diff --git a/.bumpversion.toml b/.bumpversion.toml
index f501507..3bc5813 100644
--- a/.bumpversion.toml
+++ b/.bumpversion.toml
@@ -24,4 +24,4 @@ post_commit_hooks = []
 filename = "pyproject.toml"
 
 [[tool.bumpversion.files]]
-filename = "ml_cli/version.py"
+filename = "pyml_cli/version.py"
diff --git a/.github/workflows/code-style.yaml b/.github/workflows/code-style.yaml
index 9636c02..1aae75a 100644
--- a/.github/workflows/code-style.yaml
+++ b/.github/workflows/code-style.yaml
@@ -5,13 +5,22 @@ on: [pull_request]
 
 jobs:
   linting:
+    env:
+      UV_CACHE_DIR: /tmp/.uv-cache
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v6
       - name: Setup uv
-        id: setup-uv
-        uses: astral-sh/setup-uv@v5
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+
+      - name: Setup Pixi Environment
+        uses: prefix-dev/setup-pixi@v0.9.3
         with:
-          enable-cache: true
-      - name: Run pre-commit
-        run: uvx pre-commit run --all-files
+          pixi-version: latest
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+
+      - name: Set up Python
+        run: uv python install
+
+      - uses: pre-commit/action@v3.0.1
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
index a5c5dd1..7bb64cb 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -4,6 +4,13 @@ on:
   push:
     branches:
       - main
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: write
+  pull-requests: write
 
 jobs:
   build-docs:
@@ -17,24 +24,62 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v6
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          fetch-depth: 0
 
-      - uses: prefix-dev/setup-pixi@v0.8.1
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Setup Pixi Environment
+        uses: prefix-dev/setup-pixi@v0.9.3
         with:
+          pixi-version: latest
           cache: true
-          environments: docs
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
 
       - name: Build docs
         run: pixi run build-docs
 
+      - name: Verify build output
+        run: |
+          # Verify that markdown files are NOT in the site directory
+          # (They should be processed into HTML by MkDocs)
+          # The markdown files are generated by the pre-build hook, processed by MkDocs,
+          # and only the resulting HTML files should be in ./site
+          if find ./site -name "*.md" | grep -q .; then
+            echo "ERROR: Markdown files found in site directory!"
+            find ./site -name "*.md"
+            exit 1
+          fi
+          echo "✓ Build verification passed: No markdown files in site directory"
+          echo "✓ Site directory contains HTML files ready for deployment"
+
       - name: Deploy website
-        uses: peaceiris/actions-gh-pages@v3
+        if: github.ref_name == 'main'
+        uses: peaceiris/actions-gh-pages@v4
         with:
           # https://github.com/peaceiris/actions-gh-pages#%EF%B8%8F-set-personal-access-token-personal_token
-          personal_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: site
+          # Note: This action deploys the contents of publish_dir (./site) to gh-pages.
+          # It does NOT check .gitignore - it simply takes all files in ./site and pushes them.
+          # Since ./site only contains HTML files (generated from markdown by MkDocs),
+          # no markdown files will be deployed. The markdown files exist only during
+          # the build process and are never committed to any branch.
+          personal_token: ${{ secrets.GHPAGES_DEPLOY_KEY }}
+          publish_dir: ./site
           publish_branch: gh-pages
           allow_empty_commit: false
           keep_files: false
           force_orphan: true
           enable_jekyll: false
+
+      - name: Deploy PR Preview
+        if: github.event_name == 'pull_request' && github.event.pull_request.base.ref == 'main'
+        uses: rossjrw/pr-preview-action@v1.6.3
+        with:
+          # Note: This action works similarly - it deploys the contents of source-dir (./site)
+          # to create a preview. It also does NOT check .gitignore, but since ./site only
+          # contains HTML files, no markdown files will be included in the preview.
+          source-dir: ./site
+          preview-branch: gh-pages
diff --git a/.github/workflows/pr-tests.yaml b/.github/workflows/pr-tests.yaml
index fab67d4..2b5eb8b 100644
--- a/.github/workflows/pr-tests.yaml
+++ b/.github/workflows/pr-tests.yaml
@@ -1,61 +1,84 @@
 name: Run tests on pull requests
 
-on: [pull_request]
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+
+env:
+  OPENAI_API_KEY: dummy_key
 
 jobs:
-  run-tests:
+  check-changes:
     runs-on: ubuntu-latest
-    name: Run test suite
-
-    # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
-    defaults:
-      run:
-        shell: bash -l {0}
-
+    outputs:
+      has-code-changes: ${{ steps.changes.outputs.has-code-changes }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - uses: prefix-dev/setup-pixi@v0.8.1
+        uses: actions/checkout@v6
         with:
-          cache: true
-          environments: tests
+          fetch-depth: 0
 
-      - name: Run tests
+      - name: Check for code changes
+        id: changes
         run: |
-          pixi run test
-
-      # https://github.com/codecov/codecov-action
-      - name: Upload code coverage
-        uses: codecov/codecov-action@v2
-        with:
-          # fail_ci_if_error: true # optional (default = false)
-          verbose: true # optional (default = false)
-
+          if [[ "${{ github.event_name }}" == "push" ]]; then
+            echo "has-code-changes=true" >> $GITHUB_OUTPUT
+          else
+            # For pull requests, check if there are non-docs changes
+            if git diff --name-only origin/${{ github.base_ref }}...HEAD | grep -v '^docs/' | grep -v '\.md$' | grep -q .; then
+              echo "has-code-changes=true" >> $GITHUB_OUTPUT
+            else
+              echo "has-code-changes=false" >> $GITHUB_OUTPUT
+            fi
+          fi
 
-  # This helps us check that pyproject.toml's `project` table's `dependencies`
-  # are defined completely.
-  bare-install:
+  test-matrix:
+    needs: check-changes
     runs-on: ubuntu-latest
-    name: Run bare installation test
+    name: ${{ matrix.test-type }} (Python ${{ matrix.python-version }}, ${{ matrix.environment-type }})
+    if: ${{ needs.check-changes.outputs.has-code-changes == 'true' }}
 
     strategy:
       matrix:
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
+        environment-type: ['pixi']
+        test-type: ['unit-tests', 'smoke-tests']
+
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
+
+      - name: Update apt and install curl
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y curl
 
