From c905a54ff0d50c8adfad84726cd2afc8e51721b6 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Thu, 16 Oct 2025 13:08:15 +0100
Subject: [PATCH 01/19] python/ Remove requirements_dev.txt

---
 .github/workflows/python.yml |  3 +--
 python/Makefile              |  2 +-
 python/requirements_dev.txt  | 32 --------------------------------
 python/tox.ini               | 20 ++++++++------------
 4 files changed, 10 insertions(+), 47 deletions(-)
 delete mode 100644 python/requirements_dev.txt

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 5f3ae717b..8048b2242 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -120,7 +120,6 @@ jobs:
         with:
           python-version: '3.10'
           cache: 'pip'
-          cache-dependency-path: '**/requirements_dev.txt'
 
       - name: Ensure Pip and Build
         run: |
@@ -137,7 +136,7 @@ jobs:
 
       - name: install the doc build requirements
         run: |
-          python3 -m pip install -r requirements_dev.txt
+          python3 -m pip install .[docs]
         working-directory: python
 
       - name: Build the docs 🔧
diff --git a/python/Makefile b/python/Makefile
index 78c51fa46..b88ba9d27 100644
--- a/python/Makefile
+++ b/python/Makefile
@@ -20,7 +20,7 @@ pre-commit:
 	pre-commit run -a
 
 docdeps:
-	python3 -m pip install -r requirements_dev.txt --disable-pip-version-check --quiet
+	python3 -m pip install .[docs] --disable-pip-version-check --quiet
 
 show:
 	$(MAKE) -C doc show
diff --git a/python/requirements_dev.txt b/python/requirements_dev.txt
deleted file mode 100644
index c5d5b4923..000000000
--- a/python/requirements_dev.txt
+++ /dev/null
@@ -1,32 +0,0 @@
-# Sync with .pre-commit-config.yaml
-setuptools>=77.0.3
-cffi >= 1.17.1
-numpy >= 1.23.0
-
-pre-commit >= 3.3.2
-ruff >= 0.11.2
-
-tox >= 4.6.2 # Sync with tox.ini
-pytest >= 7  # Sync with tox.ini
-pytest-cov >= 4.1.0
-virtualenv >= 20
-build
-
-sphinx >= 6.0
-pydata_sphinx_theme>=0.16.0
-jupyter
-ipykernel
-kaleido
-sphinx-gallery>=0.19.0
-sphinxcontrib-napoleon
-sphinxcontrib-bibtex
-sphinx-autodoc-typehints
-sphinx-copybutton
-sphinx-design
-jupyterlab
-ipywidgets
-
-# Gallery examples
-pandas >=2.0.0
-seaborn
-plotly
diff --git a/python/tox.ini b/python/tox.ini
index 1afa12d37..a3e89a824 100644
--- a/python/tox.ini
+++ b/python/tox.ini
@@ -1,6 +1,6 @@
 [tox]
 requires =
-    tox>=4.2
+    tox>=4.6.2
 env_list =
     numpy-v2
     py{312, 311, 310}
@@ -11,10 +11,9 @@ package = wheel
 wheel_build_env = .pkg
 deps =
     numpy<2
-    pandas>=2
-    pytest>=7
-    cov: coverage[toml]
-    cov: gcovr
+extras =
+    test
+    cov: coverage
 commands =
     pytest --doctest-modules --doctest-continue-on-failure --import-mode=importlib {envsitepackagesdir}/moocore tests
 
@@ -25,10 +24,9 @@ package = wheel
 wheel_build_env = .pkg
 deps =
     numpy>=2
-    pandas>=2
-    pytest>=7
-    cov: coverage[toml]
-    cov: gcovr
+extras =
+    test
+    cov: coverage
 commands =
     pytest --doctest-modules --doctest-continue-on-failure --import-mode=importlib {envsitepackagesdir}/moocore tests
 
@@ -51,10 +49,8 @@ commands =
 
 [testenv:docs]
 description = Build documentation
-deps =
-    -r{toxinidir}/requirements_dev.txt
 extras =
-    doc
+    docs
 commands =
     sphinx-build -M html ./doc/source ./doc/_build/ -WT --keep-going -d ./doc/_build/doctrees
 

From 31dc582d06ceb577874e36177eb4bd8043394fe3 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Thu, 16 Oct 2025 13:22:58 +0100
Subject: [PATCH 02/19] python/pyproject.toml (tool.cibuildwheel): Replace
 test-groups by test-extras.

---
 python/pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/pyproject.toml b/python/pyproject.toml
index ace69a2c8..9ddddfa86 100644
--- a/python/pyproject.toml
+++ b/python/pyproject.toml
@@ -88,8 +88,8 @@ skip = [
   "*_i686",    # Skip 32-bit builds
 ]
 build-verbosity = 2
-# Will cause the wheel to be installed with these groups of dependencies
-test-groups = [ "test" ]
+# Will cause the wheel to be installed with these optional-dependencies
+test-extras = [ "test" ]
 test-command = [
   "pytest --doctest-modules --doctest-continue-on-failure {package}/tests {package}/src/moocore/_moocore.py",
 ]

From 6f81cdfd0f1e3cc9c397562c35782fa7606af8c6 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Thu, 16 Oct 2025 13:41:52 +0100
Subject: [PATCH 03/19]  * update.bib.sh: Simplify code. Remove ids field.  *
 python/doc/source/REFERENCES.bib, r/inst/REFERENCES.bib: Regenerate.

