From 9c5777415429ce688f1b8b758449222278cf52f7 Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 12:26:07 -0700 Subject: [PATCH 01/18] use python poetry --- .github/workflows/build.yml | 83 +- MANIFEST.in | 5 - Makefile | 30 - poetry.lock | 3186 +++++++++++++++++++++++++++++++++++ pyproject.toml | 95 +- requirements.txt | 2 - runtime.txt | 1 - setup.cfg | 67 - setup.py | 6 - 9 files changed, 3330 insertions(+), 145 deletions(-) delete mode 100644 MANIFEST.in delete mode 100644 Makefile create mode 100644 poetry.lock delete mode 100644 requirements.txt delete mode 100644 runtime.txt delete mode 100644 setup.cfg delete mode 100644 setup.py diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 5809a8e8a..6ec40b928 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -30,21 +30,27 @@ jobs: uses: github/codeql-action/analyze@v1 build-reference-documentation: runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.10"] + poetry-version: ["1.8.2"] steps: - uses: actions/checkout@v2 - - name: Set up Python 3.8 + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: ${{ matrix.python-version }} + - name: Install Poetry ${{ matrix.poetry-version }} + uses: abatilo/actions-poetry@v3.0.0 + with: + poetry-version: ${{ matrix.poetry-version }} + - name: Install dependencies + run: poetry install - name: "Run Reference Documentation Generation" run: | - sudo apt install pandoc - pip install -U pip setuptools wheel - pip install -r requirements.txt - pip install pipdeptree echo "documentation" > dependencies_documentation.txt - pipdeptree >> dependencies_documentation.txt - sphinx-build -W -t build_tutorials -a docs/ docs/_build/html + poetry run pipdeptree >> dependencies_documentation.txt + poetry run poe docsWithTutorials - name: Archive documentation version artifact uses: actions/upload-artifact@v2 with: @@ -59,37 +65,51 @@ jobs: docs/_build/html code-format-check: runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.10"] + poetry-version: ["1.8.2"] steps: - uses: actions/checkout@v2 - - name: Set up Python 3.8 + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: ${{ matrix.python-version }} + - name: Install Poetry ${{ matrix.poetry-version }} + uses: abatilo/actions-poetry@v3.0.0 + with: + poetry-version: ${{ matrix.poetry-version }} + - name: Install dependencies + run: poetry install - name: Run Format Check - run: | - pip install -U pip setuptools wheel - pip install -r requirements.txt - black --check --diff ./graspologic ./tests - isort --check-only ./graspologic ./tests + run: poetry run poe format_check test-coverage: runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.10"] + poetry-version: ["1.8.2"] steps: - uses: actions/checkout@v2 - - name: Set up Python 3.8 + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: ${{ matrix.python-version }} + - name: Install Poetry ${{ matrix.poetry-version }} + uses: abatilo/actions-poetry@v3.0.0 + with: + poetry-version: ${{ matrix.poetry-version }} + - name: Install dependencies + run: poetry install - name: Run Test Coverage - run: | - pip install -U pip setuptools wheel - pip install -r requirements.txt - python -m pytest --co --cov=graspologic graspologic tests + run: poetry run poe coverage unit-and-doc-test: runs-on: ${{matrix.os}} strategy: matrix: os: [ubuntu-latest, windows-latest, macos-latest] - python_version: ["3.8", "3.9", "3.10", "3.11"] + python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + poetry-version: ["1.8.2"] fail-fast: false steps: - uses: actions/checkout@v2 @@ -97,22 +117,21 @@ jobs: uses: actions/setup-python@v2 with: python-version: ${{matrix.python_version}} - - name: Install dependencies Python ${{matrix.python_version}} ${{matrix.os}} - run: | - pip install -U pip setuptools wheel - pip install -r requirements.txt + - name: Install Poetry ${{ matrix.poetry-version }} + uses: abatilo/actions-poetry@v3.0.0 + with: + poetry-version: ${{ matrix.poetry-version }} + - name: Install dependencies + run: poetry install - name: Run Unit Tests and Doctests Python ${{matrix.python_version}} ${{matrix.os}} - run: | - pytest tests # note: should be pytest graspologic tests, but we're skipping doctests for now and re-enabling them in another PR + run: poetry run poe tests - name: Run mypy type check Python ${{matrix.python_version}} ${{matrix.os}} - run: | - mypy ./graspologic + run: poetry run poe type_check - name: Generate dependency tree run: | - pip install pipdeptree export DEPS='dependencies_${{matrix.python_version}}_${{matrix.os}}.txt' echo "${{matrix.python_version}} ${{matrix.os}}" > $DEPS - pipdeptree >> $DEPS + poetry run pipdeptree >> $DEPS shell: bash - name: Archive dependency tree uses: actions/upload-artifact@v2 diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index d4f63a8c7..000000000 --- a/MANIFEST.in +++ /dev/null @@ -1,5 +0,0 @@ -recursive-include graspologic *.typed -recursive-include graspologic/datasets *.edgelist -recursive-include graspologic/datasets *.csv -recursive-include graspologic/layouts/include colors-100.json -exclude tests/* diff --git a/Makefile b/Makefile deleted file mode 100644 