diff --git a/poetry.lock b/poetry.lock index 59535a35e..a4b3abfc5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -157,6 +157,7 @@ files = [ [package.dependencies] aiosignal = ">=1.1.2" +async-timeout = {version = ">=4.0,<5.0", markers = "python_version < \"3.11\""} attrs = ">=17.3.0" frozenlist = ">=1.1.1" multidict = ">=4.5,<7.0" @@ -220,30 +221,6 @@ typing-extensions = ">=4" [package.extras] tz = ["python-dateutil"] -[[package]] -name = "altair" -version = "5.3.0" -description = "Vega-Altair: A declarative statistical visualization library for Python." -optional = false -python-versions = ">=3.8" -files = [ - {file = "altair-5.3.0-py3-none-any.whl", hash = "sha256:7084a1dab4d83c5e7e5246b92dc1b4451a6c68fd057f3716ee9d315c8980e59a"}, - {file = "altair-5.3.0.tar.gz", hash = "sha256:5a268b1a0983b23d8f9129f819f956174aa7aea2719ed55a52eba9979b9f6675"}, -] - -[package.dependencies] -jinja2 = "*" -jsonschema = ">=3.0" -numpy = "*" -packaging = "*" -pandas = ">=0.25" -toolz = "*" - 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"sha256:20c567a7fc0c9d8e405fda2e9bce6eb3656e350f2bd8921a4b660dd53f544f10"}, ] [[package]] @@ -9368,5 +9337,5 @@ workflows = ["dataclasses-json", "dulwich", "flytekit", "google-api-python-clien [metadata] lock-version = "2.0" -python-versions = ">=3.11, <3.13" -content-hash = "6515b417ac411b998d0da76e7e48dd3cfe992e991736061e2db358568d373bd5" +python-versions = ">=3.10, <3.12" +content-hash = "d8bc392bee7cf231ab3c52dac7804d8c70278ec125a4df7d95db5d29b02190a6" diff --git a/pyproject.toml b/pyproject.toml index 2eb53ff42..74eef80c3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,40 +1,35 @@ [tool.poetry] name = "pyrovelocity" -version = "0.3.0" +version = "0.2.0" packages = [{ include = "pyrovelocity", from = "src" }] description = "A multivariate RNA Velocity model to estimate future cell states with uncertainty using probabilistic modeling with pyro." authors = ["pyrovelocity team"] license = "AGPL-3.0-only" readme = "README.md" -homepage = "https://docs.pyrovelocity.net" +homepage = "https://github.com/pinellolab/pyrovelocity" repository = "https://github.com/pinellolab/pyrovelocity" -documentation = "https://docs.pyrovelocity.net" +documentation = "https://pyrovelocity.readthedocs.io" classifiers = [ - "Development Status :: 3 - Alpha", + "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", "License :: OSI Approved :: GNU Affero General Public License v3", "Natural Language :: English", "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", ] [tool.poetry.urls] Changelog = "https://github.com/pinellolab/pyrovelocity/releases" [tool.poetry.dependencies] -python = ">=3.11, <3.13" +python = ">=3.10, <3.12" adjusttext = ">=1.1.1" -altair = ">=5.3.0" anndata = ">=0.10.5" anyio = ">=4.3.0" appdirs = ">=1.4.4" -# 0.18.0 adds a dependency on dm-tree = ">=0.1.8" -# whose build is broken and wheel attempts to -# dlopen an undeclared or broken shared library -# on Darwin arviz = ">=0.17.1" -astropy = ">=6.1.2" +astropy = ">=5.2.2" beartype = ">=0.18.5" # pinning chex>=0.1.82 may be required to avoid # dm-tree = ">=0.1.8" @@ -46,23 +41,27 @@ colorlog = ">=6.7.0" daft = ">=0.1.2" diffrax = ">=0.5.0" diskcache = ">=5.6.1" -duckdb = ">=1.0.0" +duckdb = ">=0.10.1" einops = ">=0.7.0" # requires python 3.11 -expression = ">=5.0.2" +# expression = ">=4.3.0" flax = ">=0.8.1" frozenlist = { version = ">=1.1.1", python = "<3.12" } # frozenlist = [ # { version = ">=1.1.1", python = "<3.12" }, # { version = ">=1.4.1", python = ">=3.12" }, # ] -fsspec = ">=2024.3.0" -greenlet = ">=3.0.3" httpx = ">=0.27.0" h5py = ">=3.9.0" -ibis-framework = { extras = ["duckdb"], version = ">=9.2.0" } +ibis-framework = { extras = ["duckdb"], version = ">=8.0.0" } +# jax "<0.4.27" required +# when using conda-lock +# due to https://github.com/google/jax/issues/21116 +# fixed in jax 0.4.29 but not available on conda-forge jax = ">=0.4.23" jaxlib = ">=0.4.23" +# jax = ">=0.4.23,<0.4.27" +# jaxlib = ">=0.4.23,<0.4.27" jaxtyping = ">=0.2.25" leidenalg = ">=0.9.1" llvmlite = { version = ">=0.41.1", python = "<3.12" } @@ -70,47 +69,46 @@ llvmlite = { version = ">=0.41.1", python = "<3.12" } # { version = ">=0.41.1", python = "<3.12" }, # { version = ">=0.42.0", python = ">=3.12" }, # ] -# Temporarily pin yanked matplotlib 3.9.1 -# https://github.com/matplotlib/matplotlib/issues/28551 -# for usage with pip installs -matplotlib = ">=3.9.1" +matplotlib = ">=3.8.4" mlflow = ">=2.13.0" numpyro = ">=0.15.0" pandas = ">=2.0.0" plumbum = ">=1.8.2" polars = ">=0.20.17" pyarrow = ">=14.0.2" -pydantic = ">=2.8.0" pyro-ppl = ">=1.9.1" lightning = ">=2.0.0" pytorch-lightning = ">=2.0.0" pyyaml = ">=6.0.1" -returns = ">=0.23.0" -rich = ">=13.7.1" +returns = ">=0.22.0" +rich = ">=12.6.0" scanpy = ">=1.10.1" scikit-learn = ">=1.3.1" -scipy = ">=1.10.1,<1.14.0" +# scikit-learn requires an upper bound of +# 1.2.0 when using conda-lock due to inconsistent +# dependency bounds on conda-forge and pypi +# scikit-learn = "<1.2.0" +scipy = ">=1.10.1" scvelo = ">=0.3.2" -# scvelo = { git = "https://github.com/theislab/scvelo.git", rev = "3fbce6ff6d644a44911091f498efa0c69f6b85b0" } +# scvelo = { version = ">=0.3.1", python = "<3.12", source = "pypi" } +# scvelo = [ +# { version = ">=0.3.1", python = "<3.12" }, +# # requires scikit-learn <1.2.0, which is not compatible with python 3.12 +# { version = ">0.3.1", python = ">=3.12" }, +# ] scvi-tools = ">=1.1.1" seaborn = ">=0.13.2" -sparse = ">=0.15.4" -statsmodels = ">=0.14.2" sympy = ">=1.12" termcolor = ">=2.2.0" -tiledb = ">=0.31.1" torch = { version = ">=2.1.2", python = "<3.12" } # torch = [ # { version = ">=2.1.2", python = "<3.12" }, # { version = ">=2.2.0", python = ">=3.12" }, # ] torchmetrics = ">=1.2.1" -trio = ">=0.26.0" -validators = ">=0.33.0" -vegafusion = ">=1.6.9" -vegafusion-python-embed = ">=1.6.9" -vl-convert-python = ">=1.6.0" -zstandard = ">=0.23.0" +trio = ">=0.25.0" +validators = ">=0.22.0" +zstandard = ">=0.21.0" # removed from library at # cospar = { version = ">=0.1.9", source = "pypi" } # scikit-misc = ">=0.1.4" @@ -130,7 +128,7 @@ dulwich = { version = ">=0.21.7", optional = true } # flake8-bugbear = { version = ">=21.9.2", optional = true } # flake8-docstrings = { version = ">=1.6.0", optional = true } # flake8-rst-docstrings = { version = ">=0.2.5", optional = true } -flytekit = { version = ">=1.13.3", optional = true } +flytekit = { version = ">=1.12.0", optional = true } furo = { version = ">=2023.5.20", optional = true } google-api-python-client = { version = ">=2.79.0", optional = true } hydra-core = { version = ">=1.3.2", optional = true } @@ -253,7 +251,7 @@ optional = true [tool.poetry.group.workflows.dependencies] dataclasses-json = ">=0.5.7" dulwich = ">=0.21.7" -flytekit = ">=1.13.0" +flytekit = ">=1.10.7" google-api-python-client = ">=2.79.0" google-cloud-storage = ">=2.14.0" hydra-core = ">=1.3.2" @@ -361,21 +359,8 @@ log_level = "INFO" virtual_package_spec = "conda/virtual-packages.yml" [tool.conda-lock.dependencies] -python = ">=3.11, <3.12" +python = ">=3.10, <3.11" pip = ">=23.2" -fmt = ">=10.2.1,<11.0" -# jax "<0.4.27" required -# when using conda-lock -# due to https://github.com/google/jax/issues/21116 -# fixed in jax 0.4.29 but not available on conda-forge -jax = ">=0.4.23,<0.4.27" -jaxlib = ">=0.4.23,<0.4.27" -pydantic = ">=2.1.1" -# scikit-learn requires an upper bound of -# 1.2.0 when using conda-lock due to inconsistent -# dependency bounds on conda-forge and pypi -# scikit-learn = "<1.2.0" -scikit-learn = "<1.2.0" # poethepoet = { source = "pypi" } [tool.poe.tasks.conda-lock] @@ -420,25 +405,17 @@ pyrovelocity-notebooks = "pyrovelocity.workflows.notebooks:cli" # $ pytest > test.log.py [tool.pytest.ini_options] log_level = "INFO" -# We exclude markers associated with slow tests by default -# but run them in CI with the make target `test-cov-xml` -# which overrides this behavior. addopts = """ --m "not slow and not pyensembl" +-m "not pyensembl" -rA --xdoctest --disable-warnings --cov=src/pyrovelocity/ --cov-report=term-missing ---durations=0 """ asyncio_mode = "strict" norecursedirs = ["bazel-*", ".direnv", "reproducibility", "scripts"] -markers = [ - "pyensembl: Tests that require pyensembl to run.", - "slow: Tests that are slow and should be run separately.", - "integration: Tests that use many library components.", -] +markers = ["pyensembl: Tests that require pyensembl to run."] [tool.coverage.paths] source = ["src/pyrovelocity"] @@ -579,7 +556,7 @@ force_single_line = true lines_after_imports = 2 [tool.mypy] -python_version = ">=3.11" +python_version = ">=3.10" [[tool.mypy.overrides]] module = [""]