---
 python/doc/source/REFERENCES.bib | 16 ++++++++++------
 r/inst/REFERENCES.bib            | 16 ++++++++++------
 update_bib.sh                    | 13 ++++++-------
 3 files changed, 26 insertions(+), 19 deletions(-)

diff --git a/python/doc/source/REFERENCES.bib b/python/doc/source/REFERENCES.bib
index 89f42d001..ecfb5ed1e 100644
--- a/python/doc/source/REFERENCES.bib
+++ b/python/doc/source/REFERENCES.bib
@@ -200,8 +200,7 @@ @article{DiaLop2020ejor
 
 @article{DubLopStu2011amai,
   author = { J{\'e}r{\'e}mie Dubois-Lacoste  and  Manuel L{\'o}pez-Ib{\'a}{\~n}ez  and  Thomas St{\"u}tzle },
-  title = {Improving the Anytime Behavior of Two-Phase Local
-                  Search},
+  title = {Improving the Anytime Behavior of Two-Phase Local Search},
   journal = {Annals of Mathematics and Artificial Intelligence},
   year = 2011,
   volume = 61,
@@ -233,7 +232,8 @@ @article{GueFonPaq2021hv
   year = 2021,
   volume = 54,
   number = 6,
-  pages = {1--42}
+  pages = {1--42},
+  doi = {10.1145/3453474}
 }
 
 @article{HerWer1987tabucol,
@@ -296,6 +296,9 @@ @article{LopVerDreDoe2025
                   Single-objective Black-box Optimization Algorithms},
   journal = {IEEE Transactions on Evolutionary Computation},
   year = 2025,
+  volume = 29,
+  number = 5,
+  pages = {1774--1782},
   annote = {Pre-print: \url{https://doi.org/10.48550/arXiv.2404.02031}},
   doi = {10.1109/TEVC.2024.3462758},
   abstract = {A widely accepted way to assess the performance of iterative
@@ -366,10 +369,11 @@ @article{ZitThiLauFon2003:tec
   year = 2003,
   volume = 7,
   number = 2,
-  amonth = apr,
   pages = {117--132},
-  doi = {10.1109/TEVC.2003.810758},
-  annote = {Proposed the combination of quality indicators; proposed epsilon-indicator}
+  annote = {Proposed the combination of quality indicators; proposed
+                  epsilon-indicator},
+  amonth = apr,
+  doi = {10.1109/TEVC.2003.810758}
 }
 
 @incollection{AugBadBroZit2009gecco,
diff --git a/r/inst/REFERENCES.bib b/r/inst/REFERENCES.bib
index 89f42d001..ecfb5ed1e 100644
--- a/r/inst/REFERENCES.bib
+++ b/r/inst/REFERENCES.bib
@@ -200,8 +200,7 @@ @article{DiaLop2020ejor
 
 @article{DubLopStu2011amai,
   author = { J{\'e}r{\'e}mie Dubois-Lacoste  and  Manuel L{\'o}pez-Ib{\'a}{\~n}ez  and  Thomas St{\"u}tzle },
-  title = {Improving the Anytime Behavior of Two-Phase Local
-                  Search},
+  title = {Improving the Anytime Behavior of Two-Phase Local Search},
   journal = {Annals of Mathematics and Artificial Intelligence},
   year = 2011,
   volume = 61,
@@ -233,7 +232,8 @@ @article{GueFonPaq2021hv
   year = 2021,
   volume = 54,
   number = 6,
-  pages = {1--42}
+  pages = {1--42},
+  doi = {10.1145/3453474}
 }
 
 @article{HerWer1987tabucol,
@@ -296,6 +296,9 @@ @article{LopVerDreDoe2025
                   Single-objective Black-box Optimization Algorithms},
   journal = {IEEE Transactions on Evolutionary Computation},
   year = 2025,
+  volume = 29,
+  number = 5,
+  pages = {1774--1782},
   annote = {Pre-print: \url{https://doi.org/10.48550/arXiv.2404.02031}},
   doi = {10.1109/TEVC.2024.3462758},
   abstract = {A widely accepted way to assess the performance of iterative
@@ -366,10 +369,11 @@ @article{ZitThiLauFon2003:tec
   year = 2003,
   volume = 7,
   number = 2,
-  amonth = apr,
   pages = {117--132},
-  doi = {10.1109/TEVC.2003.810758},
-  annote = {Proposed the combination of quality indicators; proposed epsilon-indicator}
+  annote = {Proposed the combination of quality indicators; proposed
+                  epsilon-indicator},
+  amonth = apr,
+  doi = {10.1109/TEVC.2003.810758}
 }
 
