[Briefly describe the problem this PR is attempting to address. Please use
@mentions or reference issue numbers if that will help. Provide a list of
top-level changes if possible.]
Before you submit a pull request, check that it meets these guidelines:
[ ] The pull request should include tests.
[ ] 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.
[ ] The pull request should work for Python 2.7, 3.4, 3.5, and 3.6.
Fixes #69
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:
[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:
[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
# Use "pushd" instead of "cd" so it's easy to pop back to the outrigger folder
pushd $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. Return to the original outrigger folder and upload to PyPI:
# Return to the outrigger directory from the `pushd`
popd
# Now upload to PyPI
python setup.py register -r pypi
python setup.py sdist upload -r pypi
Check that it appears correctly on the PyPI website.
[ ] 14. Upload to Bioconda:
cd ..
# If `bioconda-recipes` is not yet cloned, do this step. Otherwise you can
# skip it
git clone https://github.com/bioconda/bioconda-recipes
# Skip to this next line if you've already cloned bioconda-recipes
cd bioconda-recipes/recipes
git checkout -b outrigger_v0.2.1
# Remove existing outrigger folders
rm -rf outrigger
conda skeleton pypi outrigger
git add outrigger
git commit -m "Updated outrigger to v0.2.1"
git push origin outrigger_v0.2.1
# Go up two folders to return to the parent folder
cd ../../
[ ] 14. Check that a new pull request exists at bioconda-recipes
[ ] 16. 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 staged-recipes/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"
[ ] 17. Create a pull request to conda-forge using the YeoLab fork.
[Briefly describe the problem this PR is attempting to address. Please use @mentions or reference issue numbers if that will help. Provide a list of top-level changes if possible.]
Before you submit a pull request, check that it meets these guidelines:
Fixes #69
Release checklist
[x] 1. Check that version numbers in
outrigger/outrigger/__init__.pyandoutrigger/setup.pymatch[x] 2. Add release notes in
outrigger/docs/releases[x] 3. Copy release notes to
outrigger/HISTORY.rst[x] 4. Check that the
.rstfiles are valid usingrstcheckand the built-in Python RST checker:[x] 7. Do a test run of uploading to PyPI test. This assumes you have set up your PyPI configuration according to this.
[x] 8. (Optional, if there's an error) in either the
HISTORY.rstorREADME.rstfile, you will get an error. To narrow down this error, look for the corresponding line inoutrigger.egg-info. It won't be exactly the same line because of the header but it will be closer sincePKG-INFOconcatenates yourREADME.rstandHISTORY.rstfiles.condaenvironment using the PyPI test serveroutriggerfrom the right environment is getting referenced.which outriggershould have the following output:outrigger -hshould have the following output:Check that it appears correctly on the PyPI website.
[ ] 14. Check that a new pull request exists at bioconda-recipes
[ ] 16. Upload to conda-forge
conda-forgeusing the YeoLab fork.