fix_lbin_in_FIT_age #556

.github/workflows/ss3-pr-open-issues.yml

@@ -1,78 +1,78 @@
 # Opens issues to r4ss, SSI, and doc repos when changes occur in SS3.
-name: ss3-pr-open-issues.yml
-on:
-  pull_request:
-    types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review']
-#  pull_request_target:
-#    types:
-#      - closed
-jobs:
-  ss3-pr-open-issues:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GH_PAT }}
-    steps:
-      - name: Update Ubuntu packages
-        run: sudo apt update && sudo apt install -y libcurl4-openssl-dev
-      - name: Get Pull Request Number
-        run: |
-          echo github.event.pull_request.number = ${{ github.event.pull_request.number }}
-      - uses: actions/checkout@v3
-      - uses: r-lib/actions/setup-r@v2
-       # with:
-       #   use-public-rspm: true
-      - name: install the gh and curl pkgs
-        run:
-          Rscript -e "install.packages('gh')"
-      - name: Get pr info and save
-        run: |
-          Rscript -e 'info <- gh::gh("GET /repos/{owner}/{repo}/pulls/{pull_number}", 
-            owner = "nmfs-ost", 
-            repo = "ss3-source-code",
-            pull_number = "${{ github.event.pull_request.number }}")
-          saveRDS(info, file = "info.RDS")'
-      - name: Post issues, if needed
-        run: |
-          info <- readRDS("info.RDS")
-          pr_body  <- strsplit(info$body, "\n" )[[1]]
-          pr_body <- gsub("\r", "",  pr_body, fixed = TRUE)
-          # Get info on which repos need open issues, if a change log entry is needed.
-          # allow some flexibility for getting the spacing wrong, which is easy to do.
-          # look for checklist items like - []
-          needs_changes <- grep("-\\s*\\[\\s*\\]", pr_body, ignore.case = TRUE, value = TRUE)
-          issue_title <- paste0("Changes need for SS3 PR ",  info$number)
-          issue_body <- paste0("Changes will be needed in this ",
-            "repository due to the opening of SS3 Pull Request ", 
-            info$number, ".\n", 
-            "Please see ", 
-            "https://github.com/nmfs-ost/ss3-source-code/pull/", 
-            info$number, " and its associated issues for more information.",
-            "\n\nNote: this issue was created automatically via GitHub ",
-            "Action using the workflow in \n",
-            "https://github.com/nmfs-ost/ss3-source-code/blob/main/.github/workflows/ss3-pr-open-issues.yml")
-          # post r4ss issue if needed
-          if (length(grep("r4ss", needs_changes)) == 1) {
-            gh::gh("POST /repos/{owner}/{repo}/issues",
-             owner = "r4ss", 
-             repo = "r4ss", 
-             title = issue_title,
-             body = issue_body)
-          }
-          # post SSI issue if needed
-          if (length(grep("SSI", needs_changes)) == 1) {
-                      gh::gh("POST /repos/{owner}/{repo}/issues",
-             owner = "nmfs-ost", 
-             repo = "ssi", 
-             title = issue_title,
-             body = issue_body)
-          }
-          # post documentation issue, if needed
-          if (length(grep("manual", needs_changes)) == 1) {
-            gh::gh("POST /repos/{owner}/{repo}/issues",
-             owner = "nmfs-ost", 
-             repo = "ss3-doc", 
-             title = issue_title,
-             body = issue_body)
-          }
-        shell: Rscript {0}
+# name: ss3-pr-open-issues.yml
+# on:
+#   pull_request:
+#     types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review']
+#   pull_request_target:
+#     types:
+#       - closed
+# jobs:
+#   ss3-pr-open-issues:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     env:
+#       GITHUB_PAT: ${{ secrets.GH_PAT }}
+#     steps:
+#       - name: Update Ubuntu packages
+#         run: sudo apt update && sudo apt install -y libcurl4-openssl-dev
