run notebooks on coast repo (#631)

* run notebooks on coast repo * updated old dir on ls * update to run on very pull request * dropping python version to match conda * fix number 4242 * renamed to make less confusing * logging? ok this is bad but it will help see what git is doing
British-Oceanographic-Data-Centre · Nov 6, 2023 · 78a63af · 78a63af
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diff --git a/.github/workflows/markdown-altimetry.yml b/.github/workflows/markdown-altimetry.yml
@@ -0,0 +1,44 @@
+name: notebook_to_md (altimetry)
+on: pull_request
+jobs:
+  commit-notebooks:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Checkout site
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive # Fetch Hugo themes and all extra projects
+          fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod
+          path: site
+
+      - name: Checkout coast
+        uses: actions/checkout@v3
+        with:
+          repository: British-Oceanographic-Data-Centre/COAsT
+          ref: develop
+          path: external
+
+      - name: Prepare environement
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: coast
+          environment-file: external/environment.yml
+          python-version: 3.8.10
+      - name: prep exec notebooks
+        run: |
+          conda info
+          conda list
+          conda config --show
+          cd $GITHUB_WORKSPACE/external
+          sudo apt install wget unzip -y
+          wget -q https://linkedsystems.uk/erddap/files/COAsT_example_files/COAsT_example_files.zip
+          unzip COAsT_example_files.zip && mv COAsT_example_files ./example_scripts/notebook_tutorials/runnable_notebooks/altimetry/example_files
+          mkdir -p ./example_scripts/notebook_tutorials/markdown/altimetry
+          ls ./example_scripts/notebook_tutorials
+          pip install .
+          mv config ./example_scripts/notebook_tutorials/runnable_notebooks/altimetry/config
+          bash notebook_to_md.sh altimetry
+          
diff --git a/.github/workflows/markdown-general.yml b/.github/workflows/markdown-general.yml
@@ -0,0 +1,43 @@
+name: notebook_to_md (general)
+on: pull_request
+jobs:
+  commit-notebooks:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Checkout site
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive # Fetch Hugo themes and all extra projects
+          fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod
+          path: site
+
+      - name: Checkout coast
+        uses: actions/checkout@v3
+        with:
+          repository: British-Oceanographic-Data-Centre/COAsT
+          ref: develop
+          path: external
+
+      - name: Prepare environement
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: coast
+          environment-file: external/environment.yml
+          python-version: 3.8.10
+      - name: prep exec notebooks
+        run: |
+          conda info
+          conda list
+          conda config --show
+          cd $GITHUB_WORKSPACE/external
+          sudo apt install wget unzip -y
+          wget -q https://linkedsystems.uk/erddap/files/COAsT_example_files/COAsT_example_files.zip
+          unzip COAsT_example_files.zip && mv COAsT_example_files ./example_scripts/notebook_tutorials/runnable_notebooks/general/example_files          
+          mkdir -p ./example_scripts/notebook_tutorials/markdown/general
+          ls ./example_scripts/notebook_tutorials
+          pip install .
+          mv config ./example_scripts/notebook_tutorials/runnable_notebooks/general/config
+          bash notebook_to_md.sh general
diff --git a/.github/workflows/markdown-gridded.yml b/.github/workflows/markdown-gridded.yml
@@ -0,0 +1,43 @@
+name: notebook_to_md (gridded)
+on: pull_request
+jobs:
+  commit-notebooks:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Checkout site
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive # Fetch Hugo themes and all extra projects
+          fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod
+          path: site
+
+      - name: Checkout coast
+        uses: actions/checkout@v3
+        with:
+          repository: British-Oceanographic-Data-Centre/COAsT
+          ref: develop
+          path: external
+
+      - name: Prepare environement
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: coast
+          environment-file: external/environment.yml
+          python-version: 3.8.10
+      - name: prep exec notebooks
+        run: |
+          conda info
+          conda list
+          conda config --show
+          cd $GITHUB_WORKSPACE/external
+          sudo apt install wget unzip -y
+          wget -q https://linkedsystems.uk/erddap/files/COAsT_example_files/COAsT_example_files.zip
+          unzip COAsT_example_files.zip && mv COAsT_example_files ./example_scripts/notebook_tutorials/runnable_notebooks/gridded/example_files
+          mkdir -p ./example_scripts/notebook_tutorials/markdown/gridded
