5 write muskrat data prep scripts

.github/PR_get_muskrat_data.md

@@ -0,0 +1,16 @@
+## Brief description
+
+This is an **automatically generated PR**. 
+The following steps are all automatically performed:
+
+- download muskrat management data from gbif 
+- cleanup and link data with provinces & communes 
+- export neccessary files 
+
+All the steps above are triggered by `./.github/workflows/get_muskrat_data.yaml`<sup>1</sup>
+and executed by `./src/get_muskrat_data.R` and assisted by 
+`./script/install_packages_muskrat.R`. 
+
+Changes to the PR description can be made at `./.github/PR_get_muskrat_data.md`
+
+<sup>1</sup>set to trigger every monday between January & December.

.github/workflows/get_muskrat_data.yaml

@@ -0,0 +1,81 @@
+on:
+  schedule: 
+   - cron: '0 0 * 1-12 1'
+
+
+name: get_muskrat_data
+
+jobs:
+  fetch-data:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,   r: 'release'}
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_TOKEN: ${{ secrets.AUTOMATISATION }}
+      gbif_user: ${{ secrets.GBIF_USER }}
+      email: ${{ secrets.GBIF_EMAIL }}
+      gbif_pwd: ${{ secrets.GBIF_PWD }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.AUTOMATISATION }}
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install linux libraries
+        run: |
+          sudo apt install libsodium-dev
+          sudo apt-get install libcurl4-openssl-dev
+          sudo apt-get install libgdal-dev libproj-dev
+          sudo apt install libudunits2-dev
+
+      - name: Install R packages
+        run: |
+          source("src/install_packages_muskrat.R")
+        shell: Rscript {0}
+
+      - name: Management prep
+        run: |
+          source("src/get_muskrat_data.R")
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        uses: devops-infra/action-commit-push@master
+        with:
+          github_token: ${{ secrets.AUTOMATISATION }}
+          commit_prefix: "[AUTO]"
+          commit_message: "get muskrat data"
+          target_branch: automatic-management-prep
+
+      - name: Get branch name
+        run: |
+          git branch --show-current
+
+      - name: Create pull request
+        uses: devops-infra/action-pull-request@v0.4.2
+        with:
+          github_token: ${{ secrets.AUTOMATISATION }}
+          target_branch: main
+          title: "[AUTO] get muskrat data"
+          template: .github/PR_get_muskrat_data.md
+          reviewer: SanderDevisscher
+          label: automated workflow
+          get_diff: false

.gitignore

@@ -37,5 +37,9 @@ vignettes/*.pdf
 
 # R Environment Variables
 .Renviron
+
+# too large files
 data/interim/df_timeseries.tsv
 data/output/full_timeseries.csv
+*.zip
+