-      - name: Setup Python
-        uses: actions/setup-python@v4
+      # Setup Pixi if needed
+      - name: Setup Pixi Environment
+        if: ${{ matrix.environment-type == 'pixi' }}
+        uses: prefix-dev/setup-pixi@v0.9.3
         with:
-          python-version: ${{ matrix.python-version }}
+          pixi-version: latest
+          cache: true
 
-      - name: Install package
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e .
+      # Run the appropriate test based on matrix variables
+      - name: Run unit tests
+        if: ${{ matrix.test-type == 'unit-tests' }}
+        run: pixi run -e tests test
+
+      - name: Run smoke tests (pixi)
+        if: ${{ matrix.test-type == 'smoke-tests' && github.repository_owner == 'matdagommer' }}
+        run: pixi run pyml --help
 
-      - name: Run CLI as a smoke test.
-        run: "pyml-cli --help"
+      # Upload code coverage only for unit tests
+      - name: Upload code coverage
+        if: ${{ matrix.test-type == 'unit-tests' }}
+        uses: codecov/codecov-action@v4
+        with:
+          verbose: true
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fb4b302..a795240 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,19 +2,14 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
-      - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 25.11.0
-    hooks:
-      - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.11.10
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
-        exclude: ^notebooks/.*|^docs/.*$
+        exclude: ^notebooks/.*|^docs/.*|pyproject.toml|pyml_cli/templates/.*$
   - repo: https://github.com/jendrikseipp/vulture
     rev: 'v2.14'
     hooks:
@@ -23,7 +18,7 @@ repos:
     rev: 1.7.0
     hooks:
       - id: interrogate
-        exclude: ^(docs/|tests/)
+        exclude: ^(docs/|tests/|scripts/|notebooks/|pyml_cli/templates/)
         args: [-c, pyproject.toml]
   - repo: local
     hooks:
diff --git a/docs/api.md b/docs/api.md
index a43cbf3..4180c30 100644
--- a/docs/api.md
+++ b/docs/api.md
@@ -1,3 +1,3 @@
 # Top-level API for pyml-cli
 
-::: ml_cli
+::: pyml_cli
diff --git a/docs/releases/v0.1.3.md b/docs/releases/v0.1.3.md
index 168638b..9d0d9b2 100644
--- a/docs/releases/v0.1.3.md
+++ b/docs/releases/v0.1.3.md
@@ -44,8 +44,8 @@ This release introduces automated version management and improves the release wo
 ### New Features
 
 - Add `.bumpversion.toml` for automated version management, enabling consistent version bumping and tagging. (9c8dbf) (MatDagommer)
-- Add `pyproject.toml` and `ml_cli/version.py` to the files tracked by bumpversion, ensuring all relevant files are updated during version bumps. (f105e4) (MatDagommer)
-- Include `ml_cli/version.py` in the list of files updated by bumpversion. (be0d2e) (MatDagommer)
+- Add `pyproject.toml` and `pyml_cli/version.py` to the files tracked by bumpversion, ensuring all relevant files are updated during version bumps. (f105e4) (MatDagommer)
+- Include `pyml_cli/version.py` in the list of files updated by bumpversion. (be0d2e) (MatDagommer)
 
