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jeromekelleherjeromekelleher
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Merge pull request #36 from jeromekelleher/initial-circle
Initial circleCI config.
2 parents 58ace5f + 7ca664c commit 46167ef

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‎.circleci/config.yml‎

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version: 2
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jobs:
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build:
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docker:
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- image: circleci/python:3.6-stretch
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working_directory: /home/circleci/tskit
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steps:
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- checkout
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- run: sudo chown -R circleci:circleci *
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# - restore_cache:
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# key: tskit-{{ .Branch }}
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- run:
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name: Checkout submodules
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command: |
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git submodule update --init --recursive --remote
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- run:
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name: Install dependencies and set path
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command: |
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sudo apt-get install ninja-build libcunit1-dev valgrind clang doxygen libgsl-dev
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pip install --user -r python/requirements/development.txt
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pip install meson --user
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# tmp; until we have an msprime package install from here.
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pip install --user --pre --upgrade tskit
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pip install --user git+https://github.com/tskit-dev/msprime
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echo 'export PATH=/home/circleci/.local/bin:$PATH' >> $BASH_ENV
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# - save_cache:
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# key: tskit-{{ .Branch }}
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# paths:
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# - "/home/circleci/.local"
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- run:
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name: Compile Python
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command: |
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cd python
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# CFLAGS="--coverage -Wall -Wextra -Werror -Wno-unused-parameter" \
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# python setup.py build_ext --inplace
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# TODO enable these flags later.
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CFLAGS="--coverage" python setup.py build_ext --inplace
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- run:
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name: Lint Python
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command: |
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cd python
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flake8 --max-line-length 89 tskit setup.py tests
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- run:
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name: Run Python tests
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command: |
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PYTHONPATH=python nosetests -v --with-coverage --cover-package tskit \
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--cover-branches --cover-erase --cover-xml \
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--cover-inclusive python/tests
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python3 -m codecov -F python
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- run:
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name: Build Python package
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command: |
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cd python
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rm -fR build
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python setup.py sdist
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python setup.py check
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python -m venv venv
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source venv/bin/activate
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pip install --upgrade setuptools pip wheel
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python setup.py build_ext
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python setup.py egg_info
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python setup.py bdist_wheel
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# TODO This doesn't seem to be installing, fails on bdist_wheel build.
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# pip install dist/*.tar.gz
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# - run:
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# name: Compile C
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# command: |
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# CFLAGS=--coverage meson c/ build-gcc && cd build-gcc && ninja
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# - run:
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# name: Run C tests
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# command: |
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# export KASTORE_SOPATH=./build-gcc/libtskit.so
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# ./build-gcc/tests
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# ./build-gcc/dynamic_api_tests
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# ./build-gcc/malloc_tests
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# ./build-gcc/io_tests
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# - run:
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# name: Valgrind for C tests.
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# command: |
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# export KASTORE_SOPATH=./build-gcc/libtskit.so
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# valgrind --leak-check=full --error-exitcode=1 ./build-gcc/tests
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# valgrind --leak-check=full --error-exitcode=1 ./build-gcc/dynamic_api_tests
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# valgrind --leak-check=full --error-exitcode=1 ./build-gcc/malloc_tests
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# valgrind --leak-check=full --error-exitcode=1 ./build-gcc/io_tests
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# - run:
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# name: Run gcov & upload coverage.
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# command: |
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# gcov -pb -o ./python/build/temp.linux*/ python/_tskitmodule.c
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# gcov -pb ./build-gcc/tests@exe/tskit.c.gcno \
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# ./build-gcc/malloc_tests@exe/tskit.c.gcno \
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# ./build-gcc/io_tests@exe/tskit.c.gcno \
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# ./build-gcc/dynamic_api_tests@exe/tskit.c.gcno \
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# ./build-gcc/tskit@sha/tskit.c.gcno
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# codecov -X gcov -F C
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# - run:
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# name: Compile C tests under clang
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# command: |
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# CC=clang meson c/ build-clang && cd build-clang && ninja
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# - run:
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# name: Run clang C tests
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# command: |
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# export KASTORE_SOPATH=./build-clang/libtskit.so
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# ./build-clang/tests
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# ./build-clang/dynamic_api_tests
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# ./build-clang/malloc_tests
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# ./build-clang/io_tests
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# - run:
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# name: Build docs
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# command: |
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# cd docs && make

