add offset option for ENV Q #322
Workflow file for this run
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| # Build stock synthesis with all c++ compiler warnings, and fail job if the | |
| # number of warnings has increased. | |
| name: build-ss3-warnings | |
| # Controls when the action will run. | |
| on: | |
| workflow_dispatch: | |
| push: | |
| paths: | |
| - '**.tpl' | |
| branches: | |
| - main | |
| pull_request: | |
| types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review'] | |
| paths: | |
| - '**.tpl' | |
| branches: | |
| - main | |
| jobs: | |
| build-warnings: | |
| if: github.event.pull_request.draft == false | |
| runs-on: ubuntu-latest | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" | |
| steps: | |
| - name: Checkout ss3 repo | |
| uses: actions/checkout@v4 | |
| - name: Update Ubuntu packages | |
| run: sudo apt-get update | |
| - name: setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| # - name: Get admb and put in path, linux | |
| # run: | | |
| # wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip | |
| # sudo unzip admb-13.1-linux.zip -d /usr/local/bin | |
| # sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb | |
| # echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH | |
| - name: Build stock synthesis with warnings displayed in console using admb docker image | |
| run: | | |
| rm -rf SS330 | |
| rm -rf ss3_osx.tar | |
| mkdir SS330 | |
| chmod 777 SS330 | |
| /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -w | |
| - name: Build stock synthesis with warnings again to save to file | |
| run: | | |
| rm -rf SS330 | |
| rm -rf ss3_osx.tar | |
| mkdir SS330 | |
| chmod 777 SS330 | |
| /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -w &> warnings.txt | |
| # Runs a set of commands using the runners shell | |
| - name: Use R to parse warnings output | |
| run: | | |
| txt <- readLines("warnings.txt", encoding = "UTF-8") | |
| warn_line <- grep(pattern = "g++ -c -std=c++17 -O3 -Wall -Wextra -D_USE_MATH_DEFINES -DUSE_ADMB_CONTRIBS", x = txt, fixed = TRUE) | |
| end_warn_line <- grep(pattern = "*** Linking: ss3.obj ", x = txt, fixed = TRUE) | |
| if (length(warn_line) == 1 & length(end_warn_line) == 1) { | |
| txt <- txt[(warn_line+3):(end_warn_line-1)] | |
| rm_warn_start_lines <- grep(pattern = "/usr/local/admb/include/admodel.h: ", x = txt, fixed = TRUE, invert = TRUE) | |
| txt <- txt[rm_warn_start_lines] | |
| n_errors <- length(grep(pattern = "^ [0-9]", x = txt)) | |
| message("There are ", n_errors, " warning messages related to SS3.") | |
| write.table(n_errors, "n_warn.txt") | |
| } | |
| writeLines(txt, "warnings_ss.txt") | |
| # warn_line <- grep(pattern = "compiling a second time to get warnings", x = txt, fixed = TRUE) | |
| # txt <- txt[(warn_line+1):length(txt)] | |
| shell: Rscript {0} | |
| - name: Print warnings | |
| run: cat warnings_ss.txt | |
| - name: determine if fails/passes | |
| run: | | |
| ref <- readLines(".github/workflows/reference_files/warnings_ss_ref.txt") | |
| n_warn <- read.table("n_warn.txt") | |
| n_warn <- as.integer(n_warn[1,1]) | |
| if (n_warn > length(ref)) { | |
| stop("Increased number of warnings compared to reference warning file") | |
| } else { | |
| # n_warn doesn't take into account the "In file included from ss.cpp:7:" | |
| # so add 2 to add those lines back in | |
| if (n_warn+length(ref) < length(ref)){ | |
| stop("Number of warnings of decreased compared to reference warning file") | |
| } else { | |
| message("Acceptable number of warnings") | |
| } | |
| } | |
| shell: Rscript {0} | |
| - name: Archive warnings text file | |
| if: always() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: 'warnings_ss.txt' | |
| path: warnings_ss.txt |