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.gitattributes

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CONTRIBUTING.md

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+# How to develop on this project
+
+scprint welcomes contributions from the community.
+
+**You need PYTHON3!**
+
+This instructions are for linux base systems. (Linux, MacOS, BSD, etc.)
+## Setting up your own fork of this repo.
+
+- On github interface click on `Fork` button.
+- Clone your fork of this repo. `git clone [email protected]:YOUR_GIT_USERNAME/scPRINT.git`
+- Enter the directory `cd scPRINT`
+- Add upstream repo `git remote add upstream https://github.com/jkobject/scPRINT`
+
+## Setting up your own virtual environment
+
+Run `make virtualenv` to create a virtual environment.
+then activate it with `source .venv/bin/activate`.
+
+## Install the project in develop mode
+
+Run `make install` to install the project in develop mode.
+
+## Run the tests to ensure everything is working
+
+Run `make test` to run the tests.
+
+## Create a new branch to work on your contribution
+
+Run `git checkout -b my_contribution`
+
+## Make your changes
+
+Edit the files using your preferred editor. (we recommend VIM or VSCode)
+
+## Format the code
+
+Run `make fmt` to format the code.
+
+## Run the linter
+
+Run `make lint` to run the linter.
+
+## Test your changes
+
+Run `make test` to run the tests.
+
+Ensure code coverage report shows `100%` coverage, add tests to your PR.
+
+## Build the docs locally
+
+Run `make docs` to build the docs.
+
+Ensure your new changes are documented.
+
+## Commit your changes
+
+This project uses [conventional git commit messages](https://www.conventionalcommits.org/en/v1.0.0/).
+
+Example: `fix(package): update setup.py arguments 🎉` (emojis are fine too)
+
+## Push your changes to your fork
+
+Run `git push origin my_contribution`
+
+## Submit a pull request
+
+On github interface, click on `Pull Request` button.
+
+Wait CI to run and one of the developers will review your PR.
+## Makefile utilities
+
+This project comes with a `Makefile` that contains a number of useful utility.
+
+```bash 
+❯ make
+Usage: make <target>
+
+Targets:
+help:             ## Show the help.
+install:          ## Install the project in dev mode.
+fmt:              ## Format code using black & isort.
+lint:             ## Run pep8, black, mypy linters.
+test: lint        ## Run tests and generate coverage report.
+watch:            ## Run tests on every change.
+clean:            ## Clean unused files.
+virtualenv:       ## Create a virtual environment.
+release:          ## Create a new tag for release.
+docs:             ## Build the documentation.
+switch-to-poetry: ## Switch to poetry package manager.
+init:             ## Initialize the project based on an application template.
+```
+
+## Making a new release
+
+This project uses [semantic versioning](https://semver.org/) and tags releases with `X.Y.Z`
+Every time a new tag is created and pushed to the remote repo, github actions will
+automatically create a new release on github and trigger a release on PyPI.
+
+For this to work you need to setup a secret called `PIPY_API_TOKEN` on the project settings>secrets, 
+this token can be generated on [pypi.org](https://pypi.org/account/).
+
+To trigger a new release all you need to do is.
+
+1. If you have changes to add to the repo
+    * Make your changes following the steps described above.
+    * Commit your changes following the [conventional git commit messages](https://www.conventionalcommits.org/en/v1.0.0/).
+2. Run the tests to ensure everything is working.
+4. Run `make release` to create a new tag and push it to the remote repo.
+
+the `make release` will ask you the version number to create the tag, ex: type `0.1.1` when you are asked.
+
+> **CAUTION**:  The make release will change local changelog files and commit all the unstaged changes you have.

pyproject.toml

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+[tool.poetry]
+name = "scprint"
+version = "0.1.0"
+license = "MIT"
+description = ""
+authors = ["jeremie kalfon"]
+readme = ["README.md", "LICENSE"]
+repository = "https://github.com/jkobject/scPrint"
+keywords = [
+  "scRNAseq",
+  "transformer",
+  "GRN",
+  "gene regulatory network",
+  "scPrint",
+]
+
+[tool.poetry.dependencies]
+lamindb = "*"
+python = "3.10"
+cellxgene-census = "*"
+torch = ">=2.0.0"
+anndata = "*"
+matplotlib = "*"
+seaborn = "*"
+gseapy = "*"
+ipykernel = "*"
+owlready2 = "*"
+torchdata = "*"
+biomart = "*"
+scib = "*"
+scikit-learn = "*"
+scipy = "*"
+pandas = ">=2.0.0"
+numpy = "*"
+leidenalg = "*"
+decoupler = "*"
+Bio = "*"
+attridict = "*"
+gget = "*"
+torchvision = "*"
+fair-esm = { git = "https://github.com/facebookresearch/esm.git", branch = "main" }
+hydra-core = "*"
+lightning = "*"
+#torchtext = "*"
+#transformers = "*"
+pynndescent = ">=0.5.11"
+scDataLoader = "*"
+einops = "*"
+rich = "*"
+typeshed-client = "*"
+tensorboardX = "*"
+jsonargparse = "*"
+docstring-parser = "*"
+lnschema-bionty = "*"
+bionty = "*"
+wandb = "*"
+wandb-core = "*"
+pykeops = "*"
+louvain = "*"
+hdbscan = "*"
+scib-metrics = "*"
+scikit-misc = "*"
+zarr = "*"
+galore-torch = { git = "https://github.com/jiaweizzhao/GaLore", branch = "master" }
+tensorly = "*3
+
+[tool.poetry.group.flashattention.dependencies]
+# C_INCLUDE_PATH=$CONDA_HOME/envs/scprint/include
+torchtext = "0.15.1"
+triton = "2.0.0.dev20221202" #no deps
+torch = "2.0.0"
+torchvision = "0.15.0"
+torchaudio = "2.0.0"
+pytorch-fast-transformers = "*"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.4.3"
+coverage = "^7.3.2"
+flake8 = "^6.1.0"
+black = "^23.10.1"
+isort = "^5.12.0"
+pytest-cov = "^4.1.0"
+mypy = "^1.6.1"
+gitchangelog = "^3.0.4"
+mkdocs = "^1.5.3"
+mkdocs-git-revision-date-localized-plugin = "*"
+mkdocstrings = "*"
+mkdocs-git-authors-plugin = "*"
+mkdocs-jupyter = "*"
+mkdocstrings-python = "*"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry.scripts]
+scprint = 'scprint.__main__:main'