changing to cookiecutter like template

.github/ISSUE_TEMPLATE/general-purpose.md

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+Your issue may already be reported! Please search on the
+[issue tracker][issue-tracker] before creating one.
+
+## Expected behavior
+
+<!--- If you're describing a bug, tell us what should happen -->
+
+<!--- If you're suggesting a change/improvement, tell us how it should work -->
+
+## Current behavior
+
+<!--- If describing a bug, tell us what happens instead of the expected
+behavior -->
+
+<!--- If suggesting a change/improvement, explain the difference from current
+behavior -->
+
+## Possible solution
+
+<!--- Not obligatory, but suggest a fix/reason for the bug, -->
+
+<!--- or ideas how to implement the addition or change -->
+
+## Context
+
+<!--- How has this issue affected you? What are you trying to accomplish? -->
+
+<!--- Providing context helps us come up with a solution that is most useful in
+the real world -->
+
+## Steps to reproduce (FOR BUGS)
+
+<!--- Provide a link to a live example, or an unambiguous set of steps to -->
+
+<!--- reproduce this bug. Include code to reproduce, if relevant -->
+
+1.
+
+## Your environment (FOR BUGS)
+
+<!--- Include as many relevant details about the environment you experienced the
+bug in -->
+
+- Version used:
+- Browser Name and version:
+- Operating System and version (desktop or mobile):
+- Link to your project:
+
+[issue-tracker]: https://github.com/elixir-cloud-aai/ga4gh-sdk/issues

.github/actions/ci.yml

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+name: GitHub CI/CD Workflow	
+
+on: [push, pull_request]	
+
+jobs:	
+  build:	
+
+    runs-on: ubuntu-latest	
+    container:	
+      image: ubuntu:24.04	
+    env:	
+      OPENSSL_DIR: /usr/include/openssl	
+      OPENSSL_LIB_DIR: /usr/lib/x86_64-linux-gnu	
+      OPENSSL_INCLUDE_DIR: /usr/include/openssl	
+
+    steps:	
+    - name: Install dependencies	
+      run: |	
+        apt-get update	
+        apt-get install -y curl git build-essential libssl-dev 	
+        
+    - uses: actions/checkout@v4 # checkout the repository	
+    - name: Install Rust	
+      run: |
+        curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+        echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+    - name: Set up JDK 11 # required for build-models.sh	
+      uses: actions/setup-java@v3
+      with:	
+        distribution: 'adopt'	
+        java-version: '11'	
+
+    - name: Install Go	
+      uses: actions/setup-go@v4
+      with:	
+        go-version: '^1.22'  	
+    - name: Install Funnel	
+      run: |	
+          if [ -d "funnel" ]; then rm -Rf funnel; fi	
+          git clone https://github.com/ohsu-comp-bio/funnel.git	
+          cd funnel && make && make install && cd ..	
+    - uses: actions/checkout@v4 # checkout the repository	
+    - name: Build models	
+      run: |	
+        bash ./build-models.sh	
+    - name: Build	
+      run: |	
+        cargo build --verbose	
+    - name: Run tests	
+      run: |	
+        bash ./run-tests.sh	
+    - name: Lint	
+      run: |	
+        cargo clippy -- -D warnings	
+    - name: Format	
+      run: |	
+        cargo fmt -- ./lib/src/serviceinfo/models/*.rs # workaround to fix autogenerated code formatting	
+        cargo fmt -- ./lib/src/tes/models/*.rs	
+        cargo fmt -- --check

