From 39393ec98fe2f933538557276c05c6044665a379 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 07:16:51 +0200
Subject: [PATCH 01/13] CI Remove historic nogil Python 3.9 build

---
 azure-pipelines.yml                           | 36 ---------
 build_tools/azure/install.sh                  | 10 ---
 build_tools/azure/python_nogil_lock.txt       | 73 -------------------
 .../azure/python_nogil_requirements.txt       | 20 -----
 build_tools/azure/test_docs.sh                |  2 +-
 build_tools/shared.sh                         |  2 +-
 doc/developers/contributing.rst               |  1 -
 7 files changed, 2 insertions(+), 142 deletions(-)
 delete mode 100644 build_tools/azure/python_nogil_lock.txt
 delete mode 100644 build_tools/azure/python_nogil_requirements.txt

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 1ce5244124d4d..372b2033ecbe6 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -62,42 +62,6 @@ jobs:
         SKLEARN_WARNINGS_AS_ERRORS: '1'
         CHECK_PYTEST_SOFT_DEPENDENCY: 'true'
 
-- template: build_tools/azure/posix-docker.yml
-  # Experimental CPython branch without the Global Interpreter Lock:
-  # https://github.com/colesbury/nogil/
-  #
-  # The nogil build relies on a dedicated PyPI-style index to install patched
-  # versions of NumPy, SciPy and Cython maintained by @colesbury and that
-  # include specific fixes to make them run correctly without relying on the GIL.
-  #
-  # The goal of this CI entry is to make sure that we do not introduce any
-  # dependency on the GIL in scikit-learn itself. An auxiliary goal is to early
-  # detect any regression in the patched build dependencies to report them
-  # upstream. The long-term goal is to be able to stop having to maintain
-  # multiprocessing based workaround / hacks in joblib / loky to make multi-CPU
-  # computing in scikit-learn efficient by default using regular threads.
-  #
-  # If this experimental entry becomes too unstable, feel free to disable it.
-  parameters:
-    name: Linux_nogil
-    vmImage: ubuntu-20.04
-    dependsOn: [git_commit, linting]
-    condition: |
-      and(
-        succeeded(),
-        not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')),
-        or(eq(variables['Build.Reason'], 'Schedule'),
-           contains(dependencies['git_commit']['outputs']['commit.message'], '[nogil]'
-          )
-        )
-      )
-    matrix:
-      pylatest_pip_nogil:
-        DOCKER_CONTAINER: 'nogil/python'
-        DISTRIB: 'pip-nogil'
-        LOCK_FILE: './build_tools/azure/python_nogil_lock.txt'
-        COVERAGE: 'false'
-
 - job: Linux_Nightly_Pyodide
   pool:
     vmImage: ubuntu-22.04
diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
index cdaaa0c8cc965..082e5f9e8e675 100755
--- a/build_tools/azure/install.sh
+++ b/build_tools/azure/install.sh
@@ -65,11 +65,6 @@ python_environment_install_and_activate() {
         python3 -m virtualenv --system-site-packages --python=python3 $VIRTUALENV
         source $VIRTUALENV/bin/activate
         pip install -r "${LOCK_FILE}"
-
-    elif [[ "$DISTRIB" == "pip-nogil" ]]; then
-        python -m venv $VIRTUALENV
-        source $VIRTUALENV/bin/activate
-        pip install -r "${LOCK_FILE}"
     fi
 
     if [[ "$DISTRIB" == "conda-pip-scipy-dev" ]]; then
@@ -86,11 +81,6 @@ python_environment_install_and_activate() {
         pip install https://github.com/joblib/joblib/archive/master.zip
         echo "Installing pillow from latest sources"
         pip install https://github.com/python-pillow/Pillow/archive/main.zip
-
-    elif [[ "$DISTRIB" == "pip-nogil" ]]; then
-        apt-get -yq update
-        apt-get install -yq ccache
-
     fi
 }
 
diff --git a/build_tools/azure/python_nogil_lock.txt b/build_tools/azure/python_nogil_lock.txt
deleted file mode 100644
index 7f67a48842dea..0000000000000
--- a/build_tools/azure/python_nogil_lock.txt
+++ /dev/null
@@ -1,73 +0,0 @@
-#
-# This file is autogenerated by pip-compile with Python 3.9
-# by the following command:
-#
-#    pip-compile --output-file=/scikit-learn/build_tools/azure/python_nogil_lock.txt /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-#
---index-url https://d1yxz45j0ypngg.cloudfront.net/
---extra-index-url https://pypi.org/simple
-
-contourpy==1.1.1
-    # via matplotlib
-cycler==0.12.1
-    # via matplotlib
-cython==3.0.10
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-exceptiongroup==1.2.1
-    # via pytest
-execnet==2.1.1
-    # via pytest-xdist
-fonttools==4.51.0
-    # via matplotlib
-iniconfig==2.0.0
-    # via pytest
-joblib==1.4.2
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-kiwisolver==1.4.4
-    # via matplotlib
-matplotlib==3.6.2
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-meson==1.4.0
-    # via meson-python
-meson-python==0.16.0
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-ninja==1.11.1.1
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-numpy==1.24.0
-    # via
-    #   -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-    #   contourpy
-    #   matplotlib
-    #   scipy
-packaging==24.0
-    # via
-    #   matplotlib
-    #   meson-python
-    #   pyproject-metadata
-    #   pytest
-pillow==9.5.0
-    # via matplotlib
-pluggy==1.5.0
-    # via pytest
-pyparsing==3.1.2
-    # via matplotlib
-pyproject-metadata==0.8.0
-    # via meson-python
-pytest==7.4.4
-    # via
-    #   -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-    #   pytest-xdist
-pytest-xdist==3.6.1
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-python-dateutil==2.9.0.post0
-    # via matplotlib
-scipy==1.9.3
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-six==1.16.0
-    # via python-dateutil
-threadpoolctl==3.5.0
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-tomli==2.0.1
-    # via
-    #   meson-python
-    #   pytest
diff --git a/build_tools/azure/python_nogil_requirements.txt b/build_tools/azure/python_nogil_requirements.txt
deleted file mode 100644
index 2cebad9a03b25..0000000000000
--- a/build_tools/azure/python_nogil_requirements.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-# To generate python_nogil_lock.txt, use the following command:
-# docker run -v $PWD:/scikit-learn -it nogil/python bash -c 'pip install pip-tools; pip-compile --upgrade /scikit-learn/build_tools/azure/python_nogil_requirements.txt -o /scikit-learn/build_tools/azure/python_nogil_lock.txt'
-#
-# The reason behind it is that you need python-nogil to generate the pip lock
-# file. Using pip-compile --index and --extra-index will not work, for example
-# the latest cython will be picked up from PyPI, rather than the one from the
-# python-nogil index
-matplotlib
-numpy
-scipy
-cython
-joblib
-threadpoolctl
-# TODO: somehow pytest 8 does not seem to work with meson editable
-# install. Exit code is 5, i.e. no test collected
-# This would be fixed by https://github.com/mesonbuild/meson-python/pull/569
-pytest<8
-pytest-xdist
-meson-python
-ninja
diff --git a/build_tools/azure/test_docs.sh b/build_tools/azure/test_docs.sh
index 61e855425786b..b3a5ec97c4d6a 100755
--- a/build_tools/azure/test_docs.sh
+++ b/build_tools/azure/test_docs.sh
@@ -4,7 +4,7 @@ set -e
 
