Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Mutation map #711

Merged
merged 7 commits into from
Mar 24, 2020
Merged

Mutation map #711

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
0f14bc0
Add poisson and flat to RandomGenerator for testing.
jeromekelleher Feb 19, 2019
62db04c
Outline Python implementation.
jeromekelleher Feb 19, 2019
ee3a9ee
Added low-level code for mutation maps.
jeromekelleher Feb 21, 2019
b752c9e
Change intervals to same as recomb map.
jeromekelleher Mar 22, 2020
d9d81cc
Basic definition of interval_map class.
jeromekelleher Mar 22, 2020
b993263
Refactor recomb_map to use the interval_map.
jeromekelleher Mar 22, 2020
de191d5
Added the IntervalMap & update high-level code.
jeromekelleher Mar 22, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 11 additions & 10 deletions .circleci/config.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ jobs:
- run:
name: Checkout submodules
command: |
git submodule update --init --recursive
git submodule update --init --recursive
# Write out the status for debugging purposes. Are we checked out at tags?
git submodule status --recursive
- run:
Expand Down Expand Up @@ -44,7 +44,7 @@ jobs:
name: Run highlevel tests and upload coverage
command: |
nosetests -v --with-coverage --cover-package msprime \
--cover-branches --cover-erase --cover-xml --cover-inclusive tests
--cover-branches --cover-erase --cover-xml --cover-inclusive tests
codecov -X gcov -F python
rm .coverage

Expand All @@ -65,12 +65,13 @@ jobs:
gcov -pb -o ./build/temp.linux*/ _msprimemodule.c
cd build-gcc
# TODO should be able to do this with 'find', but it's tricky and opaque.
gcov -pb ./msprime@sta/fenwick.c.gcno ../lib/fenwick.c
gcov -pb ./msprime@sta/msprime.c.gcno ../lib/msprime.c
gcov -pb ./msprime@sta/mutgen.c.gcno ../lib/mutgen.c
gcov -pb ./msprime@sta/object_heap.c.gcno ../lib/object_heap.c
gcov -pb ./msprime@sta/recomb_map.c.gcno ../lib/recomb_map.c
gcov -pb ./msprime@sta/util.c.gcno ../lib/util.c
gcov -pb ./msprime@sta/fenwick.c.gcno ../lib/fenwick.c
gcov -pb ./msprime@sta/msprime.c.gcno ../lib/msprime.c
gcov -pb ./msprime@sta/mutgen.c.gcno ../lib/mutgen.c
gcov -pb ./msprime@sta/object_heap.c.gcno ../lib/object_heap.c
gcov -pb ./msprime@sta/recomb_map.c.gcno ../lib/recomb_map.c
gcov -pb ./msprime@sta/interval_map.c.gcno ../lib/interval_map.c
gcov -pb ./msprime@sta/util.c.gcno ../lib/util.c
cd ..
codecov -X gcov -F C

Expand All @@ -87,6 +88,6 @@ jobs:
name: Install from the distribution tarball
command: |
python -m venv venv
source venv/bin/activate
source venv/bin/activate
pip install --upgrade setuptools pip
pip install dist/*.tar.gz
pip install dist/*.tar.gz
Loading