From 9bb92795a8bea18b9ab5328b222ca43d682290cf Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Mon, 28 Oct 2024 13:54:55 -0400 Subject: [PATCH] Update python requirements use proper syntax for `~=` packages. --- docker/requirements.in | 7 +- docker/requirements.txt | 111 ++++++++++++++++---------------- docker/requirements_anndata.in | 2 +- docker/requirements_anndata.txt | 18 +++--- docker/requirements_scvi.in | 7 +- docker/requirements_scvi.txt | 111 ++++++++++++++++---------------- 6 files changed, 132 insertions(+), 124 deletions(-) diff --git a/docker/requirements.in b/docker/requirements.in index 5bf61cd0..61b27e34 100644 --- a/docker/requirements.in +++ b/docker/requirements.in @@ -1,8 +1,9 @@ -anndata~=0.10 +anndata~=0.10.8 etils<1.8 # v1.8 drops python 3.10 support jax[cpu] +lightning>=2.3.3 # critical security fix pandas -scanpy~=1.10 -scvi-tools~=1.1 +scanpy~=1.10.2 +scvi-tools~=1.1.5 torch torchvision diff --git a/docker/requirements.txt b/docker/requirements.txt index a45e63cb..d161d316 100644 --- a/docker/requirements.txt +++ b/docker/requirements.txt @@ -5,93 +5,96 @@ # pip-compile --no-annotate --output-file=requirements.txt --strip-extras requirements.in # absl-py==2.1.0 -aiohttp==3.9.5 +aiohappyeyeballs==2.4.3 +aiohttp==3.10.10 aiosignal==1.3.1 anndata==0.10.8 -array-api-compat==1.7.1 +array-api-compat==1.9 async-timeout==4.0.3 -attrs==23.2.0 -chex==0.1.86 +attrs==24.2.0 +chex==0.1.87 contextlib2==21.6.0 -contourpy==1.2.1 +contourpy==1.3.0 cycler==0.12.1 docrep==0.3.2 etils==1.7.0 -exceptiongroup==1.2.1 -filelock==3.15.4 -flax==0.8.5 -fonttools==4.53.1 -frozenlist==1.4.1 -fsspec==2024.6.1 -h5py==3.11.0 -idna==3.7 -importlib-resources==6.4.0 -jax==0.4.30 -jaxlib==0.4.30 +exceptiongroup==1.2.2 +filelock==3.16.1 +flax==0.10.0 +fonttools==4.54.1 +frozenlist==1.5.0 +fsspec==2024.10.0 +h5py==3.12.1 +humanize==4.11.0 +idna==3.10 +importlib-resources==6.4.5 +jax==0.4.35 +jaxlib==0.4.35 jinja2==3.1.4 joblib==1.4.2 -kiwisolver==1.4.5 +kiwisolver==1.4.7 legacy-api-wrap==1.4 -lightning==2.1.4 -lightning-utilities==0.11.3.post0 +lightning==2.4.0 +lightning-utilities==0.11.8 llvmlite==0.43.0 markdown-it-py==3.0.0 -markupsafe==2.1.5 -matplotlib==3.9.1 +markupsafe==3.0.2 +matplotlib==3.9.2 mdurl==0.1.2 ml-collections==0.1.1 -ml-dtypes==0.4.0 +ml-dtypes==0.5.0 mpmath==1.3.0 -msgpack==1.0.8 -mudata==0.2.4 -multidict==6.0.5 +msgpack==1.1.0 +mudata==0.3.1 +multidict==6.1.0 multipledispatch==1.0.0 natsort==8.4.0 nest-asyncio==1.6.0 -networkx==3.3 +networkx==3.4.2 numba==0.60.0 numpy==1.26.4 -numpyro==0.15.0 -opt-einsum==3.3.0 -optax==0.2.2 -orbax-checkpoint==0.5.20 +numpyro==0.15.3 +opt-einsum==3.4.0 +optax==0.2.3 +orbax-checkpoint==0.7.0 packaging==24.1 -pandas==2.2.2 +pandas==2.2.3 patsy==0.5.6 -pillow==10.4.0 -protobuf==5.27.2 +pillow==11.0.0 +propcache==0.2.0 +protobuf==5.28.3 pygments==2.18.0 pynndescent==0.5.13 -pyparsing==3.1.2 +pyparsing==3.2.0 pyro-api==0.1.2 pyro-ppl==1.9.1 python-dateutil==2.9.0.post0 -pytorch-lightning==2.3.3 -pytz==2024.1 -pyyaml==6.0.1 -rich==13.7.1 -scanpy==1.10.2 -scikit-learn==1.5.1 -scipy==1.14.0 -scvi-tools==1.1.5 +pytorch-lightning==2.4.0 +pytz==2024.2 +pyyaml==6.0.2 +rich==13.9.3 +scanpy==1.10.3 +scikit-learn==1.5.2 +scipy==1.14.1 +scvi-tools==1.1.6.post2 seaborn==0.13.2 session-info==1.0.0 six==1.16.0 -statsmodels==0.14.2 -stdlib-list==0.10.0 -sympy==1.13.0 -tensorstore==0.1.63 +statsmodels==0.14.4 +stdlib-list==0.11.0 +sympy==1.13.1 +tensorstore==0.1.67 threadpoolctl==3.5.0 -toolz==0.12.1 -torch==2.3.1 -torchmetrics==1.4.0.post0 -torchvision==0.18.1 -tqdm==4.66.4 +toolz==1.0.0 +torch==2.5.0 +torchmetrics==1.5.1 +torchvision==0.20.0 +tqdm==4.66.6 typing-extensions==4.12.2 -tzdata==2024.1 +tzdata==2024.2 umap-learn==0.5.6 -yarl==1.9.4 -zipp==3.19.2 +yarl==1.16.0 +zipp==3.20.2 # The following packages are considered to be unsafe in a requirements file: # setuptools diff --git a/docker/requirements_anndata.in b/docker/requirements_anndata.in index c90c929e..20de7d54 100644 --- a/docker/requirements_anndata.in +++ b/docker/requirements_anndata.in @@ -1,2 +1,2 @@ # requirements.in packages for minimal ScPCA workflows -anndata~=0.10 +anndata~=0.10.8 diff --git a/docker/requirements_anndata.txt b/docker/requirements_anndata.txt index 78ed1033..24aef767 100644 --- a/docker/requirements_anndata.txt +++ b/docker/requirements_anndata.txt @@ -4,16 +4,16 @@ # # pip-compile --no-annotate --output-file=requirements_anndata.txt --strip-extras requirements_anndata.in # -anndata==0.10.8 -array-api-compat==1.7.1 -exceptiongroup==1.2.1 -h5py==3.11.0 +anndata==0.10.9 +array-api-compat==1.9 +exceptiongroup==1.2.2 +h5py==3.12.1 natsort==8.4.0 -numpy==2.0.0 +numpy==2.1.2 packaging==24.1 -pandas==2.2.2 +pandas==2.2.3 python-dateutil==2.9.0.post0 -pytz==2024.1 -scipy==1.14.0 +pytz==2024.2 +scipy==1.14.1 six==1.16.0 -tzdata==2024.1 +tzdata==2024.2 diff --git a/docker/requirements_scvi.in b/docker/requirements_scvi.in index 47067d40..f458c3a4 100644 --- a/docker/requirements_scvi.in +++ b/docker/requirements_scvi.in @@ -1,4 +1,5 @@ # requirements.in packages for scvi-based analysis -anndata~=0.10 -scanpy~=1.10 -scvi-tools~=1.1 +anndata~=0.10.8 +lightning>=2.3.3 # critical security fix +scanpy~=1.10.2 +scvi-tools~=1.1.5 diff --git a/docker/requirements_scvi.txt b/docker/requirements_scvi.txt index eb327333..e9af6f52 100644 --- a/docker/requirements_scvi.txt +++ b/docker/requirements_scvi.txt @@ -5,92 +5,95 @@ # pip-compile --no-annotate --output-file=requirements_scvi.txt --strip-extras requirements_scvi.in # absl-py==2.1.0 -aiohttp==3.9.5 +aiohappyeyeballs==2.4.3 +aiohttp==3.10.10 aiosignal==1.3.1 anndata==0.10.8 -array-api-compat==1.7.1 +array-api-compat==1.9 async-timeout==4.0.3 -attrs==23.2.0 -chex==0.1.86 +attrs==24.2.0 +chex==0.1.87 contextlib2==21.6.0 -contourpy==1.2.1 +contourpy==1.3.0 cycler==0.12.1 docrep==0.3.2 -etils==1.7.0 -exceptiongroup==1.2.1 -filelock==3.15.4 -flax==0.8.5 -fonttools==4.53.1 -frozenlist==1.4.1 -fsspec==2024.6.1 -h5py==3.11.0 -idna==3.7 -importlib-resources==6.4.0 -jax==0.4.30 -jaxlib==0.4.30 +etils==1.10.0 +exceptiongroup==1.2.2 +filelock==3.16.1 +flax==0.10.0 +fonttools==4.54.1 +frozenlist==1.5.0 +fsspec==2024.10.0 +h5py==3.12.1 +humanize==4.11.0 +idna==3.10 +importlib-resources==6.4.5 +jax==0.4.35 +jaxlib==0.4.35 jinja2==3.1.4 joblib==1.4.2 -kiwisolver==1.4.5 +kiwisolver==1.4.7 legacy-api-wrap==1.4 -lightning==2.1.4 -lightning-utilities==0.11.3.post0 +lightning==2.4.0 +lightning-utilities==0.11.8 llvmlite==0.43.0 markdown-it-py==3.0.0 -markupsafe==2.1.5 -matplotlib==3.9.1 +markupsafe==3.0.2 +matplotlib==3.9.2 mdurl==0.1.2 ml-collections==0.1.1 -ml-dtypes==0.4.0 +ml-dtypes==0.5.0 mpmath==1.3.0 -msgpack==1.0.8 -mudata==0.2.4 -multidict==6.0.5 +msgpack==1.1.0 +mudata==0.3.1 +multidict==6.1.0 multipledispatch==1.0.0 natsort==8.4.0 nest-asyncio==1.6.0 -networkx==3.3 +networkx==3.4.2 numba==0.60.0 numpy==1.26.4 -numpyro==0.15.0 -opt-einsum==3.3.0 -optax==0.2.2 -orbax-checkpoint==0.5.20 +numpyro==0.15.3 +opt-einsum==3.4.0 +optax==0.2.3 +orbax-checkpoint==0.7.0 packaging==24.1 -pandas==2.2.2 +pandas==2.2.3 patsy==0.5.6 -pillow==10.4.0 -protobuf==5.27.2 +pillow==11.0.0 +propcache==0.2.0 +protobuf==5.28.3 pygments==2.18.0 pynndescent==0.5.13 -pyparsing==3.1.2 +pyparsing==3.2.0 pyro-api==0.1.2 pyro-ppl==1.9.1 python-dateutil==2.9.0.post0 -pytorch-lightning==2.3.3 -pytz==2024.1 -pyyaml==6.0.1 -rich==13.7.1 -scanpy==1.10.2 -scikit-learn==1.5.1 -scipy==1.14.0 -scvi-tools==1.1.5 +pytorch-lightning==2.4.0 +pytz==2024.2 +pyyaml==6.0.2 +rich==13.9.3 +scanpy==1.10.3 +scikit-learn==1.5.2 +scipy==1.14.1 +scvi-tools==1.1.6.post2 seaborn==0.13.2 session-info==1.0.0 six==1.16.0 -statsmodels==0.14.2 -stdlib-list==0.10.0 -sympy==1.13.0 -tensorstore==0.1.63 +statsmodels==0.14.4 +stdlib-list==0.11.0 +sympy==1.13.1 +tensorstore==0.1.67 threadpoolctl==3.5.0 -toolz==0.12.1 -torch==2.3.1 -torchmetrics==1.4.0.post0 -tqdm==4.66.4 +toolz==1.0.0 +torch==2.5.0 +torchmetrics==1.5.1 +tqdm==4.66.6 typing-extensions==4.12.2 -tzdata==2024.1 +tzdata==2024.2 umap-learn==0.5.6 -yarl==1.9.4 -zipp==3.19.2 +yarl==1.16.0 +zipp==3.20.2 # The following packages are considered to be unsafe in a requirements file: # setuptools