Fix build tests #63
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Fix build tests #63
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Jennit07
commented
Jul 25, 2023
Jennit07
commented
Jul 25, 2023
|
This seems to work, however, the tests now run very slowly. I think they can be sped up by extracting the data as an Arrow Table i.e. The other suggestion is that we don't always need to use |
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Aug 19, 2024
* Update to dev version * Make testthat run in parallel * Fix build tests (#63) * Update variables to pass tests * Update indiv number of variables * Change exists tests to read * Set an environment var to make testthat use multiple CPUs --------- Co-authored-by: James McMahon <james.mcmahon@phs.scot> * Bug/tidyselect not working (#85) * Allow using tidyselect helpers with `col_select` * Add some tests for tidyselect helpers * Update documentation * recid and partnership filter allow for recid and partnership filter when they are not specified to select in columns * Style package * update tests --------- Co-authored-by: Moohan <Moohan@users.noreply.github.com> Co-authored-by: Zihao Li <lizihao_anu@outlook.com> Co-authored-by: lizihao-anu <lizihao-anu@users.noreply.github.com> * Documentation (#88) * Update maintainer to Megan (#69) * Update README.Rmd (#64) Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bug - speed up `get_chi()` (#68) * Update to dev version * Make testthat run in parallel * Update variables to pass tests * Update indiv number of variables * Change exists tests to read * Set an environment var to make testthat use multiple CPUs * Revert changes and deal with NA chi/anon_chi * Update documentation * Style package * Update tests so that they pass * Style package * fix tests * Render `README.md` after changes to the `.Rmd` version * exclude from tests for now --------- Co-authored-by: James McMahon <james.mcmahon@phs.scot> Co-authored-by: Jennit07 <Jennit07@users.noreply.github.com> * Render `README.md` after changes to the `.Rmd` version (#70) Co-authored-by: github-merge-queue[bot] <github-merge-queue[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#66) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump peter-evans/create-pull-request from 4 to 5 (#65) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v4...v5) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump stefanzweifel/git-auto-commit-action from 4 to 5 (#67) Bumps [stefanzweifel/git-auto-commit-action](https://github.com/stefanzweifel/git-auto-commit-action) from 4 to 5. - [Release notes](https://github.com/stefanzweifel/git-auto-commit-action/releases) - [Changelog](https://github.com/stefanzweifel/git-auto-commit-action/blob/master/CHANGELOG.md) - [Commits](stefanzweifel/git-auto-commit-action@v4...v5) --- updated-dependencies: - dependency-name: stefanzweifel/git-auto-commit-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump JamesIves/github-pages-deploy-action from 4.4.3 to 4.5.0 (#71) Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.4.3 to 4.5.0. - [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases) - [Commits](JamesIves/github-pages-deploy-action@v4.4.3...v4.5.0) --- updated-dependencies: - dependency-name: JamesIves/github-pages-deploy-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/upload-artifact from 3 to 4 (#72) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3 to 4. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v3...v4) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump peter-evans/create-pull-request from 5 to 6 (#74) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 5 to 6. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v5...v6) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/cache from 3 to 4 (#73) Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@v3...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Update README.md (#75) Updated to include reading in LTC 'catch all' variables * change in episode file cost variable vector (#76) Co-authored-by: marjom02 <megan.mcnicol2@nhs.scot> * force keytime format to hms (#77) * force keytime format to hms * Update documentation * visible binding for global variables like ‘keytime1’ * minor changes * fix keytime in column names * import hms --------- Co-authored-by: lizihao-anu <lizihao-anu@users.noreply.github.com> * Bump JamesIves/github-pages-deploy-action from 4.5.0 to 4.6.0 (#79) Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.5.0 to 4.6.0. - [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases) - [Commits](JamesIves/github-pages-deploy-action@v4.5.0...v4.6.0) --- updated-dependencies: - dependency-name: JamesIves/github-pages-deploy-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * add vignette for SLFhelper documentation * Style package * Hide messages * remove conflict * Style package * Split up documentation into 3 vignettes * add