ci(backport): Use uv for all pip installs (#2494)

* Backport:
   - PR #2444
   - PR #2475

Author: matthewfeickert

.github/workflows/bump-version.yml

@@ -198,8 +198,9 @@ jobs:
 
     - name: Install Python dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install tbump
+        python -m pip install uv
+        uv pip install --system --upgrade pip setuptools wheel
+        uv pip install --system tbump
         python -m pip list
 
     - name: Setup Git user to push new tag

.github/workflows/ci.yml

@@ -43,17 +43,19 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install dependencies (Python 3.7)
-      if: matrix.python-version == '3.7'
+    - name: Install dependencies
+      if: matrix.python-version != '3.7' && matrix.python-version != '3.8'
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install --find-links https://storage.googleapis.com/jax-releases/jax_releases.html --upgrade .[test]
+        python -m pip install uv
+        uv pip install --system --upgrade pip setuptools wheel
+        uv pip install --system --upgrade ".[all,test]"
 
-    - name: Install dependencies
-      if: matrix.python-version != '3.7'
+      # c.f. https://github.com/astral-sh/uv/issues/2062
+    - name: Install dependencies (Python 3.7, 3.8)
+      if: matrix.python-version == '3.7' || matrix.python-version == '3.8'
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install --upgrade .[test]
+        python -m pip install --find-links https://storage.googleapis.com/jax-releases/jax_releases.html --upgrade ".[all,test]"
 
     - name: List installed Python packages
       run: python -m pip list

.github/workflows/dependencies-head.yml

@@ -29,13 +29,18 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade --pre .[test]
+        python -m pip install uv
+        uv pip install --system --upgrade pip setuptools wheel
+        uv pip --no-cache --quiet install --system --upgrade --pre ".[all,test]"
         python -m pip list
 
+    - name: List release candidates, alpha, and beta releases
+      run: |
+        python -m pip list | egrep '[0-9](rc|[ab])[0-9]'
+
     - name: Test with pytest
       run: |
-        pytest --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
+        pytest --ignore tests/contrib --ignore tests/benchmarks --ignore tests/test_notebooks.py
 
   scipy:
 
@@ -53,19 +58,19 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    # Use nightly SciPy wheels from Anaconda's PyPI
-    # c.f. https://twitter.com/ralfgommers/status/1419917265781334025
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade .[test]
-        python -m pip uninstall --yes scipy
-        python -m pip install --upgrade --index-url https://pypi.anaconda.org/scipy-wheels-nightly/simple scipy
+        python -m pip install uv
+        uv pip install --system --upgrade pip setuptools wheel
+        uv pip --no-cache --quiet install --system --upgrade ".[all,test]"
+        uv pip uninstall --system scipy
+        # uv wants to upgrade dependencies (numpy) to a dev release too, so don't --upgrade
+        uv pip install --system --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple scipy
         python -m pip list
 
     - name: Test with pytest
       run: |
-        pytest --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
+        pytest --ignore tests/contrib --ignore tests/benchmarks --ignore tests/test_notebooks.py
 
   iminuit:
 
@@ -83,15 +88,16 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade .[test]
-        python -m pip uninstall --yes iminuit
-        python -m pip install --upgrade cython
-        python -m pip install --upgrade git+https://github.com/scikit-hep/iminuit.git
+        python -m pip install uv
+        uv pip install --system --upgrade pip setuptools wheel
+        uv pip --no-cache --quiet install --system --upgrade ".[all,test]"
+        uv pip uninstall --system iminuit
+        uv pip install --system --upgrade cython
+        uv pip install --system --upgrade git+https://github.com/scikit-hep/iminuit.git
         python -m pip list
     - name: Test with pytest
       run: |
-        pytest --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
+        pytest --ignore tests/contrib --ignore tests/benchmarks --ignore tests/test_notebooks.py
 
   uproot5:
 
@@ -109,14 +115,15 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade .[test]
-        python -m pip uninstall --yes uproot
-        python -m pip install --upgrade git+https://github.com/scikit-hep/uproot4.git
+        python -m pip install uv
+        uv pip install --system --upgrade pip setuptools wheel
+        uv pip --no-cache --quiet install --system --upgrade ".[all,test]"
+        uv pip uninstall --system uproot
+        uv pip install --system --upgrade git+https://github.com/scikit-hep/uproot5.git
         python -m pip list
     - name: Test with pytest
       run: |
-        pytest --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
+        pytest --ignore tests/contrib --ignore tests/benchmarks --ignore tests/test_notebooks.py
 
   matplotlib:
 
