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Welcome to the pygtftk wiki!

For users

Please look at the git repository.

For developpers

For git hubflow usage see 'https://datasift.github.io/gitflow/GitFlowForGitHub.html'.

Creating a release

Preparing the new release tag on github

Example with release 0.9.0

When everything seems to be ok you can go for a release. Follow these rules.

• Start a new release from develop branch (THIS_VER="0.9.0"; git hf release start v$THIS_VER).
• Ensure you have all python packages required for developement pip install "pygtftk[dev]"
• Try installing the current version make install
• type make release VER=$THIS_VER
• type make release_bump VER=$THIS_VER
• type make release_test and check the tests (or use the parallelized version e.g. make test_para -j 14).
• type make release_nose and check the tests.
• type make release_doc and check the doc.
• Under OSX, check this release is pypiable.
  • rm -rf dist; python setup.py bdist_wheel
  • try to install the package using pip install dist/pygtftk-....whl
• Publish the release to master using git hf release finish vx.x.x
• On the github page. Delete the tag.
• Create the tag through the gitub interface.

Creating Pypi/manylinux compliant packages for Linux

Simply type:

• type make release_pip_unix and check the log in the wheels directory and the version.
• type make release_pip_osx. Check the version.
• Upload the package on Pypi using twine upload wheelhouse_manylinux

Creating conda build

• The sha256 needs to be computed from the archive available from github using:

      - `openssl sha256 pygtftk-0.9.10.tar.gz`
  

• Clone the bioconda/recipe repo

      - clone the bioconda-recipes forked repo at https://github.com/dputhier/bioconda-recipes
      - cd bioconda-recipes/recipes/pygtftk
  

• Change

     - Bump the version, the sha256 (set build: number to 0 ?) in the meta.yaml.
     - git add/commit/push
  

• Check everything is working:

  • For UNIX:

    • docker pull quay.io/bioconda/bioconda-utils-build-env
    • docker create --mount type=bind,source=/tmp,target=/tmp/out -i -t --name mybioconda bioconda/bioconda-utils-build-env /bin/bash
    • docker start mybioconda
    • docker attach mybioconda
    • mkdir -p /io && cd /io
    • git clone https://github.com/dputhier/bioconda-recipes . # the forked version
    • cd recipes/pygtftk && conda-build --python 3.9 .

  • Under OSX do:

    • Go to the bioconda-recipes/recipes/pygtftk folder and conda build --python 3.9 .

• Fork https://github.com/bioconda/bioconda-recipes

     - create a PR
  

Hotfix

A special case of branch starting from master with modifications not to be directly included in develop branch (but upon merge with master).

• git hf hotfix start "x.x.x"
• git hf hotfix finish "x.x.x"

Merge if required and type:

• git push origin:hotfix/x.x.x
• git push origin "x.x.x"