Merge pull request #384 from nickjcroucher/new_ska2

Add plotting and fix OSX installation bug
nickjcroucher · Sep 11, 2023 · 79da6f0 · 79da6f0
2 parents 97f24cd + 1b689a7
commit 79da6f0
Show file tree

Hide file tree

Showing 18 changed files with 1,302 additions and 43 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -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
@@ -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: