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mattcieslakmattcieslak
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Add accessor functions, multi-h5 modeling (#117)
1 parent 14ab04f commit 113b5eb

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‎.circleci/config.yml‎

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version: 2
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steps: &steps
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steps:
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- checkout
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- run:
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name: Install libraries
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command: |
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apt update \
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&& apt install -y --no-install-recommends \
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curl \
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r-cran-devtools \
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r-bioc-rhdf5 \
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r-bioc-delayedarray \
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pandoc \
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texlive-latex-recommended \
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texlive-fonts-recommended \
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texlive-fonts-extra
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- run:
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name: Install package dependencies
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command: R -e "devtools::install_deps(dep = TRUE, dependencies = TRUE)"
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- run:
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name: Check code style
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command: |
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R -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes"); if (!requireNamespace("styler", quietly = TRUE) || as.character(utils::packageVersion("styler")) != "1.11.0") remotes::install_version("styler", version = "1.11.0", upgrade = "never")'
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R -e 'result <- styler::style_pkg(dry = "on", style = styler::tidyverse_style, strict = FALSE); if (!all(result[["changed"]] == FALSE)) { message("Code style check found files that would be reformatted. Run styler::style_pkg(style = styler::tidyverse_style) locally."); print(result[result[["changed"]], "file", drop = FALSE]) }'
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- run:
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name: Build package
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command: R CMD build .
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- run:
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name: Check package
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command: R CMD check *tar.gz
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- run:
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name: Calculate and upload code coverage
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command: |
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R -e 'if (!requireNamespace("covr", quietly = TRUE)) install.packages("covr")'
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R -e 'cov <- covr::package_coverage(type = "tests"); covr::to_cobertura(cov, filename = "coverage.xml"); print(cov); cat(sprintf("Total coverage: %.2f%%\n", covr::percent_coverage(cov)))'
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if command -v curl >/dev/null 2>&1; then
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curl -Os https://uploader.codecov.io/latest/linux/codecov || echo "Codecov uploader download failed; continuing."
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else
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echo "curl not found; skipping Codecov upload."
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fi
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if [ -f codecov ]; then
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chmod +x codecov
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./codecov -f coverage.xml -n "circleci-r-tests" || echo "Codecov upload failed; continuing."
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else
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echo "Codecov uploader not available; skipping upload."
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fi
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setup_steps: &setup_steps
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- checkout
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- run:
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name: Install libraries
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command: |
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apt update \
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&& apt install -y --no-install-recommends \
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curl \
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r-cran-devtools \
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r-bioc-rhdf5 \
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r-bioc-delayedarray \
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pandoc \
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texlive-latex-recommended \
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texlive-fonts-recommended \
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texlive-fonts-extra
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- run:
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name: Install package dependencies
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command: R -e "devtools::install_deps(dep = TRUE, dependencies = TRUE)"
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- run:
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name: Check code style
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command: |
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R -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes"); if (!requireNamespace("styler", quietly = TRUE) || as.character(utils::packageVersion("styler")) != "1.11.0") remotes::install_version("styler", version = "1.11.0", upgrade = "never")'
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R -e 'result <- styler::style_pkg(dry = "on", style = styler::tidyverse_style, strict = FALSE); if (!all(result[["changed"]] == FALSE)) { message("Code style check found files that would be reformatted. Run styler::style_pkg(style = styler::tidyverse_style) locally."); print(result[result[["changed"]], "file", drop = FALSE]) }'
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- run:
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name: Build package
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command: R CMD build .
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- persist_to_workspace:
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root: .
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paths:
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- "*.tar.gz"
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jobs:
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releaseJammy:
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setup_and_build:
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docker:
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- image: rocker/r2u:jammy
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steps: *setup_steps
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check_package:
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docker:
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- image: rocker/r2u:jammy
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steps:
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- checkout
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- run:
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name: Install libraries
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command: |
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apt update \
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&& apt install -y --no-install-recommends \
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curl \
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r-cran-devtools \
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r-bioc-rhdf5 \
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r-bioc-delayedarray \
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pandoc \
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texlive-latex-recommended \
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texlive-fonts-recommended \
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texlive-fonts-extra
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- run:
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name: Install package dependencies
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command: R -e "devtools::install_deps(dep = TRUE, dependencies = TRUE)"
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- attach_workspace:
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at: .
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- run:
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name: Check package
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command: R CMD check *tar.gz
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calculate_coverage:
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docker:
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- image: rocker/r2u:jammy
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<<: *steps
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steps:
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- checkout
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- run:
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name: Install libraries
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command: |
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apt update \
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&& apt install -y --no-install-recommends \
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curl \
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r-cran-devtools \
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r-bioc-rhdf5 \
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r-bioc-delayedarray \
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pandoc \
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texlive-latex-recommended \
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texlive-fonts-recommended \
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texlive-fonts-extra
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- run:
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name: Install package dependencies
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command: R -e "devtools::install_deps(dep = TRUE, dependencies = TRUE)"
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- run:
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name: Calculate and upload code coverage
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command: |
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R -e 'if (!requireNamespace("covr", quietly = TRUE)) install.packages("covr")'
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R -e 'cov <- covr::package_coverage(type = "tests"); covr::to_cobertura(cov, filename = "coverage.xml"); print(cov); cat(sprintf("Total coverage: %.2f%%\\n", covr::percent_coverage(cov)))'
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if command -v curl >/dev/null 2>&1; then
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curl -Os https://uploader.codecov.io/latest/linux/codecov || echo "Codecov uploader download failed; continuing."
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else
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echo "curl not found; skipping Codecov upload."
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fi
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if [ -f codecov ]; then
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chmod +x codecov
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./codecov -f coverage.xml -n "circleci-r-tests" || echo "Codecov upload failed; continuing."
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else
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echo "Codecov uploader not available; skipping upload."
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fi
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build_and_deploy:
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environment:
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TZ: "/usr/share/zoneinfo/America/New_York"
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docker:
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- image: cimg/base:2020.09
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# working_directory: tmp/src/modelarray_build # the code will be check-ed out to here
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steps:
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- checkout
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- setup_remote_docker:
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version: 2
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build_test_deploy:
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jobs:
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- releaseJammy:
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- setup_and_build:
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filters:
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branches:
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ignore:
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tags:
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only: /.*/
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- build_and_deploy:
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- check_package:
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requires:
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- releaseJammy
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- setup_and_build
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filters:
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branches:
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only: main
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ignore:
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- gh-pages
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- /^gh-pages.*/
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tags: # make sure any `git tag` triggers the run
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tags:
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only: /.*/
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- calculate_coverage:
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requires:
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- setup_and_build
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filters:
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branches:
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ignore:
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- gh-pages
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- /^gh-pages.*/
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tags:
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only: /.*/
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- build_and_deploy:
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requires:
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- check_package
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- calculate_coverage
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filters:
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branches:
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only: main
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ignore:
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- gh-pages
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- /^gh-pages.*/
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tags:
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only: /.*/