 if [[ "$DISTRIB" =~ ^conda.* ]]; then
     source activate $VIRTUALENV
-elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "pip-nogil" ]]; then
+elif [[ "$DISTRIB" == "ubuntu" ]]; then
     source $VIRTUALENV/bin/activate
 fi
 
diff --git a/build_tools/shared.sh b/build_tools/shared.sh
index 4866c149d506f..dd4b0856050a7 100644
--- a/build_tools/shared.sh
+++ b/build_tools/shared.sh
@@ -29,7 +29,7 @@ show_installed_libraries(){
 activate_environment() {
     if [[ "$DISTRIB" =~ ^conda.* ]]; then
         source activate $VIRTUALENV
-    elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "debian-32" || "$DISTRIB" == "pip-nogil" ]]; then
+    elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "debian-32" ]]; then
         source $VIRTUALENV/bin/activate
     fi
 }
diff --git a/doc/developers/contributing.rst b/doc/developers/contributing.rst
index 8c8d478e6d6f5..f46051175b82d 100644
--- a/doc/developers/contributing.rst
+++ b/doc/developers/contributing.rst
@@ -518,7 +518,6 @@ Commit Message Marker  Action Taken by CI
 [cd build cirrus]      CD is run only for Cirrus CI
 [lint skip]            Azure pipeline skips linting
 [scipy-dev]            Build & test with our dependencies (numpy, scipy, etc.) development builds
-[nogil]                Build & test with the nogil experimental branches of CPython, Cython, NumPy, SciPy, ...
 [pyodide]              Build & test with Pyodide
 [azure parallel]       Run Azure CI jobs in parallel
 [cirrus arm]           Run Cirrus CI ARM test

From 3b3d1696487a258a2fe50b100c97bdb6ed38d498 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 11:15:30 +0200
Subject: [PATCH 02/13] Revert "CI Remove historic nogil Python 3.9 build"

This reverts commit 39393ec98fe2f933538557276c05c6044665a379.
---
 azure-pipelines.yml                           | 36 +++++++++
 build_tools/azure/install.sh                  | 10 +++
 build_tools/azure/python_nogil_lock.txt       | 73 +++++++++++++++++++
 .../azure/python_nogil_requirements.txt       | 20 +++++
 build_tools/azure/test_docs.sh                |  2 +-
 build_tools/shared.sh                         |  2 +-
 doc/developers/contributing.rst               |  1 +
 7 files changed, 142 insertions(+), 2 deletions(-)
 create mode 100644 build_tools/azure/python_nogil_lock.txt
 create mode 100644 build_tools/azure/python_nogil_requirements.txt

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 372b2033ecbe6..1ce5244124d4d 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -62,6 +62,42 @@ jobs:
         SKLEARN_WARNINGS_AS_ERRORS: '1'
         CHECK_PYTEST_SOFT_DEPENDENCY: 'true'
 
+- template: build_tools/azure/posix-docker.yml
+  # Experimental CPython branch without the Global Interpreter Lock:
+  # https://github.com/colesbury/nogil/
+  #
+  # The nogil build relies on a dedicated PyPI-style index to install patched
+  # versions of NumPy, SciPy and Cython maintained by @colesbury and that
+  # include specific fixes to make them run correctly without relying on the GIL.
+  #
+  # The goal of this CI entry is to make sure that we do not introduce any
+  # dependency on the GIL in scikit-learn itself. An auxiliary goal is to early
+  # detect any regression in the patched build dependencies to report them
+  # upstream. The long-term goal is to be able to stop having to maintain
+  # multiprocessing based workaround / hacks in joblib / loky to make multi-CPU
+  # computing in scikit-learn efficient by default using regular threads.
+  #
+  # If this experimental entry becomes too unstable, feel free to disable it.
+  parameters:
+    name: Linux_nogil
+    vmImage: ubuntu-20.04
+    dependsOn: [git_commit, linting]
+    condition: |
+      and(
+        succeeded(),
+        not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')),
+        or(eq(variables['Build.Reason'], 'Schedule'),
+           contains(dependencies['git_commit']['outputs']['commit.message'], '[nogil]'
+          )
+        )
+      )
+    matrix:
+      pylatest_pip_nogil:
+        DOCKER_CONTAINER: 'nogil/python'
+        DISTRIB: 'pip-nogil'
+        LOCK_FILE: './build_tools/azure/python_nogil_lock.txt'
+        COVERAGE: 'false'
+
 - job: Linux_Nightly_Pyodide
   pool:
     vmImage: ubuntu-22.04
diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
index 082e5f9e8e675..cdaaa0c8cc965 100755
--- a/build_tools/azure/install.sh
+++ b/build_tools/azure/install.sh
@@ -65,6 +65,11 @@ python_environment_install_and_activate() {
         python3 -m virtualenv --system-site-packages --python=python3 $VIRTUALENV
         source $VIRTUALENV/bin/activate
         pip install -r "${LOCK_FILE}"
+
+    elif [[ "$DISTRIB" == "pip-nogil" ]]; then
+        python -m venv $VIRTUALENV
+        source $VIRTUALENV/bin/activate
+        pip install -r "${LOCK_FILE}"
     fi
 
     if [[ "$DISTRIB" == "conda-pip-scipy-dev" ]]; then
@@ -81,6 +86,11 @@ python_environment_install_and_activate() {
         pip install https://github.com/joblib/joblib/archive/master.zip
         echo "Installing pillow from latest sources"
         pip install https://github.com/python-pillow/Pillow/archive/main.zip
+
+    elif [[ "$DISTRIB" == "pip-nogil" ]]; then
+        apt-get -yq update
+        apt-get install -yq ccache
+
     fi
 }
 
diff --git a/build_tools/azure/python_nogil_lock.txt b/build_tools/azure/python_nogil_lock.txt
new file mode 100644
index 0000000000000..7f67a48842dea
--- /dev/null
+++ b/build_tools/azure/python_nogil_lock.txt
@@ -0,0 +1,73 @@
+#
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
+#
+#    pip-compile --output-file=/scikit-learn/build_tools/azure/python_nogil_lock.txt /scikit-learn/build_tools/azure/python_nogil_requirements.txt
+#
+--index-url https://d1yxz45j0ypngg.cloudfront.net/
+--extra-index-url https://pypi.org/simple
+
+contourpy==1.1.1
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+cython==3.0.10
+    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
+exceptiongroup==1.2.1
+    # via pytest
+execnet==2.1.1
+    # via pytest-xdist
+fonttools==4.51.0
+    # via matplotlib
+iniconfig==2.0.0
+    # via pytest
+joblib==1.4.2
+    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
+kiwisolver==1.4.4
+    # via matplotlib
+matplotlib==3.6.2
+    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
+meson==1.4.0
+    # via meson-python
+meson-python==0.16.0
+    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
+ninja==1.11.1.1
+    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
+numpy==1.24.0
+    # via
+    #   -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
+    #   contourpy
+    #   matplotlib
+    #   scipy
+packaging==24.0
+    # via
+    #   matplotlib
+    #   meson-python
+    #   pyproject-metadata
+    #   pytest
+pillow==9.5.0
+    # via matplotlib
+pluggy==1.5.0
+    # via pytest
+pyparsing==3.1.2
+    # via matplotlib
+pyproject-metadata==0.8.0
+    # via meson-python
+pytest==7.4.4
+    # via
+    #   -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
+    #   pytest-xdist
+pytest-xdist==3.6.1
+    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
+python-dateutil==2.9.0.post0
+    # via matplotlib
+scipy==1.9.3
+    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
+six==1.16.0
+    # via python-dateutil
+threadpoolctl==3.5.0
+    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
+tomli==2.0.1
+    # via
+    #   meson-python
+    #   pytest
diff --git a/build_tools/azure/python_nogil_requirements.txt b/build_tools/azure/python_nogil_requirements.txt
new file mode 100644
index 0000000000000..2cebad9a03b25
--- /dev/null
+++ b/build_tools/azure/python_nogil_requirements.txt
@@ -0,0 +1,20 @@
+# To generate python_nogil_lock.txt, use the following command:
+# docker run -v $PWD:/scikit-learn -it nogil/python bash -c 'pip install pip-tools; pip-compile --upgrade /scikit-learn/build_tools/azure/python_nogil_requirements.txt -o /scikit-learn/build_tools/azure/python_nogil_lock.txt'
+#
+# The reason behind it is that you need python-nogil to generate the pip lock
+# file. Using pip-compile --index and --extra-index will not work, for example
+# the latest cython will be picked up from PyPI, rather than the one from the
+# python-nogil index
+matplotlib
+numpy
+scipy
+cython
+joblib
+threadpoolctl
+# TODO: somehow pytest 8 does not seem to work with meson editable
+# install. Exit code is 5, i.e. no test collected
+# This would be fixed by https://github.com/mesonbuild/meson-python/pull/569
+pytest<8
+pytest-xdist
+meson-python
+ninja
diff --git a/build_tools/azure/test_docs.sh b/build_tools/azure/test_docs.sh
index b3a5ec97c4d6a..61e855425786b 100755
--- a/build_tools/azure/test_docs.sh
+++ b/build_tools/azure/test_docs.sh
@@ -4,7 +4,7 @@ set -e
 
 if [[ "$DISTRIB" =~ ^conda.* ]]; then
     source activate $VIRTUALENV
-elif [[ "$DISTRIB" == "ubuntu" ]]; then
+elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "pip-nogil" ]]; then
     source $VIRTUALENV/bin/activate
 fi
 