 @incollection{AugBadBroZit2009gecco,
diff --git a/update_bib.sh b/update_bib.sh
index 22e7e134c..b9907f335 100755
--- a/update_bib.sh
+++ b/update_bib.sh
@@ -12,18 +12,17 @@ for file in $BIBFILES; do
 done
 tmpbib=$(mktemp --tmpdir tmpXXXXXXXXXX.bib)
 keys=$(paste -d '#' -s bibkeys.txt | sed 's/#/\\\|/g')
-bib2bib --warn-error --expand --expand-xrefs --no-comment --expand-xrefs $BIBFILES --remove pdf --remove alias -c "(\$key : \"$keys\")" -ob $tmpbib -oc /dev/null
+bib2bib --warn-error --expand --expand-xrefs --no-comment --expand-xrefs $BIBFILES --remove pdf --remove ids -c "(\$key : \"$keys\")" -ob $tmpbib -oc /dev/null
 if [ ! -s "${tmpbib}" ]; then
     echo "error: ${tmpbib} is empty! keys:= $keys"
     exit 1
 fi
 # Workaround https://github.com/GeoBosh/rbibutils/issues/9
-sed -i 's#\\slash #~/ #g' $tmpbib
-sed -i 's#\\hspace{0pt}#{}{}{}#g' $tmpbib
-# Work around broken URL:
-sed -i 's%researchrepository.napier.ac.uk/id/eprint/3044%lopez-ibanez.eu/publications#LopezIbanezPhD%g' $tmpbib
+sed -i -e 's#\\slash #~/ #g' \
+    -e 's#\\hspace{0pt}#{}{}{}#g' \
+    -e 's%researchrepository.napier.ac.uk/id/eprint/3044%lopez-ibanez.eu/publications#LopezIbanezPhD%g' \
+    $tmpbib
 comment='% DO NOT EDIT THIS FILE. It is auto-generated by "update_bib.sh".'
-PYTHON_DOC_DIR="./python/doc/source"
 echo $comment | cat --squeeze-blank - $tmpbib > r/inst/REFERENCES.bib
-echo $comment | cat --squeeze-blank - $tmpbib > $PYTHON_DOC_DIR/REFERENCES.bib
+cp --force r/inst/REFERENCES.bib ./python/doc/source/REFERENCES.bib
 rm -f $BIBFILES $tmpbib

From 7c77c19268f5c26f7c09cf95180949af1d185ef7 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Thu, 16 Oct 2025 14:48:53 +0100
Subject: [PATCH 04/19] .pre-commit-config.yaml: Fix roxygenize hook.

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d6062d98d..2199e5089 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
         args: [--root=r/]
         exclude: '(do\.R|vignettes/articles/.+\.Rmd)'
       - id: roxygenize
-        args: [--root=<R package root>]
+        args: [--root=r/]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0

From 281fd3c864b73949117536364cb6eab48e6bd295 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Thu, 16 Oct 2025 14:53:24 +0100
Subject: [PATCH 05/19] .pre-commit-config.yaml: Fix roxygenize hook.

---
 .pre-commit-config.yaml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2199e5089..9f2d2bd4d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -14,10 +14,13 @@ repos:
       - id: no-print-statement
       - id: no-debug-statement
       - id: deps-in-desc
-        args: [--root=r/]
+        args: [--root=./r/]
         exclude: '(do\.R|vignettes/articles/.+\.Rmd)'
       - id: roxygenize
-        args: [--root=r/]
+        args: [--root=./r/]
+        additional_dependencies:
+          - doctest
+          - Rdpack
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0

From c070f6d86ddadb7a297c6b97710fb1f83543d229 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Thu, 16 Oct 2025 14:55:12 +0100
Subject: [PATCH 06/19] Improve documentation of `generate_ndset()` in R and
 Python

---
 python/src/moocore/_moocore.py | 10 +++++-----
 r/R/generate.R                 | 11 +++++------
 r/man/generate_ndset.Rd        | 11 +++++------
 3 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/python/src/moocore/_moocore.py b/python/src/moocore/_moocore.py
index 0894c730f..44c5d6e3b 100644
--- a/python/src/moocore/_moocore.py
+++ b/python/src/moocore/_moocore.py
@@ -1024,9 +1024,9 @@ def generate_ndset(
     :footcite:p:`RubMel1998simulation`.  Values sampled from the exponential
     distribution are guaranteed to be positive.
 
-    Sampling from either the standard normal distribution, as suggested by
-    :footcite:t:`GueFonPaq2021hv`, or the uniform distribution, as suggested by
-    :footcite:t:`LacKlaFon2017box`, does not produce a uniform distribution
+    Sampling from either the standard normal distribution
+    :footcite:p:`GueFonPaq2021hv` or the uniform distribution
+    :footcite:p:`LacKlaFon2017box` does not produce a uniform distribution
     when projected into the simplex.
 
     Method ``"concave-sphere"`` uniformly samples points on the positive
@@ -1038,8 +1038,8 @@ def generate_ndset(
     :math:`z_i = \frac{|x_i|}{\|\vec{x}\|_2}`
     :footcite:p:`Muller1959sphere`. The absolute value in the numerator ensures
     that points are sampled on the positive orthant of the hyper-sphere.
-    Sampling from the uniform distribution, as suggested by
-    :footcite:t:`LacKlaFon2017box`, does not result in a uniform sampling when
+    Sampling from the uniform distribution :footcite:p:`LacKlaFon2017box`
+    does not result in a uniform sampling when
     projected onto the surface of the hyper-sphere.
 
