From 4820ced582e93a9c3d1eb5903354137dfd9c0822 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 25 Mar 2020 21:18:43 +0100 Subject: [PATCH 1/6] OSX test --- .github/workflows/osx_startup.yaml | 33 ++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 .github/workflows/osx_startup.yaml diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml new file mode 100644 index 00000000000..0d215e97d85 --- /dev/null +++ b/.github/workflows/osx_startup.yaml @@ -0,0 +1,33 @@ +name: OSX +on: [push, pull_request] +jobs: + + test: + name: Startup test + runs-on: macos-latest + strategy: + matrix: + python-version: [3.7] + steps: + - uses: actions/checkout@v2 + with: + path: 'galaxy root' + - uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Cache pip dir + uses: actions/cache@v1 + id: pip-cache + with: + path: ~/.cache/pip + key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }} + - name: Install tox + run: pip install tox + - name: fetch migrations + run: | + wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite + mv db_gx_rev_0141.sqlite database/universe.sqlite + working-directory: 'galaxy root' + - name: run tests + run: tox -e mulled + working-directory: 'galaxy root' From d709a4b9ba661d006dfe61566043e025320c64fc Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 25 Mar 2020 21:26:07 +0100 Subject: [PATCH 2/6] Test py37-first_startup --- .github/workflows/osx_startup.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml index 0d215e97d85..8bd8a74b0f8 100644 --- a/.github/workflows/osx_startup.yaml +++ b/.github/workflows/osx_startup.yaml @@ -29,5 +29,5 @@ jobs: mv db_gx_rev_0141.sqlite database/universe.sqlite working-directory: 'galaxy root' - name: run tests - run: tox -e mulled + run: tox -e py37-first_startup working-directory: 'galaxy root' From aa68c834361cfbab4c8d67e3bc288dc09d8b7034 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 26 Mar 2020 12:54:32 +0100 Subject: [PATCH 3/6] Drop .travis.yml --- .travis.yml | 29 ----------------------------- 1 file changed, 29 deletions(-) delete mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 0f690edec63..00000000000 --- a/.travis.yml +++ /dev/null @@ -1,29 +0,0 @@ -os: osx -# No version of Python is available via virtualenv on OS X workers, see https://github.com/travis-ci/travis-ci/issues/2312 -language: generic - -env: - - TOX_ENV=py27-first_startup - - TOX_ENV=py37-first_startup - -install: - - set -e - - pip install tox - - | - if [ "$TOX_ENV" == "py27-first_startup" ]; then - # Use this job to test the latest migrations - wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite - mv db_gx_rev_0141.sqlite database/universe.sqlite - elif [ "$TOX_ENV" == "py37-first_startup" ]; then - # There is now a pre-installed python3 on osx Travis workers, but use this job to test using a conda environment - MINICONDA_URL="https://repo.anaconda.com/miniconda" - MINICONDA_FILE="Miniconda3-latest-MacOSX-x86_64.sh" - curl -L -O "${MINICONDA_URL}/${MINICONDA_FILE}" - bash $MINICONDA_FILE -b - . ~/miniconda3/bin/activate - fi - -script: tox -e $TOX_ENV - -notifications: - email: false From cbe90b67a9c3803215b10fd0944e54fcbb1e83b0 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 26 Mar 2020 12:55:34 +0100 Subject: [PATCH 4/6] Keep osx-speicifc pip cache --- .github/workflows/osx_startup.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml index 8bd8a74b0f8..b54e0ce7ddd 100644 --- a/.github/workflows/osx_startup.yaml +++ b/.github/workflows/osx_startup.yaml @@ -20,7 +20,7 @@ jobs: id: pip-cache with: path: ~/.cache/pip - key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }} + key: pip-cache-osx-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }} - name: Install tox run: pip install tox - name: fetch migrations From 91794485e8a3fa2bf0ba8d98dc90b95674ad11cc Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Thu, 26 Mar 2020 14:33:23 +0100 Subject: [PATCH 5/6] Use correct location for OSX pip cache Co-Authored-By: Nicola Soranzo --- .github/workflows/osx_startup.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml index b54e0ce7ddd..dfbf85ea777 100644 --- a/.github/workflows/osx_startup.yaml +++ b/.github/workflows/osx_startup.yaml @@ -19,7 +19,7 @@ jobs: uses: actions/cache@v1 id: pip-cache with: - path: ~/.cache/pip + path: ~/Library/Caches/pip key: pip-cache-osx-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }} - name: Install tox run: pip install tox From b9dac3c485e31cad93bae616954c634c66c8bbfd Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 27 Mar 2020 15:28:38 +0000 Subject: [PATCH 6/6] Use osx_startup job to test using Python from a conda env --- .github/workflows/osx_startup.yaml | 21 ++++++++------------- tox.ini | 2 +- 2 files changed, 9 insertions(+), 14 deletions(-) diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml index dfbf85ea777..f59525e812b 100644 --- a/.github/workflows/osx_startup.yaml +++ b/.github/workflows/osx_startup.yaml @@ -5,29 +5,24 @@ jobs: test: name: Startup test runs-on: macos-latest - strategy: - matrix: - python-version: [3.7] steps: - uses: actions/checkout@v2 with: path: 'galaxy root' - - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - name: Cache pip dir uses: actions/cache@v1 id: pip-cache with: path: ~/Library/Caches/pip - key: pip-cache-osx-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }} + # scripts/common_startup.sh creates a conda env for Galaxy containing Python 3.6 + key: pip-cache-3.6-${{ hashFiles('galaxy root/requirements.txt') }} - name: Install tox run: pip install tox - - name: fetch migrations - run: | - wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite - mv db_gx_rev_0141.sqlite database/universe.sqlite - working-directory: 'galaxy root' + - name: Install and activate miniconda # use this job to test using Python from a conda environment + uses: goanpeca/setup-miniconda@v1 + with: + activate-environment: '' - name: run tests - run: tox -e py37-first_startup + run: tox -e first_startup + shell: bash -l {0} # need this to have CONDA_EXE set working-directory: 'galaxy root' diff --git a/tox.ini b/tox.ini index 65f75359293..0757e8e992a 100644 --- a/tox.ini +++ b/tox.ini @@ -17,7 +17,7 @@ passenv = CI CONDA_EXE setenv = first_startup: GALAXY_PYTHON=python first_startup: GALAXY_CONFIG_DATABASE_AUTO_MIGRATE=true - py{35,36,37}-first_startup: GALAXY_VIRTUAL_ENV=.venv3 + py{35,36,37,38}-first_startup: GALAXY_VIRTUAL_ENV=.venv3 unit: GALAXY_VIRTUAL_ENV={envdir} unit: GALAXY_ENABLE_BETA_COMPRESSED_GENBANK_SNIFFING=1 mulled: GALAXY_TEST_INCLUDE_SLOW=1