+#       - name: Get Pull Request Number
+#         run: |
+#           echo github.event.pull_request.number = ${{ github.event.pull_request.number }}
+#       - uses: actions/checkout@v3
+#       - uses: r-lib/actions/setup-r@v2
+#        # with:
+#        #   use-public-rspm: true
+#       - name: install the gh and curl pkgs
+#         run:
+#           Rscript -e "install.packages('gh')"
+#       - name: Get pr info and save
+#         run: |
+#           Rscript -e 'info <- gh::gh("GET /repos/{owner}/{repo}/pulls/{pull_number}", 
+#             owner = "nmfs-ost", 
+#             repo = "ss3-source-code",
+#             pull_number = "${{ github.event.pull_request.number }}")
+#           saveRDS(info, file = "info.RDS")'
+#       - name: Post issues, if needed
+#         run: |
+#           info <- readRDS("info.RDS")
+#           pr_body  <- strsplit(info$body, "\n" )[[1]]
+#           pr_body <- gsub("\r", "",  pr_body, fixed = TRUE)
+#           # Get info on which repos need open issues, if a change log entry is needed.
+#           # allow some flexibility for getting the spacing wrong, which is easy to do.
+#           # look for checklist items like - []
+#           needs_changes <- grep("-\\s*\\[\\s*\\]", pr_body, ignore.case = TRUE, value = TRUE)
+#           issue_title <- paste0("Changes need for SS3 PR ",  info$number)
+#           issue_body <- paste0("Changes will be needed in this ",
+#             "repository due to the opening of SS3 Pull Request ", 
+#             info$number, ".\n", 
+#             "Please see ", 
+#             "https://github.com/nmfs-ost/ss3-source-code/pull/", 
+#             info$number, " and its associated issues for more information.",
+#             "\n\nNote: this issue was created automatically via GitHub ",
+#             "Action using the workflow in \n",
+#             "https://github.com/nmfs-ost/ss3-source-code/blob/main/.github/workflows/ss3-pr-open-issues.yml")
+#           # post r4ss issue if needed
+#           if (length(grep("r4ss", needs_changes)) == 1) {
+#             gh::gh("POST /repos/{owner}/{repo}/issues",
+#              owner = "r4ss", 
+#              repo = "r4ss", 
+#              title = issue_title,
+#              body = issue_body)
+#           }
+#           # post SSI issue if needed
+#           if (length(grep("SSI", needs_changes)) == 1) {
+#                       gh::gh("POST /repos/{owner}/{repo}/issues",
+#              owner = "nmfs-ost", 
+#              repo = "ssi", 
+#              title = issue_title,
+#              body = issue_body)
+#           }
+#           # post documentation issue, if needed
+#           if (length(grep("manual", needs_changes)) == 1) {
+#             gh::gh("POST /repos/{owner}/{repo}/issues",
+#              owner = "nmfs-ost", 
+#              repo = "ss3-doc", 
+#              title = issue_title,
+#              body = issue_body)
+#           }
+#         shell: Rscript {0}

SS_write_report.tpl

@@ -2395,7 +2395,7 @@ FUNCTION void write_bigoutput()
         temp = abs(header_a_rd(f, i, 2));
         if (temp > 999)
           temp -= 1000;
-        SS2out << f << " " << fleetname(f) << " " << fleet_area(f) << Show_Time2(ALK_time) << " " << data_time(ALK_time, f, 1) << " " << data_time(ALK_time, f, 3) << " " << gen_a(f, i) << " " << mkt_a(f, i) << " " << ageerr_type_a(f, i) << " " << Lbin_lo(f, i) << " " << Lbin_hi(f, i) << " ";
+        SS2out << f << " " << fleetname(f) << " " << fleet_area(f) << Show_Time2(ALK_time) << " " << data_time(ALK_time, f, 1) << " " << data_time(ALK_time, f, 3) << " " << gen_a(f, i) << " " << mkt_a(f, i) << " " << ageerr_type_a(f, i) << " " << len_bins(Lbin_lo(f, i)) << " " << len_bins(Lbin_hi(f, i)) << " ";
         if (header_a(f, i, 2) < 0 && in_superperiod == 0)
         {
           SS2out << " start ";