 ### Bug Fixes
 
diff --git a/pixi.lock b/pixi.lock
index 3538d33..0d23659 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -22,6 +22,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/babel-2.17.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.2.0-py314h680f03e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.14.3-pyha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/binaryornot-0.4.4-pyhd8ed1ab_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/bleach-6.3.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/bleach-with-css-6.3.0-h5f6438b_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.conda
@@ -33,10 +34,12 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2025.11.12-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.0.0-py314h4a8dc5f_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cfgv-3.5.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/chardet-5.2.0-pyhd8ed1ab_3.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.4-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/comm-0.2.3-pyhe01879c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/cookiecutter-2.6.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/coverage-7.13.0-py314h67df5f8_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.2-py314hd8ed1ab_100.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cuda-cccl_linux-64-12.9.27-ha770c72_0.conda
@@ -58,6 +61,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/decorator-5.2.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/docutils-0.22.4-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda
@@ -80,6 +84,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/ipython_pygments_lexers-1.1.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.1.8-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/isoduration-20.11.0-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/itsdangerous-2.2.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/jaxlib-0.7.2-cuda129_py314h80c6225_202.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jedi-0.19.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda
@@ -141,11 +146,18 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.2.0-hdf11a46_16.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/loguru-0.7.3-pyh707e725_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/loro-1.10.3-py314h5059d10_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/marimo-0.18.4-py314h9e666f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/markdown-3.10-pyhcf101f3_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/markupsafe-3.0.3-pyh7db6752_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mistune-3.2.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ml_dtypes-0.5.4-np2py314h6477eea_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/msgspec-0.20.0-py314h5bd0f2a_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.14.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.4-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.16.6-pyhcf101f3_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbformat-5.10.4-pyhd8ed1ab_1.conda
@@ -174,6 +186,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/pure_eval-0.2.3-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyh29332c3_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.19.2-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/pymdown-extensions-10.19.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pytest-9.0.2-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pytest-cov-7.0.0-pyhcf101f3_1.conda
@@ -182,6 +195,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/python-fastjsonschema-2.21.2-pyhe01879c_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.2-h4df99d1_100.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/python-json-logger-2.0.7-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/python-slugify-8.0.4-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2025.3-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pytz-2025.2-pyhd8ed1ab_0.conda
@@ -195,21 +209,32 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/rfc3339-validator-0.1.4-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/rfc3986-validator-0.1.1-pyh9f0ad1d_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/rfc3987-syntax-1.1.0-pyhe01879c_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.2.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.30.0-py314h2e6c369_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml-0.18.17-py314h0f05182_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml.clib-0.2.15-py314h0f05182_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/scipy-1.16.3-py314hf07bd8e_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.3-pyh0d859eb_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-80.9.0-pyhff2d567_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/sh-2.1.0-pyh707e725_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/shellingham-1.5.4-pyhd8ed1ab_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/six-1.17.0-pyhe01879c_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.1-pyhd8ed1ab_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/sortedcontainers-2.4.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.8.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/stack_data-0.6.3-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/starlette-0.50.0-pyhfdc7a7d_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/terminado-0.18.1-pyhc90fa1f_1.conda
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   size: 15183
   timestamp: 1733331395943
-- pypi: https://files.pythonhosted.org/packages/c7/b0/003792df09decd6849a5e39c28b513c06e84436a54440380862b5aeff25d/tzdata-2025.3-py2.py3-none-any.whl
-  name: tzdata
-  version: '2025.3'
-  sha256: 06a47e5700f3081aab02b2e513160914ff0694bce9947d6b76ebd6bf57cfc5d1
-  requires_python: '>=2'
 - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-h8577fbf_0.conda
   sha256: 50fad5db6734d1bb73df1cf5db73215e326413d4b2137933f70708aa1840e25b
   md5: 338201218b54cadff2e774ac27733990
@@ -6032,6 +6575,21 @@ packages:
   - pkg:pypi/urllib3?source=compressed-mapping
   size: 102842
   timestamp: 1765719817255
+- conda: https://conda.anaconda.org/conda-forge/noarch/uvicorn-0.40.0-pyhc90fa1f_0.conda
+  sha256: 9cb6777bc67d43184807f8c57bdf8c917830240dd95e66fa9dbb7d65fa81f68e
+  md5: eb8fdfa0a193cfe804970d1a5470246d
+  depends:
+  - __unix
+  - click >=7.0
+  - h11 >=0.8
+  - python >=3.10
+  - typing_extensions >=4.0
+  - python
+  license: BSD-3-Clause
+  purls:
+  - pkg:pypi/uvicorn?source=hash-mapping
+  size: 54972
+  timestamp: 1766332899903
 - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.35.4-pyhd8ed1ab_0.conda
   sha256: 77193c99c6626c58446168d3700f9643d8c0dab1f6deb6b9dd039e6872781bfb
   md5: cfccfd4e8d9de82ed75c8e2c91cab375
@@ -6119,6 +6677,34 @@ packages:
   - pkg:pypi/websocket-client?source=hash-mapping
   size: 61391
   timestamp: 1759928175142
+- conda: https://conda.anaconda.org/conda-forge/linux-64/websockets-15.0.1-py314h31f8a6b_2.conda
+  sha256: 102c0acc2301908bcc0bd0c792e059cf8a6b93fc819f56c8a3b8a6b473afe58a
+  md5: e05c3cce47cc4f32f886eb17091ba6e2
+  depends:
+  - python
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - python_abi 3.14.* *_cp314
+  license: BSD-3-Clause
+  license_family: BSD
+  purls:
+  - pkg:pypi/websockets?source=hash-mapping
+  size: 380425
+  timestamp: 1756476367704
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/websockets-15.0.1-py314hf17b0b1_2.conda
+  sha256: c00677dc11e5f20e115ab7252c60893cd0bac9fc78b12678d62ba6b1b5dcb3f7
+  md5: 22ef4a8d9fdd426f7fb9d5b3bf168c2a
+  depends:
+  - python
+  - python 3.14.* *_cp314
+  - __osx >=11.0
+  - python_abi 3.14.* *_cp314
+  license: BSD-3-Clause
+  license_family: BSD
+  purls:
+  - pkg:pypi/websockets?source=hash-mapping
+  size: 383627
+  timestamp: 1756476437332
 - conda: https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-4.0.15-pyhd8ed1ab_0.conda
   sha256: 826af5e2c09e5e45361fa19168f46ff524e7a766022615678c3a670c45895d9a
   md5: dc257b7e7cad9b79c1dfba194e92297b
diff --git a/pyml_cli/__init__.py b/pyml_cli/__init__.py
index 1ca8221..97a1196 100644
--- a/pyml_cli/__init__.py
+++ b/pyml_cli/__init__.py
@@ -1,12 +1,15 @@
-"""Top-level API for pyml-cli.
+"""Top-level module for pyml-cli."""
 
-This is the file from which you can do:
+from .version import __version__
 
-    from ml_cli import some_function
+# Try importing pixi from sh, if not available, then auto-install pixi
+try:
+    from sh import pixi  # noqa: F401
+except ImportError:
+    err_msg = """To use `pyml-cli`, you need to have `pixi` installed.
 
-Use it to control the top-level API of your Python data science project.
+Please follow installation instructions available at: https://pixi.sh/latest/
 """
-
-from .version import __version__
+    raise ImportError(err_msg)
 