diff --git a/build_tools/shared.sh b/build_tools/shared.sh
index dd4b0856050a7..4866c149d506f 100644
--- a/build_tools/shared.sh
+++ b/build_tools/shared.sh
@@ -29,7 +29,7 @@ show_installed_libraries(){
 activate_environment() {
     if [[ "$DISTRIB" =~ ^conda.* ]]; then
         source activate $VIRTUALENV
-    elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "debian-32" ]]; then
+    elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "debian-32" || "$DISTRIB" == "pip-nogil" ]]; then
         source $VIRTUALENV/bin/activate
     fi
 }
diff --git a/doc/developers/contributing.rst b/doc/developers/contributing.rst
index f46051175b82d..8c8d478e6d6f5 100644
--- a/doc/developers/contributing.rst
+++ b/doc/developers/contributing.rst
@@ -518,6 +518,7 @@ Commit Message Marker  Action Taken by CI
 [cd build cirrus]      CD is run only for Cirrus CI
 [lint skip]            Azure pipeline skips linting
 [scipy-dev]            Build & test with our dependencies (numpy, scipy, etc.) development builds
+[nogil]                Build & test with the nogil experimental branches of CPython, Cython, NumPy, SciPy, ...
 [pyodide]              Build & test with Pyodide
 [azure parallel]       Run Azure CI jobs in parallel
 [cirrus arm]           Run Cirrus CI ARM test

From c979671fedc6c7a9fc9943700005b1a619b56761 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 11:32:14 +0200
Subject: [PATCH 03/13] [free-threaded] First attempt to see whether at least
 the trigger works

---
 azure-pipelines.yml          | 37 ++++++++++++++----------------------
 build_tools/azure/install.sh | 22 ++++++++++++++++-----
 2 files changed, 31 insertions(+), 28 deletions(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 1ce5244124d4d..7787f0ae1ce64 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -62,40 +62,31 @@ jobs:
         SKLEARN_WARNINGS_AS_ERRORS: '1'
         CHECK_PYTEST_SOFT_DEPENDENCY: 'true'
 
-- template: build_tools/azure/posix-docker.yml
-  # Experimental CPython branch without the Global Interpreter Lock:
-  # https://github.com/colesbury/nogil/
-  #
-  # The nogil build relies on a dedicated PyPI-style index to install patched
-  # versions of NumPy, SciPy and Cython maintained by @colesbury and that
-  # include specific fixes to make them run correctly without relying on the GIL.
-  #
-  # The goal of this CI entry is to make sure that we do not introduce any
-  # dependency on the GIL in scikit-learn itself. An auxiliary goal is to early
-  # detect any regression in the patched build dependencies to report them
-  # upstream. The long-term goal is to be able to stop having to maintain
-  # multiprocessing based workaround / hacks in joblib / loky to make multi-CPU
-  # computing in scikit-learn efficient by default using regular threads.
-  #
-  # If this experimental entry becomes too unstable, feel free to disable it.
+- template: build_tools/azure/posix.yml
+  # CPython 3.13 free-threaded build. Currently this uses CPyton 3.13
+  # free-threaded build from deadsnakes PPA together with Numpy and Scipy
+  # free-threaded development wheels.
+  # TODO Use released Numpy and Scipy versions when they are available
+  # TODO Use CPython 3.13 when it is released (planned in October 2024)
   parameters:
-    name: Linux_nogil
-    vmImage: ubuntu-20.04
+    name: Linux_free_threaded
+    vmImage: ubuntu-22.04
     dependsOn: [git_commit, linting]
     condition: |
       and(
         succeeded(),
         not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')),
         or(eq(variables['Build.Reason'], 'Schedule'),
-           contains(dependencies['git_commit']['outputs']['commit.message'], '[nogil]'
+           contains(dependencies['git_commit']['outputs']['commit.message'], '[free-threaded]'
           )
         )
       )
     matrix:
-      pylatest_pip_nogil:
-        DOCKER_CONTAINER: 'nogil/python'
-        DISTRIB: 'pip-nogil'
-        LOCK_FILE: './build_tools/azure/python_nogil_lock.txt'
+      pylatest_pip_free_threaded:
+        DOCKER_CONTAINER: ''
+        DISTRIB: 'pip-free-threaded'
+        # TODO free-threaded probably use pip lock-file
+        LOCK_FILE: './build_tools/azure/python_free_threaded_lock.txt'
         COVERAGE: 'false'
 
 - job: Linux_Nightly_Pyodide
diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
index cdaaa0c8cc965..02eb73b9ca38a 100755
--- a/build_tools/azure/install.sh
+++ b/build_tools/azure/install.sh
@@ -66,10 +66,19 @@ python_environment_install_and_activate() {
         source $VIRTUALENV/bin/activate
         pip install -r "${LOCK_FILE}"
 
-    elif [[ "$DISTRIB" == "pip-nogil" ]]; then
-        python -m venv $VIRTUALENV
+    elif [[ "$DISTRIB" == "pip-free-threaded" ]]; then
+        python3.13t -m venv $VIRTUALENV
         source $VIRTUALENV/bin/activate
-        pip install -r "${LOCK_FILE}"
+        # TODO free-threaded use a lock-file, for now done by hand
+        # TODO for now need pip 24.1b1 to find free-threaded wheels
+        pip install -U --pre pip
+        dev_anaconda_url=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+        dev_packages="numpy scipy"
+        pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url $dev_packages
+        # TODO need development Cython for now
+        pip install git+https://github.com/cython/cython
+        # Install all the other dependencies
+        pip install joblib threadpoolctl pytest meson-python
     fi
 
     if [[ "$DISTRIB" == "conda-pip-scipy-dev" ]]; then
@@ -87,10 +96,13 @@ python_environment_install_and_activate() {
         echo "Installing pillow from latest sources"
         pip install https://github.com/python-pillow/Pillow/archive/main.zip
 
