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MAINT Remove requirements files #240

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merged 9 commits into from
Mar 7, 2024
Merged

MAINT Remove requirements files #240

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19f7e51
Try to migrate CI one at a time
adam2392 Mar 6, 2024
2596111
Style
adam2392 Mar 6, 2024
990c0e9
wheels
adam2392 Mar 6, 2024
5f1b766
Try all gh actions
adam2392 Mar 6, 2024
baabb42
Try again
adam2392 Mar 6, 2024
57ffb98
Fix
adam2392 Mar 7, 2024
3e6a8b7
Address circleCI as well
adam2392 Mar 7, 2024
a6067c4
Fix circle
adam2392 Mar 7, 2024
31bd2d7
Adding style requirements back
adam2392 Mar 7, 2024
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10 changes: 6 additions & 4 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -81,12 +81,14 @@ jobs:
- run:
name: setup Python venv
command: |
pip install -r build_requirements.txt
pip install -r doc_requirements.txt
pip install --upgrade pip spin
spin setup-submodule
pip install .[build,doc]

- run:
name: build scikit-tree
command: |
python spin build -j2
spin build -j2

- save_cache:
key: deps_ccache-{{ .Branch }}
Expand Down Expand Up @@ -127,7 +129,7 @@ jobs:
echo "After..."
ls build-install/**
export PYTHONPATH=$PWD/build-install/usr/lib/python3.8/site-packages
python ./spin docs
./spin docs

- store_artifacts:
path: doc/_build/html
Expand Down
21 changes: 10 additions & 11 deletions .github/workflows/build_wheels.yml
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Expand Up @@ -60,9 +60,8 @@ jobs:

- name: Setup submodule
run: |
python -m pip install -r build_requirements.txt
python -m pip install spin
python spin setup-submodule
python -m pip install --upgrade pip spin
python -m spin setup-submodule

- name: win_amd64 - install rtools
run: |
Expand All @@ -79,7 +78,7 @@ jobs:
# configuration step to create a build directory. The subsequent wheel
# build then needs to use that directory. This can be done with pip
# using a command like:
# python -m pip wheel --config-settings builddir=build .
# pip wheel --config-settings builddir=build .
# if: >-
# ( ! contains(matrix.os[2], 'arm64' ) )
env:
Expand Down Expand Up @@ -114,10 +113,10 @@ jobs:

- name: Install cibuildwheel dependencies
run: |
python -m pip install cibuildwheel
python -m pip install -r build_requirements.txt
python -m pip install spin
python spin setup-submodule
pip install cibuildwheel
pip install spin
spin setup-submodule
pip install .[build]

- name: Build wheels
uses: pypa/cibuildwheel@v2.16.5
Expand Down Expand Up @@ -146,9 +145,9 @@ jobs:

- name: Build source distribution
run: |
python -m pip install -r build_requirements.txt
python -m pip install spin
python spin setup-submodule
pip install spin build
spin setup-submodule
pip install .[build]
python -m build

- name: Store artifacts
Expand Down
43 changes: 24 additions & 19 deletions .github/workflows/main.yml
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Expand Up @@ -46,28 +46,32 @@ jobs:
python-version: ${{ matrix.python-version }}
architecture: "x64"
cache: "pip"
cache-dependency-path: "requirements.txt"
cache-dependency-path: "pyproject.toml"

- name: show-gcc
- name: Install packages for Ubuntu
if: ${{ matrix.os == 'ubuntu-22.04'}}
run: |
gcc --version
sudo apt-get update
sudo apt-get install -y libopenblas-dev libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libsuitesparse-dev ccache libmpc-dev
sudo apt-get install -y gcc
sudo apt-get update

- name: Install Ccache for MacOSX
if: ${{ matrix.os == 'macos-latest'}}
run: |
brew install ccache
brew install gcc

- name: Install packages for Ubuntu
if: ${{ matrix.os == 'ubuntu-22.04'}}
- name: show-gcc
run: |
sudo apt-get update
sudo apt-get install -y libopenblas-dev libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libsuitesparse-dev ccache libmpc-dev
gcc --version

- name: Install Python packages
run: |
python -m pip install -r build_requirements.txt
python -m pip install spin
python -m pip install -r test_requirements.txt
python -m spin setup-submodule
python -m pip install .[build]
python -m pip install .[test]

- name: Prepare compiler cache
id: prep-ccache
Expand Down Expand Up @@ -153,7 +157,7 @@ jobs:
python-version: ${{ matrix.python-version }}
architecture: "x64"
cache: "pip"
cache-dependency-path: "requirements.txt"
cache-dependency-path: "pyproject.toml"