 __all__ = ["__version__"]
diff --git a/pyml_cli/cli/__init__.py b/pyml_cli/cli/__init__.py
index 209b705..40336a1 100644
--- a/pyml_cli/cli/__init__.py
+++ b/pyml_cli/cli/__init__.py
@@ -1 +1,50 @@
 """Initialize the CLI package."""
+
+from pathlib import Path
+
+import typer
+import yaml
+
+from ..version import __version__
+from .project import init
+from .system import status
+
+app = typer.Typer(pretty_exceptions_show_locals=False)
+
+app.command()(init)
+app.command()(status)
+
+@app.command()
+def configure(
+    name: str = typer.Option(..., help="Your name", prompt=True),
+    email: str = typer.Option(..., help="Your email address", prompt=True),
+    github_username: str = typer.Option("", help="Your GitHub username", prompt=True),
+    twitter_username: str = typer.Option("", help="Your Twitter username", prompt=True),
+    linkedin_username: str = typer.Option(
+        "", help="Your LinkedIn username", prompt=True
+    ),
+):
+    """Initial configuration for pyml.
+
+    :param name: Your name.
+    :param email: Your email address.
+    :param github_username: Your GitHub username.
+    :param twitter_username: Your Twitter username.
+    :param linkedin_username: Your LinkedIn username.
+    """
+    info = dict(
+        name=name,
+        email=email,
+        github_username=github_username,
+        twitter_username=twitter_username,
+        linkedin_username=linkedin_username,
+    )
+    config_file_path = Path.home() / ".pyml.yaml"
+    with config_file_path.open("w+") as f:
+        f.write(yaml.dump(info))
+
+
+@app.command()
+def version():
+    """Print the current version of pyml."""
+    print(__version__)
diff --git a/pyml_cli/cli/project.py b/pyml_cli/cli/project.py
new file mode 100644
index 0000000..7408705
--- /dev/null
+++ b/pyml_cli/cli/project.py
@@ -0,0 +1,16 @@
+"""Project initialization CLI."""
+
+from pathlib import Path
+
+from cookiecutter.main import cookiecutter
+from typer import Typer
+
+app = Typer()
+
+PROJECT_TEMPLATE_DIR = Path(__file__).parent.parent / "templates" / "project"
+
+
+@app.command()
+def init():
+    """Initialize project from template."""
+    cookiecutter(str(PROJECT_TEMPLATE_DIR.resolve()))
diff --git a/pyml_cli/cli/system.py b/pyml_cli/cli/system.py
new file mode 100644
index 0000000..f5eec6e
--- /dev/null
+++ b/pyml_cli/cli/system.py
@@ -0,0 +1,59 @@
+"""CLI for interacting with system tools.
+
+Because pyml relies heavily on the presence of anaconda,
+we look for environment variables such as:
+
+- `CONDA_EXE`
+- `CONDA_PYTHON_EXE`
+- `CONDA_PREFIX`
+- `anaconda`
+"""
+
+import typer
+from sh import bash, curl, which
+
+app = typer.Typer()
+
+
+@app.command()
+def status():
+    """Report status for tools that we expect to have installed.
+
+    We check for the presence of:
+
+    1. A `pixi` installation.
+    2. A `homebrew` installation.
+    3. The presence of a .pypirc file.
+    """
+    check_pixi()
+
+
+def check_pixi():
+    """Check that `pixi` is installed."""
+    out = which("pixi")
+    if out:
+        location = out.strip("\n")
+        print(f"✅ pixi found at {location}! 🎉")
+    else:
+        print(
+            "❌ pixi not found. "
+            "Please follow instructions at https://pixi.sh/install.sh to install pixi."
+        )
+
+
+@app.command()
+def init():
+    """Bootstrap user's system with necessary programs."""
+    install_pixi()
+
+
+def install_pixi():
+    """Install conda onto a user's system."""
+    # curl -fsSL https://pixi.sh/install.sh | bash
+    curl("-fsSL", "https://pixi.sh/install.sh", "-o", "/tmp/install_pixi.sh")
+    bash("/tmp/install_pixi.sh")
+
+
+def install_homebrew():
+    """Install homebrew onto a user's system."""
+    pass
diff --git a/pyml_cli/templates/project/cookiecutter.json b/pyml_cli/templates/project/cookiecutter.json
new file mode 100644
index 0000000..6dc4359
--- /dev/null
+++ b/pyml_cli/templates/project/cookiecutter.json
@@ -0,0 +1,14 @@
+{
+    "project_name": "Name of the Project",
+    "short_description": "A short description of the project",
+    "github_username": "Your GitHub username",
+    "full_name": "Your full name",
+    "email": "Your email address",
+    "__project_kebabcase": "{{ cookiecutter.project_name.lower().replace(' ', '-') }}",
+    "__project_snakecase": "{{ cookiecutter.project_name.lower().replace(' ', '_').replace('-', '_') }}",
+    "__cli_name": "{{ cookiecutter.__project_kebabcase }}",
+    "__conda_env_name": "{{ cookiecutter.__project_kebabcase }}",
+    "__repo_name": "{{ cookiecutter.__project_kebabcase }}",
+    "__module_name": "{{ cookiecutter.__project_snakecase }}",
+    "__package_name": "{{ cookiecutter.__project_kebabcase }}"
+}
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.bumpversion.toml b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.bumpversion.toml
new file mode 100644
index 0000000..59d65ca
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.bumpversion.toml	
@@ -0,0 +1,27 @@
+[tool.bumpversion]
+current_version = "0.1.0"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+moveable_tags = []
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = []
+post_commit_hooks = []
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+
+[[tool.bumpversion.files]]
+filename = "{{ cookiecutter.__module_name }}/version.py"
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.devcontainer/Dockerfile b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.devcontainer/Dockerfile
new file mode 100644
index 0000000..0ef3b5a
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.devcontainer/Dockerfile	
@@ -0,0 +1,55 @@
+#-------------------------------------------------------------------------------------------------------------
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
+#-------------------------------------------------------------------------------------------------------------
+
+FROM continuumio/miniconda3
+
+# Avoid warnings by switching to noninteractive
+ENV DEBIAN_FRONTEND=noninteractive
+
+# This Dockerfile adds a non-root user with sudo access. Use the "remoteUser"
+# property in devcontainer.json to use it. On Linux, the container user's GID/UIDs
+# will be updated to match your local UID/GID (when using the dockerFile property).
+# See https://aka.ms/vscode-remote/containers/non-root-user for details.
+ARG USERNAME=vscode
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
+
+# Copy environment.yml (if found) to a temp locaition so we update the environment. Also
+# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
+COPY environment.yml*  /tmp/conda-tmp/
+
+# Configure apt and install packages
+RUN apt-get update \
+    && apt-get -y install --no-install-recommends apt-utils dialog 2>&1 \
+    #
+    # Verify git, process tools, lsb-release (common in install instructions for CLIs) installed
+    && apt-get -y install git openssh-client less iproute2 procps iproute2 lsb-release \
+    #
+    # Install TexLive and related utilities
+    && apt-get -y install texlive texlive-publishers texlive-science latexmk cm-super texlive-xetex \
+    #
+    # Install mamba to replace conda
+    && /opt/conda/bin/conda install -c conda-forge -y mamba \
+    #
+    # Update Python environment based on environment.yml (if present)
+    && if [ -f "/tmp/conda-tmp/environment.yml" ]; then /opt/conda/bin/mamba env update -n base -f /tmp/conda-tmp/environment.yml; fi \
+    && rm -rf /tmp/conda-tmp \
+    #
+    # Create a non-root user to use if preferred - see https://aka.ms/vscode-remote/containers/non-root-user.
+    && groupadd --gid $USER_GID $USERNAME \
+    && useradd -s /bin/bash --uid $USER_UID --gid $USER_GID -m $USERNAME \
+    #
+    # [Optional] Add sudo support for the non-root user
+    && apt-get install -y sudo nano emacs vim \
+    && echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME\