-    elif [[ "$DISTRIB" == "pip-nogil" ]]; then
+    elif [[ "$DISTRIB" == "pip-free-threaded" ]]; then
         apt-get -yq update
         apt-get install -yq ccache
-
+        apt-get install software-properties-common -y
+        add-apt-repository --yes ppa:deadsnakes/nightly
+        apt-get update -y
+        apt-get install -y --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil
     fi
 }
 

From 84b62b8caef1329e2b0c90cfe8ac695f6fd2c029 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 11:37:48 +0200
Subject: [PATCH 04/13] [free-threaded] fix

---
 build_tools/azure/install.sh    | 17 +++++++++--------
 doc/developers/contributing.rst |  2 +-
 2 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
index 02eb73b9ca38a..e36f1f0718b27 100755
--- a/build_tools/azure/install.sh
+++ b/build_tools/azure/install.sh
@@ -38,6 +38,15 @@ pre_python_environment_install() {
         apt-get install -y python3-dev python3-numpy python3-scipy \
                 python3-matplotlib libatlas3-base libatlas-base-dev \
                 python3-virtualenv python3-pandas ccache git
+
+    elif [[ "$DISTRIB" == "pip-free-threaded" ]]; then
+        apt-get -yq update
+        apt-get install -yq ccache
+        apt-get install software-properties-common -y
+        add-apt-repository --yes ppa:deadsnakes/nightly
+        apt-get update -y
+        apt-get install -y --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil
+
     fi
 }
 
@@ -95,14 +104,6 @@ python_environment_install_and_activate() {
         pip install https://github.com/joblib/joblib/archive/master.zip
         echo "Installing pillow from latest sources"
         pip install https://github.com/python-pillow/Pillow/archive/main.zip
-
-    elif [[ "$DISTRIB" == "pip-free-threaded" ]]; then
-        apt-get -yq update
-        apt-get install -yq ccache
-        apt-get install software-properties-common -y
-        add-apt-repository --yes ppa:deadsnakes/nightly
-        apt-get update -y
-        apt-get install -y --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil
     fi
 }
 
diff --git a/doc/developers/contributing.rst b/doc/developers/contributing.rst
index 8c8d478e6d6f5..535983712cc8c 100644
--- a/doc/developers/contributing.rst
+++ b/doc/developers/contributing.rst
@@ -518,7 +518,7 @@ Commit Message Marker  Action Taken by CI
 [cd build cirrus]      CD is run only for Cirrus CI
 [lint skip]            Azure pipeline skips linting
 [scipy-dev]            Build & test with our dependencies (numpy, scipy, etc.) development builds
-[nogil]                Build & test with the nogil experimental branches of CPython, Cython, NumPy, SciPy, ...
+[free-threaded]        Build & test with CPython 3.13 free-threaded
 [pyodide]              Build & test with Pyodide
 [azure parallel]       Run Azure CI jobs in parallel
 [cirrus arm]           Run Cirrus CI ARM test

From 72c2e1c9fa4a4189fd70a4d198500e7afba1ad81 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 11:46:48 +0200
Subject: [PATCH 05/13] [free-threaded] fix

---
 build_tools/azure/install.sh | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
index e36f1f0718b27..65d5918c54733 100755
--- a/build_tools/azure/install.sh
+++ b/build_tools/azure/install.sh
@@ -40,13 +40,12 @@ pre_python_environment_install() {
                 python3-virtualenv python3-pandas ccache git
 
     elif [[ "$DISTRIB" == "pip-free-threaded" ]]; then
-        apt-get -yq update
-        apt-get install -yq ccache
-        apt-get install software-properties-common -y
-        add-apt-repository --yes ppa:deadsnakes/nightly
-        apt-get update -y
-        apt-get install -y --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil
-
+        sudo apt-get -yq update
+        sudo apt-get install -yq ccache
+        sudo apt-get install software-properties-common -y
+        sudo add-apt-repository --yes ppa:deadsnakes/nightly
+        sudo apt-get update -y
+        sudo apt-get install -y --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil
     fi
 }
 

From 3da8db478b75c31eb4df551a319ef19a4a2dfd8c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 11:58:31 +0200
Subject: [PATCH 06/13] [free-threaded] fix

---
 azure-pipelines.yml          | 4 +++-
 build_tools/azure/install.sh | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 7787f0ae1ce64..b1eb59e62e1f0 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -71,7 +71,9 @@ jobs:
   parameters:
     name: Linux_free_threaded
     vmImage: ubuntu-22.04
-    dependsOn: [git_commit, linting]
+    # TODO free-threading temporary optimization for quicker iteration
+    dependsOn: [git_commit]
+    # dependsOn: [git_commit, linting]
     condition: |
       and(
         succeeded(),
diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
index 65d5918c54733..bc3446785775d 100755
--- a/build_tools/azure/install.sh
+++ b/build_tools/azure/install.sh
@@ -45,7 +45,7 @@ pre_python_environment_install() {
         sudo apt-get install software-properties-common -y
         sudo add-apt-repository --yes ppa:deadsnakes/nightly
         sudo apt-get update -y
-        sudo apt-get install -y --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil
+        sudo apt-get install -y --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil meson ninja-build
     fi
 }
 

From b9255e98f618820be191fd66bd1762fcfd3179da Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 12:57:18 +0200
Subject: [PATCH 07/13] [free-threaded] fix

