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[tool .poetry ]
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name = " pyrovelocity"
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- version = " 0.4 .0"
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+ version = " 0.3 .0"
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packages = [{ include = " pyrovelocity" , from = " src" }]
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description = " A multivariate RNA Velocity model to estimate future cell states with uncertainty using probabilistic modeling with pyro."
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authors = [" pyrovelocity team" ]
@@ -45,7 +45,6 @@ click = ">=8.1.7"
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colorlog = " >=6.7.0"
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daft = " >=0.1.2"
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diffrax = " >=0.5.0"
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- dill = " >=0.3.8"
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diskcache = " >=5.6.1"
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duckdb = " >=1.0.0"
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einops = " >=0.7.0"
@@ -61,7 +60,6 @@ fsspec = ">=2024.3.0"
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greenlet = " >=3.0.3"
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httpx = " >=0.27.0"
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h5py = " >=3.9.0"
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- # hdf5plugin = ">=4.4.0"
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ibis-framework = { extras = [" duckdb" ], version = " >=9.2.0" }
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jax = " >=0.4.23"
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jaxlib = " >=0.4.23"
@@ -79,7 +77,6 @@ matplotlib = ">=3.9.1"
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mlflow = " >=2.13.0"
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numpyro = " >=0.15.0"
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pandas = " >=2.0.0"
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- pillow = " >=10.1.0"
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plumbum = " >=1.8.2"
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polars = " >=0.20.17"
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pyarrow = " >=14.0.2"
@@ -139,7 +136,6 @@ google-api-python-client = { version = ">=2.79.0", optional = true }
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hydra-core = { version = " >=1.3.2" , optional = true }
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hydra-zen = { version = " >=0.12.1" , optional = true }
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hypothesis = { version = " >=6.71.0" , optional = true }
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- ipdb = { version = " >=0.13.13" , optional = true }
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ipython = { version = " >=8.11.0" , optional = true }
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ipywidgets = { version = " >=8.0.0" , optional = true }
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# isort = { version = ">=5.10.1", optional = true }
@@ -168,7 +164,6 @@ pytest = { version = ">=6.2.5", optional = true }
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pytest-asyncio = { version = " >=0.21.1" , optional = true }
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pytest-cov = { version = " >=4.0.0" , optional = true }
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pytest-mock = { version = " >=3.10.0" , optional = true }
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- pytest-xdist = { version = " >=3.1.0" , optional = true }
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python-dotenv = { version = " >=1.0.0" , optional = true }
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# pyupgrade = { version = ">=2.29.1", optional = true }
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# pyvis = { version = ">=0.3.2", optional = true }
@@ -223,15 +218,13 @@ optional = true
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[tool .poetry .group .test .dependencies ]
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coverage = { version = " >=6.2" , extras = [" toml" ] }
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hypothesis = " >=6.72.1"
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- ipdb = " >=0.13.13"
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ipython = " >=8.11.0"
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# poethepoet = ">=0.19.0"
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pygments = " >=2.15.0"
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pytest = " >=7.3.1"
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pytest-asyncio = " >=0.21.1"
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pytest-cov = " >=4.0.0"
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pytest-mock = " >=3.10.0"
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- pytest-xdist = " >=3.1.0"
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requests-mock = " >=1.11.0"
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xdoctest = " >=1.1.1"
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@@ -308,7 +301,6 @@ test = [
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" pytest-asyncio" ,
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" pytest-cov" ,
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" pytest-mock" ,
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- " pytest-xdist" ,
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" requests-mock" ,
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" xdoctest" ,
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]
@@ -431,13 +423,8 @@ log_level = "INFO"
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# We exclude markers associated with slow tests by default
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# but run them in CI with the make target `test-cov-xml`
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# which overrides this behavior.
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- # Add these options to enable the ipdb debugger:
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- # --pdb
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- # --pdbcls=IPython.terminal.debugger:Pdb
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- # Run tests in parallel with pytest-xdist:
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- # -n auto
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addopts = """
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- -m "not slow and not pyensembl and not network "
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+ -m "not slow and not pyensembl"
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-rA
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--xdoctest
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--disable-warnings
@@ -451,7 +438,6 @@ markers = [
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" pyensembl: Tests that require pyensembl to run." ,
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" slow: Tests that are slow and should be run separately." ,
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" integration: Tests that use many library components." ,
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- " network: Tests that use network resources." ,
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]
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[tool .coverage .paths ]
@@ -624,5 +610,5 @@ exclude = [
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]
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[build-system ]
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- requires = [" poetry-core>=1.6.0,<2 " ]
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+ requires = [" poetry-core>=1.6.0" ]
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build-backend = " poetry.core.masonry.api"
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