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| *.html |
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: [dev, master, release-*] | ||
| pull_request: | ||
| branches: [dev, master] | ||
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| name: R-CMD-check | ||
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| jobs: | ||
| R-CMD-check: | ||
| runs-on: ${{ matrix.config.os }} | ||
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| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
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| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - {os: macos-latest, r: 'release'} | ||
| - {os: windows-latest, r: 'release'} | ||
| - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | ||
| - {os: ubuntu-latest, r: 'release'} | ||
| - {os: ubuntu-latest, r: 'oldrel-1'} | ||
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| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| R_KEEP_PKG_SOURCE: yes | ||
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| steps: | ||
| - uses: actions/checkout@v3 | ||
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| - uses: r-lib/actions/setup-pandoc@v2 | ||
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| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
| http-user-agent: ${{ matrix.config.http-user-agent }} | ||
| use-public-rspm: true | ||
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| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::rcmdcheck | ||
| needs: check | ||
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| - uses: r-lib/actions/check-r-package@v2 | ||
| with: | ||
| upload-snapshots: true |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: [dev, master, release-*] | ||
| pull_request: | ||
| branches: [dev, master] | ||
|
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| name: lint | ||
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| jobs: | ||
| lint: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
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| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
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| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::lintr, local::. | ||
| needs: lint | ||
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| - name: Lint | ||
| run: | | ||
| library(lintr) | ||
| style_rules <- list( | ||
| T_and_F_symbol_linter(), assignment_linter(), brace_linter(), | ||
| commas_linter(), commented_code_linter(), todo_comment_linter(), | ||
| equals_na_linter(), | ||
| function_left_parentheses_linter(), infix_spaces_linter(), | ||
| line_length_linter(), whitespace_linter(), object_usage_linter(), | ||
| absolute_path_linter(), | ||
| nonportable_path_linter(), pipe_continuation_linter(), | ||
| semicolon_linter(), seq_linter(), quotes_linter(), | ||
| spaces_inside_linter(), spaces_left_parentheses_linter(), | ||
| trailing_blank_lines_linter(), trailing_whitespace_linter(), | ||
| undesirable_function_linter(), undesirable_operator_linter(), | ||
| unnecessary_concatenation_linter() | ||
| ) | ||
| lint_package(linters = style_rules) | ||
| shell: Rscript {0} | ||
| env: | ||
| LINTR_ERROR_ON_LINT: true |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: [dev, master, release-*] | ||
| pull_request: | ||
| branches: [dev, master] | ||
|
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| name: test-coverage | ||
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| jobs: | ||
| test-coverage: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
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| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
|
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| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::covr | ||
| needs: coverage | ||
|
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| - name: Test coverage | ||
| run: | | ||
| covr::codecov( | ||
| quiet = FALSE, | ||
| clean = FALSE, | ||
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | ||
| ) | ||
| shell: Rscript {0} | ||
|
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| - name: Show testthat output | ||
| if: always() | ||
| run: | | ||
| ## -------------------------------------------------------------------- | ||
| find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true | ||
| shell: bash | ||
|
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| - name: Upload test results | ||
| if: failure() | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: coverage-test-failures | ||
| path: ${{ runner.temp }}/package |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,31 +1,35 @@ | ||
| This file documents the changes between stable releases of DIscBIO. | ||
| # DIscBIO 1.2.1 | ||
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| # Version 1.2.0 | ||
| * Fixed integration and unit tests (issue #22, #37) | ||
| * Improved coding style (issue #38) | ||
| * Removed dependency on `boot` (issue 26) | ||
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| - Added support for retrying to retrieve URLs (issue #29) | ||
| - Removed duplicated (legacy) function | ||
| - Improved detection of duplicated data on `NetAnalysis()` | ||
| - Improved I/O behavior | ||
| - Improved validation | ||
| - Bug fixes | ||
| # DIscBIO 1.2.0 | ||
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| # Version 1.1.0 | ||
| * Added support for retrying to retrieve URLs (issue #29) | ||
| * Removed use of duplicated (legacy) function _on unit tests only_ | ||
| * Improved detection of duplicated data on `NetAnalysis()` | ||
| * Improved I/O behavior | ||
| * Improved validation | ||
| * Bug fixes | ||
|
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| - Added support for more gene types | ||
| - Improved I/O behavior | ||
| - Updated Binder notebooks | ||
| # DIscBIO 1.1.0 | ||
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| # Version 1.0.1 | ||
| * Added support for more gene types | ||
| * Improved I/O behavior | ||
| * Updated Binder notebooks | ||
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| - Bug fixes | ||
| - Updated Binder notebook | ||
| # DIscBIO 1.0.1 | ||
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| # Version 1.0.0 | ||
| * Bug fixes | ||
| * Updated Binder notebook | ||
|
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| # DIscBIO 1.0.0 | ||
|
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| Contains several changes from the [original work](https://github.com/SystemsBiologist/PSCAN), the most relevant of which are listed below: | ||
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| - Several functions have been enhanced with a `quiet` argument to suppress intermediate output (essential to obtain cleaner output in batch scripts and unit tests) | ||
| - Functions have been isolated into their own R files | ||
| - Function and package documentation were added | ||
| - Test datasets were compressed to occupy less disk space | ||
| - Bugs have been fixed | ||
| * Several functions have been enhanced with a `quiet` argument to suppress intermediate output (essential to obtain cleaner output in batch scripts and unit tests) | ||
| * Functions have been isolated into their own R files | ||
| * Function and package documentation were added | ||
| * Test datasets were compressed to occupy less disk space | ||
| * Bugs have been fixed |
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