From f8300a9ae9d609c8984887a14135bbac6cc0e4bf Mon Sep 17 00:00:00 2001 From: Ishaan Desai Date: Tue, 21 May 2024 10:32:59 +0200 Subject: [PATCH] Make the steps about upgrading pip and installing dependencies for the Micro Manager consistent in all workflows --- .github/workflows/run-adaptivity-test.yml | 12 ++++++------ .../run-domain-decomposition-tests.yml | 19 +++++++++++-------- .github/workflows/run-macro-micro-dummy.yml | 18 ++++++++++++------ 3 files changed, 29 insertions(+), 20 deletions(-) diff --git a/.github/workflows/run-adaptivity-test.yml b/.github/workflows/run-adaptivity-test.yml index b5e385c8..eb78676d 100644 --- a/.github/workflows/run-adaptivity-test.yml +++ b/.github/workflows/run-adaptivity-test.yml @@ -23,8 +23,7 @@ jobs: run: | apt-get -qq update apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config - python -m pip install --upgrade pip - pip install setuptools wheel twine + pip3 install --upgrade pip - name: Install Micro Manager working-directory: micro-manager @@ -34,13 +33,15 @@ jobs: timeout-minutes: 3 working-directory: micro-manager/tests/integration/test_unit_cube run: | - micro-manager-precice micro-manager-config-local-adaptivity.json & python3 unit_cube.py + micro-manager-precice micro-manager-config-local-adaptivity.json & + python3 unit_cube.py - name: Run integration test with global adaptivity timeout-minutes: 3 working-directory: micro-manager/tests/integration/test_unit_cube run: | - micro-manager-precice micro-manager-config-global-adaptivity.json & python3 unit_cube.py + micro-manager-precice micro-manager-config-global-adaptivity.json & + python3 unit_cube.py adaptivity_unit_tests_serial: name: Run adaptivity unit tests in serial @@ -91,8 +92,7 @@ jobs: run: | apt-get -qq update apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config - python -m pip install --upgrade pip - pip install setuptools wheel twine + pip3 install --upgrade pip - name: Install Micro Manager working-directory: micro-manager diff --git a/.github/workflows/run-domain-decomposition-tests.yml b/.github/workflows/run-domain-decomposition-tests.yml index 2c6c6015..9b04b9a9 100644 --- a/.github/workflows/run-domain-decomposition-tests.yml +++ b/.github/workflows/run-domain-decomposition-tests.yml @@ -30,23 +30,27 @@ jobs: - name: Install Dependencies working-directory: micro-manager run: | + apt-get -qq update apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config - python -m pip install --upgrade pip - pip install setuptools wheel twine + pip3 install --upgrade pip - name: Install micro-manager working-directory: micro-manager run: pip3 install --user . - - name: Run integration test (variant 1) + - name: Run integration test (2 processes) timeout-minutes: 3 working-directory: micro-manager/tests/integration/test_unit_cube - run: mpiexec -n 2 --allow-run-as-root micro-manager-precice micro-manager-config-parallel-1.json & python3 unit_cube.py + run: | + mpiexec -n 2 --allow-run-as-root micro-manager-precice micro-manager-config-parallel-1.json & + python3 unit_cube.py - - name: Run integration test (variant 2) + - name: Run integration test (6 processes) timeout-minutes: 3 working-directory: micro-manager/tests/integration/test_unit_cube - run: mpiexec -n 6 --oversubscribe --allow-run-as-root micro-manager-precice micro-manager-config-parallel-2.json & python3 unit_cube.py + run: | + mpiexec -n 6 --oversubscribe --allow-run-as-root micro-manager-precice micro-manager-config-parallel-2.json & + python3 unit_cube.py domain_decomposition_unit_tests: name: Run domain decomposition unit tests @@ -63,8 +67,7 @@ jobs: run: | apt-get -qq update apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config - python -m pip install --upgrade pip - pip install setuptools wheel + pip3 install --upgrade pip - name: Install Micro Manager working-directory: micro-manager diff --git a/.github/workflows/run-macro-micro-dummy.yml b/.github/workflows/run-macro-micro-dummy.yml index 6292cd36..7930fd2d 100644 --- a/.github/workflows/run-macro-micro-dummy.yml +++ b/.github/workflows/run-macro-micro-dummy.yml @@ -25,8 +25,7 @@ jobs: apt-get -qq update apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config apt-get -qq install sudo - python -m pip install --upgrade pip - pip install setuptools wheel twine + pip3 install --upgrade pip - name: Install micro-manager working-directory: micro-manager @@ -35,12 +34,16 @@ jobs: - name: Run python macro-micro dummy timeout-minutes: 3 working-directory: micro-manager/examples - run: micro-manager-precice micro-manager-config.json & python3 macro_dummy.py + run: | + micro-manager-precice micro-manager-config.json & + python3 macro_dummy.py - name: Run adaptive python macro-micro dummy timeout-minutes: 3 working-directory: micro-manager/examples - run: micro-manager-precice micro-manager-adaptivity-config.json & python3 macro_dummy.py + run: | + micro-manager-precice micro-manager-adaptivity-config.json & + python3 macro_dummy.py - name: Run c++ macro-micro dummy timeout-minutes: 3 @@ -50,9 +53,12 @@ jobs: pip install pybind11 c++ -O3 -Wall -shared -std=c++11 -fPIC $(python3 -m pybind11 --includes) micro_cpp_dummy.cpp -o micro_dummy$(python3-config --extension-suffix) cd ../ - micro-manager-precice micro-manager-config.json & python3 macro_dummy.py + micro-manager-precice micro-manager-config.json & + python3 macro_dummy.py - name: Run adaptive c++ macro-micro dummy timeout-minutes: 3 working-directory: micro-manager/examples - run: micro-manager-precice micro-manager-adaptivity-config.json & python3 macro_dummy.py + run: | + micro-manager-precice micro-manager-adaptivity-config.json & + python3 macro_dummy.py