@@ -136,15 +143,18 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade .[test]
-        python -m pip uninstall --yes matplotlib
-        # Need to use --extra-index-url as dependencies aren't on scipy-wheels-nightly package index.
+        python -m pip install uv
+        uv pip install --system --upgrade pip setuptools wheel
+        uv pip --no-cache --quiet install --system --upgrade ".[all,test]"
+        uv pip uninstall --system matplotlib
+        # Need to use --extra-index-url as all dependencies aren't on scientific-python-nightly-wheels package index.
         # Need to use --pre as dev releases will need priority over stable releases.
-        python -m pip install \
-          --upgrade \
+        # Note that uv and pip differ on --extra-index-url priority
+        # c.f. https://github.com/scientific-python/upload-nightly-action/issues/76
+        uv pip install --system \
           --pre \
-          --extra-index-url https://pypi.anaconda.org/scipy-wheels-nightly/simple \
+          --index-url https://pypi.org/simple/ \
+          --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
           matplotlib
 
     - name: List installed Python packages
@@ -170,11 +180,12 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --upgrade .[test]
-        python -m pip uninstall --yes pytest
-        python -m pip install --upgrade git+https://github.com/pytest-dev/pytest.git
+        python -m pip install uv
+        uv pip install --system --upgrade pip setuptools wheel
+        uv pip --no-cache --quiet install --system --upgrade ".[all,test]"
+        uv pip uninstall --system pytest
+        uv pip install --system --upgrade git+https://github.com/pytest-dev/pytest.git
         python -m pip list
     - name: Test with pytest
       run: |
-        pytest --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
+        pytest --ignore tests/contrib --ignore tests/benchmarks --ignore tests/test_notebooks.py

.github/workflows/docs.yml

@@ -31,9 +31,10 @@ jobs:
 
     - name: Install Python dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip --quiet install --upgrade .[docs,test]
-        python -m pip install yq
+        python -m pip install uv
+        uv pip install --system --upgrade pip setuptools wheel
+        uv pip --quiet install --system --upgrade ".[docs,test]"
+        uv pip install --system yq
         python -m pip list
 
     - name: Install apt-get dependencies

.github/workflows/notebooks.yml

@@ -28,8 +28,10 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install --upgrade .[test]
+        python -m pip install uv
+        uv pip install --system --upgrade pip setuptools wheel
+        # FIXME: c.f. https://github.com/scikit-hep/pyhf/issues/2104
+        uv pip install --system --upgrade ".[all,test]" 'jupyter-client<8.0.0'
 
     - name: List installed Python packages
       run: python -m pip list

.github/workflows/publish-package.yml

@@ -41,19 +41,20 @@ jobs:
 
     - name: Install python-build and twine
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install build twine
+        python -m pip install uv
+        uv pip install --system --upgrade pip
+        uv pip install --system build twine
         python -m pip list
 
     - name: Build a sdist and wheel
       if: github.event_name != 'schedule'
       run: |
-        python -m build .
+        python -m build --installer uv .
 
     - name: Build a sdist and wheel and check for warnings
       if: github.event_name == 'schedule'
       run: |
-        PYTHONWARNINGS=error,default::DeprecationWarning python -m build .
+        PYTHONWARNINGS=error,default::DeprecationWarning python -m build --installer uv .
 
     - name: Verify untagged commits have dev versions
       if: "!startsWith(github.ref, 'refs/tags/')"

.github/workflows/release_tests.yml

@@ -37,9 +37,10 @@ jobs:
 
     - name: Install from PyPI
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install --pre pyhf[backends,xmlio]
-        python -m pip install pytest pytest-cov
+        python -m pip install uv
+        uv pip install --system --upgrade pip setuptools wheel
+        uv pip install --system --pre 'pyhf[backends,xmlio]'
+        uv pip install --system pytest
         python -m pip list
 
     - name: Canary test public API
@@ -49,6 +50,6 @@ jobs:
       # FIXME: c.f. https://github.com/proycon/codemetapy/issues/24
     - name: Verify requirements in codemeta.json
       run: |
-        python -m pip install jq "codemetapy>=2.4.1"
+        uv pip install --system jq "codemetapy>=2.3.0"
         codemetapy --inputtype python --no-extras pyhf > codemeta_generated.json
         diff <(jq -S .softwareRequirements codemeta.json) <(jq -S .softwareRequirements codemeta_generated.json)

.readthedocs.yaml

@@ -9,22 +9,21 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
   apt_packages:
     - curl
     - jq
+  jobs:
+    post_create_environment:
+      - pip install uv
+    post_install:
+      # VIRTUAL_ENV needs to be set manually for now.
+      # See https://github.com/readthedocs/readthedocs.org/pull/11152/
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install '.[docs]'
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/conf.py
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF and ePub
 formats: all
-
-# python -m pip install .[docs]
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs