From 8dbce7a9f3b12911229e0384f6b7d046d4732d7d Mon Sep 17 00:00:00 2001
From: Nicholas Junge <n.junge@appliedai-institute.de>
Date: Thu, 10 Oct 2024 19:16:08 +0200
Subject: [PATCH 1/6] Add uv lockfile, bump pre-commit hooks

---
 .pre-commit-config.yaml |   24 +-
 pyproject.toml          |    8 -
 uv.lock                 | 1271 +++++++++++++++++++++++++++++++++++++++
 3 files changed, 1274 insertions(+), 29 deletions(-)
 create mode 100644 uv.lock

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d4c9591..2a8bde5 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -22,25 +22,7 @@ repos:
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.4.17
+    rev: 0.4.20
     hooks:
-      - id: pip-compile
-        name: pip-compile requirements-dev.txt
-        args:
-          - --no-annotate
-          - --no-strip-extras
-          - --python-version=3.10
-          - --extra=dev
-          - --output-file=requirements-dev.txt
-          - pyproject.toml
-        files: ^(pyproject\.toml|requirements-dev\.txt)$
-      - id: pip-compile
-        name: pip-compile requirements-docs.txt
-        args:
-          - --no-annotate
-          - --no-strip-extras
-          - --python-version=3.10
-          - --extra=docs
-          - --output-file=requirements-docs.txt
-          - pyproject.toml
-        files: ^(pyproject\.toml|requirements-docs\.txt)$
+      - id: uv-lock
+        name: Lock project dependencies
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 317af6f..0d09d44 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -111,14 +111,6 @@ ignore = [
 # Ignore unused imports in all `__init__.py` files
 "__init__.py" = ["F401"]
 
-[tool.bandit]
-exclude_dirs = ["examples", "tests"]
-skips = ["B101", "B404"]
-
 [tool.pytest.ini_options]
 log_cli = true
 log_cli_level = "DEBUG"
-
-[tool.pydoclint]
-style = 'numpy'
-exclude = '\.git|venv'
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 0000000..088f1cf
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,1271 @@
+version = 1
+requires-python = ">=3.10"
+
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From bcc307a0d57ba61243939016fc3bcb00468e9fc2 Mon Sep 17 00:00:00 2001
From: Nicholas Junge <n.junge@appliedai-institute.de>
Date: Thu, 10 Oct 2024 19:15:40 +0200
Subject: [PATCH 2/6] Remove requirement files

---
 requirements-dev.txt  | 27 ------------------
 requirements-docs.txt | 64 -------------------------------------------
 2 files changed, 91 deletions(-)
 delete mode 100644 requirements-dev.txt
 delete mode 100644 requirements-docs.txt