     Method ``"convex-sphere"`` is quivalent to ``1 - generate_ndset(...,
diff --git a/r/R/generate.R b/r/R/generate.R
index 87b3e890c..103242ebb 100644
--- a/r/R/generate.R
+++ b/r/R/generate.R
@@ -42,10 +42,9 @@
 #' \eqn{z_i = x_i / \sum_{i=1}^d x_i} \citep{RubMel1998simulation}.  Values
 #' sampled from the exponential distribution are guaranteed to be positive.
 #'
-#' Sampling from either the standard normal distribution, as suggested by
-#' \citet{GueFonPaq2021hv}, or the uniform distribution, as suggested by
-#' \citet{LacKlaFon2017box}, does not produce a uniform distribution when
-#' projected into the simplex.
+#' Sampling from either the standard normal distribution
+#' \citep{GueFonPaq2021hv} or the uniform distribution \citep{LacKlaFon2017box}
+#' does not produce a uniform distribution when projected into the simplex.
 #'
 #' Method `"concave-sphere"` uniformly samples points on the positive orthant
 #' of the hyper-sphere, which is concave when all objectives are minimised.
@@ -55,8 +54,8 @@
 #' then dividing each value by the l2-norm of the vector, \eqn{z_i =
 #' \frac{|x_i|}{\|\vec{x}\|_2}} \citep{Muller1959sphere}. The absolute value in
 #' the numerator ensures that points are sampled on the positive orthant of the
-#' hyper-sphere.  Sampling from the uniform distribution, as suggested by
-#' \citet{LacKlaFon2017box}, does not result in a uniform sampling when
+#' hyper-sphere.  Sampling from the uniform distribution
+#' \citep{LacKlaFon2017box} does not result in a uniform sampling when
 #' projected onto the surface of the hyper-sphere.
 #'
 #' Method `"convex-sphere"` is quivalent to `1 - generate_ndset(...,
diff --git a/r/man/generate_ndset.Rd b/r/man/generate_ndset.Rd
index 421d28b08..1f3a60226 100644
--- a/r/man/generate_ndset.Rd
+++ b/r/man/generate_ndset.Rd
@@ -55,10 +55,9 @@ distribution, then dividing each value by the L1-norm of the vector,
 \eqn{z_i = x_i / \sum_{i=1}^d x_i} \citep{RubMel1998simulation}.  Values
 sampled from the exponential distribution are guaranteed to be positive.
 
-Sampling from either the standard normal distribution, as suggested by
-\citet{GueFonPaq2021hv}, or the uniform distribution, as suggested by
-\citet{LacKlaFon2017box}, does not produce a uniform distribution when
-projected into the simplex.
+Sampling from either the standard normal distribution
+\citep{GueFonPaq2021hv} or the uniform distribution \citep{LacKlaFon2017box}
+does not produce a uniform distribution when projected into the simplex.
 
 Method \code{"concave-sphere"} uniformly samples points on the positive orthant
 of the hyper-sphere, which is concave when all objectives are minimised.
@@ -68,8 +67,8 @@ sampling \eqn{d} independent and identically distributed values
 then dividing each value by the l2-norm of the vector, \eqn{z_i =
 \frac{|x_i|}{\|\vec{x}\|_2}} \citep{Muller1959sphere}. The absolute value in
 the numerator ensures that points are sampled on the positive orthant of the
-hyper-sphere.  Sampling from the uniform distribution, as suggested by
-\citet{LacKlaFon2017box}, does not result in a uniform sampling when
+hyper-sphere.  Sampling from the uniform distribution
+\citep{LacKlaFon2017box} does not result in a uniform sampling when
 projected onto the surface of the hyper-sphere.
 
 Method \code{"convex-sphere"} is quivalent to \code{1 - generate_ndset(..., method="concave-sphere")}, which is convex for minimisation problems.  It

From e6513677d5a20435f4cca4b421c304f5a71a9312 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Fri, 17 Oct 2025 10:02:38 +0100
Subject: [PATCH 07/19]  * python/pyproject.toml: Build universal2 for macos,
 native wheels for the rest.  * .github/workflows/python.yml: Simplify wheels
 job. Build ubuntu-22.04-arm.

---
 .github/workflows/python.yml | 16 ++++------------
 python/pyproject.toml        | 18 +++++++-----------
 2 files changed, 11 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 8048b2242..5169d2eff 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -202,10 +202,11 @@ jobs:
       matrix:
         # FIXME: add windows-11-arm and ubuntu-24.04-arm
         # https://github.com/scipy/scipy/blob/6b79a4dec1f9ca2db4e49c328d04d293880991c6/.github/workflows/wheels.yml#L78
-        # macos-14 is apple silicon
-        os: [ubuntu-22.04, windows-2025, macos-14]
+        # https://github.com/numpy/numpy-release/blob/main/.github/workflows/wheels.yml
+        # macos-14 is Apple Silicon (arm64), but we build an universal2 wheel.
+        # The configuration of cibuildwheel can be found in pyproject.toml
+        os: [ubuntu-22.04, ubuntu-22.04-arm, windows-2025, macos-14]
         python-version: ['3.10']
-        CIBW_ARCHS_MACOS: ['universal2']
 
     steps:
       - uses: actions/checkout@v5
@@ -215,17 +216,8 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Set up QEMU
-        if: runner.os == 'Linux'
-        uses: docker/setup-qemu-action@v3
-        with:
-          platforms: arm64
-
       - name: Build wheels
         uses: pypa/cibuildwheel@v2.23.3
-        env:
-          CIBW_ARCHS_MACOS: ${{ matrix.CIBW_ARCHS_MACOS }}
-          CIBW_TEST_SKIP: ${{ matrix.CIBW_TEST_SKIP }}
         with:
           package-dir: python
           output-dir: wheelhouse
diff --git a/python/pyproject.toml b/python/pyproject.toml
index 9ddddfa86..73941ff4e 100644
--- a/python/pyproject.toml
+++ b/python/pyproject.toml
@@ -93,14 +93,14 @@ test-extras = [ "test" ]
 test-command = [
   "pytest --doctest-modules --doctest-continue-on-failure {package}/tests {package}/src/moocore/_moocore.py",
 ]
-test-skip = "*-*linux_{aarch64,ppc64le,s390x}"
+#test-skip = "*-*linux_{aarch64,ppc64le,s390x}"
 
