom
villegar:v6.3.3-dev

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@villegar villegar commented Jul 24, 2025

This pull request mainly adds a couple of workflow files to be used with Github Actions:

  • dsBase_test_suite.yaml: checks, tests and deploys report onto datashield/testStatus
  • pkgdown.yaml: builds and deploys website with documentation for the package
  • Add skip_on_os("mac", arch = "aarch64") to skip test on macOS when running on ARM architecture (unresolved issue)

villegar added 30 commits July 21, 2025 13:30
@villegar
Skip these tests on Apple M1 architecture, unresolved issue
918477c
@villegar
Add CRAN release badge, title, installation instructions and references
a1f1178
@villegar
Correct title and citation for main package
5582620
@villegar
Add new workflow based on old azure-pipelines.yml file
c5088ce
@villegar
Update token variable name
1a24b75
@villegar
Replace test_package call by test_local
74a120b
@villegar
Use r-lib custom actions to setup deployment environment and customis…
408a736 
…e the location of logs
@villegar
Install missing package to run checks and tests
06daac3
@villegar
Add missing environment variable
4ead1cf
@villegar
Add step with new approach to install devtools
a4f0077
@villegar
Add missing workind directory
d66c37a
@villegar
Simplify workflow removing unnecessary step
a8269e5
@villegar
Remove additional double quote mark
f489302
@villegar
Ammend wrong file path and add commands to check current file tree
7a81c04
@villegar
Replace the location of testStatus for development purposes
a21b0c4
@villegar
Update path ../logs >>> logs
f5ac4bc
@villegar
Update working directories
5d2c5cd
@villegar
Update git config command and paths to local files
4cfa058
@villegar
Rename workflow and update documentation
b872950
@villegar
Add recursive and verbose flags to cp command
0b8a9c6
@villegar
Simplify copying command for log files
b8c437d
@villegar
Update user.name for git push
a51f681
@villegar
Rename branchName >> BRANCH_NAME
d961ac0
@villegar
Rename environment variables from cammel case to all upper case and a…
2c11650 
…dd new REPO_OWNER variable
@villegar
Ammend token secret variable name and structure of files
b5eada4
@villegar
Update location of symbolic link
9a47b4d
@villegar
Test a new way to get GitHub authentication token
6680411
@villegar
Revert to secrets.DATASHIELD_DEV for token
4023d03
@villegar
Change function call for tests: testthat::test_local >> testthat::tes…
152de9b 
…t_package
@villegar
Add GHA workflow for deployment of package documentation website gene…
678940b 
…rated with pkgdown
villegar and others added 21 commits July 23, 2025 12:36
@villegar
Revert changes with single/double quotes surrounding code snip
d755066
@villegar
Merge branch 'datashield:v6.3.3-dev' into v6.3.3-dev
674ad9b
@villegar
Regenerate documentation with pkgdown::build_site()
e41608d
@villegar
Merge conflicting changes
d22f91f 
Merge remote-tracking branch 'refs/remotes/origin/v6.3.3-dev' into v6.3.3-dev

# Conflicts:
#	docs/authors.html
#	docs/pkgdown.yml
@villegar
Remove superfluous text
fb2780a
@villegar
Fix path for reporter output
db49482
@villegar
Update symbolic link
1a6a741
@villegar
Add additional dependencies to run the parser for test results
771a91c
@villegar
Change working directory to prevent error message when calling git2r:…
e8fed4d 
…:remote_url()
@villegar
Add additional packages to render test report in HTML format
c61416b
@villegar
Correct function call render >> quarto_render
1c46394
@villegar
Remove additional quotation marks
36c3160
@villegar
Update command to render quarto report
dbc689c
@villegar
Fix location of input for quarto_render command
23a22bf
@villegar
Add line for debugging
f9b4ca7
@villegar
Set up local environment variables
b6f86df
@villegar
Add missing portion of path
510422a
@villegar
Rename DATETIME to WORKFLOW_ID and update path to logs: ../logs >> logs
2c26a06
@villegar
Revert path to match the working directory structure of the quarto_re…
fdfca18 
…nder command
@villegar
Add missing dependencies and change output file for quarto_render
4078d70
@villegar
Correct name of output file from quarto_render: index.html >> test_re…
5e779b8 
…port.html
@StuartWheater StuartWheater changed the base branch from v6.3.3-dev to v6.3.4-dev July 24, 2025 13:54
StuartWheater
StuartWheater reviewed Jul 24, 2025
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Do we know why the "corTestDS::smk" is failing on Apple M1 mac?

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villegar commented Jul 24, 2025

Do we know why the "corTestDS::smk" on Apple M1 mac?

Still unknown, as the error message itself is not very useful and I failed to reproduce locally (running on Apple M4 Pro). Needs further investigation.

@StuartWheater StuartWheater merged commit 56c19d2 into datashield:v6.3.4-dev Jul 25, 2025
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