diff --git a/requirements-dev.txt b/requirements-dev.txt
deleted file mode 100644
index 73f6088..0000000
--- a/requirements-dev.txt
+++ /dev/null
@@ -1,27 +0,0 @@
-# This file was autogenerated by uv via the following command:
-#    uv pip compile --no-annotate --no-strip-extras --python-version=3.10 --extra=dev --output-file=requirements-dev.txt pyproject.toml
-build==1.2.2
-cfgv==3.4.0
-distlib==0.3.8
-exceptiongroup==1.2.2
-filelock==3.16.1
-fsspec==2024.9.0
-identify==2.6.1
-importlib-metadata==8.5.0
-iniconfig==2.0.0
-nodeenv==1.9.1
-numpy==2.1.1
-packaging==24.1
-platformdirs==4.3.6
-pluggy==1.5.0
-pre-commit==3.8.0
-psutil==6.0.0
-pyarrow==17.0.0
-pyproject-hooks==1.2.0
-pytest==8.3.3
-pyyaml==6.0.2
-tabulate==0.9.0
-tomli==2.0.1
-typing-extensions==4.12.2
-virtualenv==20.26.6
-zipp==3.20.2
diff --git a/requirements-docs.txt b/requirements-docs.txt
deleted file mode 100644
index 3095bfd..0000000
--- a/requirements-docs.txt
+++ /dev/null
@@ -1,64 +0,0 @@
-# This file was autogenerated by uv via the following command:
-#    uv pip compile --no-annotate --no-strip-extras --python-version=3.10 --extra=docs --output-file=requirements-docs.txt pyproject.toml
-anyio==4.6.0
-babel==2.16.0
-black==24.8.0
-certifi==2024.8.30
-charset-normalizer==3.3.2
-click==8.1.7
-colorama==0.4.6
-docstring-parser==0.16
-essentials==1.1.5
-essentials-openapi==1.0.9
-exceptiongroup==1.2.2
-ghp-import==2.1.0
-griffe==1.3.2
-h11==0.14.0
-httpcore==1.0.5
-httpx==0.27.2
-idna==3.10
-importlib-metadata==8.5.0
-importlib-resources==6.4.5
-jinja2==3.1.4
-markdown==3.7
-markdown-it-py==3.0.0
-markupsafe==2.1.5
-mdurl==0.1.2
-mergedeep==1.3.4
-mike==2.1.3
-mkdocs==1.6.1
-mkdocs-autorefs==1.2.0
-mkdocs-callouts==1.14.0
-mkdocs-gen-files==0.5.0
-mkdocs-get-deps==0.2.0
-mkdocs-include-dir-to-nav==1.2.0
-mkdocs-literate-nav==0.6.1
-mkdocs-material==9.5.39
-mkdocs-material-extensions==1.3.1
-mkdocs-section-index==0.3.9
-mkdocstrings[python]==0.26.1
-mkdocstrings-python==1.11.1
-mypy-extensions==1.0.0
-neoteroi-mkdocs==1.1.0
-packaging==24.1
-paginate==0.5.7
-pathspec==0.12.1
-platformdirs==4.3.6
-pygments==2.18.0
-pymdown-extensions==10.11.1
-pyparsing==3.1.4
-python-dateutil==2.9.0.post0
-pyyaml==6.0.2
-pyyaml-env-tag==0.1
-regex==2024.9.11
-requests==2.32.3
-rich==13.9.1
-six==1.16.0
-sniffio==1.3.1
-tabulate==0.9.0
-tomli==2.0.1
-typing-extensions==4.12.2
-urllib3==2.2.3
-verspec==0.1.0
-watchdog==5.0.3
-zipp==3.20.2

From e1aaef8877a7b8edcb85a91c6f60ccdb5daf374b Mon Sep 17 00:00:00 2001
From: Nicholas Junge <n.junge@appliedai-institute.de>
Date: Thu, 10 Oct 2024 20:00:10 +0200
Subject: [PATCH 3/6] Switch all actions to uv

Migrated over from lakefs-spec. Everything is as we have it there -
uv installation, running everything via `uv run`, etc.

The mike setup means that the mike action can only be run after a uv setup.
---
 .github/actions/mike-docs/action.yaml |  2 +-
 .github/workflows/lint-and-test.yaml  | 85 +++++++++------------------
 .github/workflows/release.yaml        | 22 +++----
 3 files changed, 37 insertions(+), 72 deletions(-)

diff --git a/.github/actions/mike-docs/action.yaml b/.github/actions/mike-docs/action.yaml
index 0ed90ee..1cf2783 100644
--- a/.github/actions/mike-docs/action.yaml
+++ b/.github/actions/mike-docs/action.yaml
@@ -31,5 +31,5 @@ runs:
       if [ "true" = "${{ inputs.push }}" ]; then
         MIKE_OPTIONS+=( "--push" )
       fi
-      mike deploy ${{ inputs.version }} ${{ inputs.alias }} "${MIKE_OPTIONS[@]}"
+      uv run mike deploy ${{ inputs.version }} ${{ inputs.alias }} "${MIKE_OPTIONS[@]}"
     shell: bash
diff --git a/.github/workflows/lint-and-test.yaml b/.github/workflows/lint-and-test.yaml
index af24027..55cebb0 100644
--- a/.github/workflows/lint-and-test.yaml
+++ b/.github/workflows/lint-and-test.yaml
@@ -10,38 +10,18 @@ on:
 
