From a2ca8c3a0d2e5343c9cc882230f2b8b80a82da2b Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 20 Aug 2014 06:24:57 -0400 Subject: [PATCH 1/4] catching up with recent changes --- doc/dev/release.txt | 31 ++++++++++++++++++++----------- 1 file changed, 20 insertions(+), 11 deletions(-) diff --git a/doc/dev/release.txt b/doc/dev/release.txt index a32f1e4c47..c10f188e82 100644 --- a/doc/dev/release.txt +++ b/doc/dev/release.txt @@ -21,7 +21,7 @@ release makers, following this checklist by MRC. #. (Optional) Check for updates to versioneer:: - pip install versioneer + pip install --upgrade versioneer versioneer-installer git diff @@ -77,37 +77,45 @@ release makers, following this checklist by MRC. source bin/activate git clone --depth 1 --branch v${new_version}-${rc} https://github.com/ged-lab/khmer.git cd khmer + make install-dependencies make install - nosetests khmer --attr '!known_failing' make test - normalize-by-median.py --version # double-check version number + normalize-by-median.py --version 2>&1 | grep ${new_version}-${rc} && \ + echo 1st manual version check passed + cd .. + nosetests khmer --attr '!known_failing' + # Secondly we test via pip - cd ../../testenv2 + cd ../testenv2 source bin/activate pip install -U setuptools==3.4.1 pip install -e git+https://github.com/ged-lab/khmer.git@v${new_version}-${rc}#egg=khmer cd src/khmer + make install-dependencies make dist make install - nosetests khmer --attr '!known_failing' make test - normalize-by-median.py --version # double-check version number + normalize-by-median.py --version 2>&1 | grep ${new_version}-${rc} && \ + echo 2nd manual version check passed cp dist/khmer*tar.gz ../../../testenv3/ - + cd ../.. + nosetests khmer --attr '!known_failing' + # Is the distribution in testenv2 complete enough to build another # functional distribution? - cd ../../../testenv3/ + cd ../testenv3/ source bin/activate pip install -U setuptools==3.4.1 pip install khmer*tar.gz - nosetests khmer --attr '!known_failing' + pip install nose tar xzf khmer*tar.gz cd khmer* make dist make test + pushd .. ; nosetests khmer --attr '!known_failing' ; popd #. Publish the new release on the testing PyPI server. You will need to change your PyPI credentials as documented here: @@ -127,9 +135,10 @@ release makers, following this checklist by MRC. pip install screed nose pip install -i https://testpypi.python.org/pypi --pre --no-clean khmer nosetests khmer --attr '!known_failing' - normalize-by-median.py --version 2>&1 | awk ' { print $2 } ' + normalize-by-median.py --version 2>&1 | grep ${new_version}-${rc} && \ + echo 3rd manual version check passed cd build/khmer - ./setup.py nosetests + make test #. Do any final testing (BaTLab and/or acceptance tests). From e376a7bad597ff6a0293a5c668d34bfa30b4eb19 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 2 Sep 2014 10:01:22 -0400 Subject: [PATCH 2/4] add API checks --- doc/dev/coding-guidelines-and-review.txt | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/doc/dev/coding-guidelines-and-review.txt b/doc/dev/coding-guidelines-and-review.txt index 27d3d2f8ad..f5d92e71e6 100644 --- a/doc/dev/coding-guidelines-and-review.txt +++ b/doc/dev/coding-guidelines-and-review.txt @@ -63,7 +63,11 @@ ready for review:: - [ ] If it introduces new functionality in scripts/ is it tested? Check for code coverage. - [ ] Is it well formatted? Look at `make pep8`, `make diff_pylint_report`, - `make cppcheck`, and `make doc` output. Use `make format` and manual fixing as needed. + `make cppcheck`, and `make doc` output. Use `make format` and manual + fixing as needed. + - [ ] Did it change the command-line interface? Only additions are allowed + without a major version increment. Changing file formats also requires a + major version number increment. - [ ] Is it documented in the ChangeLog? - [ ] Was a spellchecker run on the source code and documentation after changes were made? From 80423e76dc3cbbc18e6efc1dfe0f64a6bb716630 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 2 Sep 2014 10:01:41 -0400 Subject: [PATCH 3/4] include the sandbox --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index c87cd0f52b..ea77197f51 100644 --- a/Makefile +++ b/Makefile @@ -105,7 +105,7 @@ pylint: $(PYSOURCES) $(wildcard tests/*.py) pylint_report.txt: ${PYSOURCES} $(wildcard tests/*.py) pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \ setup.py khmer/[!_]*.py khmer/__init__.py scripts/*.py tests \ - > pylint_report.txt || true + sandbox/*.py > pylint_report.txt || true diff_pylint_report: pylint_report.txt diff-quality --violations=pylint pylint_report.txt From 57ba15c9e78f9ba3d1716b7e920749204090a24c Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 3 Dec 2014 14:23:03 -0500 Subject: [PATCH 4/4] doc doc updates --- ChangeLog | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/ChangeLog b/ChangeLog index f4aa5f7bc4..93b53eaf1d 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,10 @@ +2014-12-07 Michael R. Crusoe + + * Makefile: add sandbox scripts to the pylint_report.txt target + * doc/dev/coding-guidelines-and-review.txt: Add question about command + line API to the checklist + * doc/dev/release.txt: refresh release procedure + 2014-12-05 Michael R. Crusoe * CITATIONS,khmer/khmer_args.py: update citations for Qingpeng's paper