index 3c86d6263..000000000 --- a/Makefile +++ /dev/null @@ -1,30 +0,0 @@ -clean: - rm -rf docs/_build - -docs: - sphinx-build -W -a docs/ docs/_build/html - -docsWithTutorials: - sphinx-build -W -t build_tutorials -a docs/ docs/_build/html - -coverage: - python -m pytest --co --cov=graspologic graspologic tests - -lint: - black --check --diff ./graspologic ./tests - isort --check-only ./graspologic ./tests -format: - black ./graspologic ./tests - isort ./graspologic ./tests -test: - pytest tests - -fast-test: - pytest tests 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statistics" +repository = "https://github.com/microsoft/graspologic" +authors = [ + "Eric Bridgeford", + "Jaewon Chung ", + "Benjamin Pedigo", + "Bijan Varjavand", +] +maintainers = [ + "Dax Pryce " +] +license = "MIT" +readme = "README.md" +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "Topic :: Scientific/Engineering :: Mathematics", +] +include = [ + "graspologic", + "graspologic/**/*.typed", + "graspologic/datasets/**/*.edgelist", + "graspologic/datasets/**/*.csv", + "graspologic/layouts/include/**/colors-100.json" +] +exclude = [ + "tests" +] + +[tool.poetry.dependencies] +python = "^3.8" +anytree = "^2.8.0" +beartype = "^0.10.0" +gensim = "^4.0.0,!=4.2.0" +graspologic-native = "^1.1.1" +hyppo = "^0.3.2" +joblib = "^0.17.0" +matplotlib = "^3,!=3.3.*,!=3.6.1" +networkx = "^2.1" +numpy = "^1.11.0" +POT = "^0.7.0" +seaborn = "^0.11.0" +scikit-learn = "^1" +scipy = "^1.9.0,<1.13.0" +statsmodels = "^0.13.2" +typing-extensions = "^4.4.0" +umap-learn = "^0.4.6" + +[tool.poetry.group.dev.dependencies] +ipykernel = "^5.1.0" +ipython = "^7.4.0,!=8.7.0" # https://github.com/spatialaudio/nbsphinx/issues/687#issuecomment-1339271312 +isort = "^5.9.3" +mypy = "^0.910" +nbsphinx = "^0.8.7" +numpydoc = "^1.1.0" +pandoc = "^1.1.0" +pytest = "^6.2.5" +pytest-cov = "^3.0.0" +sphinx = "^4.2.0" +sphinxcontrib-rawfiles = "^0.1.1" +sphinx-rtd-theme = "^1.0.0" +testfixtures = "^6.18.3" +pipdeptree = "^2.20.0" + [build-system] -requires = ["setuptools >= 24.2.0"] -build-backend = "setuptools.build_meta" +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + +[tool.poe.tasks] +_black = "black ./graspologic ./tests" +_isort = "isort ./graspologic ./tests" +_black_check = "black --check --diff ./graspologic ./tests" +_isort_check = "isort --check-only ./graspologic ./tests" +clean = "rm -rf docs/_build" +type_check = "mypy ./graspologic" + +# Formatting +format = ["_black", "_isort"] +format_check = ["_black_check", "_isort_check"] + +# Docs Tasks +docs = "sphinx-build -W -a docs/ docs/_build/html" +docsWithTutorials = "sphinx-build -W -t build_tutorials -a docs/ docs/_build/html" + +# Testing Tasks +tests = "pytest tests" +coverage = "python -m pytest --co --cov=graspologic graspologic tests" +fast_test = "pytest tests --ignore=tests/test_latentdistributiontest.py --ignore=tests/test_latentpositiontest.py" + +lint = ["format_check", "type_check"] +validate = ["lint", "coverage", "docs", "tests"] [tool.isort] profile = "black" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index b0920f98d..000000000 --- a/requirements.txt +++ /dev/null @@ -1,2 +0,0 @@ --e .[dev] - diff --git a/runtime.txt b/runtime.txt deleted file mode 100644 index cc1923a40..000000000 --- a/runtime.txt +++ /dev/null @@ -1 +0,0 @@ -3.8 diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 62868ad09..000000000 --- a/setup.cfg +++ /dev/null @@ -1,67 +0,0 @@ -[metadata] -name = graspologic -version = 3.3.0 - -description = A set of python modules for graph statistics -long_description = file: README.md -long_description_content_type = text/markdown -author = Eric Bridgeford, Jaewon Chung, Benjamin Pedigo, Bijan Varjavand -author_email = j1c@jhu.edu -maintainer = Dax Pryce -maintainer_email = daxpryce@microsoft.com -url = https://github.com/microsoft/graspologic -license = MIT -classifiers = - Development Status :: 5 - Production/Stable - Intended Audience :: Science/Research - Topic :: Scientific/Engineering :: Mathematics - License :: OSI Approved :: MIT License - Programming Language :: Python :: 3 - Programming Language :: Python :: 3.8 - Programming Language :: Python :: 3.9 - Programming Language :: Python :: 3.10 - Programming Language :: Python :: 3.11 - -[options] -packages = find: -include_package_data = True -python_requires = >=3.8, <3.12 -install_requires = - anytree>=2.8.0 - beartype>=0.10.0 - gensim>=4.0.0,!=4.2.0 # bug with 4.2.0 on some platforms, issue #998 - graspologic-native>=1.1.1 - hyppo>=0.3.2 # bug with lower versions and scipy>=1.8 - joblib>=0.17.0 # Older versions of joblib cause issue #806. Transitive dependency of hyppo. - matplotlib>=3.0.0,!=3.3.*,!=3.6.1 - networkx>=2.1 - numpy>=1.8.1 - POT>=0.7.0 - seaborn>= 0.11.0 - scikit-learn>=0.22.0 - scipy>=1.9.0 - statsmodels>=0.13.2 - typing-extensions>=4.4.0 - umap-learn>=0.4.6 - -[options.packages.find] -exclude = - tests - -[options.extras_require] -dev = - black - ipykernel>=5.1.0 - ipython>=7.4.0,!