 [tool.cibuildwheel.linux]
-archs = [
-  "x86_64",
-  #  "aarch64", FAILS doctests
-]
+archs = [ "native" ]
 manylinux-x86_64-image = "manylinux_2_28"
+manylinux-aarch64-image = "manylinux_2_28"
+musllinux-x86_64-image = "musllinux_1_2"
+musllinux-aarch64-image = "musllinux_1_2"
 # Use abi3audit to catch issues with Limited API wheels
 repair-wheel-command = [
   "auditwheel repair -w {dest_dir} {wheel}",
@@ -108,9 +108,7 @@ repair-wheel-command = [
 ]
 
 [tool.cibuildwheel.windows]
-archs = [
-  "AMD64",
-]
+archs = [ "native" ]
 # Use delvewheel on windows
 before-build = "pip install delvewheel"
 repair-wheel-command = [
@@ -119,9 +117,7 @@ repair-wheel-command = [
 ]
 
 [tool.cibuildwheel.macos]
-archs = [
-  "universal2",
-]
+archs = [ "universal2" ]
 repair-wheel-command = [
   "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
   #  "pipx run abi3audit --verbose --strict --report {wheel}",

From 9767862aac0de36af91b6ff081d93cab05452973 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Fri, 17 Oct 2025 11:16:36 +0100
Subject: [PATCH 08/19]  * python/benchmarks/bench_ndom.py: Make sure that
 numba is available.  * python/benchmarks/python-requirements.txt: Add numba,
 sort lines.

---
 python/benchmarks/bench_ndom.py           |  4 ++--
 python/benchmarks/python-requirements.txt | 13 +++++++------
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/python/benchmarks/bench_ndom.py b/python/benchmarks/bench_ndom.py
index aa81f4f2f..ed4f90f38 100644
--- a/python/benchmarks/bench_ndom.py
+++ b/python/benchmarks/bench_ndom.py
@@ -65,7 +65,7 @@ def get_dataset(name):
                 z, maximise=True, keep_weakly=False
             ),
             "botorch": lambda z: botorch_is_nondominated(z, deduplicate=True),
-            "paretoset": lambda z: paretoset(
+            "paretoset (numba)": lambda z: paretoset(
                 z, sense=z.shape[1] * ["max"], distinct=True, use_numba=True
             ),
         },
@@ -116,7 +116,7 @@ def get_dataset(name):
             "botorch": lambda z: bool2pos(
                 botorch_is_nondominated(z, deduplicate=False)
             ),
-            "paretoset": lambda z: bool2pos(
+            "paretoset (numba)": lambda z: bool2pos(
                 paretoset(
                     z,
                     sense=z.shape[1] * ["max"],
diff --git a/python/benchmarks/python-requirements.txt b/python/benchmarks/python-requirements.txt
index 33fe23d4c..bf2dcd640 100644
--- a/python/benchmarks/python-requirements.txt
+++ b/python/benchmarks/python-requirements.txt
@@ -1,10 +1,11 @@
+botorch
 cpuinfo
+desdeo
+jmetal
+matplotlib
+nevergrad
+numba
 numpy
 pandas
-matplotlib
-botorch
-pymoo
-jmetal
-desdeo
 paretoset
-nevergrad
+pymoo

From 3f3dee90fe1a61d865db97a8955bb30b44ac6292 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Fri, 17 Oct 2025 11:17:15 +0100
Subject: [PATCH 09/19]  * .github/workflows/python.yml: Build wheels for
 windows_arm64.  * .github/windows_arm64_steps/action.yml: New.

---
 .github/windows_arm64_steps/action.yml | 22 ++++++++++++++++++++++
 .github/workflows/python.yml           |  9 +++++++--
 2 files changed, 29 insertions(+), 2 deletions(-)
 create mode 100644 .github/windows_arm64_steps/action.yml

diff --git a/.github/windows_arm64_steps/action.yml b/.github/windows_arm64_steps/action.yml
new file mode 100644
index 000000000..14b7f41a1
--- /dev/null
+++ b/.github/windows_arm64_steps/action.yml
@@ -0,0 +1,22 @@
+name: Build Dependencies(Win-ARM64)
+description: "Setup LLVM for Win-ARM64 builds"
+# https://github.com/numpy/numpy-release/blob/295d6a70a867972774ff05ae98d7a560a659e2b4/.github/windows_arm64_steps/action.yml
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install LLVM with checksum verification
+      shell: pwsh
+      run: |
+        Invoke-WebRequest https://github.com/llvm/llvm-project/releases/download/llvmorg-20.1.6/LLVM-20.1.6-woa64.exe -UseBasicParsing -OutFile LLVM-woa64.exe
+        $expectedHash = "92f69a1134e32e54b07d51c6e24d9594852f6476f32c3d70471ae00fffc2d462"
+        $fileHash = (Get-FileHash -Path "LLVM-woa64.exe" -Algorithm SHA256).Hash
+        if ($fileHash -ne $expectedHash) {
+            Write-Error "Checksum verification failed. The downloaded file may be corrupted or tampered with."
+            exit 1
+        }
+        Start-Process -FilePath ".\LLVM-woa64.exe" -ArgumentList "/S" -Wait
+        echo "C:\Program Files\LLVM\bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+        echo "CC=clang-cl" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+        echo "CXX=clang-cl" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+        echo "FC=flang-new" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 5169d2eff..76f3f73e3 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -98,7 +98,7 @@ jobs:
       - name: Publish artifacts
         uses: actions/upload-artifact@v4
         with:
-          name: moocore-wheels-${{ matrix.os }}-${{ matrix.python-version }}
+          name: moocore-wheels-sdist-${{ matrix.os }}-${{ matrix.python-version }}
           path: python/dist/*.tar.gz
 
