From 9d1fd33b4cff48d28533a7231e7cb186592a2cc7 Mon Sep 17 00:00:00 2001 From: Daniel Bolin Date: Mon, 25 Mar 2024 10:19:10 -0400 Subject: [PATCH] Use PyPi for popv --- containers/popv/Dockerfile | 2 +- .../popv/context/requirements-freeze.txt | 267 +++++++----------- containers/popv/context/requirements.txt | 6 +- 3 files changed, 101 insertions(+), 174 deletions(-) diff --git a/containers/popv/Dockerfile b/containers/popv/Dockerfile index 7bda49d..45b51cd 100644 --- a/containers/popv/Dockerfile +++ b/containers/popv/Dockerfile @@ -1,4 +1,4 @@ -FROM tensorflow/tensorflow:2.11.1 +FROM tensorflow/tensorflow:2.16.1 RUN apt-get -y update && apt-get -y install python3-dev g++ git wget && apt-get clean diff --git a/containers/popv/context/requirements-freeze.txt b/containers/popv/context/requirements-freeze.txt index 045a828..942c967 100644 --- a/containers/popv/context/requirements-freeze.txt +++ b/containers/popv/context/requirements-freeze.txt @@ -1,109 +1,75 @@ -absl-py==2.0.0 -aiohttp==3.8.6 +absl-py==2.1.0 +aiohttp==3.9.3 aiosignal==1.3.1 -alabaster==0.7.13 -anndata==0.8.0 +anndata==0.10.6 annoy==1.17.3 -asttokens==2.4.1 +array_api_compat==1.4.1 astunparse==1.6.3 -async-timeout==4.0.3 -attrs==23.1.0 -Babel==2.13.1 -backcall==0.2.0 -bbknn==1.5.1 -beautifulsoup4==4.12.2 -bleach==6.1.0 -cached-property==1.5.2 -cachetools==5.3.2 -celltypist==1.6.1 -certifi==2023.7.22 -charset-normalizer==3.3.1 -chex==0.1.7 +attrs==23.2.0 +bbknn==1.6.0 +beautifulsoup4==4.12.3 +celltypist==1.6.2 +certifi==2024.2.2 +charset-normalizer==3.3.2 +chex==0.1.85 click==8.1.7 -comm==0.1.4 contextlib2==21.6.0 -contourpy==1.1.1 +contourpy==1.2.0 cycler==0.12.1 -Cython==3.0.4 -decorator==5.1.1 -defusedxml==0.7.1 +Cython==3.0.9 dm-tree==0.1.8 docrep==0.3.2 -docutils==0.17.1 -entrypoints==0.4 et-xmlfile==1.1.0 -etils==1.3.0 -executing==2.0.0 -fastjsonschema==2.18.1 +etils==1.7.0 fbpca==1.0 -filelock==3.12.4 -flatbuffers==23.5.26 -flax==0.7.2 -fonttools==4.43.1 -frozenlist==1.4.0 -fsspec==2023.10.0 -gast==0.4.0 -gdown==4.7.1 +filelock==3.13.1 +flatbuffers==24.3.7 +flax==0.8.1 +fonttools==4.49.0 +frozenlist==1.4.1 +fsspec==2024.2.0 +gast==0.5.4 +gdown==5.1.0 geosketch==1.2 -google-auth==2.23.3 -google-auth-oauthlib==1.0.0 google-pasta==0.2.0 -grpcio==1.59.0 +grpcio==1.62.1 h5py==3.10.0 -harmony-pytorch==0.1.7 -huggingface-hub==0.11.1 -idna==3.4 -igraph==0.10.8 -imagesize==1.4.1 -imgkit==1.2.2 -importlib-metadata==4.2.0 -importlib-resources==6.1.0 +harmony-pytorch==0.1.8 +huggingface-hub==0.21.4 +idna==3.6 +igraph==0.11.4 +importlib_resources==6.2.0 intervaltree==3.1.0 -ipython==8.12.3 -ipywidgets==8.1.1 -jax==0.4.10 -jaxlib==0.4.10 -jedi==0.19.1 -Jinja2==3.1.2 +jax==0.4.25 +jaxlib==0.4.25 +Jinja2==3.1.3 joblib==1.3.2 -jsonschema==4.19.1 -jsonschema-specifications==2023.7.1 -jupyter_client==7.4.9 -jupyter_core==5.4.0 -jupyterlab-pygments==0.2.2 -jupyterlab-widgets==3.0.9 -keras==2.13.1 +keras==3.0.5 kiwisolver==1.4.5 -leidenalg==0.10.1 +leidenalg==0.10.2 libclang==16.0.6 -lightning-utilities==0.9.0 -llvmlite==0.41.1 -Markdown==3.3.4 +lightning==2.1.4 +lightning-utilities==0.10.1 +llvmlite==0.42.0 +Markdown==3.5.2 markdown-it-py==3.0.0 -MarkupSafe==2.1.3 -matplotlib==3.7.3 -matplotlib-inline==0.1.6 +MarkupSafe==2.1.5 +matplotlib==3.8.3 mdurl==0.1.2 -mistune==3.0.2 -ml-collections==0.1.1 -ml-dtypes==0.2.0 +ml-dtypes==0.3.2 +ml_collections==0.1.1 mpmath==1.3.0 -msgpack==1.0.7 +msgpack==1.0.8 mudata==0.2.3 -multidict==6.0.4 +multidict==6.0.5 multipledispatch==1.0.0 +namex==0.0.7 natsort==8.4.0 -nbclient==0.8.0 -nbconvert==7.9.2 -nbformat==5.9.2 -nbsphinx==0.9.3 -nbsphinx-link==1.3.0 -nest-asyncio==1.5.8 -networkx==3.1 -nltk==3.8.1 -numba==0.58.1 -numpy==1.24.3 -numpyro==0.12.1 +nest-asyncio==1.6.0 +networkx==3.2.1 +numba==0.59.0 +numpy==1.26.4 +numpyro==0.14.0 nvidia-cublas-cu12==12.1.3.1 nvidia-cuda-cupti-cu12==12.1.105 nvidia-cuda-nvrtc-cu12==12.1.105 @@ -113,107 +79,72 @@ nvidia-cufft-cu12==11.0.2.54 nvidia-curand-cu12==10.3.2.106 nvidia-cusolver-cu12==11.4.5.107 nvidia-cusparse-cu12==12.1.0.106 -nvidia-nccl-cu12==2.18.1 -nvidia-nvjitlink-cu12==12.3.52 +nvidia-nccl-cu12==2.19.3 +nvidia-nvjitlink-cu12==12.4.99 nvidia-nvtx-cu12==12.1.105 -oauthlib==3.2.2 obonet==1.0.0 -OnClass==1.2 +OnClass==1.3 openpyxl==3.1.2 opt-einsum==3.3.0 -optax==0.1.7 -orbax-checkpoint==0.2.3 -packaging==23.2 +optax==0.2.1 +orbax-checkpoint==0.5.5 +packaging==24.0 pandas==1.5.3 -pandocfilters==1.5.0 -parso==0.8.3 -patsy==0.5.3 -pexpect==4.8.0 -pickleshare==0.7.5 -Pillow==10.1.0 -pkgutil_resolve_name==1.3.10 -platformdirs==3.11.0 -popv @ git+https://github.com/czbiohub/PopV@6b95ddf68226658bdc0c07f3f89de8e8b6669c6b -prompt-toolkit==3.0.39 -protobuf==4.24.4 -psutil==5.9.6 -ptyprocess==0.7.0 -pure-eval==0.2.2 -pyasn1==0.5.0 -pyasn1-modules==0.3.0 -Pygments==2.16.1 -pynndescent==0.5.10 -pyparsing==3.1.1 +patsy==0.5.6 +pillow==10.2.0 +PopV==0.4.2 +protobuf==4.25.3 +psutil==5.9.8 +Pygments==2.17.2 +pynndescent==0.5.11 +pyparsing==3.1.2 pyro-api==0.1.2 -pyro-ppl==1.8.6 +pyro-ppl==1.9.0 