.github/actions/local.yml

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+name: Local CI/CD Workflow	
+
+on: workflow_dispatch
+
+jobs:	
+  build:	
+
+    runs-on: ubuntu-latest	
+    container:	
+      image: ubuntu:24.04	
+    env:	
+      OPENSSL_DIR: /usr/include/openssl	
+      OPENSSL_LIB_DIR: /usr/lib/x86_64-linux-gnu	
+      OPENSSL_INCLUDE_DIR: /usr/include/openssl	
+
+    steps:	
+
+    - name: Cache Rust dependencies	
+      uses: actions/cache@v3
+      with:	
+        path: ~/.cargo	
+        key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}	
+        restore-keys: ${{ runner.os }}-cargo-	
+
+    - name: Cache Rust build output	
+      uses: actions/cache@v3
+      with:	
+        path: target	
+        key: ${{ runner.os }}-build-${{ hashFiles('**/Cargo.lock') }}	
+        restore-keys: ${{ runner.os }}-build-	
+
+    - name: Cache Maven dependencies	
+      uses: actions/cache@v3
+      with:	
+        path: ~/.m2/repository	
+        key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}	
+        restore-keys: ${{ runner.os }}-maven-	
+
+    - name: Cache Go modules	
+      uses: actions/cache@v3
+      with:	
+        path: ~/.cache/go-build	
+        key: ${{ runner.os }}-go-${{ hashFiles('**/go.sum') }}	
+        restore-keys: ${{ runner.os }}-go-	
+
+    - name: Cache Funnel dependencies	
+      uses: actions/cache@v3
+      with:	
+        path: ~/funnel/build	
+        key: ${{ runner.os }}-funnel-${{ hashFiles('**/funnel/*') }}	
+        restore-keys: ${{ runner.os }}-funnel-	
+
+    - uses: actions/checkout@v4 # checkout the repository	
+    - name: Install Rust	
+      run: |
+        curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+        echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+    - name: Set up JDK 11 # required for build-models.sh	
+      uses: actions/setup-java@v3
+      with:	
+        distribution: 'adopt'	
+        java-version: '11'	
+
+    - name: Install Go	
+      uses: actions/setup-go@v4
+      with:	
+        go-version: '^1.22'  	
+    - name: Install Funnel	
+      run: |	
+          if [ -d "funnel" ]; then rm -Rf funnel; fi	
+          git clone https://github.com/ohsu-comp-bio/funnel.git	
+          cd funnel && make && make install && cd ..	
+    - uses: actions/checkout@v4 # checkout the repository	
+    - name: Build models	
+      run: |	
+        . $HOME/.cargo/env	
+        bash ./build-models.sh	
+    - name: Build	
+      run: |	
+        . $HOME/.cargo/env	
+        cargo build --verbose	
+    - name: Run tests	
+      run: |	
+        . $HOME/.cargo/env	
+        bash ./run-tests.sh	
+    - name: Lint	
+      run: |	
+        . $HOME/.cargo/env	
+        cargo clippy -- -D warnings	
+    - name: Format	
+      run: |	
+        . $HOME/.cargo/env	
+        # rustup install nightly – fails for some reason	
+        # rustup default nightly	
+        cargo fmt -- ./lib/src/serviceinfo/models/*.rs # workaround to fix autogenerated code formatting	
+        cargo fmt -- ./lib/src/tes/models/*.rs	
+        cargo fmt -- --check # --config-path ./rustfmt.toml	