   build-doc:
@@ -205,7 +205,7 @@ jobs:
         # https://github.com/numpy/numpy-release/blob/main/.github/workflows/wheels.yml
         # macos-14 is Apple Silicon (arm64), but we build an universal2 wheel.
         # The configuration of cibuildwheel can be found in pyproject.toml
-        os: [ubuntu-22.04, ubuntu-22.04-arm, windows-2025, macos-14]
+        os: [ubuntu-22.04, ubuntu-22.04-arm, windows-2025, windows-11-arm, macos-14]
         python-version: ['3.10']
 
     steps:
@@ -215,6 +215,11 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Setup LLVM for Windows ARM64
+        if: ${{ matrix.os == 'windows-11-arm' }}
+        uses: ./.github/windows_arm64_steps
 
       - name: Build wheels
         uses: pypa/cibuildwheel@v2.23.3

From b9170b64a5e7fbfb6eee02307e2b9d24282c7b15 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Fri, 17 Oct 2025 11:35:00 +0100
Subject: [PATCH 10/19] .github/workflows/python.yml: Use Python 3.11 for
 Windows ARM64.

---
 .github/workflows/python.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 76f3f73e3..dfd76f0be 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -205,8 +205,12 @@ jobs:
         # https://github.com/numpy/numpy-release/blob/main/.github/workflows/wheels.yml
         # macos-14 is Apple Silicon (arm64), but we build an universal2 wheel.
         # The configuration of cibuildwheel can be found in pyproject.toml
-        os: [ubuntu-22.04, ubuntu-22.04-arm, windows-2025, windows-11-arm, macos-14]
+        os: [ubuntu-22.04, ubuntu-22.04-arm, windows-2025, macos-14]
         python-version: ['3.10']
+        include:
+          # 3.11 is the earliest version on windows-arm
+          - os: windows-11-arm
+            python-version: "3.11"
 
     steps:
       - uses: actions/checkout@v5

From a7507ed549d42a91851c6f67b8767c5a281178cb Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Fri, 17 Oct 2025 12:12:31 +0100
Subject: [PATCH 11/19] .github/workflows/python.yml: Simplify.

---
 .github/workflows/python.yml | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index dfd76f0be..baa90411b 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -95,6 +95,7 @@ jobs:
         run: python3 -m build
         working-directory: python
 
+        # This is needed for publishing to PyPI
       - name: Publish artifacts
         uses: actions/upload-artifact@v4
         with:
@@ -130,13 +131,8 @@ jobs:
         run: python3 -m build
         working-directory: python
 
-      - name: install the package
-        run: python3 -m pip install .
-        working-directory: python
-
-      - name: install the doc build requirements
-        run: |
-          python3 -m pip install .[docs]
+      - name: Install the package and the doc build requirements
+        run: python3 -m pip install .[docs]
         working-directory: python
 
       - name: Build the docs 🔧
@@ -160,7 +156,6 @@ jobs:
     name: Coverage ${{ matrix.os }} (${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     strategy:
-      # When set to true, GitHub cancels all in-progress jobs if any matrix job fails.
       matrix:
         os: [ubuntu-latest]
         python-version: ['3.10']

From 1664f361f5134bf103ada87012a9e12f9b653a70 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Fri, 17 Oct 2025 12:13:08 +0100
Subject: [PATCH 12/19] python/doc/source/whatsnew/index.rst: Document new
 wheels.

---
 python/doc/source/whatsnew/index.rst | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/python/doc/source/whatsnew/index.rst b/python/doc/source/whatsnew/index.rst
index d0144e3a1..49780a49f 100644
--- a/python/doc/source/whatsnew/index.rst
+++ b/python/doc/source/whatsnew/index.rst
@@ -7,15 +7,20 @@ What's new
 Version 0.1.9 (dev)
 -------------------
 
-- :func:`~moocore.hv_contributions` ignores dominated points by default.  Set ``ignore_dominated=False`` to restore the previous behavior.  The 3D case uses the HVC3D algorithm.
+- :func:`~moocore.hv_contributions` ignores dominated points by default.
+  Set ``ignore_dominated=False`` to restore the previous behavior.
+  The 3D case uses the HVC3D algorithm.
 - New function :func:`~moocore.any_dominated` to quickly detect if a set is
   nondominated.
 - New function :func:`~moocore.generate_ndset` to generate random nondominated
   sets with different shapes.
 - New example :ref:`sphx_glr_auto_examples_plot_generate.py`.
-- :func:`~moocore.is_nondominated`, :func:`~moocore.any_dominated`, :func:`~moocore.pareto_rank` now handle single-objective inputs correctly (:issue:`27`, :issue:`29`).
+- :func:`~moocore.is_nondominated`, :func:`~moocore.any_dominated`,
+  :func:`~moocore.pareto_rank` now handle single-objective inputs correctly (:issue:`27`, :issue:`29`).
 - Ranks returned by :func:`~moocore.pareto_rank` are 0-based.
 - :func:`~moocore.is_nondominated` and :func:`~moocore.filter_dominated` are faster for dimensions larger than 3.
+- ``moocore`` wheels are now built for ``aarch64`` (ARM64) in Linux and Windows.
+  See the `installation instructions <https://github.com/multi-objective/moocore/tree/main/python#install>`_.
 
 Version 0.1.8 (15/07/2025)
 --------------------------

From 6ec7c6eb7c0cb9e29276809d53a21723dfbd2619 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Fri, 17 Oct 2025 12:13:44 +0100
Subject: [PATCH 13/19]  * python/src/moocore/_ffi_build.py: Build C code with
 /arch:AVX on Windows and    -march=x86-64-v2 on x86-64 Linux and MacOS to
 enable basic vectorization.

---
 python/src/moocore/_ffi_build.py | 27 +++++++++++++--------------
 1 file changed, 13 insertions(+), 14 deletions(-)

diff --git a/python/src/moocore/_ffi_build.py b/python/src/moocore/_ffi_build.py
index 3f120aec8..7f8990438 100644
--- a/python/src/moocore/_ffi_build.py
+++ b/python/src/moocore/_ffi_build.py
@@ -47,9 +47,6 @@
 sources = [sources_path + f for f in sources]
 
 
-is_windows = platform.system() == "Windows"
-
-
 def get_config():
     from distutils.core import Distribution
     from distutils.sysconfig import get_config_vars
@@ -64,8 +61,8 @@ def uses_msvc():
     return config.try_compile('#ifndef _MSC_VER\n#error "not MSVC"\n#endif')
 
 
-# Try to detect cross-compilation.
-def _get_target_platform(arch_flags, default):
+def _get_target_platform():
+    arch_flags = os.environ.get("ARCHFLAGS", "")
     flags = [f for f in arch_flags.split(" ") if f.strip() != ""]
     try:
         pos = flags.index("-arch")
@@ -74,9 +71,14 @@ def _get_target_platform(arch_flags, default):
     except ValueError:
         pass
 
-    return default
+    return platform.machine()
 
 
+is_windows = platform.system() == "Windows"
+target_platform = _get_target_platform()
+is_x86_64 = target_platform in ("i686", "x86", "x86_64", "AMD64")
+
+# Compiler flags.
 MSVC_CFLAGS = ["/GL", "/O2", "/GS-", "/wd4996"]
 MSVC_LDFLAGS = ["/LTCG"]
 GCC_CFLAGS = ["-flto", "-O3"]
@@ -86,17 +88,14 @@ def _get_target_platform(arch_flags, default):
 if is_windows and uses_msvc():
     extra_compile_args.extend(MSVC_CFLAGS)
     extra_link_args.extend(MSVC_LDFLAGS)
+    if is_x86_64:
+        extra_compile_args.append("/arch:AVX")
 else:
     extra_compile_args.extend(GCC_CFLAGS)
     extra_link_args.extend(GCC_CFLAGS)
-    target_platform = _get_target_platform(
-        os.environ.get("ARCHFLAGS", ""), platform.machine()
-    )
-    # Optimized version requires SSE2 extensions. They have been around since
-    # 2001 so we try to compile it on every recent-ish x86.
-    sse2 = target_platform in ("i686", "x86", "x86_64", "AMD64")
-    if sse2:
-        extra_compile_args.append("-msse2")
+    # Compile for sufficiently old x86-64 architecture.
+    if is_x86_64:
+        extra_compile_args.append("-march=x86-64-v2")
 
 cflags = os.environ.get("CFLAGS", "")
 if cflags != "":

From 29936d303a3a350fe7866f3ec53211f357b3a505 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Fri, 17 Oct 2025 13:23:13 +0100
Subject: [PATCH 14/19] python/src/moocore/_ffi_build.py: Add
 /DMOOCORE_SHARED_LIB to MSVC_CFLAGS.

---
 python/src/moocore/_ffi_build.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/src/moocore/_ffi_build.py b/python/src/moocore/_ffi_build.py
index 7f8990438..d80ab7fc9 100644
--- a/python/src/moocore/_ffi_build.py
+++ b/python/src/moocore/_ffi_build.py
@@ -79,7 +79,7 @@ def _get_target_platform():
 is_x86_64 = target_platform in ("i686", "x86", "x86_64", "AMD64")
 
 # Compiler flags.
-MSVC_CFLAGS = ["/GL", "/O2", "/GS-", "/wd4996"]
+MSVC_CFLAGS = ["/GL", "/O2", "/GS-", "/wd4996", "/DMOOCORE_SHARED_LIB"]
 MSVC_LDFLAGS = ["/LTCG"]
 GCC_CFLAGS = ["-flto", "-O3"]
 

From 7c3602e2a6899fe2e38b8d15b7e102155fad4e60 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Fri, 17 Oct 2025 16:07:09 +0100
Subject: [PATCH 15/19] pyproject.toml: Run abi3audit on wheels.

---
 python/pyproject.toml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/python/pyproject.toml b/python/pyproject.toml
index 73941ff4e..658c4fef1 100644
--- a/python/pyproject.toml
+++ b/python/pyproject.toml
@@ -86,6 +86,8 @@ skip = [
   "*_ppc64le",
   "*_s390x",
   "*_i686",    # Skip 32-bit builds
+  "cp313t-*",
+  "cp314t-*",  # Skip free-threaded builds
 ]
 build-verbosity = 2
 # Will cause the wheel to be installed with these optional-dependencies
@@ -104,7 +106,7 @@ musllinux-aarch64-image = "musllinux_1_2"
 # Use abi3audit to catch issues with Limited API wheels
 repair-wheel-command = [
   "auditwheel repair -w {dest_dir} {wheel}",
-  #  "pipx run abi3audit --verbose --strict --report {wheel}",
+  "pipx run abi3audit --verbose --strict --report {wheel}",
 ]
 
