Use PyPi for popv

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
 

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

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