.github/actions/setup/poetry/action.yaml

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+# ---
+# name: Setup Python and Poetry Action
+# description: Configure system, Python, Poetry and deps and cache management.
+
+# inputs:
+#   os:
+#     default: ubuntu-latest
+#     description: The operating system to use
+#   python-version:
+#     default: '3.11'
+#     description: The version of Python to use
+#   poetry-version:
+#     default: '1.8.2'
+#     description: The version of Poetry to install
+#   poetry-install-options:
+#     default: ''
+#     description: Additional options to pass to poetry install
+#   poetry-export-options:
+#     default: ''
+#     description: Options to pass to poetry export for hash generation for cache
+#                  invalidation
+
+# runs:
+#   using: composite
+#   steps:
+#     - uses: 'actions/setup-python@v5'
+#       id: setup-python
+#       with:
+#         python-version: '${{ inputs.python-version }}'
+
+#     - name: Setup pipx environment Variables
+#       id: pipx-env-setup
+#       # pipx default home and bin dir are not writable by the cache action
+#       # so override them here and add the bin dir to PATH for later steps.
+#       # This also ensures the pipx cache only contains poetry
+#       run: |
+#         SEP="${{ !startsWith(runner.os, 'windows') && '/' || '\\' }}"
+#         PIPX_CACHE="${{ github.workspace }}${SEP}pipx_cache"
+#         echo "pipx-cache-path=${PIPX_CACHE}" >> $GITHUB_OUTPUT
+#         echo "pipx-version=$(pipx --version)" >> $GITHUB_OUTPUT
+#         echo "PIPX_HOME=${PIPX_CACHE}${SEP}home" >> $GITHUB_ENV
+#         echo "PIPX_BIN_DIR=${PIPX_CACHE}${SEP}bin" >> $GITHUB_ENV
+#         echo "PIPX_MAN_DIR=${PIPX_CACHE}${SEP}man" >> $GITHUB_ENV
+#         echo "${PIPX_CACHE}${SEP}bin" >> $GITHUB_PATH
+#       shell: bash
+
+#     - name: Pipx cache
+#       id: pipx-cache
+#       uses: actions/cache@v4
+#       with:
+#         path: ${{ steps.pipx-env-setup.outputs.pipx-cache-path }}
+#         key: ${{ runner.os }}-python-
+#              ${{ steps.setup-python.outputs.python-version }}-
+#              pipx-${{ steps.pipx-env-setup.outputs.pipx-version }}-
+#              poetry-${{ inputs.poetry-version }}
+
+#     - name: Install poetry
+#       if: steps.pipx-cache.outputs.cache-hit != 'true'
+#       id: install-poetry
+#       shell: bash
+#       run: |
+#         pipx install poetry \
+#         --python "${{ steps.setup-python.outputs.python-path }}"
+
+#     - name: Read poetry cache location
+#       id: poetry-cache-location
+#       shell: bash
+#       run: |
+#         echo "poetry-venv-location=$(poetry config virtualenvs.path)" \
+#         >> $GITHUB_OUTPUT
+
+#     - name: Generate hash only for required deps
+#       run: |
+#         poetry export ${{ inputs.poetry-export-options }} \
+#         --format=requirements.txt --output=requirements.txt
+#         echo "DEP_HASH=$(sha256sum requirements.txt | cut -d ' ' -f 1)" \
+#          >> $GITHUB_ENV
+#       shell: bash
+
+#     - uses: actions/cache@v4
+#       name: Poetry cache
+#       with:
+#         path: ${{ steps.poetry-cache-location.outputs.poetry-venv-location }}
+#         key: ${{ runner.os }}-[python-
+#              ${{ steps.setup-python.outputs.python-version }}]-[
+#              ${{ env.DEP_HASH }}]-[${{ inputs.poetry-install-options }}]
+
+#     - name: 'Poetry install'
+#       if: steps.poetry-cache.outputs.cache-hit != 'true'
+#       shell: bash
+#       run: poetry install ${{ inputs.poetry-install-options }} --no-interaction
+# ...

.github/workflows/code_quality.yaml

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+---
+name: Code quality
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      cargo-path: ${{ steps.export-cargo-path.outputs.path }}
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: |
+          apt-get update
+          apt-get install -y curl git build-essential libssl-dev
+
+      - name: Install Rust
+        id: install-rust
+        run: |
+          curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      - name: Export cargo path
+        id: export-cargo-path
+        run: echo "path=$HOME/.cargo/bin" >> $GITHUB_OUTPUT
+
+  lint:
+    needs: setup
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Rust
+        run: echo "$GITHUB_PATH" >> $GITHUB_PATH
+
+      - name: Lint
+        run: cargo clippy -- -D warnings
+
+  format:
+    needs: setup
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Rust
+        run: echo "$GITHUB_PATH" >> $GITHUB_PATH
+
+      - name: Format
+        run: |
+          cargo fmt -- ./lib/src/serviceinfo/models/*.rs # workaround to fix autogenerated code formatting
+          cargo fmt -- ./lib/src/tes/models/*.rs
+          cargo fmt -- --check
+
+  spell-check:
+    needs: setup
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Rust
+        run: echo "$GITHUB_PATH" >> $GITHUB_PATH
+
+      - name: Check spellings
+        run: cargo spellcheck
+...