 [tool.cibuildwheel.windows]
@@ -113,14 +115,14 @@ archs = [ "native" ]
 before-build = "pip install delvewheel"
 repair-wheel-command = [
   "delvewheel repair -w {dest_dir} {wheel}",
-  #  "pipx run abi3audit --verbose --strict --report {wheel}",
+  "pipx run abi3audit --verbose --strict --report {wheel}",
 ]
 
 [tool.cibuildwheel.macos]
 archs = [ "universal2" ]
 repair-wheel-command = [
   "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
-  #  "pipx run abi3audit --verbose --strict --report {wheel}",
+  "pipx run abi3audit --verbose --strict --report {wheel}",
 ]
 
 [tool.ruff]

From 10b2405155ed68c4a97ac550902627736791a407 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Fri, 17 Oct 2025 16:35:12 +0100
Subject: [PATCH 16/19] enabled abi3audit

---
 python/pyproject.toml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/python/pyproject.toml b/python/pyproject.toml
index 658c4fef1..6fefe3ef0 100644
--- a/python/pyproject.toml
+++ b/python/pyproject.toml
@@ -104,25 +104,27 @@ manylinux-aarch64-image = "manylinux_2_28"
 musllinux-x86_64-image = "musllinux_1_2"
 musllinux-aarch64-image = "musllinux_1_2"
 # Use abi3audit to catch issues with Limited API wheels
+before-build = "pip install abi3audit"
 repair-wheel-command = [
   "auditwheel repair -w {dest_dir} {wheel}",
-  "pipx run abi3audit --verbose --strict --report {wheel}",
+  "abi3audit --verbose --strict --report {wheel}",
 ]
 
 [tool.cibuildwheel.windows]
 archs = [ "native" ]
 # Use delvewheel on windows
-before-build = "pip install delvewheel"
+before-build = "pip install delvewheel abi3audit"
 repair-wheel-command = [
   "delvewheel repair -w {dest_dir} {wheel}",
-  "pipx run abi3audit --verbose --strict --report {wheel}",
+  "abi3audit --verbose --strict --report {wheel}",
 ]
 
 [tool.cibuildwheel.macos]
 archs = [ "universal2" ]
+before-build = "pip install abi3audit"
 repair-wheel-command = [
   "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
-  "pipx run abi3audit --verbose --strict --report {wheel}",
+  "abi3audit --verbose --strict --report {wheel}",
 ]
 
 [tool.ruff]

From f7253138df20a391e8b0404dcf7d441c519ce8d4 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Fri, 17 Oct 2025 16:35:45 +0100
Subject: [PATCH 17/19] Bump cibuildwheel to v3.2.1

---
 .github/workflows/python.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index baa90411b..51c826c0d 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -216,12 +216,12 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
 
-      - name: Setup LLVM for Windows ARM64
+      - name: Setup LLVM for Windows ARM64 (NOT WORKING/FIXME)
         if: ${{ matrix.os == 'windows-11-arm' }}
         uses: ./.github/windows_arm64_steps
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.3
+        uses: pypa/cibuildwheel@v3.2.1
         with:
           package-dir: python
           output-dir: wheelhouse

From 7da3108855d9f7189104a944d1cb8c9856387023 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 17 Oct 2025 15:53:05 +0000
Subject: [PATCH 18/19] Initial plan


From c69566e4e6abbbd482971e883ed2237e16319207 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 17 Oct 2025 16:04:57 +0000
Subject: [PATCH 19/19] Fix limited-API (abi3) wheels configuration

Co-authored-by: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
---
 python/setup.py                  | 16 +++++++++-------
 python/src/moocore/_ffi_build.py |  3 ++-
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/python/setup.py b/python/setup.py
index 40c41b354..ac7925f0b 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -3,17 +3,19 @@
 from wheel.bdist_wheel import bdist_wheel as _bdist_wheel
 
 
-class bdist_wheel_abi_none(_bdist_wheel):
+class bdist_wheel_abi3(_bdist_wheel):
     def finalize_options(self):
         _bdist_wheel.finalize_options(self)
-        self.root_is_pure = False
-
-    def get_tag(self):
-        _python, _abi, plat = _bdist_wheel.get_tag(self)
-        return "py3", "none", plat
+        # Automatically detect py_limited_api from extension modules
+        if not self.py_limited_api:
+            for ext in self.distribution.ext_modules or []:
+                if getattr(ext, "py_limited_api", False):
+                    # Use cp310 as the minimum Python version for abi3
+                    self.py_limited_api = "cp310"
+                    break
 
 
 setup(
     cffi_modules=["src/moocore/_ffi_build.py:ffibuilder"],
-    cmdclass={"bdist_wheel": bdist_wheel_abi_none},
+    cmdclass={"bdist_wheel": bdist_wheel_abi3},
 )
diff --git a/python/src/moocore/_ffi_build.py b/python/src/moocore/_ffi_build.py
index d80ab7fc9..a7d53c1a7 100644
--- a/python/src/moocore/_ffi_build.py
+++ b/python/src/moocore/_ffi_build.py
@@ -118,7 +118,8 @@ def _get_target_platform():
     sources=sources,
     include_dirs=[libmoocore_path],
     extra_compile_args=extra_compile_args,
-    extra_link_args=extra_compile_args,
+    extra_link_args=extra_link_args,
+    py_limited_api=True,
 )
 
 if __name__ == "__main__":