Initial commit: Add core functionality

.clabot

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+{
+  "contributors": "https://script.google.com/macros/s/AKfycbxMTfPIVni3XIT1gWJyt6ujOe3xMw3kdWpFbVQ6zZ1MS4eLiJCB2Jth3a1mrkoYHTIW/exec",
+  "message": "Thank you for your contribution. We require contributors to sign our Contributor License Agreement (CLA). We do not have a signed CLA on file for you. In order for us to review and merge your code, please sign our CLA [here](https://forms.gle/o5F7YiLCZ96vfhQ18). After you signed, you can comment on this PR with `@cla-bot check` to trigger another check.",
+  "label": "CLA signed",
+  "recheckComment": "Thanks for tagging me. I looked for a signed form under your signature again, and updated the status on this PR. If the check was successful, no further action is needed. If the check was unsuccessful, please see the instructions in my first comment."
+}

.github/workflows/build.yml

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+name: Python package
+
+on:
+  push:
+    branches:
+      - main 
+      - 'main*'
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.8]
+        include:
+          - os: ubuntu-latest
+            path: ~/.cache/pip
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          
+      - name: Run the formatter
+        run: |
+          make format
+
+      - name: Check that no binary files have been added to repo
+        run: |
+          make check_for_binary
+
+      - name: Build package
+        run: |
+          make build
+
+        run: |
+          make test

.github/workflows/doc-coverage.yml

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+name: PR Status
+# Adapted from https://github.com/shift-happens-benchmark/icml-2022/blob/main/.github/workflows/pr-status.yml
+# Apache 2.0 licensed
+
+
+on:
+  pull_request:
+    branches:
+      - main 
+      - 'main*'
+
+jobs:
+  documentation-status:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8']
+
+    steps:
+    # NOTE(stes) currently not used, we check
+    # the entire codebase now by default. 
+    #- uses: actions/checkout@v3
+    #  with:
+    #    ref: main
+    - uses: actions/checkout@v3
+    - uses: actions/cache@v1
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip
+        restore-keys: |
+          ${{ runner.os }}-pip
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package 
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install interrogate==1.5.0
+    - name: documentation
+      id: documentation
+      run: |
+        RESULT=$(make --silent interrogate)
+        RESULT=$(tail -n +3 <<< $RESULT)
+        STATUS=$(tail -n1 <<< $RESULT)
+        STATUS=$(sed 's/-//g' <<< $STATUS)
+        # trim
+        STATUS=$(echo $STATUS | xargs echo -n)
+        RESULT=$(head -n -1 <<< $RESULT)
+        # remove second to last line
+        RESULTA=$(head -n -2 <<< $RESULT)
+        RESULTB=$(tail -n1 <<< $RESULT)
+        NL=$'\n'
+        RESULT="$RESULTA${NL}||||||${NL}$RESULTB"
+        RESULT="$RESULT${NL}${NL}$STATUS"
+        RESULT="${RESULT//'%'/'%25'}"
+        RESULT="${RESULT//$'\n'/'%0A'}"
+        RESULT="${RESULT//$'\r'/'%0D'}"
+        echo "::set-output name=result::$RESULT"
+      continue-on-error: true
+    - name: comment documentation result on PR
+      uses: thollander/actions-comment-pull-request@v1
+      with:
+        message: |
+          ## Docstring Coverage Report
+          ${{ steps.documentation.outputs.result }}
+        comment_includes: '## Docstring Coverage Report'
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    # following snippet borrowed from
+    # https://stackoverflow.com/a/58003436
+    # CC BY-SA 4.0, Peter Evans
+    - name: Fail on insufficient coverage
+      if: steps.documentation.outcome != 'success'
+      run: exit 1

.github/workflows/docs.yml

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+name: Build docs
+
+on:
+  push:
+    branches:
+      - main 
+  pull_request:
+    branches:
+      - main 
+      - 'main*'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Cache dependencies
+        id: pip-cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip
+
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Checkout cebra figures 
+        uses: actions/checkout@v3
+        with:
+          repository: AdaptiveMotorControlLab/cebra-figures
+          path: docs/source/cebra-figures
+          ref: main
+          token: ${{ secrets.GH_PAT_FIGURES }}
+
+      - name: Checkout assets
+        uses: actions/checkout@v3
+        with:
+          repository: AdaptiveMotorControlLab/cebra-assets
+          path: assets
+          ref: main
+          token: ${{ secrets.GH_PAT_FIGURES }}
+
+      - name: Add assets to repo
+        run: |
+          cp -r assets/* .
+          rm -r assets
+
+      - name: Checkout cebra demos 
+        uses: actions/checkout@v3
+        with:
+          repository: AdaptiveMotorControlLab/cebra-demos
+          path: docs/source/demo_notebooks
+          ref: main
+          token: ${{ secrets.GH_PAT_FIGURES }}
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          sudo apt-get install -y pandoc
+          pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
+          pip install '.[docs]'
+
+      - name: Build docs
+        run: |
+          ls docs/source/cebra-figures
+          # later also add the -n option to check for broken links
+          export SPHINXOPTS="-W --keep-going -n"
+          make docs
+
+      - name: Deploy docs (staging)
+        uses: cpina/github-action-push-to-another-repository@main
+        if: github.ref != 'refs/heads/main'
+        env:
+          API_TOKEN_GITHUB: ${{ secrets.GH_PAT_FIGURES }}
+        with:
+          source-directory: 'docs/page'
+          destination-github-username: 'stes'
+          destination-repository-name: 'cebra-ai'
+          user-name: stes
+          user-email: [email protected]
+          target-branch: staging
+
+      - name: Deploy docs (production)
+        uses: cpina/github-action-push-to-another-repository@main
+        if: github.ref == 'refs/heads/main'
+        env:
+          API_TOKEN_GITHUB: ${{ secrets.GH_PAT_FIGURES }}
+        with:
+          source-directory: 'docs/page'
+          destination-github-username: 'stes'
+          destination-repository-name: 'cebra-ai'
+          user-name: stes
+          user-email: [email protected]
+          target-branch: main 
+

.github/workflows/release-pypi.yml

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+name: Update internal release
+
+on:
+  push:
+    tags:
+      - 'v*.*.*'
+  pull_request:
+    branches: [ main ]
+    types:
+      - labeled
+      - opened
+      - edited
+      - synchronize
+      - reopened
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Cache dependencies
+        id: pip-cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip
+
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Build and publish to Test PyPI
+        if: ${{ (github.ref != 'refs/heads/main') && (github.event.label.name == 'release') }}
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
+        run: |
+          make dist
+          ls dist/
+          tar tvf dist/cebra-*.tar.gz
+          python3 -m twine upload --repository testpypi dist/*
+
+      - name: Build and publish to PyPI
+        if: ${{ github.event_name == 'push' }}
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          make dist
+          ls dist/
+          tar tvf dist/cebra-*.tar.gz
+          python3 -m twine upload dist/*