From a0c98536d398c5ba75661b26ecdc87a9a270e51d Mon Sep 17 00:00:00 2001 From: Lee-Ping Wang Date: Mon, 25 Sep 2023 13:01:35 -0700 Subject: [PATCH 1/7] Update ci.yml from Use micromamba in CI (#273) --- .github/workflows/ci.yml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b62efbb25..58461edb4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,15 +34,14 @@ jobs: - name: Checkout uses: actions/checkout@v3 - - name: Install dependencies with Miniconda - uses: conda-incubator/setup-miniconda@v2 + - name: Set up conda environment + uses: mamba-org/provision-with-micromamba@main with: - python-version: ${{ matrix.python-version }} - mamba-version: "*" - activate-environment: forcebalance-test environment-file: devtools/conda-envs/test_env.yaml - auto-activate-base: false - + channel-priority: "flexible" + extra-specs: + python=${{ matrix.python-version }} + - name: Additional info about the build shell: bash run: | @@ -115,7 +114,7 @@ jobs: - name: Run tests run: | - pytest -v --cov=forcebalance --cov-config=setup.cfg --durations=0 --cov-report=xml + pytest -vx --cov=forcebalance --cov-config=setup.cfg --durations=0 --cov-report=xml src/tests/ - name: Run water study run: | From 3a325924f95cdb6734eeb438798529fcc6eb2341 Mon Sep 17 00:00:00 2001 From: Lee-Ping Wang Date: Mon, 25 Sep 2023 15:00:40 -0700 Subject: [PATCH 2/7] Exclude TestEvaluatorBromineStudy --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 58461edb4..71474b230 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -114,7 +114,7 @@ jobs: - name: Run tests run: | - pytest -vx --cov=forcebalance --cov-config=setup.cfg --durations=0 --cov-report=xml src/tests/ + pytest -vx --cov=forcebalance --cov-config=setup.cfg --durations=0 --cov-report=xml -k "not TestEvaluatorBromineStudy" src/tests/ - name: Run water study run: | From 70e120b9d91cb6826e15f2cf252e9b29ed2a096a Mon Sep 17 00:00:00 2001 From: Lee-Ping Wang Date: Mon, 25 Sep 2023 18:18:27 -0700 Subject: [PATCH 3/7] Remove openeye-toolkits from test_env.yaml --- devtools/conda-envs/test_env.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index f1730b205..c9ae7f06a 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -28,4 +28,4 @@ dependencies: - openff-evaluator-base >= 0.4.1 - pint =0.20 # - openff-recharge - - openeye-toolkits + # - openeye-toolkits (Don't have a license file to use with GH Actions.) From 8061849817e1e47c5d9ccafad9838ca238664c4c Mon Sep 17 00:00:00 2001 From: Lee-Ping Wang Date: Tue, 26 Sep 2023 11:08:57 -0700 Subject: [PATCH 4/7] Replace provision-with-micromamba in ci.yml --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 71474b230..9d11540ae 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -35,7 +35,7 @@ jobs: uses: actions/checkout@v3 - name: Set up conda environment - uses: mamba-org/provision-with-micromamba@main + uses: mamba-org/setup-micromamba@v1 with: environment-file: devtools/conda-envs/test_env.yaml channel-priority: "flexible" From ce10eaa3c0619871e4a0771a259f479c6eb021d8 Mon Sep 17 00:00:00 2001 From: Lee-Ping Wang Date: Tue, 26 Sep 2023 11:25:13 -0700 Subject: [PATCH 5/7] Address setup-micromamba warnings --- .github/workflows/ci.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9d11540ae..7a5ffea22 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -38,8 +38,7 @@ jobs: uses: mamba-org/setup-micromamba@v1 with: environment-file: devtools/conda-envs/test_env.yaml - channel-priority: "flexible" - extra-specs: + create-args: >- # beware the >- instead of |, we don't split on newlines but on spaces python=${{ matrix.python-version }} - name: Additional info about the build From d760e3c65066e904a98d740cb32fe9f07ac7621b Mon Sep 17 00:00:00 2001 From: Lee-Ping Wang Date: Tue, 26 Sep 2023 11:52:20 -0700 Subject: [PATCH 6/7] Set -DGMX_USE_RDTSCP=OFF when building Gromacs in ci.yml Seems to cause a hardware-dependent crash . --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7a5ffea22..13785ac9d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -89,10 +89,10 @@ jobs: cd gromacs-5.1.5 cp -r cmake cmake_s cd cmake - cmake -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/opt/gromacs/5.1.5 -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON .. + cmake -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/opt/gromacs/5.1.5 -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_USE_RDTSCP=OFF .. make -j 8 && make install cd ../cmake_s - cmake -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/opt/gromacs/5.1.5 -DGMX_BUILD_OWN_FFTW=ON .. + cmake -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/opt/gromacs/5.1.5 -DGMX_BUILD_OWN_FFTW=ON -DGMX_USE_RDTSCP=OFF .. make -j 8 && make install cd .. . $GITHUB_WORKSPACE/opt/gromacs/5.1.5/bin/GMXRC.bash From 9a02da99b309bc14084e14bfa531df5a1a497a67 Mon Sep 17 00:00:00 2001 From: Lee-Ping Wang Date: Tue, 26 Sep 2023 12:36:31 -0700 Subject: [PATCH 7/7] codecov should not cause workflow failure in ci.yml --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 13785ac9d..e6712f8e5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -126,4 +126,4 @@ jobs: uses: codecov/codecov-action@v3 with: file: ./coverage.xml - fail_ci_if_error: true + fail_ci_if_error: false