Add bigwig hdf5-backed dataset

.gitignore

@@ -0,0 +1,161 @@
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py|src/grelu/resources'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v5.0.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -36,12 +36,13 @@ repos:
 #     ]
 
 - repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
   - id: isort
+    args: ["--profile", "black"]
 
 - repo: https://github.com/psf/black
-  rev: 23.3.0
+  rev: 24.10.0
   hooks:
   - id: black
     language_version: python3
@@ -54,7 +55,7 @@ repos:
 #     additional_dependencies: [black]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
+  rev: 7.1.1
   hooks:
   - id: flake8
   ## You can add flake8 plugins via `additional_dependencies`:

Dockerfile

@@ -1,4 +1,4 @@
-FROM pytorchlightning/pytorch_lightning:base-cuda-py3.11-torch2.2-cuda12.1.0
+FROM pytorch/pytorch:2.4.1-cuda12.1-cudnn9-devel
 
 
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
@@ -31,27 +31,20 @@ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/gff3
 
 
 # Install python packages
+RUN pip install flash-attn --no-build-isolation
 RUN pip install cython setuptools jupyterlab pandas scikit-learn tables lxml html5lib
 RUN pip install pytest pytest-cov pre-commit
 RUN pip install black flake8 isort
 RUN pip install captum==0.5.0 wandb tensorboard plotnine
 
 RUN pip install bioframe biopython genomepy scanpy \
-                pyjaspar pymemesuite pyBigWig pyfaidx pytabix
-RUN pip install bpnet-lite>=0.5.7 ledidi enformer-pytorch genomepy
+                pyjaspar pyBigWig pyfaidx pytabix
+RUN pip install bpnet-lite>=0.5.7 ledidi enformer-pytorch genomepy statsmodels
 RUN pip install pygenomeviz
 
 # Install modiscolite
 RUN pip install modisco-lite@git+https://github.com/jmschrei/tfmodisco-lite.git
 
-# Install MEME suite
-RUN wget https://meme-suite.org/meme/meme-software/5.5.1/meme-5.5.1.tar.gz && \
-    tar -xvzf meme-5.5.1.tar.gz && \
-    cd meme-5.5.1 && \
-    ./configure --prefix=/usr --enable-build-libxml2 --enable-build-libxslt && \
-    make && \
-    make install
-
 # Run jupyterlab
 WORKDIR /
 CMD jupyter lab --no-browser --allow-root --port 8891 --ip 0.0.0.0 --NotebookApp.token=''

README.md

@@ -19,6 +19,15 @@ To install using pip:
 ```shell
 pip install gReLU
 ```
+Typical installation time including all dependencies is under 10 minutes.
+
+To train or use transformer models containing flash attention layers, [flash-attn](https://github.com/Dao-AILab/flash-attention) needs to be installed first:
+```shell
+conda install -c conda-forge cudatoolkit-dev -y
+pip install torch ninja
+pip install flash-attn --no-build-isolation
+pip install gReLU
+```
 
 ## Contributing
 
@@ -64,3 +73,7 @@ bioconda::ucsc-bedtogenepred    \
 bioconda::ucsc-gtftogenepred    \
 bioconda::ucsc-gff3togenepred
 ```
+
+## Citation
+
+Please cite our preprint: https://www.biorxiv.org/content/10.1101/2024.09.18.613778v1