fix output error in Index_2, plus two minor output tweaks (#647) #431
Workflow file for this run
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| # Builds the stock synthesis executables for testing and distribution using the admb docker image. | |
| # for macOS 12, and macos-14 (arm64 architecture), linux, Windows | |
| # Runs on every push and PR (even draft PRs) | |
| name: build-ss3 | |
| on: | |
| push: | |
| paths: | |
| - '**.tpl' | |
| - '**.sh' | |
| workflow_dispatch: | |
| jobs: | |
| build-ss3: | |
| if: ${{ github.event_name == 'workflow_dispatch' || github.event == 'push' || github.event.workflow_run.conclusion == 'failure' }} | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: windows-latest} | |
| - {os: macos-13} | |
| - {os: macos-latest} | |
| - {os: ubuntu-latest} | |
| # Limit run time to 90 min to avoid wasting action minutes. | |
| # was set to 15 and then 30 minutes previously, but compiling admb | |
| # on mac took too long | |
| timeout-minutes: 90 | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - name: checkout ss3 repo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'nmfs-ost/ss3-source-code' | |
| # Checkout ADMB repository | |
| - name: Checkout admb for macos-13 build | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: admb-project/admb | |
| path: admb | |
| ref: admb-13.2 | |
| - name: Update Ubuntu packages | |
| if: matrix.config.os == 'ubuntu-latest' | |
| run: sudo apt-get update | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Fetch git tags | |
| run: | | |
| git fetch --tags | |
| git fetch --prune --unshallow || true | |
| # Build ADMB for macos-13 | |
| - name: Build ADMB for macos-13 and put in path | |
| if: matrix.config.os == 'macos-13' || matrix.config.os == 'macos-latest' | |
| run: | | |
| cd admb && make clean | |
| - name: See where admb is | |
| if: matrix.config.os == 'macos-13' || matrix.config.os == 'macos-latest' | |
| run: | | |
| cd admb && ls | |
| - name: Compile admb, macOS | |
| if: matrix.config.os == 'macos-13' || matrix.config.os == 'macos-latest' | |
| run: | | |
| cd admb && make -j 4 | |
| - name: Change permissions of admb and put in path, macOS | |
| if: matrix.config.os == 'macos-13' || matrix.config.os == 'macos-latest' | |
| run: | | |
| sudo mv admb /usr/local/bin | |
| sudo chmod 755 /usr/local/bin/admb | |
| echo "/usr/local/bin/admb" >> $GITHUB_PATH | |
| - name: Get the last tag on Windows | |
| id: get-latest-tag-win | |
| if: matrix.config.os == 'windows-latest' | |
| run: | | |
| git tag | |
| $latest_tag = (git describe --abbrev=0 --tags) | |
| $latest_tag_commit = ( git rev-list -n 1 $latest_tag) | |
| $latest_commit = (git rev-list HEAD -n 1) | |
| echo "tag=${latest_tag}" >> $env:GITHUB_OUTPUT | |
| echo "tag_commit=${latest_tag_commit}" >> $env:GITHUB_OUTPUT | |
| echo "commit=${latest_commit}" >> $env:GITHUB_OUTPUT | |
| - name: Pull the last tag value to use in the Rscript on Windows | |
| id: get-version-win | |
| if: matrix.config.os == 'windows-latest' | |
| run: | | |
| Out-File -InputObject ${{ steps.get-latest-tag-win.outputs.tag }} -FilePath .github/last_tag.txt | |
| Out-File -InputObject ${{ steps.get-latest-tag-win.outputs.tag_commit }} -FilePath .github/last_tag_commit.txt | |