 jobs:
   lint:
+    name: Run code checks and formatting hooks
     runs-on: ubuntu-latest
-    env:
-      MYPY_CACHE_DIR: "${{ github.workspace }}/.cache/mypy"
-      RUFF_CACHE_DIR: "${{ github.workspace }}/.cache/ruff"
-      PRE_COMMIT_HOME: "${{ github.workspace }}/.cache/pre-commit"
     steps:
       - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-      - name: Set up Python and dependencies
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.11
-          cache: pip
-          cache-dependency-path: |
-            requirements-dev.txt
-            requirements-docs.txt
-            pyproject.toml
-      - name: Install dependencies
-        run: |
-          pip install -r requirements-dev.txt
-          pip install -e . --no-deps
-      - name: Cache pre-commit tools
-        uses: actions/cache@v4
-        with:
-          path: |
-            ${{ env.MYPY_CACHE_DIR }}
-            ${{ env.RUFF_CACHE_DIR }}
-            ${{ env.PRE_COMMIT_HOME }}
-          key: ${{ hashFiles('requirements-dev.txt', '.pre-commit-config.yaml') }}-linter-cache
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+      - name: Install Python 3.10 interpreter
+        run: uv python install 3.10
+      - name: Install the project
+        run: uv sync --extra dev
       - name: Run pre-commit checks
-        run: pre-commit run --all-files --verbose --show-diff-on-failure
+        run: uvx pre-commit run --all-files --verbose --show-diff-on-failure
   test:
     name: Test nnbench on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
@@ -50,35 +30,28 @@ jobs:
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up oldest supported Python on ${{ matrix.os }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.10"
-    - name: Run tests on oldest supported Python
-      run: |
-        python -m pip install ".[dev]"
-        pytest
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+      - name: Install Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+      - name: Install the project in developer mode
+        run: uv sync --extra dev
+      - name: Execute python tests
+        run: uv run pytest -s
   docs:
     name: Publish latest documentation for nnbench
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python and dependencies
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3.11
-        cache: pip
-        cache-dependency-path: |
-          requirements-dev.txt
-          requirements-docs.txt
-          pyproject.toml
-    - name: Install dependencies
-      run: |
-        pip install -r requirements-dev.txt -r requirements-docs.txt
-        pip install -e . --no-deps
-    - uses: ./.github/actions/mike-docs
-      with:
-        version: latest
-        pre_release: true # include pre-release notification banner
-        push: ${{ github.ref == 'refs/heads/main' }} # build always, publish on 'main' only to prevent version clutter
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+      - name: Install Python 3.11 interpreter
+        run: uv python install 3.11
+      - name: Install the project
+        run: uv sync --extra docs
+      - name: Build documentation using mike
+        uses: ./.github/actions/mike-docs
+        with:
+          version: latest
+          pre_release: true # include pre-release notification banner
+          push: ${{ github.ref == 'refs/heads/main' }} # build always, publish on 'main' only to prevent version clutter
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index 17c2a76..007ae73 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -15,22 +15,14 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Set up Python and dependencies
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.11
-          cache: pip
-          cache-dependency-path: |
-            requirements-dev.txt
-            requirements-docs.txt
-            pyproject.toml
-      - name: Install dependencies
-        run: |
-          pip install -r requirements-dev.txt -r requirements-docs.txt
-          pip install -e . --no-deps
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+      - name: Install Python 3.11 interpreter
+        run: uv python install 3.11
+      - name: Install the project
+        run: uv sync --all-extras
       - name: Build and check
-        run: |
-          python -m build
+        run: uv run -m build
       - name: Upload build artifacts
         uses: actions/upload-artifact@v4
         with:

