diff --git a/poetry.lock b/poetry.lock index 8d63cda..232ba89 100644 --- a/poetry.lock +++ b/poetry.lock @@ -15,9 +15,9 @@ pandas = ">=1.1.1" scipy = ">1.4" [package.extras] -dev = ["setuptools-scm", "black (>=20.8b1)", "docutils"] -doc = ["sphinx (>=4.1,<4.2)", "sphinx-rtd-theme", "sphinx-autodoc-typehints (>=1.11.0)", "sphinx-issues", "nbsphinx", "scanpydoc (>=0.7.3)", "typing-extensions"] -test = ["loompy (>=3.0.5)", "pytest (>=6.0)", "pytest-cov (>=2.10)", "zarr", "matplotlib", "sklearn", "openpyxl", "joblib", "boltons", "scanpy", "dask"] +dev = ["black (>=20.8b1)", "docutils", "setuptools_scm"] +doc = ["nbsphinx", "scanpydoc (>=0.7.3)", "sphinx (>=4.1,<4.2)", "sphinx-autodoc-typehints (>=1.11.0)", "sphinx-rtd-theme", "sphinx_issues", "typing_extensions"] +test = ["boltons", "dask[array]", "joblib", "loompy (>=3.0.5)", "matplotlib", "openpyxl", "pytest (>=6.0)", "pytest-cov (>=2.10)", "scanpy", "sklearn", "zarr"] [[package]] name = "annoy" @@ -52,9 +52,9 @@ optional = false python-versions = ">=3.7" [package.extras] -all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"] +all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"] graphite = ["lz4 (>=1.7.4.2)"] -interpolatable = ["scipy", "munkres"] +interpolatable = ["munkres", "scipy"] lxml = ["lxml (>=4.0,<5)"] pathops = ["skia-pathops (>=0.5.0)"] plot = ["matplotlib"] @@ -62,7 +62,7 @@ symfont = ["sympy"] type1 = ["xattr"] ufo = ["fs (>=2.2.0,<3)"] unicode = ["unicodedata2 (>=14.0.0)"] -woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"] +woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] [[package]] name = "forceatlas2" @@ -97,7 +97,7 @@ texttable = ">=1.6.2" [package.extras] doc = ["Sphinx (>=4.2.0)", "sphinxbootstrap4theme (>=0.6.0)"] plotting = ["cairocffi (>=1.2.0)"] -test = ["networkx (>=2.5)", "pytest (>=6.2.5)", "numpy (>=1.19.0)", "pandas (>=1.1.0)", "scipy (>=1.5.0)"] +test = ["networkx (>=2.5)", "numpy (>=1.19.0)", "pandas (>=1.1.0)", "pytest (>=6.2.5)", "scipy (>=1.5.0)"] [[package]] name = "joblib" @@ -174,11 +174,11 @@ optional = false python-versions = ">=3.7" [package.extras] -default = ["numpy (>=1.19)", "scipy (>=1.5,!=1.6.1)", "matplotlib (>=3.3)", "pandas (>=1.1)"] +default = ["matplotlib (>=3.3)", "numpy (>=1.19)", "pandas (>=1.1)", "scipy (>=1.5,!=1.6.1)"] developer = ["black (==21.5b1)", "pre-commit (>=2.12)"] -doc = ["sphinx (>=4.0,<5.0)", "pydata-sphinx-theme (>=0.6,<1.0)", "sphinx-gallery (>=0.9,<1.0)", "numpydoc (>=1.1)", "pillow (>=8.2)", "nb2plots (>=0.6)", "texext (>=0.6.6)"] -extra = ["lxml (>=4.5)", "pygraphviz (>=1.7)", "pydot (>=1.4.1)"] -test = ["pytest (>=6.2)", "pytest-cov (>=2.12)", "codecov (>=2.1)"] +doc = ["nb2plots (>=0.6)", "numpydoc (>=1.1)", "pillow (>=8.2)", "pydata-sphinx-theme (>=0.6,<1.0)", "sphinx (>=4.0,<5.0)", "sphinx-gallery (>=0.9,<1.0)", "texext (>=0.6.6)"] +extra = ["lxml (>=4.5)", "pydot (>=1.4.1)", "pygraphviz (>=1.7)"] +test = ["codecov (>=2.1)", "pytest (>=6.2)", "pytest-cov (>=2.12)"] [[package]] name = "numba" @@ -191,6 +191,7 @@ python-versions = ">=3.7,<3.11" [package.dependencies] llvmlite = ">=0.38.0rc1,<0.39" numpy = ">=1.18,<1.23" +setuptools = "*" [[package]] name = "numexpr" @@ -214,11 +215,11 @@ python-versions = ">=3.8" [[package]] name = "openTSNE" -version = "0.6.2" +version = "1.0.1" description = "Extensible, parallel implementations of t-SNE" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" develop = false [package.dependencies] @@ -233,8 +234,8 @@ pynndescent = ["pynndescent (>=0.5.0,<0.6.0)"] [package.source] type = "git" url = "https://github.com/pavlin-policar/openTSNE" -reference = "master" -resolved_reference = "30b07f1b60129fc74bb937eb4632c6d424f49c4d" +reference = "HEAD" +resolved_reference = "8c62e662d974a563842102b59be38bfb7cb7b0bc" [[package]] name = "packaging" @@ -337,7 +338,7 @@ optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [package.extras] -test = ["ipaddress", "mock", "unittest2", "enum34", "pywin32", "wmi"] +test = ["enum34", "ipaddress", "mock", "pywin32", "unittest2", "wmi"] [[package]] name = "pynndescent" @@ -403,11 +404,11 @@ python-versions = "*" [[package]] name = "s2a" -version = "0.3.4" +version = "0.3.5" description = "glue to link Seurat to anndata objects" category = "main" optional = false -python-versions = "^3.8,<3.10" +python-versions = ">=3.8.3,<3.10" develop = false [package.dependencies] @@ -419,8 +420,8 @@ scipy = "^1.7" [package.source] type = "git" url = "https://github.com/milescsmith/s2a" -reference = "0.3.4" -resolved_reference = "a71326bc860a5799390416b6ca2f8b4ec917b7ab" +reference = "eb38ae3aba23bdebffd1f13d1282bfed5d2f64af" +resolved_reference = "eb38ae3aba23bdebffd1f13d1282bfed5d2f64af" [[package]] name = "scanpy" @@ -453,17 +454,17 @@ umap-learn = ">=0.3.10" [package.extras] bbknn = ["bbknn"] -dev = ["setuptools-scm", "pytoml", "black (>=20.8b1)", "docutils"] -doc = ["sphinx (>=3.2,<4.1.0)", "sphinx-rtd-theme (>=0.3.1)", "sphinx-autodoc-typehints", "scanpydoc (==0.7.2)", "typing-extensions", "python-igraph"] +dev = ["black (>=20.8b1)", "docutils", "pytoml", "setuptools_scm"] +doc = ["python-igraph", "scanpydoc (==0.7.2)", "sphinx (>=3.2,<4.1.0)", "sphinx-autodoc-typehints", "sphinx-rtd-theme (>=0.3.1)", "typing_extensions"] harmony = ["harmonypy"] -leiden = ["python-igraph", "leidenalg"] -louvain = ["python-igraph", "louvain (>=0.6,!=0.6.2)"] +leiden = ["leidenalg", "python-igraph"] +louvain = ["louvain (>=0.6,!=0.6.2)", "python-igraph"] magic = ["magic-impute (>=2.0)"] -rapids = ["cudf (>=0.9)", "cuml (>=0.9)", "cugraph (>=0.9)"] +rapids = ["cudf (>=0.9)", "cugraph (>=0.9)", "cuml (>=0.9)"] scanorama = ["scanorama"] scrublet = ["scrublet"] skmisc = ["scikit-misc (>=0.1.3)"] -test = ["pytest (>=4.4)", "pytest-nunit", "dask[array] (!=2.17.0)", "fsspec", "zappy", "zarr", "profimp", "flit-core"] +test = ["dask[array] (!=2.17.0)", "flit_core", "fsspec", "profimp", "pytest (>=4.4)", "pytest-nunit", "zappy", "zarr"] [[package]] name = "scikit-learn" @@ -480,10 +481,10 @@ scipy = ">=1.1.0" threadpoolctl = ">=2.0.0" [package.extras] -benchmark = ["matplotlib (>=2.2.3)", "pandas (>=0.25.0)", "memory-profiler (>=0.57.0)"] -docs = ["matplotlib (>=2.2.3)", "scikit-image (>=0.14.5)", "pandas (>=0.25.0)", "seaborn (>=0.9.0)", "memory-profiler (>=0.57.0)", "sphinx (>=4.0.1)", "sphinx-gallery (>=0.7.0)", "numpydoc (>=1.0.0)", "Pillow (>=7.1.2)", "sphinx-prompt (>=1.3.0)", "sphinxext-opengraph (>=0.4.2)"] -examples = ["matplotlib (>=2.2.3)", "scikit-image (>=0.14.5)", "pandas (>=0.25.0)", "seaborn (>=0.9.0)"] -tests = ["matplotlib (>=2.2.3)", "scikit-image (>=0.14.5)", "pandas (>=0.25.0)", "pytest (>=5.0.1)", "pytest-cov (>=2.9.0)", "flake8 (>=3.8.2)", "black (>=21.6b0)", "mypy (>=0.770)", "pyamg (>=4.0.0)"] +benchmark = ["matplotlib (>=2.2.3)", "memory-profiler (>=0.57.0)", "pandas (>=0.25.0)"] +docs = ["Pillow (>=7.1.2)", "matplotlib (>=2.2.3)", "memory-profiler (>=0.57.0)", "numpydoc (>=1.0.0)", "pandas (>=0.25.0)", "scikit-image (>=0.14.5)", "seaborn (>=0.9.0)", "sphinx (>=4.0.1)", "sphinx-gallery (>=0.7.0)", "sphinx-prompt (>=1.3.0)", "sphinxext-opengraph (>=0.4.2)"] +examples = ["matplotlib (>=2.2.3)", "pandas (>=0.25.0)", "scikit-image (>=0.14.5)", "seaborn (>=0.9.0)"] +tests = ["black (>=21.6b0)", "flake8 (>=3.8.2)", "matplotlib (>=2.2.3)", "mypy (>=0.770)", "pandas (>=0.25.0)", "pyamg (>=4.0.0)", "pytest (>=5.0.1)", "pytest-cov (>=2.9.0)", "scikit-image (>=0.14.5)"] [[package]] name = "scipy" @@ -510,6 +511,19 @@ numpy = ">=1.15" pandas = ">=0.23" scipy = ">=1.0" +[[package]] +name = "setuptools" +version = "69.0.3" +description = "Easily download, build, install, upgrade, and uninstall Python packages" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"] +testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] +testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] + [[package]] name = "setuptools-scm" version = "6.4.2" @@ -520,6 +534,7 @@ python-versions = ">=3.6" [package.dependencies] packaging = ">=20.0" +setuptools = "*" tomli = ">=1.0.0" [package.extras] @@ -562,7 +577,7 @@ scipy = ">=1.3" [package.extras] build = ["cython (>=0.29.22)"] develop = ["cython (>=0.29.22)"] -docs = ["sphinx", "nbconvert", "jupyter-client", "ipykernel", "matplotlib", "nbformat", "numpydoc", "pandas-datareader"] +docs = ["ipykernel", "jupyter_client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"] [[package]] name = "stdlib-list" @@ -589,7 +604,7 @@ numpy = ">=1.19.0" packaging = "*" [package.extras] -doc = ["sphinx (>=1.1)", "sphinx-rtd-theme", "numpydoc", "ipython"] +doc = ["ipython", "numpydoc", "sphinx (>=1.1)", "sphinx-rtd-theme"] [[package]] name = "texttable" @@ -648,13 +663,13 @@ scipy = ">=1.0" tqdm = "*" [package.extras] -parametric_umap = ["tensorflow (>=2.1)", "tensorflow-probability (>=0.10)"] -plot = ["pandas", "matplotlib", "datashader", "bokeh", "holoviews", "colorcet", "seaborn", "scikit-image"] +parametric-umap = ["tensorflow (>=2.1)", "tensorflow-probability (>=0.10)"] +plot = ["bokeh", "colorcet", "datashader", "holoviews", "matplotlib", "pandas", "scikit-image", "seaborn"] [metadata] lock-version = "1.1" python-versions = ">3.8.3,<3.10" -content-hash = "051e567ef07f35454ed42e3b1900d62ba9255ef1965144b09ede1c32f25865c5" +content-hash = "0a8c64e95ccb1ae6a161d6e4baa0939471803197da60c88a59d5a5901da0890d" [metadata.files] anndata = [ @@ -1173,6 +1188,10 @@ seaborn = [ {file = "seaborn-0.11.2-py3-none-any.whl", hash = "sha256:85a6baa9b55f81a0623abddc4a26b334653ff4c6b18c418361de19dbba0ef283"}, {file = "seaborn-0.11.2.tar.gz", hash = "sha256:cf45e9286d40826864be0e3c066f98536982baf701a7caa386511792d61ff4f6"}, ] +setuptools = [ + {file = "setuptools-69.0.3-py3-none-any.whl", hash = "sha256:385eb4edd9c9d5c17540511303e39a147ce2fc04bc55289c322b9e5904fe2c05"}, + {file = "setuptools-69.0.3.tar.gz", hash = "sha256:be1af57fc409f93647f2e8e4573a142ed38724b8cdd389706a867bb4efcf1e78"}, +] setuptools-scm = [ {file = "setuptools_scm-6.4.2-py3-none-any.whl", hash = "sha256:acea13255093849de7ccb11af9e1fb8bde7067783450cee9ef7a93139bddf6d4"}, {file = "setuptools_scm-6.4.2.tar.gz", hash = "sha256:6833ac65c6ed9711a4d5d2266f8024cfa07c533a0e55f4c12f6eff280a5a9e30"}, diff --git a/pyproject.toml b/pyproject.toml index ae189c7..22ba633 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ opentsne = {git = "https://github.com/pavlin-policar/openTSNE"} pacmap = "^0.5.0" PhenoGraph = {git = "https://github.com/milescsmith/PhenoGraph", rev = "1.6.1"} scanpy = "^1.8" -s2a = {git = "https://github.com/milescsmith/s2a", rev = "0.3.4"} +s2a = {git = "https://github.com/milescsmith/s2a", rev = "eb38ae3aba23bdebffd1f13d1282bfed5d2f64af"} [tool.poetry.dev-dependencies]