| Out-File -InputObject ${{ steps.get-latest-tag-win.outputs.commit}} -FilePath .github/last_commit.txt | |
| - name: Get the last tag on unix (macOS and linux) | |
| id: get-latest-tag-unix | |
| if: matrix.config.os == 'macos-13' || matrix.config.os == 'macos-latest' || matrix.config.os == 'ubuntu-latest' | |
| run: | | |
| git tag | |
| latest_tag=$(git describe --abbrev=0 --tags) | |
| latest_tag_commit=$(git rev-list -n 1 $latest_tag) | |
| latest_commit=$(git rev-list HEAD -n 1) | |
| echo "tag=${latest_tag}" >> $GITHUB_OUTPUT | |
| echo "tag_commit=${latest_tag_commit}" >> $GITHUB_OUTPUT | |
| echo "commit=${latest_commit}" >> $GITHUB_OUTPUT | |
| - name: Pull the last tag value to use in the Rscript on unix (macOS and linux) | |
| id: get-version-unix | |
| if: matrix.config.os == 'macos-13' || matrix.config.os == 'macos-latest' || matrix.config.os == 'ubuntu-latest' | |
| run: | | |
| echo "${{ steps.get-latest-tag-unix.outputs.tag }}" > .github/last_tag.txt | |
| echo "${{ steps.get-latest-tag-unix.outputs.tag_commit }}" > .github/last_tag_commit.txt | |
| echo "${{ steps.get-latest-tag-unix.outputs.commit }}" > .github/last_commit.txt | |
| - name: Edit the version info for safe version using R code | |
| run: | | |
| # Get the version | |
| # get the last tag from the repository | |
| tag_label <- readLines(".github/last_tag.txt") | |
| # get commits from from the repository | |
| tag_commit <- readLines(".github/last_tag_commit.txt") | |
| last_commit <- readLines(".github/last_commit.txt") | |
| message("The tag_label is ", tag_label) | |
| if (substr(tag_label, start = 1, stop = 6) == "v3.30.") { | |
| ver_num_full <- strsplit(tag_label, split = "v3.30", fixed = TRUE)[[1]][2] | |
| ver_num <- strsplit(ver_num_full, split = ".", fixed = TRUE)[[1]][2] | |
| if(length(grep("-", ver_num)) > 0) { | |
| ver_num <- strsplit(ver_num, split = "-", fixed = TRUE)[[1]][1] | |
| } | |
| } else { | |
| ver_num <- "unknown" | |
| } | |
| message("tag commit: ", tag_commit) | |
| message("last commit: ", last_commit) | |
| if(tag_commit == last_commit) { | |
| # figure out the version using the tag | |
| if(ver_num == "unknown") { | |
| fix_ver_num <- "unknown" | |
| } else { | |
| ver_num_full_split <- strsplit(ver_num_full, split = ".", fixed = TRUE)[[1]] | |
| if(length(ver_num_full_split) == 3) { | |
| fix_ver_num <- ver_num_full_split[3] | |
| } else if(length(ver_num_full_split) == 2) { | |
| if(length(grep("-", ver_num_full_split, fixed = TRUE)) > 0) { | |
| fix_ver_num <- strsplit(ver_num_full_split[2], split = "-", fixed = TRUE)[[1]][2] | |
| fix_ver_num <- paste0("00-", fix_ver_num) | |
| } else { | |
| fix_ver_num <- "00" | |
| } | |
| } else { | |
| fix_ver_num <- "unknown" | |
| } | |
| } | |
| } else { | |
| fix_ver_num <- "beta: not an official version of SS" | |
| } | |
| message("The minor version label is ", ver_num) | |
| message("The patch version label is ", fix_ver_num) | |
| # add version numbers to files | |
| # safe file | |
| ver_info <- readLines("SS_versioninfo_330safe.tpl") | |
| ver_info_start <- grep('Create string with version info', ver_info, fixed = TRUE) | |
| ver_info[ver_info_start + 1] <- | |
| gsub('\\.xx', paste0('\\.', ver_num), ver_info[ver_info_start + 1]) | |
