v1.0.0rc1 - Version 1.0.0, release candidate 1

[olgabot]

This pull request is meant to collect all the final tasks that are required to create a v1.0.0 release

Before you submit a pull request, check that it meets these guidelines:

• [x] The pull request should include tests.
• [x] If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.md and README.rst.
• [x] The pull request should work for Python 2.7, 3.4, and 3.5.

Release checklist

• [x] 1. Check that version numbers in outrigger/outrigger/__init__.py and outrigger/setup.py match

• [x] 2. Add release notes in outrigger/docs/releases

• [x] 3. Copy release notes to outrigger/HISTORY.rst

• [x] 4. Check that the .rst files are valid using rstcheck and the built-in Python RST checker:

python setup.py check --restructuredtext
rstcheck README.rst
rstcheck HISTORY.rst

• [x] 5. Create an annotated tag for git and push it:

git tag -a v0.2.1 -m "v0.2.1 - Release *with* requirements.txt"
git push origin v0.2.1

• [x] 6. (Optional, only if you messed up) and made the tag too early and later made changes that should be added to the tag, remove the remote tag and force re-add the local tag:

git push origin :refs/tags/v0.2.1
git tag -fa v0.2.1
git push --tags

• [x] 7. Do a test run of uploading to PyPI test. This assumes you have set up your PyPI configuration according to this.

  python setup.py register -r pypitest
  python setup.py sdist upload -r pypitest

• [x] 8. (Optional, if there's an error) in either the HISTORY.rst or README.rst file, you will get an error. To narrow down this error, look for the corresponding line in outrigger.egg-info. It won't be exactly the same line because of the header but it will be closer since PKG-INFO concatenates your README.rst and HISTORY.rst files.

warning: unexpected indent on line 615 blah blah I'm pypi RST and I'm way too strict

• [x] 9. Check the PyPI test server and make sure everything is there and the RST is rendered correctly.
• [x] 10. Do a test installation in a conda environment using the PyPI test server

conda create --yes -n outrigger_pypi_test_v0.2.1 --file conda_requirements.txt
# Change to a different directory to make sure you're not importing the `outrigger` folder
cd $HOME
source activate outrigger_pypi_test_v0.2.1
pip install --index-url https://testpypi.python.org/pypi outrigger --extra-index-url https://pypi.python.org/simple

• [x] 11. Make sure that the correct outrigger from the right environment is getting referenced. which outrigger should have the following output:

$ which outrigger
/Users/olga/anaconda3/envs/outrigger_pypi_v0.2.1/bin/outrigger

• [x] 12. Check that the installation was successful. outrigger -h should have the following output:

$ outrigger -h
usage: outrigger [-h] {index,validate,psi} ...

Calculate "percent-spliced in" (Psi) scores of alternative splicing on a *de
novo*, custom-built splicing index

positional arguments:
  {index,validate,psi}  Sub-commands
    index               Build an index of splicing events using a graph
                        database on your junction reads and an annotation
    validate            Ensure that the splicing events found all have the
                        correct splice sites
    psi                 Calculate "percent spliced-in" (Psi) values using the
                        splicing event index built with "outrigger index"

optional arguments:
  -h, --help            show this help message and exit

• [x] 13. Upload to PyPI:

python setup.py register -r pypi
python setup.py sdist upload -r pypi

• [x] 14. Upload to Bioconda:

git clone https://github.com/bioconda/bioconda-recipes
cd bioconda-recipes/recipes
git checkout -b outrigger_v0.2.1
conda skeleton pypi outrigger
git add outrigger
git commit -m "Updated outrigger to v0.2.1"

• [x] 15. Upload to conda-forge

# Clone your forked repo of https://github.com/conda-forge/staged-recipes
git clone https://github.com/YeoLab/staged-recipes
cd recipes
git checkout -b outrigger_v0.2.1
conda skeleton pypi outrigger
# Get md5 hash from PyPI
git add outrigger
git commit -m "Updated outrigger to v0.2.1"

EDIT: update bioconda and conda-forge uploading in release checklist, remove README.md --> README.rst step

[willingc]

Hi @olgabot, you may consider adding 17. Upload to conda-forge too :smile:

[olgabot]

Added instructions for uploading to bioconda: https://github.com/YeoLab/outrigger/issues/43

[willingc]

Looking like you are getting very close to 1.0.0 :heart:

[olgabot]

yes, almost there!!

On Mon, Dec 19, 2016 at 11:32 AM Carol Willing notifications@github.com wrote:

Looking like you are getting very close to 1.0.0 ❤️

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/YeoLab/outrigger/pull/63#issuecomment-268056364, or mute the thread https://github.com/notifications/unsubscribe-auth/AAxNcELB-o31pGQlEkFDtolPvh1SBMW-ks5rJtvigaJpZM4LFxJd .

--

Olga Botvinnik PhD Program in Bioinformatics and Systems Biology http://bioinformatics.ucsd.edu/ Gene Yeo Laboratory http://yeolab.ucsd.edu/yeolab/Home.html | Sanford Consortium for Regenerative Medicine http://www.sanfordconsortium.org/ University of California, San Diego http://ucsd.edu/ www http://olgabotvinnik.com/ | blog http://blog.olgabotvinnik.com/ | github http://github.com/olgabot | twitter http://twitter.com/olgabot | linkedin http://www.linkedin.com/in/olgabotvinnik

[geneyeo]

Yay!!!

Sent from my iPhone

On Dec 19, 2016, at 10:57 AM, Olga Botvinnik notifications@github.com wrote:

yes, almost there!!

On Mon, Dec 19, 2016 at 11:32 AM Carol Willing notifications@github.com wrote:

Looking like you are getting very close to 1.0.0 ❤️

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/YeoLab/outrigger/pull/63#issuecomment-268056364, or mute the thread https://github.com/notifications/unsubscribe-auth/AAxNcELB-o31pGQlEkFDtolPvh1SBMW-ks5rJtvigaJpZM4LFxJd .

--

Olga Botvinnik PhD Program in Bioinformatics and Systems Biology http://bioinformatics.ucsd.edu/ Gene Yeo Laboratory http://yeolab.ucsd.edu/yeolab/Home.html | Sanford Consortium for Regenerative Medicine http://www.sanfordconsortium.org/ University of California, San Diego http://ucsd.edu/ www http://olgabotvinnik.com/ | blog http://blog.olgabotvinnik.com/ | github http://github.com/olgabot | twitter http://twitter.com/olgabot | linkedin http://www.linkedin.com/in/olgabotvinnik — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[willingc]

Way to go @olgabot on 1.0.0!!! :cake: :dress: :crown:

[olgabot]

Yay thanks!

[LeenMachine]

Congrats!!!! 🎉

On Mon, Apr 3, 2017 at 9:12 PM Olga Botvinnik notifications@github.com wrote:

Yay thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/YeoLab/outrigger/pull/63#issuecomment-291388527, or mute the thread https://github.com/notifications/unsubscribe-auth/ADSJ-g2Zh1zL4d85n5sufC1CQOyUkDDeks5rscMggaJpZM4LFxJd .