- name: show-gcc
run: |
Expand All @@ -172,9 +176,10 @@ jobs:

- name: Install Python packages
run: |
python -m pip install -r build_requirements.txt
python -m pip install spin
python -m pip install -r test_requirements.txt
python -m spin setup-submodule
python -m pip install .[build]
python -m pip install .[test]

- name: Prepare compiler cache
id: prep-ccache
Expand Down Expand Up @@ -232,7 +237,7 @@ jobs:
- name: Upload coverage stats to codecov
uses: codecov/codecov-action@v4
with:
# python spin goes into the INSTALLED path in order to run pytest
# spin goes into the INSTALLED path in order to run pytest
files: ./coverage.xml
fail_ci_if_error: true
verbose: true
Expand All @@ -258,7 +263,7 @@ jobs:
# python-version: "3.10"
# architecture: "x64"
# cache: "pip"
# cache-dependency-path: "requirements.txt"
# cache-dependency-path: "pyproject.toml"

# - name: install-rtools
# run: |
Expand Down Expand Up @@ -287,8 +292,8 @@ jobs:

# - name: pip-packages
# run: |
# pip install -r build_requirements.txt
# pip install -r test_requirements.txt
# pip install .[build]
# pip install .[test]
# pip install spin
# pip install numpy==1.22.4

Expand Down Expand Up @@ -319,8 +324,8 @@ jobs:
# run: |
# echo "SCIPY_USE_PROPACK=1" >> $env:GITHUB_ENV
# echo "FORCE_SUBMODULE=True" >> $env:GITHUB_ENV
# python spin setup_submodule --forcesubmodule
# python spin build -j 2
# spin setup_submodule --forcesubmodule
# spin build -j 2
# # Necessary because GitHub Actions checks out the repo to D:\ while OpenBLAS
# # got installed to C:\ higher up. The copying with `--win-cp-openblas` fails
# # when things are split over drives.
Expand All @@ -329,4 +334,4 @@ jobs:

# - name: test
# run: |
# python spin test
# spin test
4 changes: 3 additions & 1 deletion .github/workflows/style.yml
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Expand Up @@ -41,7 +41,9 @@ jobs:
sudo apt-get install -y libopenblas-dev libatlas-base-dev liblapack-dev

- name: Install dependencies
run: pip install -r style_requirements.txt
run: |
pip install --upgrade pip
pip install -r style_requirements.txt

# check formatting of the code style
- name: Check code formatting
Expand Down
8 changes: 4 additions & 4 deletions DEVELOPING.md
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Expand Up @@ -43,10 +43,10 @@ If you are developing locally, you will need the build dependencies to compile t

Other requirements can be installed as such:

pip install -r requirements.txt
pip install -r style_requirements.txt
pip install -r test_requirements.txt
pip install -r doc_requirements.txt
pip install .
pip install .[style]
pip install .[test]
pip install .[doc]

# Building the project from source

Expand Down
4 changes: 2 additions & 2 deletions build_requirements.txt
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@@ -1,9 +1,9 @@
meson
meson-python
cython==0.29.36
cython>=3.0.8
ninja
numpy
scikit-learn>=1.3.1
scikit-learn>=1.4.1
click
rich-click
doit
Expand Down
15 changes: 0 additions & 15 deletions doc_requirements.txt
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This file was deleted.

16 changes: 8 additions & 8 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
[build-system]
build-backend = "mesonpy"
requires = [
"meson-python>=0.13.0",
"meson-python>=0.15.0",
'ninja',
# `wheel` is needed for non-isolated builds, given that `meson-python`
# doesn't list it as a runtime requirement (at least in 0.10.0)
# See https://github.com/FFY00/meson-python/blob/main/pyproject.toml#L4
"wheel",
"setuptools<=65.5",
"packaging",
"Cython>=0.29.24",
"scikit-learn>=1.4",
"Cython>=3.0.8",
"scikit-learn>=1.4.1",
"scipy>=1.5.0",
"numpy>=1.25; python_version>='3.9'"
]
Expand Down Expand Up @@ -49,9 +49,9 @@ include = [
{path = "meson.build", format = "sdist"}
]
dependencies = [
'numpy',
'numpy>=1.25.0',
'scipy>=1.5.0',
'scikit-learn>=1.3.1'
'scikit-learn>=1.4.1'
]