| ver_info[ver_info_start + 1] <- | |
| gsub('\\.yy', paste0('\\.', fix_ver_num), ver_info[ver_info_start+1]) | |
| writeLines(ver_info, "SS_versioninfo_330safe.tpl") | |
| #opt file | |
| ver_info <- readLines("SS_versioninfo_330opt.tpl") | |
| ver_info_start <- grep('Create string with version info', ver_info, fixed = TRUE) | |
| ver_info[ver_info_start + 1] <- | |
| gsub('\\.xx', paste0('\\.', ver_num), ver_info[ver_info_start + 1]) | |
| ver_info[ver_info_start + 1] <- | |
| gsub('\\.yy', paste0('\\.', fix_ver_num), ver_info[ver_info_start+1]) | |
| writeLines(ver_info, "SS_versioninfo_330opt.tpl") | |
| shell: Rscript {0} | |
| - name: Build stock synthesis for windows with admb docker image | |
| if: matrix.config.os == 'windows-latest' | |
| run: | | |
| cd Compile | |
| ./Make_SS_fast.bat || true | |
| ./Make_SS_safe.bat || true | |
| cd .. | |
| - name: Move exes to a new folder on windows | |
| if: matrix.config.os == 'windows-latest' | |
| run: | | |
| mkdir SS330 | |
| chmod 777 SS330 | |
| mv Compile/ss3.exe SS330/ | |
| mv Compile/ss3_opt.exe SS330/ | |
| mv SS330/ss3.exe SS330/ss3_win.exe | |
| mv SS330/ss3_opt.exe SS330/ss3_opt_win.exe | |
| - name: Build stock synthesis for mac with admb from source | |
| if: matrix.config.os == 'macos-13' || matrix.config.os == 'macos-latest' | |
| run: | | |
| rm -rf SS330 | |
| rm -rf ss3_osx.tar | |
| mkdir SS330 | |
| chmod 777 SS330 | |
| /bin/bash ./Make_SS_330_new.sh -b SS330 | |
| /bin/bash ./Make_SS_330_new.sh -b SS330 -o | |
| # - name: Build stock synthesis for mac m2 with admb docker image | |
| # if: matrix.config.os == 'macos-latest' | |
| # run: | | |
| # brew update | |
| # brew install docker | |
| # brew install --head colima | |
| # colima start --arch x86_64 | |
| # docker pull johnoel/admb-13.2:linux | |
| # rm -rf SS330 | |
| # rm -rf ss3_osx.tar | |
| # mkdir SS330 | |
| # chmod 777 SS330 | |
| # /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 | |
| # /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -o | |
| - name: Verify binary on mac | |
| if: matrix.config.os == 'macos-13' || matrix.config.os == 'macos-latest' | |
| run: | | |
| shasum -a 256 SS330/ss3 | |
| shasum -a 256 SS330/ss3_opt | |
| - name: Delete unneeded files and change exe names on mac | |
| if: matrix.config.os == 'macos-13' || matrix.config.os == 'macos-latest' | |
| run: | | |
| cd SS330 | |
| rm *.obj *.htp *.cpp ss3_opt.tpl ss3.tpl | |
| mv ss3 ss3_osx | |
| mv ss3_opt ss3_opt_osx | |
| - name: Build stock synthesis for linux with p flag and admb docker image | |
| if: matrix.config.os == 'ubuntu-latest' | |
| 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 -p | |
| /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -o -p | |
| - name: Verify binary on linux | |
| if: matrix.config.os == 'ubuntu-latest' | |
| run: | | |
| sha256sum SS330/ss3 | |
| sha256sum SS330/ss3_opt | |
| - name: Delete unneeded files and change exe names on linux | |
| if: matrix.config.os == 'ubuntu-latest' | |
| run: | | |
| cd SS330 | |
| rm *.obj *.htp *.cpp ss3_opt.tpl ss3.tpl | |
| mv ss3 ss3_linux | |
| mv ss3_opt ss3_opt_linux | |
| - name: Archive binaries | |
| if: success() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ss3-${{ matrix.config.os }} | |
| path: SS330/ |