+    && chmod 0440 /etc/sudoers.d/$USERNAME \
+    #
+    # Clean up
+    && apt-get autoremove -y \
+    && apt-get clean -y \
+    && rm -rf /var/lib/apt/lists/*
+
+# Switch back to dialog for any ad-hoc use of apt-get
+ENV DEBIAN_FRONTEND=dialog
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.devcontainer/devcontainer.json b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..c201f0a
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.devcontainer/devcontainer.json	
@@ -0,0 +1,25 @@
+{
+    "name": "{{ cookiecutter.project_name }}",
+    "build": {
+        "dockerfile": "Dockerfile",
+        "context": ".."
+    },
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "ms-azuretools.vscode-docker",
+                "ms-toolsai.jupyter",
+                "arcticicestudio.nord-visual-studio-code",
+                "ms-python.vscode-pylance",
+                "ms-python.python",
+                "redhat.vscode-yaml"
+            ]
+        }
+    },
+    "forwardPorts": [
+        8888
+    ],
+    "postCreateCommand": "pre-commit install && python -m ipykernel install --user --name {{ cookiecutter.__package_name }} }}",
+    // Use 'postStartCommand' to run commands after the container is _started_.
+    "postStartCommand": "jupyter lab --allow-root"
+}
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/copilot-instructions.md b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/copilot-instructions.md
new file mode 100644
index 0000000..63024b4
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/copilot-instructions.md	
@@ -0,0 +1,3 @@
+These are instructions for copilot to help it understand the code you write.
+Anything you would tell a human being to pay attention to
+with respect to the code you write can be put here.
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/dependabot.yml b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/dependabot.yml
new file mode 100644
index 0000000..0f96f8d
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/dependabot.yml	
@@ -0,0 +1,9 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/code-style.yaml b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/code-style.yaml
new file mode 100644
index 0000000..9636c02
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/code-style.yaml	
@@ -0,0 +1,17 @@
+# Run code style checks on each pull request.
+name: Code style checks
+
+on: [pull_request]
+
+jobs:
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup uv
+        id: setup-uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+      - name: Run pre-commit
+        run: uvx pre-commit run --all-files
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/docs.yaml b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/docs.yaml
new file mode 100644
index 0000000..574b028
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/docs.yaml	
@@ -0,0 +1,40 @@
+name: Build documentation
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    name: Build documentation
+
+    # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          cache: true
+          environments: docs
+
+      - name: Build docs
+        run: pixi run build-docs
+
+      - name: Deploy website
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          # https://github.com/peaceiris/actions-gh-pages#%EF%B8%8F-set-personal-access-token-personal_token
+          personal_token: {{ '${{ secrets.GITHUB_TOKEN }}' }}
+          publish_dir: site
+          publish_branch: gh-pages
+          allow_empty_commit: false
+          keep_files: false
+          force_orphan: true
+          enable_jekyll: false
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/pr-tests.yaml b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/pr-tests.yaml
new file mode 100644
index 0000000..fed531f
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/pr-tests.yaml	
@@ -0,0 +1,61 @@
+name: Run tests on pull requests
+
+on: [pull_request]
+
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+    name: Run test suite
+
+    # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          cache: true
+          environments: tests
+
+      - name: Run tests
+        run: |
+          pixi run test
+
+      # https://github.com/codecov/codecov-action
+      - name: Upload code coverage
+        uses: codecov/codecov-action@v2
+        with:
+          # fail_ci_if_error: true # optional (default = false)
+          verbose: true # optional (default = false)
+
+
+  # This helps us check that pyproject.toml's `project` table's `dependencies`
+  # are defined completely.
+  bare-install:
+    runs-on: ubuntu-latest
+    name: Run bare installation test
+
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: {{ '${{ matrix.python-version }}' }}
+
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .
+
+      - name: Run CLI as a smoke test.
+        run: "{{ cookiecutter.__package_name }} --help"
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/release-pypi-package.yaml b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/release-pypi-package.yaml
new file mode 100644
index 0000000..5e7fe44
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.github/workflows/release-pypi-package.yaml	
@@ -0,0 +1,133 @@
+name: Release Python Package
+
+on:
+  workflow_dispatch:
+    inputs:
+      version_name:
+        description: "One of major, minor, or patch"
+        required: true
+        type: choice
+        options:
+          - major
+          - minor
+          - patch
+        default: patch
+  pull_request:
+    branches:
+      - '**'
+
+permissions:
+  contents: write
+  id-token: write
+
+env:
+  UV_SYSTEM_PYTHON: 1
+  DEFAULT_VERSION_NAME: patch
+
+jobs:
+  deploy-package:
+    runs-on: ubuntu-latest
+    name: {{ "${{ github.event_name == 'pull_request' && '(Dry Run) ' || '' }}" }}Publish Python Package to PyPI
+    permissions:
+      id-token: write
+      contents: write
+
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+
+      - name: Setup Python environment
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Setup Pixi Environment
+        uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          pixi-version: latest
+          cache: true
+          cache-write: {{ "${{ github.event_name == 'push' }}" }}
+
+      - name: Set up Python
+        run: |
+          uv tool install bump-my-version
+
+      - name: Set version name
+        run: echo "VERSION_NAME={{ '${{ github.event.inputs.version_name || env.DEFAULT_VERSION_NAME }}' }}" >> $GITHUB_ENV
+
+      - name: Show new version bump-my-version
+        run: |
+          bump-my-version show --increment {{ '${{ env.VERSION_NAME }}' }} new_version
+
+      - name: Store new version number
+        run: echo "version_number=`bump-my-version show --increment {{ '${{ env.VERSION_NAME }}' }} new_version | sed -r s,\"^.*=\",,`" >> $GITHUB_ENV
+
+      - name: Display new version number
+        run: |
+          echo "version_name: {{ '${{ env.VERSION_NAME }}' }}"
+          echo "version_number: v{{ '${{ env.version_number }}' }}"
+
+      - name: Ensure repo status is clean
+        run: git status
+
+      - name: Configure Git
+        run: |
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+
+      - name: Run bump-my-version
+        run: bump-my-version bump {{ '${{ env.VERSION_NAME }}' }} --verbose
+
+      - name: Ensure tag creation
+        run: git tag | grep {{ '${{ env.version_number }}' }}
+
+      - name: Write release notes
+        if: github.event_name != 'pull_request'
+        env:
+          OPENAI_API_KEY: {{ '${{ secrets.OPENAI_API_KEY }}' }}
+        run: |
+          uv tool install llamabot[cli] --python 3.12 --python-preference only-managed --force
+          llamabot configure default-model --model-name="{{ '${{ secrets.DEFAULT_LANGUAGE_MODEL }}' }}"
+          llamabot git write-release-notes
+
+      - name: Commit release notes