‎.codecov.yml‎

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coverage:
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status:
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project:
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python:
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target: 95%
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flags: python
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patch:
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python:
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target: 90%
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flags: python

‎python/requirements/development.txt‎

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codecov
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coverage
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flake8
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h5py
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mock
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newick
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nose
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numpy
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six
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kastore>=0.2.2
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jsonschema
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sphinx
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sphinx-argparse
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sphinx_rtd_theme
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svgwrite
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# Seems to be a problem with Python 3. svgwrite imports
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# pyparsing.
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pyparsing < 2.1
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# We need pysam and PyVCF for testing VCF output.
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# Pin pysam at 0.9 version as there are problems with building py33 version
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# on travis.
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pysam==0.9.1.4
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PyVCF
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# We use JSON-schema to test out metadata handling.
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python_jsonschema_objects

‎python/tests/test_file_format.py‎

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CURRENT_FILE_MAJOR = 12
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test_data_dir = os.path.join(os.path.dirname(__file__), "data")
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def single_locus_no_mutation_example():
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return msprime.simulate(10, random_seed=10)
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def test_format_too_old_raised_for_hdf5(self):
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files = [
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"tests/data/hdf5-formats/msprime-0.3.0_v2.0.hdf5",
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"tests/data/hdf5-formats/msprime-0.4.0_v3.1.hdf5",
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"tests/data/hdf5-formats/msprime-0.5.0_v10.0.hdf5"]
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"msprime-0.3.0_v2.0.hdf5", "msprime-0.4.0_v3.1.hdf5",
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"msprime-0.5.0_v10.0.hdf5"]
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for filename in files:
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self.assertRaises(exceptions.VersionTooOldError, tskit.load, filename)
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path = os.path.join(test_data_dir, "hdf5-formats", filename)
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self.assertRaises(exceptions.VersionTooOldError, tskit.load, path)
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def test_msprime_v_0_5_0(self):
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ts = tskit.load_legacy("tests/data/hdf5-formats/msprime-0.5.0_v10.0.hdf5")
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path = os.path.join(test_data_dir, "hdf5-formats", "msprime-0.5.0_v10.0.hdf5")
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ts = tskit.load_legacy(path)
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self.verify_tree_sequence(ts)
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def test_msprime_v_0_4_0(self):
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ts = tskit.load_legacy("tests/data/hdf5-formats/msprime-0.4.0_v3.1.hdf5")
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path = os.path.join(test_data_dir, "hdf5-formats", "msprime-0.4.0_v3.1.hdf5")
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ts = tskit.load_legacy(path)
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self.verify_tree_sequence(ts)
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def test_msprime_v_0_3_0(self):
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ts = tskit.load_legacy("tests/data/hdf5-formats/msprime-0.3.0_v2.0.hdf5")
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path = os.path.join(test_data_dir, "hdf5-formats", "msprime-0.3.0_v2.0.hdf5")
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ts = tskit.load_legacy(path)
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self.verify_tree_sequence(ts)
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‎python/tests/test_highlevel.py‎

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self.assertGreater(num_mutations, 0)
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def test_simplify_bugs(self):
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prefix = "tests/data/simplify-bugs/"
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prefix = os.path.join(
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os.path.dirname(__file__), "data", "simplify-bugs")
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j = 1
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while True:
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nodes_file = os.path.join(prefix, "{:02d}-nodes.txt".format(j))

‎python/tests/test_provenance.py‎

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"""
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def test_file_equal(self):
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s1 = provenance.get_schema()
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with open(os.path.join("tskit", "provenance.schema.json")) as f:
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base = os.path.join(os.path.dirname(__file__), "..", "tskit")
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with open(os.path.join(base, "provenance.schema.json")) as f:
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s2 = json.load(f)
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self.assertEqual(s1, s2)
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