From 56db6ebc4aa8626c83247169459e8785909efb2a Mon Sep 17 00:00:00 2001
From: Nicholas Junge <n.junge@appliedai-institute.de>
Date: Thu, 10 Oct 2024 20:05:47 +0200
Subject: [PATCH 4/6] Add Python version matrix, fix EOF in pre-commit config

---
 .github/workflows/lint-and-test.yaml | 3 ++-
 .pre-commit-config.yaml              | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/lint-and-test.yaml b/.github/workflows/lint-and-test.yaml
index 55cebb0..8199e5f 100644
--- a/.github/workflows/lint-and-test.yaml
+++ b/.github/workflows/lint-and-test.yaml
@@ -23,12 +23,13 @@ jobs:
       - name: Run pre-commit checks
         run: uvx pre-commit run --all-files --verbose --show-diff-on-failure
   test:
-    name: Test nnbench on ${{ matrix.os }}
+    name: Test nnbench on ${{ matrix.os }} on Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
+        python-version: [ "3.10", 3.11, 3.12 ]
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2a8bde5..0ce65f9 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -25,4 +25,4 @@ repos:
     rev: 0.4.20
     hooks:
       - id: uv-lock
-        name: Lock project dependencies
\ No newline at end of file
+        name: Lock project dependencies

From 861bfe5ddb33a47615805b0b364def522ebc2d9f Mon Sep 17 00:00:00 2001
From: Nicholas Junge <n.junge@appliedai-institute.de>
Date: Thu, 10 Oct 2024 20:12:44 +0200
Subject: [PATCH 5/6] Check out repo to depth 0 in docs job

---
 .github/workflows/lint-and-test.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/lint-and-test.yaml b/.github/workflows/lint-and-test.yaml
index 8199e5f..18f1ed1 100644
--- a/.github/workflows/lint-and-test.yaml
+++ b/.github/workflows/lint-and-test.yaml
@@ -44,6 +44,9 @@ jobs:
     name: Publish latest documentation for nnbench
     runs-on: ubuntu-latest
     steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
       - name: Install uv
         uses: astral-sh/setup-uv@v3
       - name: Install Python 3.11 interpreter

From 9a43b730759fc6012506f1e7305443332ceb8d93 Mon Sep 17 00:00:00 2001
From: Nicholas Junge <n.junge@appliedai-institute.de>
Date: Thu, 10 Oct 2024 20:14:22 +0200
Subject: [PATCH 6/6] Fix Self import for Python >=3.11

---
 src/nnbench/types/benchmark.py | 6 +++++-
 src/nnbench/types/interface.py | 6 +++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/nnbench/types/benchmark.py b/src/nnbench/types/benchmark.py
index a18dc63..566b15f 100644
--- a/src/nnbench/types/benchmark.py
+++ b/src/nnbench/types/benchmark.py
@@ -1,12 +1,16 @@
 """Type interfaces for benchmarks and benchmark collections."""
 
 import copy
+import sys
 from collections.abc import Callable, Mapping
 from dataclasses import dataclass, field
 from types import MappingProxyType
 from typing import Any, Literal
 
-from typing_extensions import Self
+if sys.version_info >= (3, 11):
+    from typing import Self
+else:
+    from typing_extensions import Self
 
 from nnbench.context import Context
 from nnbench.types.interface import Interface
diff --git a/src/nnbench/types/interface.py b/src/nnbench/types/interface.py
index da0a381..21380f1 100644
--- a/src/nnbench/types/interface.py
+++ b/src/nnbench/types/interface.py
@@ -1,11 +1,15 @@
 """Type interface for the function interface"""
 
 import inspect
+import sys
 from collections.abc import Callable
 from dataclasses import dataclass
 from typing import Any, TypeVar
 
-from typing_extensions import Self
+if sys.version_info >= (3, 11):
+    from typing import Self
+else:
+    from typing_extensions import Self
 
 T = TypeVar("T")
 Variable = tuple[str, type, Any]