a comparison table to show the efficiency improvement * Update - round memory size * replace columns by col_select and add tidyselect * Style package * update ep_file_vars and indiv_file_vars * add session memory recommendation * Update R-CMD-check.yaml * fix cmd build error --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: James McMahon <james.mcmahon@phs.scot> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> Co-authored-by: Jennit07 <Jennit07@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-merge-queue[bot] <github-merge-queue[bot]@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Megan McNicol <43570769+SwiftySalmon@users.noreply.github.com> Co-authored-by: marjom02 <megan.mcnicol2@nhs.scot> Co-authored-by: lizihao-anu <lizihao-anu@users.noreply.github.com> Co-authored-by: Jennifer Thom <jennifer.thom@phs.scot> * Update documentation (#90) Co-authored-by: github-merge-queue[bot] <118344674+github-merge-queue[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump JamesIves/github-pages-deploy-action from 4.6.0 to 4.6.3 (#82) Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.6.0 to 4.6.3. - [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases) - [Commits](JamesIves/github-pages-deploy-action@v4.6.0...v4.6.3) --- updated-dependencies: - dependency-name: JamesIves/github-pages-deploy-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Increment version number to 0.10.2 (#81) * Increment version number to 0.10.2 * update description * Update R-CMD-check.yaml * Update yaml --------- Co-authored-by: Zihao Li <zihao.li@phs.scot> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: James McMahon <james.mcmahon@phs.scot> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> Co-authored-by: Moohan <Moohan@users.noreply.github.com> Co-authored-by: lizihao-anu <lizihao-anu@users.noreply.github.com> Co-authored-by: Jennit07 <Jennit07@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-merge-queue[bot] <github-merge-queue[bot]@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Megan McNicol <43570769+SwiftySalmon@users.noreply.github.com> Co-authored-by: marjom02 <megan.mcnicol2@nhs.scot> Co-authored-by: Jennifer Thom <jennifer.thom@phs.scot> Co-authored-by: github-merge-queue[bot] <118344674+github-merge-queue[bot]@users.noreply.github.com>
github-merge-queue bot
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Sep 9, 2024
* Update to dev version * Make testthat run in parallel * Fix build tests (#63) * Update variables to pass tests * Update indiv number of variables * Change exists tests to read * Set an environment var to make testthat use multiple CPUs --------- Co-authored-by: James McMahon <james.mcmahon@phs.scot> * Bug/tidyselect not working (#85) * Allow using tidyselect helpers with `col_select` * Add some tests for tidyselect helpers * Update documentation * recid and partnership filter allow for recid and partnership filter when they are not specified to select in columns * Style package * update tests --------- Co-authored-by: Moohan <Moohan@users.noreply.github.com> Co-authored-by: Zihao Li <lizihao_anu@outlook.com> Co-authored-by: lizihao-anu <lizihao-anu@users.noreply.github.com> * Documentation (#88) * Update maintainer to Megan (#69) * Update README.Rmd (#64) Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bug - speed up `get_chi()` (#68) * Update to dev version * Make testthat run in parallel * Update variables to pass tests * Update indiv number of variables * Change exists tests to read * Set an environment var to make testthat use multiple CPUs * Revert changes and deal with NA chi/anon_chi * Update documentation * Style package * Update tests so that they pass * Style package * fix tests * Render `README.md` after changes to the `.Rmd` version * exclude from tests for now --------- Co-authored-by: James McMahon <james.mcmahon@phs.scot> Co-authored-by: Jennit07 <Jennit07@users.noreply.github.com> * Render `README.md` after changes to the `.Rmd` version (#70) Co-authored-by: github-merge-queue[bot] <github-merge-queue[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#66) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump peter-evans/create-pull-request from 4 to 5 (#65) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v4...v5) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump stefanzweifel/git-auto-commit-action from 4 to 5 (#67) Bumps [stefanzweifel/git-auto-commit-action](https://github.com/stefanzweifel/git-auto-commit-action) from 4 to 5. - [Release notes](https://github.com/stefanzweifel/git-auto-commit-action/releases) - [Changelog](https://github.com/stefanzweifel/git-auto-commit-action/blob/master/CHANGELOG.md) - [Commits](stefanzweifel/git-auto-commit-action@v4...v5) --- updated-dependencies: - dependency-name: stefanzweifel/git-auto-commit-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump JamesIves/github-pages-deploy-action from 4.4.3 to 4.5.0 (#71) Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.4.3 to 4.5.0. - [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases) - [Commits](JamesIves/github-pages-deploy-action@v4.4.3...v4.5.0) --- updated-dependencies: - dependency-name: JamesIves/github-pages-deploy-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/upload-artifact from 3 to 4 (#72) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3 to 4. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v3...v4) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump peter-evans/create-pull-request from 5 to 6 (#74) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 5 to 6. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v5...v6) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/cache from 3 to 4 (#73) Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@v3...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Update README.md (#75) Updated to include reading in LTC 'catch all' variables * change in episode file cost variable vector (#76) Co-authored-by: marjom02 <megan.mcnicol2@nhs.scot> * force keytime format to hms (#77) * force keytime format to hms * Update documentation * visible binding for global variables like ‘keytime1’ * minor changes * fix keytime in column names * import hms --------- Co-authored-by: lizihao-anu <lizihao-anu@users.noreply.github.com> * Bump JamesIves/github-pages-deploy-action from 4.5.0 to 4.6.0 (#79) Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.5.0 to 4.6.0. - [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases) - [Commits](JamesIves/github-pages-deploy-action@v4.5.0...v4.6.0) --- updated-dependencies: - dependency-name: JamesIves/github-pages-deploy-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * add vignette for SLFhelper documentation * Style package * Hide messages * remove conflict * Style package * Split up documentation into 3 vignettes * add a comparison table to show the efficiency improvement * Update - round memory size * replace columns by col_select and add tidyselect * Style package * update ep_file_vars and indiv_file_vars * add session memory recommendation * Update R-CMD-check.yaml * fix cmd build error --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: James McMahon <james.mcmahon@phs.scot> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> Co-authored-by: Jennit07 <Jennit07@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-merge-queue[bot] <github-merge-queue[bot]@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Megan McNicol <43570769+SwiftySalmon@users.noreply.github.com> Co-authored-by: marjom02 <megan.mcnicol2@nhs.scot> Co-authored-by: lizihao-anu <lizihao-anu@users.noreply.github.com> Co-authored-by: Jennifer Thom <jennifer.thom@phs.scot> * Update documentation (#90) Co-authored-by: github-merge-queue[bot] <118344674+github-merge-queue[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Bump JamesIves/github-pages-deploy-action from 4.6.0 to 4.6.3 (#82) Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.6.0 to 4.6.3. - [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases) - [Commits](JamesIves/github-pages-deploy-action@v4.6.0...v4.6.3) --- updated-dependencies: - dependency-name: JamesIves/github-pages-deploy-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Increment version number to 0.10.2 (#81) * Increment version number to 0.10.2 * update description * Update R-CMD-check.yaml * Update yaml --------- Co-authored-by: Zihao Li <zihao.li@phs.scot> * Fix the tidyselect feature bug (#95) * reconstruct read_slf to fix bug of selecting feature * Update documentation * remove TODO add a filter by recid as it has been done * Style package * update ep and individual file variables --------- Co-authored-by: lizihao-anu <lizihao-anu@users.noreply.github.com> Co-authored-by: Jennit07 <67372904+Jennit07@users.noreply.github.com> * Increment version number to 0.10.4 * Update NEWS --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: James McMahon <james.mcmahon@phs.scot> Co-authored-by: Moohan <Moohan@users.noreply.github.com> Co-authored-by: Zihao Li <lizihao_anu@outlook.com> Co-authored-by: lizihao-anu <lizihao-anu@users.noreply.github.com> Co-authored-by: Zihao Li <zihao.li@phs.scot> Co-authored-by: Jennit07 <Jennit07@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-merge-queue[bot] <github-merge-queue[bot]@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Megan McNicol <43570769+SwiftySalmon@users.noreply.github.com> Co-authored-by: marjom02 <megan.mcnicol2@nhs.scot> Co-authored-by: github-merge-queue[bot] <118344674+github-merge-queue[bot]@users.noreply.github.com>
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Some outstanding but opening a PR to view the changes. Some issues with variables not matching the number of variables within the file. This is due to the older files not matching the newly updated files.