+          ls ./example_scripts/notebook_tutorials
+          pip install .
+          mv config ./example_scripts/notebook_tutorials/runnable_notebooks/gridded/config
+          bash notebook_to_md.sh gridded
diff --git a/.github/workflows/markdown-profile.yml b/.github/workflows/markdown-profile.yml
@@ -0,0 +1,43 @@
+name: notebook_to_md (profile)
+on: pull_request
+jobs:
+  commit-notebooks:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Checkout site
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive # Fetch Hugo themes and all extra projects
+          fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod
+          path: site
+
+      - name: Checkout coast
+        uses: actions/checkout@v3
+        with:
+          repository: British-Oceanographic-Data-Centre/COAsT
+          ref: develop
+          path: external
+
+      - name: Prepare environement
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: coast
+          environment-file: external/environment.yml
+          python-version: 3.8.10
+      - name: prep exec notebooks
+        run: |
+          conda info
+          conda list
+          conda config --show
+          cd $GITHUB_WORKSPACE/external
+          sudo apt install wget unzip rsync -y
+          wget -q https://linkedsystems.uk/erddap/files/COAsT_example_files/COAsT_example_files.zip
+          unzip COAsT_example_files.zip && mv COAsT_example_files ./example_scripts/notebook_tutorials/runnable_notebooks/profile/example_files          
+          mkdir -p ./example_scripts/notebook_tutorials/markdown
+          ls ./example_scripts/notebook_tutorials
+          pip install .
+          mv config ./example_scripts/notebook_tutorials/runnable_notebooks/profile/config
+          bash notebook_to_md.sh profile
diff --git a/.github/workflows/markdown-tidegauge.yml b/.github/workflows/markdown-tidegauge.yml
@@ -0,0 +1,43 @@
+name: notebook_to_md (tidegauge)
+on: pull_request
+jobs:
+  commit-notebooks:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Checkout site
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive # Fetch Hugo themes and all extra projects
+          fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod
+          path: site
+
+      - name: Checkout coast
+        uses: actions/checkout@v3
+        with:
+          repository: British-Oceanographic-Data-Centre/COAsT
+          ref: develop
+          path: external
+
+      - name: Prepare environement
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: coast
+          environment-file: external/environment.yml
+          python-version: 3.8.10
+      - name: prep exec notebooks
+        run: |
+          conda info
+          conda list
+          conda config --show
+          cd $GITHUB_WORKSPACE/external
+          sudo apt install wget unzip -y
+          wget -q https://linkedsystems.uk/erddap/files/COAsT_example_files/COAsT_example_files.zip
+          unzip COAsT_example_files.zip && mv COAsT_example_files ./example_scripts/notebook_tutorials/runnable_notebooks/tidegauge/example_files
+          mkdir -p ./example_scripts/notebook_tutorials/markdown/tidegauge
+          ls ./example_scripts/notebook_tutorials
+          pip install .
+          mv config ./example_scripts/notebook_tutorials/runnable_notebooks/tidegauge/config
+          bash notebook_to_md.sh tidegauge
diff --git a/.github/workflows/pylint_checking.yml b/.github/workflows/pylint_checking.yml
@@ -1,7 +1,7 @@
 name: Pylint
 on: pull_request
 jobs:
-  formatting:
+  pylinting:
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -31,11 +31,14 @@ jobs:
             git config --global user.email "[email protected]"
             git config --global author.email "[email protected]"
             git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY
+            git status
             git checkout -b $GITHUB_HEAD_REF
             git pull --rebase origin $GITHUB_HEAD_REF
+            git status
             echo "NEW_SCORE is greater than THREESHOLD_SCORE"
             echo "Updating THREESHOLD_SCORE"
             echo "$NEW_SCORE" > .pylint-score
+            git status
             git commit -am "Update pylint threeshold score"
             git push --set-upstream origin $GITHUB_HEAD_REF
           elif [ "$(echo "$NEW_SCORE == $THREESHOLD_SCORE" | bc -l)" -eq 1 ] ; then

diff --git a/README.md b/README.md
@@ -24,6 +24,9 @@ It's aim is to deliver a flexible, community-ready framework for assessing kilom
 
 Documentation can be found [here](https://british-oceanographic-data-centre.github.io/COAsT/docs/).
 
+![PyPI version](https://badge.fury.io/py/COAsT.svg)
+![Anaconda version](https://anaconda.org/bodc/coast/badges/version.svg)
+
 ## Notes on Object Structure and Loading (for contributors):
 
 COAsT is an object-orientated package, meaning that data is stored within Python object