+        if: github.event_name != 'pull_request'
+        run: |
+          uv tool install pre-commit
+          pre-commit run --all-files || pre-commit run --all-files
+          git add .
+          git commit -m "Add release notes for {{ '${{ env.version_number }}' }}"
+
+      - name: Build package
+        run: |
+          uv build --sdist --wheel
+
+      - name: Publish package (trusted publishing)
+        if: github.event_name != 'pull_request'
+        run: uv publish --trusted-publishing always
+
+      - name: Push changes with tags
+        if: github.event_name != 'pull_request'
+        run: |
+          git push && git push --tags
+
+      - name: Create release in GitHub repo
+        if: github.event_name != 'pull_request'
+        uses: ncipollo/release-action@v1
+        with:
+          bodyFile: "docs/releases/v{{ '${{ env.version_number }}' }}.md"
+          token: {{ '${{ secrets.GITHUB_TOKEN }}' }}
+          tag: {{ 'v${{ env.version_number }}' }}
+
+      - name: Ensure complete
+        if: github.event_name != 'pull_request'
+        run: echo "Auto-release complete!"
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.gitignore b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.gitignore
new file mode 100644
index 0000000..59d65ca
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.gitignore	
@@ -0,0 +1,27 @@
+[tool.bumpversion]
+current_version = "0.1.0"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+moveable_tags = []
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = []
+post_commit_hooks = []
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+
+[[tool.bumpversion.files]]
+filename = "{{ cookiecutter.__module_name }}/version.py"
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.pre-commit-config.yaml b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.pre-commit-config.yaml
new file mode 100644
index 0000000..212b3e2
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/.pre-commit-config.yaml	
@@ -0,0 +1,32 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.10
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+        exclude: ^notebooks/.*|^docs/.*|pyproject.toml$
+  - repo: https://github.com/jendrikseipp/vulture
+    rev: 'v2.14'
+    hooks:
+      - id: vulture
+  - repo: https://github.com/econchick/interrogate
+    rev: 1.7.0
+    hooks:
+      - id: interrogate
+        exclude: ^(docs/|tests/|scripts/|notebooks/)
+        args: [-c, pyproject.toml]
+  - repo: local
+    hooks:
+      - id: pixi-install
+        name: Keep lockfile up-to-date
+        entry: pixi install
+        language: system
+        always_run: true
+        require_serial: true
+        pass_filenames: false
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/MANIFEST.in b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/MANIFEST.in
new file mode 100644
index 0000000..6767f80
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/MANIFEST.in	
@@ -0,0 +1,3 @@
+# Some references to help:
+# https://wiki.python.org/moin/Distutils/Tutorial
+# https://stackoverflow.com/a/24727824/1274908
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/README.md b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/README.md
new file mode 100644
index 0000000..cef3204
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/README.md	
@@ -0,0 +1,15 @@
+# {{ cookiecutter.project_name }}
+
+{{ cookiecutter.short_description }}
+
+Made with ❤️ by {{ cookiecutter.full_name }} (@{{ cookiecutter.github_username }}).
+
+## Get started for development
+
+To get started:
+
+```bash
+git clone git@github.com:{{ cookiecutter.github_username }}/{{ cookiecutter.__repo_name}}
+cd {{ cookiecutter.__repo_name }}
+pixi install
+```
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/api.md b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/api.md
new file mode 100644
index 0000000..0ab9405
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/api.md	
@@ -0,0 +1,3 @@
+# Top-level API for {{ cookiecutter.project_name }}
+
+::: {{ cookiecutter.__module_name }}
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/apidocs.css b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/apidocs.css
new file mode 100644
index 0000000..f21e19e
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/apidocs.css	
@@ -0,0 +1,14 @@
+/* https://mkdocstrings.github.io/theming/#css-classes */
+.doc-property { border-radius: 15px; padding: 0 5px; }
+.doc-property-special { background-color: blue; color: white; }
+.doc-property-private { background-color: red; color: white; }
+.doc-property-property { background-color: green; color: white; }
+.doc-property-read-only { background-color: yellow; color: black; }
+
+/* https://mkdocstrings.github.io/handlers/python/#recommended-style-material */
+/* Indentation. */
+div.doc-contents:not(.first) {
+    padding-left: 25px;
+    border-left: 4px solid rgba(230, 230, 230);
+    margin-bottom: 80px;
+  }
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/config.js b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/config.js
new file mode 100644
index 0000000..66ce477
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/config.js	
@@ -0,0 +1 @@
+hljs.highlightAll();
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/index.md b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/index.md
new file mode 100644
index 0000000..a25153d
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/docs/index.md	
@@ -0,0 +1,30 @@
+# {{ cookiecutter.project_name }} }}
+
+Welcome to the repository for the {{ cookiecutter.project_name }} }} project!
+
+## Quickstart
+
+<!-- uncomment if relevant
+### Install from PyPI
+
+```python
+pip install {{ cookiecutter.__package_name }}
+```
+-->
+### Install from source
+
+```bash
+pip install git@github.com:MatDagommer/{{ cookiecutter.__package_name }}
+```
+
+### Build and preview docs
+
+```bash
+mkdocs serve
+```
+
+## Why this project exists
+
+Place your reasons here for why this project exists.
+
+What benefits does this project give to users?
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/mkdocs.yaml b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/mkdocs.yaml
new file mode 100644
index 0000000..7bc185f
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/mkdocs.yaml	
@@ -0,0 +1,50 @@
+site_name: "{{ cookiecutter.project_name }}"
+site_url: https://{{ cookiecutter.github_username }}.github.io/{{ cookiecutter.__project_kebabcase }}
+
+docs_dir: docs/
+
+# For more configuration on the theme, see https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/
+theme:
+  name: material
+  icon:
+    logo: "fontawesome/solid/book"
+  features:
+    - instant
+    - tabs
+  language: en
+
+# We customize the navigation by hand to control the order
+# in which pages show up.
+
+plugins:
+  - search
+  - mknotebooks:
+      execute: true
+      write_markdown: true
+      allow_errors: false
+      timeout: 1200
+      binder: true
+      binder_service_name: "gh"
+      binder_branch: "master"
+      binder_ui: "lab"
+
+# Taken from here: https://squidfunk.github.io/mkdocs-material/extensions/codehilite/
+markdown_extensions:
+  - codehilite
+  - admonition
+  - pymdownx.superfences
+  - markdown.extensions.attr_list
+
+extra_css:
+  - apidocs.css
+
+extra_javascript:
+  - config.js
+
+repo_name: "{{ cookiecutter.github_username }}/{{ cookiecutter.__project_kebabcase }}"
+repo_url: "https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.__project_kebabcase }}"
+
+extra:
+  social:
+    - icon: "fontawesome/brands/github"
+      link: "https://github.com/{{ cookiecutter.github_username }}"
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/notebooks/marimo_nb.py b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/notebooks/marimo_nb.py
new file mode 100644
index 0000000..81f42dc
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/notebooks/marimo_nb.py	