=8.7.0 # https://github.com/spatialaudio/nbsphinx/issues/687#issuecomment-1339271312 - isort>=5.9.3 - mypy>=0.910 - nbsphinx>=0.8.7 - numpydoc>=1.1.0 - pandoc>=1.1.0 - pytest>=6.2.5 - pytest-cov>=3.0.0 - sphinx>=4.2.0 - sphinxcontrib-rawfiles>=0.1.1 - sphinx-rtd-theme>=1.0.0 - testfixtures>=6.18.3 - diff --git a/setup.py b/setup.py deleted file mode 100644 index 9222603af..000000000 --- a/setup.py +++ /dev/null @@ -1,6 +0,0 @@ -# Copyright (c) Microsoft Corporation and contributors. -# Licensed under the MIT License. - -import setuptools - -setuptools.setup() From d6fbc4793375b23c87db9f161f539cc90ea0355f Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 12:31:14 -0700 Subject: [PATCH 02/18] add poethepoet to dev --- poetry.lock | 31 ++++++++++++++++++++++++++++++- pyproject.toml | 1 + 2 files changed, 31 insertions(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 8fbd9b91b..01686e653 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1803,6 +1803,17 @@ files = [ qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"] testing = ["docopt", "pytest"] +[[package]] +name = "pastel" +version = "0.2.1" +description = "Bring colors to your terminal." +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "pastel-0.2.1-py2.py3-none-any.whl", hash = "sha256:4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364"}, + {file = "pastel-0.2.1.tar.gz", hash = "sha256:e6581ac04e973cac858828c6202c1e1e81fee1dc7de7683f3e1ffe0bfd8a573d"}, +] + [[package]] name = "patsy" version = "0.5.6" @@ -2034,6 +2045,24 @@ files = [ {file = 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"59aaf899d35e468c610c868a3d61d510256b40f60809ccdaed32a23677325dd6" diff --git a/pyproject.toml b/pyproject.toml index 270a1bc5e..450ddb8ed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,6 +64,7 @@ sphinxcontrib-rawfiles = "^0.1.1" sphinx-rtd-theme = "^1.0.0" testfixtures = "^6.18.3" pipdeptree = "^2.20.0" +poethepoet = "^0.26.1" [build-system] requires = ["poetry-core"] From f88cad4664875eb31bdae60e24ab6d56789be3e4 Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 13:05:34 -0700 Subject: [PATCH 03/18] refine some lib versions --- poetry.lock | 755 +++++++++++++++++++++---------------------------- pyproject.toml | 26 +- 2 files changed, 342 insertions(+), 439 deletions(-) diff --git a/poetry.lock b/poetry.lock index 01686e653..60c73c95e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "alabaster" -version = "0.7.13" -description = "A configurable sidebar-enabled Sphinx theme" +version = "0.7.16" +description = "A light, 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"p [metadata] lock-version = "2.0" -python-versions = "^3.8" -content-hash = "59aaf899d35e468c610c868a3d61d510256b40f60809ccdaed32a23677325dd6" +python-versions = "^3.9,<3.13" +content-hash = "ef0640e1d196dee513abeaccb3455da744fe147e91a2d650716355c880ba628a" diff --git a/pyproject.toml b/pyproject.toml index 450ddb8ed..d053afc1f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,20 +31,20 @@ exclude = [ ] [tool.poetry.dependencies] -python = "^3.8" -anytree = "^2.8.0" -beartype = "^0.10.0" -gensim = "^4.0.0,!=4.2.0" -graspologic-native = "^1.1.1" +python = "^3.9,<3.13" +anytree = "^2.12.1" +beartype = "^0.10.4" +gensim = "^4.3.2" +graspologic-native = "^1.2.1" hyppo = "^0.3.2" joblib = "^0.17.0" -matplotlib = "^3,!=3.3.*,!=3.6.1" -networkx = "^2.1" -numpy = "^1.11.0" +matplotlib = "^3.8.4" +networkx = "^2.8.8" +numpy = "^1.26.4" POT = "^0.7.0" -seaborn = "^0.11.0" -scikit-learn = "^1" -scipy = "^1.9.0,<1.13.0" +seaborn = "^0.11.2" +scikit-learn = "^1.0.2" +scipy = "1.12.0" statsmodels = "^0.13.2" typing-extensions = "^4.4.0" umap-learn = "^0.4.6" @@ -57,8 +57,8 @@ mypy = "^0.910" nbsphinx = "^0.8.7" numpydoc = "^1.1.0" pandoc = "^1.1.0" -pytest = "^6.2.5" -pytest-cov = "^3.0.0" +pytest = "^8.2.0" +pytest-cov = "^5.0.0" sphinx = "^4.2.0" sphinxcontrib-rawfiles = "^0.1.1" sphinx-rtd-theme = "^1.0.0" From fd6e1877524c3367f521fc4c71bef6cd5fb6f621 Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 13:15:43 -0700 Subject: [PATCH 04/18] update umap --- poetry.lock | 56 +++++++++++++++++++++++++++++++++++++++++++------- pyproject.toml | 2 +- 2 files changed, 50 insertions(+), 8 deletions(-) diff --git a/poetry.lock b/poetry.lock index 60c73c95e..fc70e6d76 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2035,6 +2035,24 @@ files = [ [package.extras] windows-terminal = ["colorama (>=0.4.6)"] +[[package]] +name = "pynndescent" +version = "0.5.12" +description = "Nearest Neighbor Descent" +optional = false +python-versions = "*" +files = [ + {file = "pynndescent-0.5.12-py3-none-any.whl", hash = "sha256:9023dc5fea520a4e84d0633ae735db97d2509da927bfa86c897e61f3315473c7"}, + {file = "pynndescent-0.5.12.tar.gz", hash = "sha256:0736291fcbbedfd5e0a3a280f71a63f8eb2f8bd9670d4c0b51ac1b4d081adf70"}, +] + +[package.dependencies] +joblib = ">=0.11" +llvmlite = ">=0.30" +numba = ">=0.51.2" +scikit-learn = ">=0.18" +scipy = ">=1.0" + [[package]] name = "pyparsing" version = "3.1.2" @@ -2922,6 +2940,26 @@ files = [ {file = "tornado-6.4.tar.gz", hash = "sha256:72291fa6e6bc84e626589f1c29d90a5a6d593ef5ae68052ee2ef000dfd273dee"}, ] +[[package]] +name = "tqdm" +version = "4.66.4" +description = "Fast, Extensible Progress Meter" +optional = false +python-versions = ">=3.7" +files = [ + {file = "tqdm-4.66.4-py3-none-any.whl", hash = "sha256:b75ca56b413b030bc3f00af51fd2c1a1a5eac6a0c1cca83cbb37a5c52abce644"}, + {file = "tqdm-4.66.4.tar.gz", hash = "sha256:e4d936c9de8727928f3be6079590e97d9abfe8d39a590be678eb5919ffc186bb"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} + +[package.extras] +dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"] +notebook = ["ipywidgets (>=6)"] +slack = ["slack-sdk"] +telegram = ["requests"] + [[package]] name = "traitlets" version = "5.14.3" @@ -2961,23 +2999,27 @@ files = [ [[package]] name = "umap-learn" -version = "0.4.6" +version = "0.5.6" description = "Uniform Manifold Approximation and Projection" optional = false python-versions = "*" files = [ - {file = "umap-learn-0.4.6.tar.gz", hash = "sha256:4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3"}, + {file = "umap-learn-0.5.6.tar.gz", hash = "sha256:5b3917a862c23ba0fc83bfcd67a7b719dec85b3d9c01fdc7d894cce455df4e03"}, + {file = "umap_learn-0.5.6-py3-none-any.whl", hash = "sha256:881cc0c2ee845b790bf0455aa1664f9f68b838d9d0fe12a1291b85c5a559c913"}, ] [package.dependencies] -numba = ">=0.46,<0.47 || >0.47" +numba = ">=0.51.2" numpy = ">=1.17" -scikit-learn = ">=0.20" +pynndescent = ">=0.5" +scikit-learn = ">=0.22" scipy = ">=1.3.1" +tqdm = "*" [package.extras] -performance = ["pynndescent (>=0.4)", "tbb (>=2019.5)"] -plot = ["bokeh", "colorcet", "datashader", "holoviews", "matplotlib", "pandas"] +parametric-umap = ["tensorflow (>=2.1)"] +plot = ["bokeh", "colorcet", "datashader", "holoviews", "matplotlib", "pandas", "scikit-image", "seaborn"] +tbb = ["tbb (>=2019.0)"] [[package]] name = "urllib3" @@ -3115,4 +3157,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.9,<3.13" -content-hash = "ef0640e1d196dee513abeaccb3455da744fe147e91a2d650716355c880ba628a" +content-hash = "e2aaa0f23667eac37138095c65c2500b9ac6a8a07e682016352cdcbb90ed0a7a" diff --git a/pyproject.toml b/pyproject.toml index d053afc1f..78a4fcacd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,7 +47,7 @@ scikit-learn = "^1.0.2" scipy = "1.12.0" statsmodels = "^0.13.2" typing-extensions = "^4.4.0" -umap-learn = "^0.4.6" +umap-learn = "^0.5.6" [tool.poetry.group.dev.dependencies] ipykernel = "^5.1.0" From c08864c2849f70c153e57b4e134c81c5420d9fcd Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 13:20:25 -0700 Subject: [PATCH 05/18] update contributing docs --- CONTRIBUTING.md | 76 +++++++------------------------------------------ 1 file changed, 10 insertions(+), 66 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 6fd47a13f..3f22195bd 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -62,6 +62,10 @@ follow these guidelines! This will make it a lot faster for us to respond to you # Contributing code +## Prerequisites +* [Python 3.9+](https://www.python.org/) +* [Poetry 1.8.2+](https://python-poetry.org/docs/) + ## Setting up for development The preferred workflow for contributing to `graspologic` is to fork the main repository on GitHub, clone, and develop on a @@ -87,44 +91,7 @@ branch using a virtual environment. Steps: Always use a `feature` branch. Pull requests directly to either `dev` or `main` will be rejected until you create a feature branch based on `dev`. -4. From the project root, create a [virtual environment](https://docs.python.org/3/library/venv.html) and install all development dependencies. Examples using various terminals are provided below. These examples use Python 3.8 but you may use any Python version supported by graspologic. If using Python 3.8 does not work feel free to type the same command simply using "Python" instead of "Python 3.8".These commands should install `graspologic` in editable mode, as well as all of its dependencies and several tools you need for developing `graspologic`. These commands assume that your operating system has already activated virtual environments which will allow virtual environments to be created. - - **Bash** - ```bash - # Create virtual environment - python3.8 -m venv venv - - # Activate the virtual environment - source venv/bin/activate - - # Install development dependencies - pip install -U pip setuptools - pip install -r requirements.txt - ``` - **CMD (Windows)** - ```cmd - rem Create virtual environment. Depending on your installation you might need "py -3 -m venv venv" instead - python3.8 -m venv venv - - rem Activate the virtual environment - .\venv\Scripts\activate.bat - - rem Install development dependencies - pip install -U pip setuptools - pip install -r requirements.txt - ``` - **PowerShell** - ```powershell - # Create virtual environment - python3.8 -m venv venv - - # Activate the virtual environment - .