---
 build_tools/azure/test_docs.sh | 2 +-
 build_tools/shared.sh          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/build_tools/azure/test_docs.sh b/build_tools/azure/test_docs.sh
index 61e855425786b..1258ecf69f080 100755
--- a/build_tools/azure/test_docs.sh
+++ b/build_tools/azure/test_docs.sh
@@ -4,7 +4,7 @@ set -e
 
 if [[ "$DISTRIB" =~ ^conda.* ]]; then
     source activate $VIRTUALENV
-elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "pip-nogil" ]]; then
+elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "pip-free-threaded" ]]; then
     source $VIRTUALENV/bin/activate
 fi
 
diff --git a/build_tools/shared.sh b/build_tools/shared.sh
index 4866c149d506f..958c6ca1408e7 100644
--- a/build_tools/shared.sh
+++ b/build_tools/shared.sh
@@ -29,7 +29,7 @@ show_installed_libraries(){
 activate_environment() {
     if [[ "$DISTRIB" =~ ^conda.* ]]; then
         source activate $VIRTUALENV
-    elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "debian-32" || "$DISTRIB" == "pip-nogil" ]]; then
+    elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "debian-32" || "$DISTRIB" == "pip-free-threaded" ]]; then
         source $VIRTUALENV/bin/activate
     fi
 }

From 82083cc152ab1561740b0e2ad0e9596de20ce358 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 13:38:01 +0200
Subject: [PATCH 08/13] [free-threaded] fix

---
 azure-pipelines.yml          | 2 +-
 build_tools/azure/install.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index b1eb59e62e1f0..71fcd2fba67c4 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -85,7 +85,7 @@ jobs:
       )
     matrix:
       pylatest_pip_free_threaded:
-        DOCKER_CONTAINER: ''
+        PYTHON_GIL: '0'
         DISTRIB: 'pip-free-threaded'
         # TODO free-threaded probably use pip lock-file
         LOCK_FILE: './build_tools/azure/python_free_threaded_lock.txt'
diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
index bc3446785775d..34895997f0a17 100755
--- a/build_tools/azure/install.sh
+++ b/build_tools/azure/install.sh
@@ -86,7 +86,7 @@ python_environment_install_and_activate() {
         # TODO need development Cython for now
         pip install git+https://github.com/cython/cython
         # Install all the other dependencies
-        pip install joblib threadpoolctl pytest meson-python
+        pip install joblib threadpoolctl pytest meson-python pytest-xdist
     fi
 
     if [[ "$DISTRIB" == "conda-pip-scipy-dev" ]]; then

From 942db7811456d7634cf623794113d06ae270d8b5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 14:00:33 +0200
Subject: [PATCH 09/13] [free-threaded] apparently setuptools is needed for
 part of the tests ...

---
 build_tools/azure/install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
index 34895997f0a17..4b528bbf6a700 100755
--- a/build_tools/azure/install.sh
+++ b/build_tools/azure/install.sh
@@ -86,7 +86,7 @@ python_environment_install_and_activate() {
         # TODO need development Cython for now
         pip install git+https://github.com/cython/cython
         # Install all the other dependencies
-        pip install joblib threadpoolctl pytest meson-python pytest-xdist
+        pip install joblib threadpoolctl pytest meson-python pytest-xdist setuptools
     fi
 
     if [[ "$DISTRIB" == "conda-pip-scipy-dev" ]]; then

From 83e7f181bc7bf06509d5182467ffeb21e298616a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 17:04:33 +0200
Subject: [PATCH 10/13] [free-threaded] Try to use lock file

---
 azure-pipelines.yml                           |  3 +-
 .../azure/cpython_free_threaded_lock.txt      | 39 ++++++++++
 .../cpython_free_threaded_requirements.txt    | 16 ++++
 build_tools/azure/python_nogil_lock.txt       | 73 -------------------
 .../azure/python_nogil_requirements.txt       | 20 -----
 5 files changed, 56 insertions(+), 95 deletions(-)
 create mode 100644 build_tools/azure/cpython_free_threaded_lock.txt
 create mode 100644 build_tools/azure/cpython_free_threaded_requirements.txt
 delete mode 100644 build_tools/azure/python_nogil_lock.txt
 delete mode 100644 build_tools/azure/python_nogil_requirements.txt

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 71fcd2fba67c4..c2133ea441958 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -87,8 +87,7 @@ jobs:
       pylatest_pip_free_threaded:
         PYTHON_GIL: '0'
         DISTRIB: 'pip-free-threaded'
-        # TODO free-threaded probably use pip lock-file
-        LOCK_FILE: './build_tools/azure/python_free_threaded_lock.txt'
+        LOCK_FILE: './build_tools/azure/cpython_free_threaded_lock.txt'
         COVERAGE: 'false'
 