@@ -0,0 +1,38 @@
+import marimo
+
+__generated_with = "0.18.4"
+app = marimo.App(width="medium")
+
+
+@app.cell
+def _():
+    import numpy as np
+    return (np,)
+
+
+@app.cell
+def _(np):
+    A = np.array([0, 1, 2])
+    B = np.array([3, 4, 5])
+    return A, B
+
+
+@app.cell
+def _(A, B):
+    C = A + B
+    return (C,)
+
+
+@app.cell
+def _(C):
+    print(C)
+    return
+
+
+@app.cell
+def _():
+    return
+
+
+if __name__ == "__main__":
+    app.run()
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/pyproject.toml b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/pyproject.toml
new file mode 100644
index 0000000..5adb6a1
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/pyproject.toml	
@@ -0,0 +1,164 @@
+# https://setuptools.pypa.io/en/latest/userguide/quickstart.html
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.black]
+line-length = 88
+target-version = ['py39']
+include = '\.pyi?$'
+exclude = '''
+
+(
+  /(
+      \.eggs         # exclude a few common directories in the
+    | \.git          # root of the project
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | _build
+    | buck-out
+    | build
+    | dist
+  )/
+  | foo.py           # also separately exclude a file named foo.py in
+                     # the root of the project
+)
+'''
+
+[tool.interrogate]
+ignore-init-method = true
+ignore-init-module = false
+ignore-magic = false
+ignore-semiprivate = false
+ignore-private = false
+ignore-property-decorators = false
+ignore-module = false
+fail-under = 100
+exclude = ["setup.py", "docs", "build", "examples"]
+ignore-regex = ["^get$", "^mock_.*", ".*BaseClass.*"]
+verbose = 2
+quiet = false
+whitelist-regex = []
+color = true
+
+[tool.pytest.ini_options]
+addopts = "-v --cov --cov-report term-missing"
+testpaths = [
+    "tests",
+]
+
+[tool.isort]
+profile = "black"
+
+[tool.ruff]
+# See https://docs.astral.sh/ruff/rules/ for a list of rules.
+# See https://docs.astral.sh/ruff/configuration/#using-pyprojecttoml for configuration documentation
+lint.select = ["E", "F", "I"]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
+namespaces = false
+
+[project]
+name = "{{ cookiecutter.project_name }}"
+version = "0.1.0"
+# NOTE: move dependencies into this section if you need to distribute the project as a Python package.
+requires-python = ">=3.10"
+dependencies = [
+    "matplotlib",
+    "pandas",
+    "scikit-learn",
+    "numpy",
+    "pyprojroot",
+    "scipy",
+    "seaborn",
+    "python-dotenv",
+    "typer",
+    "loguru",
+    "marimo"
+]
+readme = "README.md"
+
+[project.scripts]
+{{ cookiecutter.__cli_name }} = "{{ cookiecutter.__module_name }}.cli:app"
+
+
+[tool.coverage.run]
+omit = [
+    "tests/*",
+]
+
+[tool.vulture]
+paths = ["{{ cookiecutter.__module_name }}", "scripts"]
+min_confidence = 80
+
+[tool.pixi.workspace]
+channels = ["conda-forge"]
+platforms = ["osx-arm64", "linux-64"]
+
+[tool.pixi.pypi-dependencies]
+{{ cookiecutter.__package_name }} = { path = ".", editable = true }
+
+# NOTE: Core dependencies (needed for running the program) go here.
+[tool.pixi.dependencies]
+typer = ">=0.21.0,<0.22"
+loguru = ">=0.7.3,<0.8"
+cookiecutter = ">=2.6.0,<3"
+sh = ">=2.2.2,<3"
+
+# NOTE: Testing dependencies (not needed for running program) go here.
+[tool.pixi.feature.tests.dependencies]
+pytest = "*"
+pytest-cov = "*"
+hypothesis = "*"
+
+# NOTE: Docs dependencies (needed for documentation and notebooks) go here.
+[tool.pixi.feature.docs.dependencies]
+mkdocs = "*"
+mkdocs-material = "*"
+mknotebooks = "*"
+
+[tool.pixi.feature.notebook.dependencies]
+ipykernel = "*"
+ipython = "*"
+jupyter = "*"
+pixi-kernel = "*"
+
+[tool.pixi.feature.devtools.dependencies]
+pre-commit = "*"
+
+[tool.pixi.feature.api.dependencies]
+fastapi = "*"
+
+# NOTE: CUDA feature is inspired by https://github.com/prefix-dev/pixi/issues/1051#issuecomment-2088820974
+[tool.pixi.feature.cuda]
+system-requirements = { cuda = "12" }
+
+[tool.pixi.feature.cuda.target.linux-64.dependencies]
+jaxlib = { version = "*", build = "*cuda12*" }
+
+[tool.pixi.feature.tests.tasks]
+test = "pytest"
+
+[tool.pixi.feature.devtools.tasks]
+lint = "pre-commit run --all-files"
+commit = "git commit"
+
+[tool.pixi.feature.docs.tasks]
+build-docs = "mkdocs build"
+serve-docs = "mkdocs serve"
+
+[tool.pixi.feature.setup.tasks]
+setup = "pre-commit autoupdate && pre-commit install --install-hooks"
+update = "pre-commit autoupdate"
+
+[tool.pixi.environments]
+default = { features = ["tests", "devtools", "notebook", "setup"] }
+docs = { features = ["docs"] }
+tests = { features = ["tests", "setup"] }
+cuda = { features = ["tests", "devtools", "notebook", "setup", "cuda"] }
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/scripts/app.py b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/scripts/app.py
new file mode 100644
index 0000000..3d990db
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/scripts/app.py	
@@ -0,0 +1,11 @@
+"""FastAPI application script."""
+
+from fastapi import FastAPI
+
+app = FastAPI()
+
+
+@app.get("/health")
+def health_check():
+    """Health check endpoint."""
+    return {"status": "healthy"}
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/{{ cookiecutter.__module_name }}/__init__.py b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/{{ cookiecutter.__module_name }}/__init__.py
new file mode 100644
index 0000000..c41cc66
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/{{ cookiecutter.__module_name }}/__init__.py	
@@ -0,0 +1,5 @@
+"""Initialize the parent module."""
+
+from .version import __version__
+
+__all__ = ["__version__"]
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/{{ cookiecutter.__module_name }}/cli/__init__.py b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/{{ cookiecutter.__module_name }}/cli/__init__.py
new file mode 100644
index 0000000..18f82e7
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/{{ cookiecutter.__module_name }}/cli/__init__.py	
@@ -0,0 +1,5 @@
+"""Initialize the CLI module."""
+
+from typer import Typer
+
+app = Typer(help="Command-line interface for {{ cookiecutter.project_name }}.")
diff --git a/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/{{ cookiecutter.__module_name }}/version.py b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/{{ cookiecutter.__module_name }}/version.py
new file mode 100644
index 0000000..ad1e36e
--- /dev/null
+++ b/pyml_cli/templates/project/{{ cookiecutter.__repo_name }}/{{ cookiecutter.__module_name }}/version.py	
@@ -0,0 +1,3 @@
+"""Version information for the package."""
+
+__version__ = "0.1.0"
diff --git a/pyml_cli/utils/__init__.py b/pyml_cli/utils/__init__.py
new file mode 100644
index 0000000..412d343
--- /dev/null
+++ b/pyml_cli/utils/__init__.py
@@ -0,0 +1,24 @@
+"""Utility functions for pyml."""
+
+from pathlib import Path
+
+import ruamel.yaml
+
+
+def read_config():
+    """Read PyML configuration file.
+
+    The PyML configuration file is always located in the home directory
+    and has the name `.pyml.yaml`.
+
+    :returns: A dictionary of PyML configurations.
+    :raises FileNotFoundError: when the pyml config file cannot be found.
+    """
+    try:
+        config_path = Path.home() / ".pyml.yaml"
+        yaml = ruamel.yaml.YAML()  # defaults to round-trip
+
+        with config_path.open("r+") as f:
+            return yaml.load(f.read())
+    except FileNotFoundError:
+        raise FileNotFoundError("❗️Please run `pyml configure` to configure pyml!")
diff --git a/pyproject.toml b/pyproject.toml
index 39cbe44..ae4cd23 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,7 +55,7 @@ profile = "black"
 [tool.ruff]
 # See https://docs.astral.sh/ruff/rules/ for a list of rules.
 # See https://docs.astral.sh/ruff/configuration/#using-pyprojecttoml for configuration documentation
-select = ["E", "F", "I"]
+lint.select = ["E", "F", "I"]
 
