sync dev and main

.github/PULL_REQUEST_TEMPLATE/dev_pr.md

@@ -0,0 +1,25 @@
+PRs into `dev` contained all necessary info. They have already been approved.
+Please provide the information below so `main` can be synced with `dev`:
+
+### List PRs
+
+List the PRs that were merged into `dev` that will be pulled into `main` and any issues they fix:
+
+* PR #? which fixes #?
+
+### Types of changes
+
+What types of changes does this pull request introduce? Put an `x` in the boxes that apply.
+This will inform the new release number.
+
+- [ ] Fix (non-breaking change which fixes a bug)
+- [ ] Feature (non-breaking change which adds or changes functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Other change (if none of the other choices apply)
+
+### Reviewer instructions
+
+The underlying PRs should have been reviewed. Please check that the proposed merge is correct before approving.
+If any checkboxes other than "Other change" have been selected please prepare the following file changes for a new release version:
+- [ ] NEWS.md - add release notes
+- [ ] DESCRIPTION - increment the version number according to [Semantic Versioning](https://semver.org)

.github/pull_request_template.md

@@ -0,0 +1,36 @@
+Your commits explain the `who`, `what`, `where` and `when` of these changes. Your code shows the `how`. You do not need to reiterate this. This PR should complete the picture by explaining `why` these changes are necessary.
+Please complete the fields below, replacing or removing placeholder text where necessary:
+
+### Justification
+
+Please describe the importance/impact of the problem and a description of how the changes in this pull request will address, resolve or improve it. This section should sufficiently explain to reviewers why these changes should be approved.
+If the proposed changes should close an issue, be sure to link to it below:  
+Fixes #?
+
+### Types of changes
+
+What types of changes does this pull request introduce? Put an `x` in the boxes that apply.
+This will inform the new release number.
+
+- [ ] Fix (non-breaking change which fixes a bug)
+- [ ] Feature (non-breaking change which adds or changes functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Other change (if none of the other choices apply)
+
+### Further comments
+
+If this is a relatively large or complex change, kick off a discussion by explaining why you chose the solution you did, what alternatives you considered, problems you may have encountered, etc.
+
+### Reviewer instructions
+
+Assign at least 2 reviewers: 
+* one of which should be a maintainer of this repo, 
+* the others should be familiar with the subject or problem.
+
+Please detail the process reviewers will need to follow to properly test these changes. It is especially helpful to identify the exact code needed to conduct a local build/review/test and to specify any aspects of the testing that may not be obvious.
+
+### Formatting
+
+This repo contains an `air.toml` file that automatically formats code to a set of standards.
+It is preferred that contributors and reviewers install the [Air](https://posit-dev.github.io/air/) formatting tool.
+Code submitted in this pull request will be automatically checked for correct formatting.

.github/workflows/R-CMD-check.yaml

@@ -30,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/format-check.yml

@@ -0,0 +1,24 @@
+# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+  workflow_dispatch:
+
+name: format-check.yaml
+
+permissions: read-all
+
+jobs:
+  format-check:
+    name: format-check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install
+        uses: posit-dev/setup-air@v1
+
+      - name: Check
+        run: air format . --check

.github/workflows/format-suggest.yml

@@ -0,0 +1,31 @@
+# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
+
+on:
+  pull_request:
+
+name: format-suggest.yaml
+
+jobs:
+  format-suggest:
+    name: format-suggest
+    runs-on: ubuntu-latest
+
+    permissions:
+      # Required to push suggestion comments to the PR
+      pull-requests: write
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install
+        uses: posit-dev/setup-air@v1
+
+      - name: Format
+        run: air format .
+
+      - name: Suggest
+        uses: reviewdog/action-suggester@v1
+        with:
+          level: error
+          fail_level: error
+          tool_name: air

.github/workflows/pkgdown.yml

@@ -11,7 +11,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
       - uses: r-lib/actions/setup-r@v2
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -23,7 +23,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v3
+        uses: actions/cache@v5
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

.github/workflows/update_mdat_data.yaml

@@ -0,0 +1,69 @@
+name: pull data from MDAT data hub
+
+on:
+  workflow_dispatch:
+  schedule:
+    # uses UTC/GMT time (+ 5 hrs)
+    ## put on HOLD temporarily
+    - cron: "0 17 * * 6" # Every Saturday at 1200 hrs = 1700 UTC
+
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+      pull-requests: write
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Set up pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.2.0'
+
+      - name: Install system dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+
+      - name: Install command line packages
+        run: |
+          sudo apt update
+          sudo apt-get install libcurl4-openssl-dev libgit2-dev libudunits2-dev
+        shell: bash
+
+      - name: Install packages
+        run: |
+          install.packages(c("remotes","here","httr2","jsonlite","dplyr","glue"))
+          remotes::install_github("NEFSC/NEFSC-Spatial")
+        shell: Rscript {0}
+
+      - name: Pull MDAT data and save to repo
+        run: |
+          options(timeout = 60 * 60 * 6)
+          source(here::here("data-raw/get_mdat_for_package.R"))
+          get_mdat_for_package(overwrite = TRUE)
+        shell: Rscript {0}
+
+      # Create the Pull Request from dev if changes are detected
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v8.1.1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "chore: update external data"
+          title: "Automated Data Update"
+          body: |
+            This is an automated pull request containing the latest fetched data.
+            Please review the changes before merging.
+          branch: automated-data-update
+          base: dev
+          delete-branch: false