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Cromshell Package Releases

Cromshell can be installed from a brew tap or through pypi. Instructions on how to publish to these repos are detailed below.

Steps Summary

  1. Set the correct version for the repository using bumpversion and merge changes to main. (e.g. bumpversion --new-version 2.1.1 minor)
  2. Create a GitHub release. The release notes may be subdivided by "Feature Additions" and "Bug Fixes".
  3. Publish on Brew.
  4. Publish on PyPi.

Brew Tap

Regular update of broadinstitute/dsp tap is needed as new releases of Cromshell are made. Once a release occurs a new formula for that release should be created in broadinstitute/homebrew-dsp git repository in the Formula directory.

The name of the formula file should have the following structure: cromshell@[version].rb. For example:

[email protected]

The following should be updated regularly in a new formula file:

  • Git release tar file url
  • Git release tar file hash (e.g. shasum -a 256 /path/to/tar/cromshell-2.0.0.beta.1.tar.gz)
  • List of required python package url and their hash

Here is an example of the content of the Formula file.

class CromshellAT200Alpha1 < Formula
  include Language::Python::Virtualenv

  desc "Python tool to interact with a Cromwell server"
  homepage "https://github.com/broadinstitute/cromshell"
  url "https://github.com/broadinstitute/cromshell/archive/refs/tags/2.0.0.alpha.1.tar.gz"
  sha256 "0ac3604ff362fdf2107f91c886887856098f1731d2d1a9e9cff59278b7b292b9"
  license "BSD-3-Clause"
  depends_on "[email protected]"

  resource "termcolor" do
    url "https://files.pythonhosted.org/packages/8a/48/a76be51647d0eb9f10e2a4511bf3ffb8cc1e6b14e9e4fab46173aa79f981/termcolor-1.1.0.tar.gz"
    sha256 "1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b"
  end
  resource "click>=8.0.0" do
    url "https://files.pythonhosted.org/packages/f4/09/ad003f1e3428017d1c3da4ccc9547591703ffea548626f47ec74509c5824/click-8.0.3.tar.gz"
    sha256 "410e932b050f5eed773c4cda94de75971c89cdb3155a72a0831139a79e5ecb5b"
  end

  def install
    virtualenv_install_with_resources
  end

  # `test do` will create, run in, and delete a temporary directory.
  test do
    system "#{bin}/cromshell-alpha", "--help"
  end
end

Note:

  1. All packages listed in the requirements.txt file should be listed in the formula. Sometimes packages in the file have their own dependencies, you can identify this by using a tool like pipdeptree to list whether it has dependencies.

        >pipdeptree -p requests
    requests==2.27.1
    - certifi [required: >=2017.4.17, installed: 2020.12.5]
    - charset-normalizer [required: ~=2.0.0, installed: 2.0.12]
    - idna [required: >=2.5,<4, installed: 2.10]
    - urllib3 [required: >=1.21.1,<1.27, installed: 1.26.2]

  2. The package url and hash can be obtained from the package pypi site or using a tool like homebrew-pypi-poet.

    poet requests

    results to:

      resource "certifi" do
    url "https://files.pythonhosted.org/packages/06/a9/cd1fd8ee13f73a4d4f491ee219deeeae20afefa914dfb4c130cfc9dc397a/certifi-2020.12.5.tar.gz"
    sha256 "1a4995114262bffbc2413b159f2a1a480c969de6e6eb13ee966d470af86af59c"
  end

  resource "charset-normalizer" do
    url "https://files.pythonhosted.org/packages/56/31/7bcaf657fafb3c6db8c787a865434290b726653c912085fbd371e9b92e1c/charset-normalizer-2.0.12.tar.gz"
    sha256 "2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597"
  end

  resource "idna" do
    url "https://files.pythonhosted.org/packages/ea/b7/e0e3c1c467636186c39925827be42f16fee389dc404ac29e930e9136be70/idna-2.10.tar.gz"
    sha256 "b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6"
  end

  resource "requests" do
    url "https://files.pythonhosted.org/packages/60/f3/26ff3767f099b73e0efa138a9998da67890793bfa475d8278f84a30fec77/requests-2.27.1.tar.gz"
    sha256 "68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61"
  end

  resource "urllib3" do
    url "https://files.pythonhosted.org/packages/29/e6/d1a1d78c439cad688757b70f26c50a53332167c364edb0134cadd280e234/urllib3-1.26.2.tar.gz"
    sha256 "19188f96923873c92ccb987120ec4acaa12f0461fa9ce5d3d0772bc965a39e08"
  end

Test Install

Test installation using formula.

brew install --build-from-source [email protected]

Test installation using brew tap

brew tap broadinstitute/dsp
brew install cromshell

Pypi

Use steps below to release on either PyPi or testPyPi, the latter is primarily used for draft releases.

  1. Install the following tools

    python3 -m pip install --upgrade pip twine build

  2. Update the version tag and project name in pyproject.toml. If creating a release in testPyPi use project name cromshell-draft-release, if creating a release in PyPi use project name cromshell.

  3. In the root repository directory build cromshell. This will create a folder called /dist with tar files of the cromshell build.

    python3 -m build

  4. Publish build using twine. The PYPI Token is obtained from your pypi account, your account will need access permission to the cromshell project in pypi (you will have different tokens for testpypi and pypi repos).

    python3 -m twine upload --username __token__ --password <PYPI_TOKEN> --repository <testpypi/pypi> dist/*

Pypi git action [Not Available]

Because this git yml is only initiated through workflow dispatch, the action will not be functional until the cromshell2 branch is merged to main.

A git action has been created to help easily send a release to pypi. The action needs to be executed manually with PyPI_Repo (by default set to "testpypi" for now) and version inputs.

Once a release version is created in the pypi repository, it is not possible rewrite over it (like in the case of a bug fix) so it's best to allow a release to have in the 'wild' for testing before adding the release to pypi.