PySocks==1.7.1 -python-dateutil==2.8.2 -pytorch-lightning==1.9.5 -pytz==2023.3.post1 +python-dateutil==2.9.0.post0 +pytorch-lightning==2.2.1 +pytz==2024.1 PyYAML==6.0.1 -pyzmq==25.1.1 -referencing==0.30.2 -regex==2023.10.3 +regex==2023.12.25 requests==2.31.0 -requests-oauthlib==1.3.1 -rich==13.6.0 -rpds-py==0.10.6 -rsa==4.9 +rich==13.7.1 +safetensors==0.4.2 scanorama==1.7.4 -scanpy==1.9.5 -scikit-learn==0.24.2 -scikit-misc==0.2.0 -scipy==1.10.1 -scvi-tools==0.20.3 -seaborn==0.13.0 -sentence-transformers==2.2.2 -sentencepiece==0.1.99 -session-info==1.0.0 -six==1.15.0 -snowballstemmer==2.2.0 +scanpy==1.9.8 +scikit-learn==1.1.3 +scikit-misc==0.3.1 +scipy==1.12.0 +scvi-tools==1.1.2 +seaborn==0.13.2 +sentence-transformers==2.5.1 +session_info==1.0.0 +six==1.16.0 sortedcontainers==2.4.0 soupsieve==2.5 -Sphinx==4.3.2 -sphinxcontrib-applehelp==1.0.4 -sphinxcontrib-devhelp==1.0.2 -sphinxcontrib-htmlhelp==2.0.1 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.3 -sphinxcontrib-serializinghtml==1.1.5 -stack-data==0.6.3 -statsmodels==0.14.0 -stdlib-list==0.9.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 sympy==1.12 -tbb==2021.10.0 -tensorboard==2.13.0 +tensorboard==2.16.2 tensorboard-data-server==0.7.2 -tensorflow==2.13.1 -tensorflow-estimator==2.13.0 -tensorflow-io-gcs-filesystem==0.34.0 -tensorstore==0.1.45 -termcolor==2.3.0 +tensorflow==2.16.1 +tensorflow-io-gcs-filesystem==0.36.0 +tensorstore==0.1.54 +termcolor==2.4.0 texttable==1.7.0 -threadpoolctl==3.2.0 -tinycss2==1.2.1 -tokenizers==0.13.3 -toolz==0.12.0 -torch==2.1.0 -torchmetrics==1.2.0 -torchvision==0.16.0 -tornado==6.3.3 -tqdm==4.64.0 -traitlets==5.12.0 -transformers==4.29.0 -triton==2.1.0 -typing_extensions==4.2.0 -umap-learn==0.5.4 -urllib3==2.0.7 -wcwidth==0.2.8 -webencodings==0.5.1 +threadpoolctl==3.3.0 +tokenizers==0.15.2 +toolz==0.12.1 +torch==2.2.1 +torchmetrics==1.3.1 +tqdm==4.66.2 +transformers==4.38.2 +triton==2.2.0 +typing_extensions==4.10.0 +umap-learn==0.5.5 +urllib3==2.2.1 Werkzeug==3.0.1 wget==3.2 -widgetsnbextension==4.0.9 -wrapt==1.15.0 -yarl==1.9.2 +wrapt==1.16.0 +yarl==1.9.4 zenodo-get==1.4.0 zipp==3.17.0 diff --git a/containers/popv/context/requirements.txt b/containers/popv/context/requirements.txt index a6f3dc6..4c3b1ca 100644 --- a/containers/popv/context/requirements.txt +++ b/containers/popv/context/requirements.txt @@ -1,6 +1,2 @@ -anndata==0.8.* -numpy==1.24.* -pandas<2.0 -popv @ git+https://github.com/czbiohub/PopV -scanpy==1.9.* +popv==0.4.* zenodo_get==1.4.0