 - job: Linux_Nightly_Pyodide
diff --git a/build_tools/azure/cpython_free_threaded_lock.txt b/build_tools/azure/cpython_free_threaded_lock.txt
new file mode 100644
index 0000000000000..f1c58b65a59d6
--- /dev/null
+++ b/build_tools/azure/cpython_free_threaded_lock.txt
@@ -0,0 +1,39 @@
+#
+# This file is autogenerated by pip-compile with Python 3.13
+# by the following command:
+#
+#    pip-compile --allow-unsafe --output-file=/scikit-learn/build_tools/azure/cpython_free_threaded_lock.txt /scikit-learn/build_tools/azure/cpython_free_threaded_requirements.txt
+#
+execnet==2.1.1
+    # via pytest-xdist
+iniconfig==2.0.0
+    # via pytest
+joblib==1.4.2
+    # via -r /scikit-learn/build_tools/azure/cpython_free_threaded_requirements.txt
+meson==1.4.1
+    # via meson-python
+meson-python==0.16.0
+    # via -r /scikit-learn/build_tools/azure/cpython_free_threaded_requirements.txt
+ninja==1.11.1.1
+    # via -r /scikit-learn/build_tools/azure/cpython_free_threaded_requirements.txt
+packaging==24.0
+    # via
+    #   meson-python
+    #   pyproject-metadata
+    #   pytest
+pluggy==1.5.0
+    # via pytest
+pyproject-metadata==0.8.0
+    # via meson-python
+pytest==8.2.2
+    # via
+    #   -r /scikit-learn/build_tools/azure/cpython_free_threaded_requirements.txt
+    #   pytest-xdist
+pytest-xdist==3.6.1
+    # via -r /scikit-learn/build_tools/azure/cpython_free_threaded_requirements.txt
+threadpoolctl==3.5.0
+    # via -r /scikit-learn/build_tools/azure/cpython_free_threaded_requirements.txt
+
+# The following packages are considered to be unsafe in a requirements file:
+setuptools==70.0.0
+    # via -r /scikit-learn/build_tools/azure/cpython_free_threaded_requirements.txt
diff --git a/build_tools/azure/cpython_free_threaded_requirements.txt b/build_tools/azure/cpython_free_threaded_requirements.txt
new file mode 100644
index 0000000000000..5561e6c28ca5e
--- /dev/null
+++ b/build_tools/azure/cpython_free_threaded_requirements.txt
@@ -0,0 +1,16 @@
+# To generate cpython_free_threaded_lock.txt, use the following command:
+# docker run -v $PWD:/scikit-learn -it ubuntu bash -c 'export DEBIAN_FRONTEND=noninteractive; apt-get -yq update; apt-get install software-properties-common ccache -y; add-apt-repository --yes ppa:deadsnakes/nightly; apt-get update -y; apt-get install -y --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil; python3.13t -m venv /venvs/myenv; source /venvs/myenv/bin/activate; pip install pip-tools; pip-compile --allow-unsafe /scikit-learn/build_tools/azure/cpython_free_threaded_requirements.txt -o /scikit-learn/build_tools/azure/cpython_free_threaded_lock.txt'
+
+# The reason behind it is that you need python-3.13t to generate the pip lock
+# file. For pure Python wheel this does not really matter. But when there are
+# cython, numpy and scipy releases that have a CPython 3.13 free-threaded
+# wheel, we can add them here and this is important that the Python 3.13
+# free-threaded wheel is picked up in the lock-file
+joblib
+threadpoolctl
+pytest
+pytest-xdist
+ninja
+meson-python
+# For some reason some of our tests require setuptools
+setuptools
diff --git a/build_tools/azure/python_nogil_lock.txt b/build_tools/azure/python_nogil_lock.txt
deleted file mode 100644
index 7f67a48842dea..0000000000000
--- a/build_tools/azure/python_nogil_lock.txt
+++ /dev/null
@@ -1,73 +0,0 @@
-#
-# This file is autogenerated by pip-compile with Python 3.9
-# by the following command:
-#
-#    pip-compile --output-file=/scikit-learn/build_tools/azure/python_nogil_lock.txt /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-#
---index-url https://d1yxz45j0ypngg.cloudfront.net/
---extra-index-url https://pypi.org/simple
-
-contourpy==1.1.1
-    # via matplotlib
-cycler==0.12.1
-    # via matplotlib
-cython==3.0.10
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-exceptiongroup==1.2.1
-    # via pytest
-execnet==2.1.1
-    # via pytest-xdist
-fonttools==4.51.0
-    # via matplotlib
-iniconfig==2.0.0
-    # via pytest
-joblib==1.4.2
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-kiwisolver==1.4.4
-    # via matplotlib
-matplotlib==3.6.2
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-meson==1.4.0
-    # via meson-python
-meson-python==0.16.0
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-ninja==1.11.1.1
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-numpy==1.24.0
-    # via
-    #   -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-    #   contourpy
-    #   matplotlib
-    #   scipy
-packaging==24.0
-    # via
-    #   matplotlib
-    #   meson-python
-    #   pyproject-metadata
-    #   pytest
-pillow==9.5.0
-    # via matplotlib
-pluggy==1.5.0
-    # via pytest
-pyparsing==3.1.2
-    # via matplotlib
-pyproject-metadata==0.8.0
-    # via meson-python
-pytest==7.4.4
-    # via
-    #   -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-    #   pytest-xdist
-pytest-xdist==3.6.1
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-python-dateutil==2.9.0.post0
-    # via matplotlib
-scipy==1.9.3
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-six==1.16.0
-    # via python-dateutil
-threadpoolctl==3.5.0
-    # via -r /scikit-learn/build_tools/azure/python_nogil_requirements.txt
-tomli==2.0.1
-    # via
-    #   meson-python
-    #   pytest
diff --git a/build_tools/azure/python_nogil_requirements.txt b/build_tools/azure/python_nogil_requirements.txt
deleted file mode 100644
index 2cebad9a03b25..0000000000000
--- a/build_tools/azure/python_nogil_requirements.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-# To generate python_nogil_lock.txt, use the following command:
-# docker run -v $PWD:/scikit-learn -it nogil/python bash -c 'pip install pip-tools; pip-compile --upgrade /scikit-learn/build_tools/azure/python_nogil_requirements.txt -o /scikit-learn/build_tools/azure/python_nogil_lock.txt'
-#
-# The reason behind it is that you need python-nogil to generate the pip lock
-# file. Using pip-compile --index and --extra-index will not work, for example
-# the latest cython will be picked up from PyPI, rather than the one from the
-# python-nogil index
-matplotlib
-numpy
-scipy
-cython
-joblib
-threadpoolctl
-# TODO: somehow pytest 8 does not seem to work with meson editable
-# install. Exit code is 5, i.e. no test collected
-# This would be fixed by https://github.com/mesonbuild/meson-python/pull/569
-pytest<8
-pytest-xdist
-meson-python
-ninja

From caeff2a011d644bd57111e043b67c2a5059d4dc0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 17:16:06 +0200
Subject: [PATCH 11/13] [free-threaded] Actually try to use lock file

