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Upgrade to using ska2 #383

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Upgrade to using ska2 #383

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1da11b9
Mask repeats with ska2
nickjcroucher Jun 22, 2023
9d3ab7b
Add R plotting script
nickjcroucher Sep 7, 2023
8f54050
Update R dependencies for plotting
nickjcroucher Sep 7, 2023
406e18a
Add plotting test
nickjcroucher Sep 7, 2023
2f7b077
Remove jellyfish deletion command
nickjcroucher Sep 7, 2023
f50cb93
Update obsolete macro
nickjcroucher Sep 7, 2023
a65ca7d
Update from setup.py to pip
nickjcroucher Sep 7, 2023
3af2159
Correct interpreter path
nickjcroucher Sep 7, 2023
e9eddf4
Remove obsolete deletion command
nickjcroucher Sep 7, 2023
4f2b2d3
Add unique sequences for ska test
nickjcroucher Sep 7, 2023
b1774f9
Define prototype for main
nickjcroucher Sep 7, 2023
5880fae
Add sequences to test
nickjcroucher Sep 7, 2023
5470b83
Fix kmer length
nickjcroucher Sep 7, 2023
59456ac
Fix annotation
nickjcroucher Sep 8, 2023
4b75805
Ensure latest llvm
nickjcroucher Sep 8, 2023
f04a3b2
Remove coverage flag from OSX compilation
nickjcroucher Sep 8, 2023
4146c8f
Distribute libclang across clang versions
nickjcroucher Sep 8, 2023
1bf8b49
Remove sudo to prevent cache permissions problems
nickjcroucher Sep 8, 2023
a0b3fb4
Enable taxon label size adjustment
nickjcroucher Sep 8, 2023
f3893f4
Enable direct annotation of the tree
nickjcroucher Sep 8, 2023
7de52b9
Add clade annotation to plotting test
nickjcroucher Sep 8, 2023
35498c0
Add input validation
nickjcroucher Sep 8, 2023
865cfb1
Annotate main function
nickjcroucher Sep 8, 2023
72fbefa
Ensure compatibility with different inputs
nickjcroucher Sep 9, 2023
1ebe4e5
Add comprehensive plotting tests
nickjcroucher Sep 9, 2023
5492366
Fix type in commands
nickjcroucher Sep 10, 2023
62958a0
Update with links to plotting advice
nickjcroucher Sep 10, 2023
fc6ee52
Add plotting documentation
nickjcroucher Sep 11, 2023
abf65c6
Add necessary plotting commands
nickjcroucher Sep 11, 2023
1b689a7
Fix broken link
nickjcroucher Sep 11, 2023
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8 changes: 4 additions & 4 deletions .github/workflows/build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,9 @@ jobs:
- name: Install dependencies with conda
run: |
sudo chown -R $UID $CONDA && source $CONDA/etc/profile.d/conda.sh && conda env update --file environment.yml
- name: Run C++ and python tests
- name: Run C and python tests
run: |
source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && export PATH=$PATH:/lib/python3.9/site-packages/ && autoreconf -i && ./configure --prefix=$CONDA_PREFIX --exec_prefix $CONDA_PREFIX CFLAGS="-O0 --coverage -I${CONDA_PREFIX}/include/" LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/" --host=x86_64-apple-darwin --build=x86_64-apple-darwin && make && sudo make install && make check
source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && FILES=`ls -l1 $CONDA_PREFIX/lib/clang/*/lib/darwin/*`; for clang_dir in $(ls -d1 $CONDA_PREFIX/lib/clang/*); do if [[ ! -d "$clang_dir/lib/darwin" ]]; then mkdir -p $clang_dir/lib/darwin; for clang_file in $(echo $FILES); do ln -s $clang_file $clang_dir/lib/darwin/; done; fi; done && export PATH=$PATH:/lib/python3.9/site-packages/ && autoreconf -i && ./configure --prefix=$CONDA_PREFIX --exec_prefix $CONDA_PREFIX CFLAGS="-O0 -I${CONDA_PREFIX}/include/" LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/" --host=x86_64-apple-darwin --build=x86_64-apple-darwin && make && make install && make check

test-linux:
runs-on: ubuntu-latest
Expand All @@ -36,9 +36,9 @@ jobs:
- name: Install subunit from source
run: |
source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && export LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/" && export CFLAGS="-I${CONDA_PREFIX}/include/" && export CPPUNIT_CFLAGS="-I${CONDA_PREFIX}/include/" && export CPPUNIT_LIBS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/" && conda install -c conda-forge testtools extras six testscenarios fixtures traceback2 python-mimeparse iso8601 && git clone https://github.com/testing-cabal/subunit.git && cd subunit && autoreconf -vi && CXXFLAGS="${CXXFLAGS} -I${CONDA_PREFIX}/include/" LDFLAGS="${LDFLAGS} -L${CONDA_PREFIX}/lib/ -lcppunit" ./configure --prefix=$CONDA_PREFIX && sudo make install && make check && cd ..
- name: Run C++ and python tests
- name: Run C and python tests
run: |
source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && export LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/ --coverage" && export CFLAGS="-I${CONDA_PREFIX}/include/ --coverage" && export PATH=$PATH:/lib/python3.9/site-packages/ && export NUMBA_DISABLE_JIT=1 && autoreconf -i && ./configure --prefix=$CONDA_PREFIX --exec_prefix $CONDA_PREFIX -enable-code-coverage CFLAGS="$CFLAGS" LDFLAGS="$LDFLAGS" --host=x86_64-linux-gnu --build=x86_64-linux-gnu && make && sudo make install && export CODE_COVERAGE_OUTPUT_FILE="gubbins_coverage.info" && make check && make check-code-coverage
source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && export LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/ --coverage" && export CFLAGS="-I${CONDA_PREFIX}/include/ --coverage" && export PATH=$PATH:/lib/python3.9/site-packages/ && export NUMBA_DISABLE_JIT=1 && autoreconf -i && ./configure --prefix=$CONDA_PREFIX --exec_prefix $CONDA_PREFIX -enable-code-coverage CFLAGS="$CFLAGS" LDFLAGS="$LDFLAGS" --host=x86_64-linux-gnu --build=x86_64-linux-gnu && make && make install && export CODE_COVERAGE_OUTPUT_FILE="gubbins_coverage.info" && make check && make check-code-coverage
- name: Upload python code coverage analysis
uses: codecov/codecov-action@v2
with:
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