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Merge branch 'main' into predator_fleet
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@k-doering-NOAA
k-doering-NOAA authored Sep 21, 2021
2 parents 35f1bea + cfbe093 commit 48a5543
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123 changes: 116 additions & 7 deletions .github/workflows/build-centos.yml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,12 @@
name: build-centos

# Controls when the action will run. Triggers the workflow on push or pull request
# events but only for the main branch
on: [workflow_dispatch]
# on: Controls when the action will run. workflow_dispatch is a manual trigger.
# This workflow also runs when a tag begining with v is pushed.
on:
workflow_dispatch:
push:
tags:
- "v*"

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
Expand All @@ -12,11 +16,9 @@ jobs:
# Limit run time to 15 min to avoid wasting action minutes.
timeout-minutes: 15
container:
image: centos:7.9.2009
image: centos:8.3.2011
# 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
- uses: actions/checkout@v2

- name: Get essential tools needed on docker
run: |
Expand All @@ -25,12 +27,117 @@ jobs:
yum install -y zip unzip
yum install -y sudo
yum install -y gcc-c++
yum install -y git
- name: see git version
run: git --version

- uses: actions/checkout@v2

- name: install R
run: |
dnf install -y epel-release
yum install -y dnf-plugins-core
dnf install -y 'dnf-command(config-manager)'
dnf config-manager --set-enabled powertools
yum install -y R
- name: Get admb and put in path
run: |
wget https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-linux.zip
sudo unzip admb-12.3-linux.zip -d /usr/local/bin
sudo chmod 755 /usr/local/bin/admb-12.3/bin/admb
echo "/usr/local/bin/admb-12.3/bin" >> $GITHUB_PATH
- name: Fetch tags
run: |
git fetch --tags
git fetch --prune --unshallow || true
- name: Get the last tag
id: get-latest-tag
run: |
git tag
latest_tag=$(git describe --abbrev=0 --tags)
latest_tag_commit=$(git rev-list -n 1 $latest_tag)
latest_commit=$(git rev-list HEAD -n 1)
echo "::set-output name=tag::${latest_tag}"
echo "::set-output name=tag_commit::${latest_tag_commit}"
echo "::set-output name=commit::${latest_commit}"
# uses: actions-ecosystem/action-get-latest-tag@v1 # for linux


- name: pull the last tag value to use in the Rscript
id: get-version
run: |
echo "${{ steps.get-latest-tag.outputs.tag }}" > .github/last_tag.txt
echo "${{ steps.get-latest-tag.outputs.tag_commit }}" > .github/last_tag_commit.txt
echo "${{ steps.get-latest-tag.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}

# Runs a set of commands using the runners shell
- name: Build stock synthesis
Expand All @@ -46,10 +153,12 @@ jobs:
sha256sum SS330/ss
sha256sum SS330/ss_opt
- name: Delete unneeded files
- name: Delete unneeded files and change exe names
run: |
cd SS330
rm *.obj *.htp *.cpp ss_opt.tpl
mv ss ss_linux
mv ss_opt ss_opt_linux
- name: Archive the exes as tar.
if: success()
Expand Down
105 changes: 103 additions & 2 deletions .github/workflows/build-mac.yml
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,12 @@
name: build-mac

# on: Controls when the action will run. workflow_dispatch is a manual trigger.
on: [workflow_dispatch]
# This workflow also runs when a tag begining with v is pushed.
on:
workflow_dispatch:
push:
tags:
- "v*"

jobs:
build-mac:
Expand All @@ -18,6 +23,100 @@ jobs:
unzip admb-12.3.zip -d /usr/local/bin
ls /usr/local/bin
echo "/usr/local/bin/admb-12.3/bin" >> $GITHUB_PATH
- name: Set up R
uses: r-lib/actions/setup-r@master
with:
r-version: 'release'

- name: Fetch tags
run: |
git fetch --tags
git fetch --prune --unshallow || true
- name: Get the last tag
id: get-latest-tag
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 "::set-output name=tag::${latest_tag}"
echo "::set-output name=tag_commit::${latest_tag_commit}"
echo "::set-output name=commit::${latest_commit}"
# uses: actions-ecosystem/action-get-latest-tag@v1 # for linux


- name: pull the last tag value to use in the Rscript
id: get-version
run: |
echo "${{ steps.get-latest-tag.outputs.tag }}" > .github/last_tag.txt
echo "${{ steps.get-latest-tag.outputs.tag_commit }}" > .github/last_tag_commit.txt
echo "${{ steps.get-latest-tag.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
run: |
Expand All @@ -32,10 +131,12 @@ jobs:
shasum -a 256 SS330/ss
shasum -a 256 SS330/ss_opt
- name: Delete unneeded files
- name: Delete unneeded files and change exe names
run: |
cd SS330
rm *.obj *.htp *.cpp ss_opt.tpl
mv ss ss_osx
mv ss_opt ss_opt_osx
- name: Archive the binaries
if: success()
Expand Down
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