‎DESCRIPTION‎

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rlang,
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tibble,
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tidyr
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RoxygenNote: 7.3.1
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RoxygenNote: 7.3.2
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Suggests:
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rmarkdown,
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knitr,

‎NAMESPACE‎

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# Generated by roxygen2: do not edit by hand
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S3method(print,h5summary)
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export("%>%")
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export(ModelArray)
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export(ModelArray.gam)
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export(analyseOneElement.gam)
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export(analyseOneElement.lm)
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export(analyseOneElement.wrap)
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export(analysisNames)
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export(elementMetadata)
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export(exampleElementData)
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export(gen_gamFormula_contIx)
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export(gen_gamFormula_fxSmooth)
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export(h5summary)
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export(mergeModelArrays)
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export(nElements)
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export(nInputFiles)
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export(numElementsTotal)
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export(results)
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export(scalarNames)
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export(scalars)
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export(sources)
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export(writeResults)
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exportMethods(analysisNames)
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exportMethods(elementMetadata)
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exportMethods(exampleElementData)
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exportMethods(nElements)
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exportMethods(nInputFiles)
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exportMethods(results)
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exportMethods(scalarNames)
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exportMethods(scalars)
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exportMethods(show)
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exportMethods(sources)
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import(tibble)
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importClassesFrom(DelayedArray,DelayedArray)
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importFrom(DelayedArray,DelayedArray)
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importFrom(DelayedArray,acbind)
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importFrom(DelayedArray,realize)
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importFrom(HDF5Array,HDF5ArraySeed)
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importFrom(crayon,black)
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importFrom(stats,p.adjust)
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importFrom(stats,p.adjust.methods)
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importFrom(stats,terms)
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importFrom(utils,head)

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