---
 build_tools/azure/install.sh | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
index 4b528bbf6a700..2cda0f6948571 100755
--- a/build_tools/azure/install.sh
+++ b/build_tools/azure/install.sh
@@ -45,7 +45,7 @@ pre_python_environment_install() {
         sudo apt-get install software-properties-common -y
         sudo add-apt-repository --yes ppa:deadsnakes/nightly
         sudo apt-get update -y
-        sudo apt-get install -y --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil meson ninja-build
+        sudo apt-get install -y --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil
     fi
 }
 
@@ -77,16 +77,22 @@ python_environment_install_and_activate() {
     elif [[ "$DISTRIB" == "pip-free-threaded" ]]; then
         python3.13t -m venv $VIRTUALENV
         source $VIRTUALENV/bin/activate
-        # TODO free-threaded use a lock-file, for now done by hand
+        pip install -r "${LOCK_FILE}"
         # TODO for now need pip 24.1b1 to find free-threaded wheels
         pip install -U --pre pip
+        # TODO When there are CPython 3.13 free-threaded wheels for numpy and
+        # scipy move this to
+        # build_tools/azure/cpython_free_threaded_requirements.txt. For now we
+        # install them from scientific-python-nightly-wheels
         dev_anaconda_url=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
         dev_packages="numpy scipy"
         pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url $dev_packages
-        # TODO need development Cython for now
+        # TODO Move cython to
+        # build_tools/azure/cpython_free_threaded_requirements.txt where there
+        # is a CPython 3.13 free-threaded wheel
+        # For now, we need the development version of Cython which has CPython
+        # 3.13 free-threaded fixes so we install it from source
         pip install git+https://github.com/cython/cython
-        # Install all the other dependencies
-        pip install joblib threadpoolctl pytest meson-python pytest-xdist setuptools
     fi
 
     if [[ "$DISTRIB" == "conda-pip-scipy-dev" ]]; then

From 52e6cb5b4190f00e7e5901083da8a04da5f60d28 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Wed, 5 Jun 2024 17:33:58 +0200
Subject: [PATCH 12/13] [free-threaded] Tweaks

---
 azure-pipelines.yml          | 10 ++--------
 build_tools/azure/install.sh | 11 +++++++----
 2 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index c2133ea441958..b65d17faafc66 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -63,17 +63,11 @@ jobs:
         CHECK_PYTEST_SOFT_DEPENDENCY: 'true'
 
 - template: build_tools/azure/posix.yml
-  # CPython 3.13 free-threaded build. Currently this uses CPyton 3.13
-  # free-threaded build from deadsnakes PPA together with Numpy and Scipy
-  # free-threaded development wheels.
-  # TODO Use released Numpy and Scipy versions when they are available
-  # TODO Use CPython 3.13 when it is released (planned in October 2024)
+  # CPython 3.13 free-threaded build
   parameters:
     name: Linux_free_threaded
     vmImage: ubuntu-22.04
-    # TODO free-threading temporary optimization for quicker iteration
-    dependsOn: [git_commit]
-    # dependsOn: [git_commit, linting]
+    dependsOn: [git_commit, linting]
     condition: |
       and(
         succeeded(),
diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
index 2cda0f6948571..c67446dfc2d24 100755
--- a/build_tools/azure/install.sh
+++ b/build_tools/azure/install.sh
@@ -39,13 +39,16 @@ pre_python_environment_install() {
                 python3-matplotlib libatlas3-base libatlas-base-dev \
                 python3-virtualenv python3-pandas ccache git
 
+    # TODO for now we use CPython 3.13 from Ubuntu deadsnakes PPA. When CPython
+    # 3.13 is released (scheduled October 2024) we can use something more
+    # similar to other conda+pip based builds
     elif [[ "$DISTRIB" == "pip-free-threaded" ]]; then
         sudo apt-get -yq update
         sudo apt-get install -yq ccache
-        sudo apt-get install software-properties-common -y
+        sudo apt-get install -yq software-properties-common
         sudo add-apt-repository --yes ppa:deadsnakes/nightly
-        sudo apt-get update -y
-        sudo apt-get install -y --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil
+        sudo apt-get update -yq
+        sudo apt-get install -yq --no-install-recommends python3.13-dev python3.13-venv python3.13-nogil
     fi
 }
 
@@ -88,7 +91,7 @@ python_environment_install_and_activate() {
         dev_packages="numpy scipy"
         pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url $dev_packages
         # TODO Move cython to
-        # build_tools/azure/cpython_free_threaded_requirements.txt where there
+        # build_tools/azure/cpython_free_threaded_requirements.txt when there
         # is a CPython 3.13 free-threaded wheel
         # For now, we need the development version of Cython which has CPython
         # 3.13 free-threaded fixes so we install it from source

From a8a84e076c1be3b7434a1586e25c1d4c08471399 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Est=C3=A8ve?= <loic.esteve@ymail.com>
Date: Mon, 10 Jun 2024 09:05:29 +0200
Subject: [PATCH 13/13] Update
 build_tools/azure/cpython_free_threaded_requirements.txt

Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
---
 build_tools/azure/cpython_free_threaded_requirements.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/build_tools/azure/cpython_free_threaded_requirements.txt b/build_tools/azure/cpython_free_threaded_requirements.txt
index 5561e6c28ca5e..b48f69abbc283 100644
--- a/build_tools/azure/cpython_free_threaded_requirements.txt
+++ b/build_tools/azure/cpython_free_threaded_requirements.txt
@@ -12,5 +12,6 @@ pytest
 pytest-xdist
 ninja
 meson-python
-# For some reason some of our tests require setuptools
+# For some reason some of our tests require setuptools.
+# TODO: update those tests to remove the dependency.
 setuptools