 [tool.setuptools]
 include-package-data = true
@@ -81,11 +81,12 @@ dependencies = [
     "python-dotenv",
     "typer",
     "jax",
+    "sh ==2.1",
 ]
 readme = "README.md"
 
 [project.scripts]
-pyml-cli = "ml_cli.cli:app"
+pyml = "pyml_cli.cli:app"
 
 
 [tool.coverage.run]
@@ -93,6 +94,10 @@ omit = [
     "tests/*",
 ]
 
+[tool.vulture]
+paths = ["pyml_cli"]
+min_confidence = 80
+
 [tool.pixi.workspace]
 channels = ["conda-forge"]
 platforms = ["osx-arm64", "linux-64"]
@@ -102,6 +107,12 @@ pyml-cli = { path = ".", editable = true }
 
 # NOTE: Core dependencies (needed for running the program) go here.
 [tool.pixi.dependencies]
+typer = ">=0.21.0,<0.22"
+loguru = ">=0.7.3,<0.8"
+cookiecutter = ">=2.6.0,<3"
+sh = "==2.1"
+marimo = ">=0.18.4,<0.19"
+"ruamel.yaml" = ">=0.18.17,<0.19"
 
 # NOTE: Testing dependencies (not needed for running program) go here.
 [tool.pixi.feature.tests.dependencies]
diff --git a/tests/test___init__.py b/tests/test___init__.py
deleted file mode 100644
index 18ef8da..0000000
--- a/tests/test___init__.py
+++ /dev/null
@@ -1 +0,0 @@
-"""Tests for pyml-cli."""
diff --git a/tests/test__init__.py b/tests/test__init__.py
new file mode 100644
index 0000000..00592ec
--- /dev/null
+++ b/tests/test__init__.py
@@ -0,0 +1,25 @@
+"""Tests for the top-level CLI."""
+
+from typer.testing import CliRunner
+
+from pyml_cli.cli import app
+from pyml_cli.utils import read_config
+
+runner = CliRunner()
+
+
+def test_configure():
+    """Test for configuring the pyml CLI."""
+    result = runner.invoke(
+        app,
+        ["configure"],
+        input="GitHub Tester\ngithub@tester.com\ngh.tester\ngh.tester\ngh.tester\n",
+    )
+    assert result.exit_code == 0
+    config = read_config()
+
+    assert config["name"] == "GitHub Tester"
+    assert config["email"] == "github@tester.com"
+    assert config["twitter_username"] == "gh.tester"
+    assert config["linkedin_username"] == "gh.tester"
+    assert config["github_username"] == "gh.tester"
diff --git a/tests/test_cli.py b/tests/test_cli.py
deleted file mode 100644
index 06869fa..0000000
--- a/tests/test_cli.py
+++ /dev/null
@@ -1 +0,0 @@
-"""Tests for ml_cli.cli."""
diff --git a/tests/test_models.py b/tests/test_models.py
deleted file mode 100644
index 72c1dca..0000000
--- a/tests/test_models.py
+++ /dev/null
@@ -1 +0,0 @@
-"""Tests for pyml-cli's machine learning models."""