\venv\Scripts\Activate.ps1 - - # Install development dependencies - pip install -U pip setuptools - pip install -r requirements.txt - ``` +4. From the project root, run `poetry install`, which will create a virtual environment and install necessary dependencies. ## Code Changes @@ -155,44 +122,25 @@ tools to help make sure your changes meet the standards for our repository. #### Code formatting Please use `black` and `isort` so that the format of your code is compatible with our project. Format your code prior to committing using one of the following methods: ```bash -# Run "black" and "isort" using Make -make format -``` -OR -```bash -# Run "black" and "isort" -black graspologic/ tests/ -isort graspologic/ tests/ +poetry run poe format ``` #### Type checking Validate your typehinting by running: ```bash -make type-check -``` -OR -```bash -mypy ./graspologic +poetry run poe type_check ``` #### Unit testing To check if your code runs correctly, we recommend using unit testing that locally tests your code by implementing test cases. Execute these unit tests by running: ```bash -make test -``` -OR -```bash -pytest tests +poetry run poe tests ``` #### Creating documentation Build the documentation with the use of [sphinx](https://www.sphinx-doc.org/en/master/usage/index.html) by running: ```bash -make docs -``` -OR -```bash -sphinx-build -W -t build_tutorials -a docs/ docs/_build/html +poetry run poe docs ``` Please verify that the built documentation looks appropriate. You can view the `html` from the `docs/_build/html` folder; click on `index.html` to see what the homepage would @@ -202,11 +150,7 @@ If you have made any changes that could affect the tutorials, please also build This can take a bit longer because the code in each notebook actually needs to execute. You can build the documentation and tutorials by running: ```bash -make docsWithTutorials -``` -OR -```bash -sphinx-build -W -t build_tutorials -a docs/ docs/_build/html +poetry run poe docsWithTutorials ``` ## Publishing Changes From f9989b982beefc8187d0ccdfef453678fa95e417 Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 13:28:17 -0700 Subject: [PATCH 06/18] update seaborn --- poetry.lock | 24 ++++++++++++++---------- pyproject.toml | 2 +- 2 files changed, 15 insertions(+), 11 deletions(-) diff --git a/poetry.lock b/poetry.lock index fc70e6d76..c14eac3b8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2496,20 +2496,24 @@ test = ["asv", "gmpy2", "hypothesis", "mpmath", "pooch", "pytest", "pytest-cov", [[package]] name = "seaborn" -version = "0.11.2" -description = "seaborn: statistical data visualization" +version = "0.13.2" +description = "Statistical data visualization" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" files = [ - {file = 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"statsmodels (>=0.12)"] [[package]] name = "setuptools" @@ -3157,4 +3161,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.9,<3.13" -content-hash = "e2aaa0f23667eac37138095c65c2500b9ac6a8a07e682016352cdcbb90ed0a7a" +content-hash = "ee2492aafadf9a176ffb2742bf882861bbbfd8c0de6987494c2d5b892d5e47ba" diff --git a/pyproject.toml b/pyproject.toml index 78a4fcacd..5b8525c94 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,7 +42,7 @@ matplotlib = "^3.8.4" networkx = "^2.8.8" numpy = "^1.26.4" POT = "^0.7.0" -seaborn = "^0.11.2" +seaborn = "^0.13.2" scikit-learn = "^1.0.2" scipy = "1.12.0" statsmodels = "^0.13.2" From f9972b6d9fd1142f219f281541f3e3001d5ab9d7 Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 13:35:29 -0700 Subject: [PATCH 07/18] update balck, sphinx, pandoc --- poetry.lock | 166 +++++++++++++++++++++++++++++++++++++------------ pyproject.toml | 7 ++- 2 files changed, 131 insertions(+), 42 deletions(-) diff --git a/poetry.lock b/poetry.lock index c14eac3b8..0e5af9274 100644 --- a/poetry.lock +++ b/poetry.lock @@ -134,6 +134,52 @@ charset-normalizer = ["charset-normalizer"] html5lib = ["html5lib"] lxml = ["lxml"] +[[package]] +name = "black" +version = "24.4.2" +description = "The uncompromising code formatter." +optional = false +python-versions = ">=3.8" +files = [ + {file = "black-24.4.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:dd1b5a14e417189db4c7b64a6540f31730713d173f0b63e55fabd52d61d8fdce"}, + {file = "black-24.4.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8e537d281831ad0e71007dcdcbe50a71470b978c453fa41ce77186bbe0ed6021"}, + {file = "black-24.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eaea3008c281f1038edb473c1aa8ed8143a5535ff18f978a318f10302b254063"}, + {file = "black-24.4.2-cp310-cp310-win_amd64.whl", hash = "sha256:7768a0dbf16a39aa5e9a3ded568bb545c8c2727396d063bbaf847df05b08cd96"}, + 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"tabulate-0.9.0-py3-none-any.whl", hash = "sha256:024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f"}, + {file = "tabulate-0.9.0.tar.gz", hash = "sha256:0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c"}, +] + +[package.extras] +widechars = ["wcwidth"] + [[package]] name = "testfixtures" version = "6.18.5" @@ -3161,4 +3249,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.9,<3.13" -content-hash = "ee2492aafadf9a176ffb2742bf882861bbbfd8c0de6987494c2d5b892d5e47ba" +content-hash = "48eabea437137d263a972b01923cc444d7c7c4528b8212dee61d91f5422765ff" diff --git a/pyproject.toml b/pyproject.toml index 5b8525c94..8bf3302b1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -56,15 +56,16 @@ isort = "^5.9.3" mypy = "^0.910" nbsphinx = "^0.8.7" numpydoc = "^1.1.0" -pandoc = "^1.1.0" +pandoc = "^2.3.0" pytest = "^8.2.0" pytest-cov = "^5.0.0" -sphinx = "^4.2.0" +sphinx = "^7.3.7" sphinxcontrib-rawfiles = "^0.1.1" -sphinx-rtd-theme = "^1.0.0" +sphinx-rtd-theme = "^2.0.0" testfixtures = "^6.18.3" pipdeptree = "^2.20.0" poethepoet = "^0.26.1" +black = "^24.4.2" [build-system] requires = ["poetry-core"] From 19d1ef3e3e3dd9a48dd8400ae44bcf921b0f896d Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 13:37:09 -0700 Subject: [PATCH 08/18] run formatter --- graspologic/pipeline/__init__.py | 1 + graspologic/pipeline/embed/omnibus_embedding.py | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/graspologic/pipeline/__init__.py b/graspologic/pipeline/__init__.py index 8b90689bd..56813acd2 100644 --- a/graspologic/pipeline/__init__.py +++ b/graspologic/pipeline/__init__.py @@ -15,6 +15,7 @@ is to bridge this gap. """ + # Copyright (c) Microsoft Corporation. # Licensed under the MIT license. diff --git a/graspologic/pipeline/embed/omnibus_embedding.py b/graspologic/pipeline/embed/omnibus_embedding.py index cffe2bcb0..cdd7a988a 100644 --- a/graspologic/pipeline/embed/omnibus_embedding.py +++ b/graspologic/pipeline/embed/omnibus_embedding.py @@ -165,9 +165,9 @@ def omnibus_embedding_pairwise( for graph in graphs[1:]: union_graph.add_edges_from(graph.edges()) - union_graph_lcc: Union[ - nx.Graph, nx.Digraph, nx.OrderedGraph, nx.OrderedDiGraph - ] = largest_connected_component(union_graph) + union_graph_lcc: Union[nx.Graph, nx.Digraph, nx.OrderedGraph, nx.OrderedDiGraph] = ( + largest_connected_component(union_graph) + ) union_graph_lcc_nodes: Set[Any] = set(list(union_graph_lcc.nodes())) union_node_ids = np.array(list(union_graph_lcc_nodes)) From 187ddcad6994f9da6e66b475bc9d017ca2e605e1 Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 13:49:10 -0700 Subject: [PATCH 09/18] apt install pandoc in docs job --- .github/workflows/build.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 6ec40b928..e631ea644 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -35,6 +35,7 @@ jobs: python-version: ["3.10"] poetry-version: ["1.8.2"] steps: + - run: sudo apt-get install -y pandoc - uses: actions/checkout@v2 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 From 856220e24e261a1dbae6b7cd72ed30a0d39e001b Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 14:23:19 -0700 Subject: [PATCH 10/18] update sk-learn --- graspologic/cluster/autogmm.py | 4 +- graspologic/cluster/base.py | 3 +- poetry.lock | 83 +++++++++++++++------------------- pyproject.toml | 5 +- 4 files changed, 44 insertions(+), 51 deletions(-) diff --git a/graspologic/cluster/autogmm.py b/graspologic/cluster/autogmm.py index 65548e616..2f4357ac9 100644 --- a/graspologic/cluster/autogmm.py +++ b/graspologic/cluster/autogmm.py @@ -569,8 +569,10 @@ def fit(self, X: np.ndarray, y: Optional[np.ndarray] = None) -> "AutoGMMCluster" if self.label_init is None: for p_ag in param_grid_ag: if p_ag["affinity"] != "none": + p_ag_without_affinity = p_ag.copy() + p_ag_without_affinity.pop("affinity", None) agg = AgglomerativeClustering( - n_clusters=self.min_components, **p_ag + n_clusters=self.min_components, **p_ag_without_affinity ) agg.fit(X_subset) hierarchical_labels = _hierarchical_labels( diff --git a/graspologic/cluster/base.py b/graspologic/cluster/base.py index a4ce4f192..72dc4da75 100644 --- a/graspologic/cluster/base.py +++ b/graspologic/cluster/base.py @@ -6,11 +6,12 @@ import numpy as np from sklearn.base import BaseEstimator, ClusterMixin +from sklearn.cluster import AffinityPropagation from sklearn.metrics import adjusted_rand_score from sklearn.utils.validation import check_is_fitted -class BaseCluster(ABC, BaseEstimator, ClusterMixin): +class BaseCluster(ABC, AffinityPropagation): """ Base clustering class. 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[metadata] lock-version = "2.0" python-versions = "^3.9,<3.13" -content-hash = "a1e6d5e3c1d6f9d923c8fa9d52813360607de03af399810526a5f9271d9adc3a" +content-hash = "3a8ac5d2986647a3408c4ced88e358207188452a47d3b46a8c3ff3a71a06515f" diff --git a/pyproject.toml b/pyproject.toml index 769012a6f..f973f7678 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,7 +45,7 @@ POT = "^0.7.0" seaborn = "^0.13.2" scikit-learn = "^1.4.2" scipy = "1.12.0" -statsmodels = "^0.13.2" +statsmodels = "^0.14.2" typing-extensions = "^4.4.0" umap-learn = "^0.5.6" From 13a919112a5d4b3243b6cd0db63248f7b843b36d Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 14:32:33 -0700 Subject: [PATCH 12/18] remove 3.8 from build --- .github/workflows/build.yml | 2 +- .github/workflows/publish.yml | 4 ++-- .readthedocs.yml | 2 +- README.md | 3 ++- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index e631ea644..afec275cb 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -109,7 +109,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, windows-latest, macos-latest] - python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + python_version: ["3.9", "3.10", "3.11", "3.12"] poetry-version: ["1.8.2"] fail-fast: false steps: diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index c32da9c45..eba53ca5b 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -16,10 +16,10 @@ jobs: if: github.ref=='refs/heads/main' || github.ref=='refs/heads/dev' steps: - uses: actions/checkout@v2 - - name: Set up Python 3.8 + - name: Set up Python 3.9 uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: 3.9 - name: Install dependencies run: | python -m pip install --upgrade pip setuptools wheel twine diff --git a/.readthedocs.yml b/.readthedocs.yml index f1ad56f2b..77964e9e0 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -3,7 +3,7 @@ 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{file = "mypy_extensions-0.4.4.tar.gz", hash = "sha256:c8b707883a96efe9b4bb3aaf0dcc07e7e217d7d8368eec4db4049ee9e142f4fd"}, + {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"}, + {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"}, ] [[package]] @@ -2931,17 +2938,6 @@ webencodings = ">=0.4" doc = ["sphinx", "sphinx_rtd_theme"] test = ["pytest", "ruff"] -[[package]] -name = "toml" -version = "0.10.2" -description = "Python Library for Tom's Obvious, Minimal Language" -optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" -files = [ - {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"}, - {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"}, -] - [[package]] name = "tomli" version = "2.0.1" @@ -3190,4 +3186,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.9,<3.13" -content-hash = "3a8ac5d2986647a3408c4ced88e358207188452a47d3b46a8c3ff3a71a06515f" +content-hash = "2e5e2d44a0a5e64211290dd13009332fc77473294471109c3dbe7ec9adc36167" diff --git a/pyproject.toml b/pyproject.toml index f973f7678..f29f76d26 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -53,7 +53,7 @@ umap-learn = "^0.5.6" ipykernel = "^5.1.0" ipython = "^7.4.0,!=8.7.0" # https://github.com/spatialaudio/nbsphinx/issues/687#issuecomment-1339271312 isort = "^5.9.3" -mypy = "^0.910" +mypy = "^1.10.0" nbsphinx = "^0.8.7" numpydoc = "^1.1.0" pandoc = "^2.3.0" From c1bc448213853501801f67c074cb67a6ed1e4204 Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 15:56:20 -0700 Subject: [PATCH 14/18] dynamic versioning plugin --- .github/workflows/publish.yml | 57 +++++++++++++++++++++-------------- pyproject.toml | 10 ++++-- 2 files changed, 43 insertions(+), 24 deletions(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index eba53ca5b..48d6d327c 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -1,5 +1,13 @@ name: graspologic Publish on: + # + # When a release tag is created (e.g. v1.0.0), this workflow will be triggered. The `poetry dynamic-version` plugin will use the correct version tag. + # + release: + types: [created] + # + # On pushes to main and dev, a prerelease version will be cut for the branch. e.g. v1.0.0-pre.10+ + # push: paths-ignore: - '.all-contributorsrc' @@ -14,35 +22,40 @@ jobs: runs-on: ubuntu-latest needs: build if: github.ref=='refs/heads/main' || github.ref=='refs/heads/dev' + strategy: + matrix: + python-version: ["3.10"] + poetry-version: ["1.8.2"] steps: - uses: actions/checkout@v2 - - name: Set up Python 3.9 + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: - python-version: 3.9 + python-version: ${{ matrix.python-version }} + - name: Install Poetry ${{ matrix.poetry-version }} + uses: abatilo/actions-poetry@v3.0.0 + with: + poetry-version: ${{ matrix.poetry-version }} + # + # This plugin will append version hashes unless we're on a release tag + # + - name: Add poetry-dynamic-versioning plugin + run: poetry self add "poetry-dynamic-versioning[plugin]" - name: Install dependencies - run: | - python -m pip install --upgrade pip setuptools wheel twine - pip install -r requirements.txt + run: poetry install - name: Create version environment variable run: | - echo "GRASPOLOGIC_VERSION=`python setup.py --version`" >> $GITHUB_ENV - echo "GRASPOLOGIC_TAG=v`python setup.py --version`" >> $GITHUB_ENV - - name: Build Release with setuptools - if: github.ref=='refs/heads/main' - run: | - python setup.py sdist - - name: Build Prerelease with setuptools - if: github.ref=='refs/heads/dev' - run: | - python setup.py egg_info -b "dev$GITHUB_RUN_ID" sdist - - name: Publish with twine - if: github.ref=='refs/heads/main' || github.ref=='refs/heads/dev' - env: - TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} - TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} - run: | - twine upload dist/* + echo "GRASPOLOGIC_VERSION=`poetry version --short`" >> $GITHUB_ENV + echo "GRASPOLOGIC_TAG=v`poetry version --short`" >> $GITHUB_ENV + - name: Build Artifacts + run: poetry build + # Note: need to set up a Trusted Publisher on PyPi + - name: Publish package distributions to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + packages-dir: dist + skip-existing: true + verbose: true - name: Download documentation artifact uses: actions/download-artifact@v2 with: diff --git a/pyproject.toml b/pyproject.toml index f29f76d26..fe66a8ecb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,8 +68,14 @@ poethepoet = "^0.26.1" black = "^24.4.2" [build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"] +build-backend = "poetry_dynamic_versioning.backend" + +[tool.poetry-dynamic-versioning] +enable = true +style = "semver" +vcs = "git" +bump = true [tool.poe.tasks] _black = "black ./graspologic ./tests" From b98c2fb3780e2fa6f5672752ce1e3c1bc4f5187b Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 16:05:21 -0700 Subject: [PATCH 15/18] restore original python range --- poetry.lock | 5 ++--- pyproject.toml | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index 246593c53..c2cd3f61c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1719,7 +1719,6 @@ files = [ numpy = [ {version = ">=1.22.4", markers = "python_version < \"3.11\""}, {version = ">=1.23.2", markers = "python_version == \"3.11\""}, - {version = ">=1.26.0", markers = "python_version >= \"3.12\""}, ] python-dateutil = ">=2.8.2" pytz = ">=2020.1" @@ -3185,5 +3184,5 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" -python-versions = "^3.9,<3.13" -content-hash = "2e5e2d44a0a5e64211290dd13009332fc77473294471109c3dbe7ec9adc36167" +python-versions = "^3.9,<3.12" +content-hash = "559f15a1ba4713ea3b3ad59d720b31bc55c0508566b7faf384309bb4e844ea36" diff --git a/pyproject.toml b/pyproject.toml index fe66a8ecb..2311b887c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,7 @@ exclude = [ ] [tool.poetry.dependencies] -python = "^3.9,<3.13" +python = "^3.9,<3.12" anytree = "^2.12.1" beartype = "^0.10.4" gensim = "^4.3.2" From 8eea017cdcdab477fda83bf50212c9fa51ced92a Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Tue, 7 May 2024 16:06:30 -0700 Subject: [PATCH 16/18] update py range --- poetry.lock | 5 +++-- pyproject.toml | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index c2cd3f61c..246593c53 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1719,6 +1719,7 @@ files = [ numpy = [ {version = ">=1.22.4", markers = "python_version < \"3.11\""}, {version = ">=1.23.2", markers = "python_version == \"3.11\""}, + {version = ">=1.26.0", markers = "python_version >= \"3.12\""}, ] python-dateutil = ">=2.8.2" pytz = ">=2020.1" @@ -3184,5 +3185,5 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" -python-versions = "^3.9,<3.12" -content-hash = "559f15a1ba4713ea3b3ad59d720b31bc55c0508566b7faf384309bb4e844ea36" +python-versions = "^3.9,<3.13" +content-hash = "2e5e2d44a0a5e64211290dd13009332fc77473294471109c3dbe7ec9adc36167" diff --git a/pyproject.toml b/pyproject.toml index 2311b887c..fe66a8ecb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,7 @@ exclude = [ ] [tool.poetry.dependencies] -python = "^3.9,<3.12" +python = "^3.9,<3.13" anytree = "^2.12.1" beartype = "^0.10.4" gensim = "^4.3.2" From 673c093288562033f573fe60755c21bab87c0467 Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Wed, 8 May 2024 10:16:16 -0700 Subject: [PATCH 17/18] affinity=>metric in agglomorativeclustering --- graspologic/cluster/autogmm.py | 4 ++-- graspologic/cluster/base.py | 3 +-- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/graspologic/cluster/autogmm.py b/graspologic/cluster/autogmm.py index 2f4357ac9..98dca8c82 100644 --- a/graspologic/cluster/autogmm.py +++ b/graspologic/cluster/autogmm.py @@ -570,9 +570,9 @@ def fit(self, X: np.ndarray, y: Optional[np.ndarray] = None) -> "AutoGMMCluster" for p_ag in param_grid_ag: if p_ag["affinity"] != "none": p_ag_without_affinity = p_ag.copy() - p_ag_without_affinity.pop("affinity", None) + affinity = p_ag_without_affinity.pop("affinity", None) agg = AgglomerativeClustering( - n_clusters=self.min_components, **p_ag_without_affinity + n_clusters=self.min_components, metric=affinity, **p_ag_without_affinity ) agg.fit(X_subset) hierarchical_labels = _hierarchical_labels( diff --git a/graspologic/cluster/base.py b/graspologic/cluster/base.py index 72dc4da75..a4ce4f192 100644 --- a/graspologic/cluster/base.py +++ b/graspologic/cluster/base.py @@ -6,12 +6,11 @@ import numpy as np from sklearn.base import BaseEstimator, ClusterMixin -from sklearn.cluster import AffinityPropagation from sklearn.metrics import adjusted_rand_score from sklearn.utils.validation import check_is_fitted -class BaseCluster(ABC, AffinityPropagation): +class BaseCluster(ABC, BaseEstimator, ClusterMixin): """ Base clustering class. """ From ad67d4900843062316b8f76cde6b0e68698179fb Mon Sep 17 00:00:00 2001 From: Chris Trevino Date: Wed, 8 May 2024 10:19:29 -0700 Subject: [PATCH 18/18] formatting --- graspologic/cluster/autogmm.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/graspologic/cluster/autogmm.py b/graspologic/cluster/autogmm.py index 98dca8c82..85b66fe5e 100644 --- a/graspologic/cluster/autogmm.py +++ b/graspologic/cluster/autogmm.py @@ -572,7 +572,9 @@ def fit(self, X: np.ndarray, y: Optional[np.ndarray] = None) -> "AutoGMMCluster" p_ag_without_affinity = p_ag.copy() affinity = p_ag_without_affinity.pop("affinity", None) agg = AgglomerativeClustering( - n_clusters=self.min_components, metric=affinity, **p_ag_without_affinity + n_clusters=self.min_components, + metric=affinity, + **p_ag_without_affinity ) agg.fit(X_subset) hierarchical_labels = _hierarchical_labels(