From 974c0be9fd8ebdb37c94fabb9ab6d0572ee7fb29 Mon Sep 17 00:00:00 2001 From: Andrew Ramirez Date: Mon, 16 Sep 2024 12:23:22 -0700 Subject: [PATCH] Change to rye --- .github/workflows/build.yml | 11 +- .github/workflows/test.yml | 30 - makefile | 29 +- poetry.lock | 2147 ----------------------------------- pyproject.toml | 92 +- requirements-dev.lock | 311 +++++ requirements.lock | 298 +++++ 7 files changed, 695 insertions(+), 2223 deletions(-) delete mode 100644 .github/workflows/test.yml delete mode 100644 poetry.lock create mode 100644 requirements-dev.lock create mode 100644 requirements.lock diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 39c1e2f..0ecd69d 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -8,8 +8,13 @@ jobs: runs-on: self-hosted steps: - uses: actions/checkout@v4 - - name: Install dependencies - run: poetry install + - name: Setup rye + uses: eifinger/setup-rye@v4 + with: + enable-cache: true + version: '0.39.0' + - name: Setup environment + run: make .venv - name: Build figures run: make all -j 2 - name: Upload files @@ -17,4 +22,4 @@ jobs: with: name: files path: | - output/*.svg + output/*.svg \ No newline at end of file diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml deleted file mode 100644 index 3a1119c..0000000 --- a/.github/workflows/test.yml +++ /dev/null @@ -1,30 +0,0 @@ -# This workflow will install Python dependencies, run tests and lint with a variety of Python versions -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -name: Test - -on: push - -jobs: - build: - runs-on: self-hosted - steps: - - uses: actions/checkout@v4 - - name: Install dependencies - run: poetry install - - name: Run mypy check - run: make mypy - - name: Run ruff check - run: poetry run ruff check spatialpf2 - - name: Run ruff format check - run: poetry run ruff format --check spatialpf2 - - name: Test with pytest - run: make coverage.xml - - name: Upload coverage to Codecov - uses: codecov/codecov-action@v4 - with: - token: ${{ secrets.CODECOV_TOKEN }} - files: ./coverage.xml - flags: unittests - name: codecov-umbrella - fail_ci_if_error: true diff --git a/makefile b/makefile index 9eded07..315acbf 100644 --- a/makefile +++ b/makefile @@ -1,6 +1,4 @@ -SHELL := /bin/bash - -.PHONY: clean test +.PHONY: clean test pyright flist = $(wildcard spatialpf2/figures/figure*.py) allOutput = $(patsubst spatialpf2/figures/figure%.py, output/figure%.svg, $(flist)) @@ -9,21 +7,20 @@ all: $(allOutput) output/figure%.svg: spatialpf2/figures/figure%.py @ mkdir -p ./output - poetry run fbuild $* + rye run fbuild $* -test: - poetry run pytest -s -x -v +test: .venv + rye run pytest -s -v -x -coverage.xml: - poetry run pytest --cov=spatialpf2 --cov-report=xml +.venv: + rye sync -clean: - rm -rf output profile profile.svg - rm -rf factor_cache +coverage.xml: .venv + rye run pytest --junitxml=junit.xml --cov=spatialpf2 --cov-report xml:coverage.xml -testprofile: - 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"^1.10" -pacmap = "^0.7.1" -leidenalg = "^0.10.1" -tqdm = "^4.66.1" -tlviz = "^0.1.1" -statsmodels = "^0.14.1" -dask = {extras = ["dataframe"], version = "^2024.3.1"} -ruff = "^0.4.2" - -[tool.poetry.scripts] -fbuild = "spatialpf2.figures.common:genFigure" \ No newline at end of file + +dependencies = [ + "pandas>=2.1.3", + "scanpy>=1.9.6", + "matplotlib>=3.9", + "scikit-learn>=1.5", + "tensorly>=0.8.1", + "numpy>=1.26.2", + "parafac2 @ git+https://github.com/meyer-lab/parafac2.git@793f8ad06791ffcc698105d80941774741722574", + "pacmap>=0.7.3", + "anndata>=0.10.3", + "tlviz>=0.1.1", + "datashader>=0.16.2", + "dask[dataframe]>=2024.5.0", + "setuptools>=69.5", + "doubletdetection>=4.2", + "networkx>=3.3" +] + + +readme = "README.md" + +[project.scripts] +fbuild = "spatialpf2.figures.common:genFigure" +factor = "spatialpf2.imports:factorSave" + +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[tool.rye] +managed = true +dev-dependencies = [ + "pytest>=8.0", + "pytest-cov>=5.0", + "pyright>=1.1", +] + +[tool.hatch.metadata] +allow-direct-references = true + +[tool.hatch.build.targets.wheel] +packages = ["spatialpf2"] + +[tool.ruff.lint] +select = [ + # pycodestyle + "E", + # Pyflakes + "F", + # pyupgrade + "UP", + # flake8-bugbear + "B", + # flake8-simplify + "SIM", + # isort + "I", + # Unused arguments + "ARG", +] diff --git a/requirements-dev.lock b/requirements-dev.lock new file mode 100644 index 0000000..02a0f3e --- /dev/null +++ b/requirements-dev.lock @@ -0,0 +1,311 @@ +# generated by rye +# use `rye lock` or `rye sync` to update this lockfile +# +# last locked with the following flags: +# pre: false +# features: [] +# all-features: false +# with-sources: false +# generate-hashes: false +# universal: false + +-e file:. +anndata==0.10.9 + # via doubletdetection + # via parafac2 + # via scanpy + # via spatialpf2 +annoy==1.17.3 + # via pacmap +array-api-compat==1.8 + # via anndata +asttokens==2.4.1 + # via stack-data +certifi==2024.8.30 + # via requests +charset-normalizer==3.3.2 + # via requests +click==8.1.7 + # via dask +cloudpickle==3.0.0 + # via dask +colorcet==3.1.0 + # via datashader +comm==0.2.2 + # via ipywidgets +contourpy==1.3.0 + # via matplotlib +coverage==7.6.1 + # via pytest-cov +cupy-cuda12x==13.3.0 + # via parafac2 +cycler==0.12.1 + # via matplotlib +dask==2024.9.0 + # via dask-expr + # via datashader + # via spatialpf2 +dask-expr==1.1.14 + # via dask +datashader==0.16.3 + # via spatialpf2 +decorator==5.1.1 + # via ipython +doubletdetection==4.2 + # via spatialpf2 +executing==2.1.0 + # via stack-data +fastrlock==0.8.2 + # via cupy-cuda12x +fonttools==4.53.1 + # via matplotlib +fsspec==2024.9.0 + # via dask +h5py==3.11.0 + # via anndata + # via scanpy +idna==3.10 + # via requests +igraph==0.11.6 + # via leidenalg + # via louvain +importlib-metadata==8.5.0 + # via dask +iniconfig==2.0.0 + # via pytest +ipython==8.27.0 + # via ipywidgets +ipywidgets==8.1.5 + # via doubletdetection +jedi==0.19.1 + # via ipython +joblib==1.4.2 + # via pynndescent + # via scanpy + # via scikit-learn +jupyterlab-widgets==3.0.13 + # via ipywidgets +kiwisolver==1.4.7 + # via matplotlib +legacy-api-wrap==1.4 + # via scanpy +leidenalg==0.10.2 + # via doubletdetection + # via phenograph +llvmlite==0.43.0 + # via numba + # via pynndescent +locket==1.0.0 + # via partd +louvain==0.8.2 + # via doubletdetection +matplotlib==3.9.2 + # via doubletdetection + # via scanpy + # via seaborn + # via spatialpf2 + # via tlviz +matplotlib-inline==0.1.7 + # via ipython +multipledispatch==1.0.0 + # via datashader +natsort==8.4.0 + # via anndata + # via scanpy +networkx==3.3 + # via scanpy + # via spatialpf2 +nodeenv==1.9.1 + # via pyright +numba==0.60.0 + # via datashader + # via pacmap + # via pynndescent + # via scanpy + # via umap-learn +numpy==1.26.4 + # via anndata + # via contourpy + # via cupy-cuda12x + # via dask + # via datashader + # via doubletdetection + # via h5py + # via matplotlib + # via numba + # via pacmap + # via pandas + # via parafac2 + # via patsy + # via phenograph + # via pyarrow + # via scanpy + # via scikit-learn + # via scipy + # via seaborn + # via spatialpf2 + # via statsmodels + # via tensorly + # via tlviz + # via umap-learn + # via xarray +packaging==24.1 + # via anndata + # via dask + # via datashader + # via matplotlib + # via pytest + # via scanpy + # via statsmodels + # via xarray +pacmap==0.7.3 + # via parafac2 + # via spatialpf2 +pandas==2.2.2 + # via anndata + # via dask + # via dask-expr + # via datashader + # via doubletdetection + # via scanpy + # via seaborn + # via spatialpf2 + # via statsmodels + # via tlviz + # via xarray +parafac2 @ git+https://github.com/meyer-lab/parafac2.git@793f8ad06791ffcc698105d80941774741722574 + # via spatialpf2 +param==2.1.1 + # via datashader + # via pyct +parso==0.8.4 + # via jedi +partd==1.4.2 + # via dask +patsy==0.5.6 + # via scanpy + # via statsmodels +pexpect==4.9.0 + # via ipython +phenograph==1.5.7 + # via doubletdetection +pillow==10.4.0 + # via datashader + # via matplotlib +pluggy==1.5.0 + # via pytest +prompt-toolkit==3.0.47 + # via ipython +psutil==6.0.0 + # via phenograph +ptyprocess==0.7.0 + # via pexpect +pure-eval==0.2.3 + # via stack-data +pyarrow==17.0.0 + # via dask-expr +pyct==0.5.0 + # via datashader +pygments==2.18.0 + # via ipython +pynndescent==0.5.13 + # via scanpy + # via umap-learn +pyparsing==3.1.4 + # via matplotlib +pyright==1.1.380 +pytest==8.3.3 + # via pytest-cov +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 + # via matplotlib + # via pandas +pytz==2024.2 + # via pandas +pyyaml==6.0.2 + # via dask +requests==2.32.3 + # via datashader + # via tlviz +scanpy==1.10.2 + # via doubletdetection + # via spatialpf2 +scikit-learn==1.5.2 + # via pacmap + # via parafac2 + # via phenograph + # via pynndescent + # via scanpy + # via spatialpf2 + # via umap-learn +scipy==1.14.1 + # via anndata + # via datashader + # via doubletdetection + # via parafac2 + # via phenograph + # via pynndescent + # via scanpy + # via scikit-learn + # via statsmodels + # via tensorly + # via tlviz + # via umap-learn +seaborn==0.13.2 + # via scanpy +session-info==1.0.0 + # via scanpy +setuptools==75.1.0 + # via phenograph + # via spatialpf2 +six==1.16.0 + # via asttokens + # via patsy + # via python-dateutil +stack-data==0.6.3 + # via ipython +statsmodels==0.14.3 + # via scanpy + # via tlviz +stdlib-list==0.10.0 + # via session-info +tensorly==0.8.1 + # via parafac2 + # via spatialpf2 +texttable==1.7.0 + # via igraph +threadpoolctl==3.5.0 + # via scikit-learn +tlviz==0.1.1 + # via spatialpf2 +toolz==0.12.1 + # via dask + # via datashader + # via partd +tqdm==4.66.5 + # via doubletdetection + # via parafac2 + # via scanpy + # via umap-learn +traitlets==5.14.3 + # via comm + # via ipython + # via ipywidgets + # via matplotlib-inline +typing-extensions==4.12.2 + # via ipython +tzdata==2024.1 + # via pandas +umap-learn==0.5.6 + # via scanpy +urllib3==2.2.3 + # via requests +wcwidth==0.2.13 + # via prompt-toolkit +widgetsnbextension==4.0.13 + # via ipywidgets +xarray==2024.9.0 + # via datashader + # via tlviz +zipp==3.20.2 + # via importlib-metadata diff --git a/requirements.lock b/requirements.lock new file mode 100644 index 0000000..a70d000 --- /dev/null +++ b/requirements.lock @@ -0,0 +1,298 @@ +# generated by rye +# use `rye lock` or `rye sync` to update this lockfile +# +# last locked with the following flags: +# pre: false +# features: [] +# all-features: false +# with-sources: false +# generate-hashes: false +# universal: false + +-e file:. +anndata==0.10.9 + # via doubletdetection + # via parafac2 + # via scanpy + # via spatialpf2 +annoy==1.17.3 + # via pacmap +array-api-compat==1.8 + # via anndata +asttokens==2.4.1 + # via stack-data +certifi==2024.8.30 + # via requests +charset-normalizer==3.3.2 + # via requests +click==8.1.7 + # via dask +cloudpickle==3.0.0 + # via dask +colorcet==3.1.0 + # via datashader +comm==0.2.2 + # via ipywidgets +contourpy==1.3.0 + # via matplotlib +cupy-cuda12x==13.3.0 + # via parafac2 +cycler==0.12.1 + # via matplotlib +dask==2024.9.0 + # via dask-expr + # via datashader + # via spatialpf2 +dask-expr==1.1.14 + # via dask +datashader==0.16.3 + # via spatialpf2 +decorator==5.1.1 + # via ipython +doubletdetection==4.2 + # via spatialpf2 +executing==2.1.0 + # via stack-data +fastrlock==0.8.2 + # via cupy-cuda12x +fonttools==4.53.1 + # via matplotlib +fsspec==2024.9.0 + # via dask +h5py==3.11.0 + # via anndata + # via scanpy +idna==3.10 + # via requests +igraph==0.11.6 + # via leidenalg + # via louvain +importlib-metadata==8.5.0 + # via dask +ipython==8.27.0 + # via ipywidgets +ipywidgets==8.1.5 + # via doubletdetection +jedi==0.19.1 + # via ipython +joblib==1.4.2 + # via pynndescent + # via scanpy + # via scikit-learn +jupyterlab-widgets==3.0.13 + # via ipywidgets +kiwisolver==1.4.7 + # via matplotlib +legacy-api-wrap==1.4 + # via scanpy +leidenalg==0.10.2 + # via doubletdetection + # via phenograph +llvmlite==0.43.0 + # via numba + # via pynndescent +locket==1.0.0 + # via partd +louvain==0.8.2 + # via doubletdetection +matplotlib==3.9.2 + # via doubletdetection + # via scanpy + # via seaborn + # via spatialpf2 + # via tlviz +matplotlib-inline==0.1.7 + # via ipython +multipledispatch==1.0.0 + # via datashader +natsort==8.4.0 + # via anndata + # via scanpy +networkx==3.3 + # via scanpy + # via spatialpf2 +numba==0.60.0 + # via datashader + # via pacmap + # via pynndescent + # via scanpy + # via umap-learn +numpy==1.26.4 + # via anndata + # via contourpy + # via cupy-cuda12x + # via dask + # via datashader + # via doubletdetection + # via h5py + # via matplotlib + # via numba + # via pacmap + # via pandas + # via parafac2 + # via patsy + # via phenograph + # via pyarrow + # via scanpy + # via scikit-learn + # via scipy + # via seaborn + # via spatialpf2 + # via statsmodels + # via tensorly + # via tlviz + # via umap-learn + # via xarray +packaging==24.1 + # via anndata + # via dask + # via datashader + # via matplotlib + # via scanpy + # via statsmodels + # via xarray +pacmap==0.7.3 + # via parafac2 + # via spatialpf2 +pandas==2.2.2 + # via anndata + # via dask + # via dask-expr + # via datashader + # via doubletdetection + # via scanpy + # via seaborn + # via spatialpf2 + # via statsmodels + # via tlviz + # via xarray +parafac2 @ git+https://github.com/meyer-lab/parafac2.git@793f8ad06791ffcc698105d80941774741722574 + # via spatialpf2 +param==2.1.1 + # via datashader + # via pyct +parso==0.8.4 + # via jedi +partd==1.4.2 + # via dask +patsy==0.5.6 + # via scanpy + # via statsmodels +pexpect==4.9.0 + # via ipython +phenograph==1.5.7 + # via doubletdetection +pillow==10.4.0 + # via datashader + # via matplotlib +prompt-toolkit==3.0.47 + # via ipython +psutil==6.0.0 + # via phenograph +ptyprocess==0.7.0 + # via pexpect +pure-eval==0.2.3 + # via stack-data +pyarrow==17.0.0 + # via dask-expr +pyct==0.5.0 + # via datashader +pygments==2.18.0 + # via ipython +pynndescent==0.5.13 + # via scanpy + # via umap-learn +pyparsing==3.1.4 + # via matplotlib +python-dateutil==2.9.0.post0 + # via matplotlib + # via pandas +pytz==2024.2 + # via pandas +pyyaml==6.0.2 + # via dask +requests==2.32.3 + # via datashader + # via tlviz +scanpy==1.10.2 + # via doubletdetection + # via spatialpf2 +scikit-learn==1.5.2 + # via pacmap + # via parafac2 + # via phenograph + # via pynndescent + # via scanpy + # via spatialpf2 + # via umap-learn +scipy==1.14.1 + # via anndata + # via datashader + # via doubletdetection + # via parafac2 + # via phenograph + # via pynndescent + # via scanpy + # via scikit-learn + # via statsmodels + # via tensorly + # via tlviz + # via umap-learn +seaborn==0.13.2 + # via scanpy +session-info==1.0.0 + # via scanpy +setuptools==75.1.0 + # via phenograph + # via spatialpf2 +six==1.16.0 + # via asttokens + # via patsy + # via python-dateutil +stack-data==0.6.3 + # via ipython +statsmodels==0.14.3 + # via scanpy + # via tlviz +stdlib-list==0.10.0 + # via session-info +tensorly==0.8.1 + # via parafac2 + # via spatialpf2 +texttable==1.7.0 + # via igraph +threadpoolctl==3.5.0 + # via scikit-learn +tlviz==0.1.1 + # via spatialpf2 +toolz==0.12.1 + # via dask + # via datashader + # via partd +tqdm==4.66.5 + # via doubletdetection + # via parafac2 + # via scanpy + # via umap-learn +traitlets==5.14.3 + # via comm + # via ipython + # via ipywidgets + # via matplotlib-inline +typing-extensions==4.12.2 + # via ipython +tzdata==2024.1 + # via pandas +umap-learn==0.5.6 + # via scanpy +urllib3==2.2.3 + # via requests +wcwidth==0.2.13 + # via prompt-toolkit +widgetsnbextension==4.0.13 + # via ipywidgets +xarray==2024.9.0 + # via datashader + # via tlviz +zipp==3.20.2 + # via importlib-metadata