[project.optional-dependencies]
Expand All @@ -68,10 +68,10 @@ build = [
'meson-python',
'spin',
'doit',
'scikit-learn>=1.3.1',
'Cython>=0.29.36',
'scikit-learn>=1.4.1',
'Cython>=3.0.8',
'ninja',
'numpy',
'numpy>=1.25.0',
'rich-click',
'pydevtool'
]
Expand Down
4 changes: 0 additions & 4 deletions requirements.txt
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2 changes: 1 addition & 1 deletion sktree/_lib/sklearn_fork
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Submodule sklearn_fork updated 68 files
+1 −1 build_tools/azure/debian_atlas_32bit_lock.txt
+21 −21 build_tools/azure/pylatest_conda_forge_mkl_linux-64_conda.lock
+12 −12 build_tools/azure/pylatest_conda_forge_mkl_osx-64_conda.lock
+4 −4 build_tools/azure/pylatest_conda_mkl_no_openmp_osx-64_conda.lock
+10 −10 build_tools/azure/pylatest_pip_openblas_pandas_linux-64_conda.lock
+13 −9 build_tools/azure/pymin_conda_defaults_openblas_linux-64_conda.lock
+13 −13 build_tools/azure/pymin_conda_forge_mkl_win-64_conda.lock
+17 −17 build_tools/azure/pymin_conda_forge_openblas_ubuntu_2204_linux-64_conda.lock
+4 −4 build_tools/azure/pypy3_linux-64_conda.lock
+1 −1 build_tools/azure/ubuntu_atlas_lock.txt
+33 −33 build_tools/circle/doc_linux-64_conda.lock
+16 −16 build_tools/circle/doc_min_dependencies_linux-64_conda.lock
+4 −4 build_tools/cirrus/pymin_conda_forge_linux-aarch64_conda.lock
+1 −0 doc/glossary.rst
+2 −0 doc/metadata_routing.rst
+626 −550 doc/modules/clustering.rst
+2 −2 doc/modules/linear_model.rst
+10 −0 doc/whats_new/v1.4.rst
+45 −0 doc/whats_new/v1.5.rst
+4 −4 sklearn/cluster/_agglomerative.py
+8 −0 sklearn/cluster/_hdbscan/hdbscan.py
+3 −1 sklearn/cluster/_optics.py
+2 −2 sklearn/cluster/_spectral.py
+21 −0 sklearn/cluster/tests/test_optics.py
+15 −5 sklearn/compose/_target.py
+9 −1 sklearn/compose/tests/test_target.py
+2 −2 sklearn/datasets/_arff_parser.py
+34 −2 sklearn/datasets/_base.py
+27 −3 sklearn/datasets/_california_housing.py
+19 −2 sklearn/datasets/_covtype.py
+28 −3 sklearn/datasets/_kddcup99.py
+48 −5 sklearn/datasets/_lfw.py
+19 −2 sklearn/datasets/_olivetti_faces.py
+22 −3 sklearn/datasets/_rcv1.py
+14 −0 sklearn/datasets/_samples_generator.py
+31 −5 sklearn/datasets/_species_distributions.py
+43 −4 sklearn/datasets/_twenty_newsgroups.py
+28 −0 sklearn/datasets/tests/test_base.py
+10 −1 sklearn/decomposition/_dict_learning.py
+1 −1 sklearn/ensemble/_bagging.py
+1 −1 sklearn/ensemble/_iforest.py
+1 −1 sklearn/linear_model/_huber.py
+130 −27 sklearn/linear_model/_ransac.py
+4 −4 sklearn/linear_model/tests/test_ransac.py
+157 −118 sklearn/manifold/_locally_linear.py
+37 −9 sklearn/manifold/_spectral_embedding.py
+1 −1 sklearn/manifold/_t_sne.py
+1 −1 sklearn/metrics/pairwise.py
+1 −1 sklearn/model_selection/_split.py
+2 −2 sklearn/model_selection/_validation.py
+115 −54 sklearn/multioutput.py
+4 −4 sklearn/neighbors/_graph.py
+5 −1 sklearn/neighbors/_nca.py
+16 −4 sklearn/neighbors/tests/test_nca.py
+2 −2 sklearn/preprocessing/_label.py
+17 −7 sklearn/tests/metadata_routing_common.py
+5 −3 sklearn/tests/test_metadata_routing.py
+118 −20 sklearn/tests/test_metaestimators_metadata_routing.py
+62 −33 sklearn/tests/test_multioutput.py
+7 −1 sklearn/tests/test_public_functions.py
+9 −287 sklearn/utils/__init__.py
+175 −0 sklearn/utils/_chunking.py
+115 −0 sklearn/utils/_mask.py
+2 −2 sklearn/utils/_metadata_requests.py
+73 −0 sklearn/utils/tests/test_chunking.py
+5 −0 sklearn/utils/tests/test_param_validation.py
+0 −69 sklearn/utils/tests/test_utils.py
+7 −2 sklearn/utils/validation.py
6 changes: 0 additions & 6 deletions test_requirements.txt
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