From 70bae358e3b3fdb1227af0de5d2989f81df6f14b Mon Sep 17 00:00:00 2001 From: IAlibay Date: Tue, 15 Aug 2023 01:56:38 +0100 Subject: [PATCH 1/6] Add tarball install tests and make sure we use clang with macos --- .github/workflows/gh-ci-cron.yaml | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 12b409f012d..5f03ed6fae9 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -3,6 +3,9 @@ on: schedule: # 3 am Tuesdays and Fridays - cron: "0 3 * * 2,5" + pull_request: + branches: + - develop concurrency: # Probably overly cautious group naming. @@ -211,16 +214,21 @@ jobs: conda-latest-release: # A set of runner to check that the latest conda release works as expected if: "github.repository == 'MDAnalysis/mdanalysis'" - runs-on: ${{ matrix.os }} + runs-on: ${{ matrix.os }}-latest timeout-minutes: 60 strategy: fail-fast: false matrix: - os: [ubuntu-latest, macos-latest] + os: [ubuntu, macos] python-version: ["3.9", "3.10", "3.11"] steps: - uses: actions/checkout@v3 + - name: setup_os + uses: ./.github/actions/setup-os + with: + os-type: ${{ matrix.os }} + - name: setup_micromamba uses: mamba-org/setup-micromamba@v1 with: @@ -253,14 +261,22 @@ jobs: pypi-latest-release: # A set of runner to check that the latest conda release works as expected if: "github.repository == 'MDAnalysis/mdanalysis'" - runs-on: ${{ matrix.os }} + runs-on: ${{ matrix.os }}-latest timeout-minutes: 60 strategy: fail-fast: false matrix: - os: [ubuntu-latest, macos-latest, windows-latest] + os: [ubuntu, macos, windows] python-version: ["3.9", "3.10", "3.11"] + wheels: ['true', 'false'] steps: + - uses: actions/checkout@v3 + + - name: setup_os + uses: ./.github/actions/setup-os + with: + os-type: ${{ matrix.os }} + - uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} @@ -268,7 +284,10 @@ jobs: - name: install_mdanalysis shell: bash run: | - pip install mdanalysis mdanalysistests pytest-xdist pytest-timeout "gsd<3.0" + if [ "${{ matrix.wheels }}" == "false" ]; then + INSTALL_FLAGS="--no-binary -v" + fi + pip install ${INSTALL_FLAGS} mdanalysis mdanalysistests pytest-xdist pytest-timeout "gsd<3.0" - name: run_tests shell: bash From 539b8b4c3b5b747021a7aa0978799530f07a80a7 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Tue, 15 Aug 2023 01:57:41 +0100 Subject: [PATCH 2/6] increase verbosity --- .github/workflows/gh-ci-cron.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 5f03ed6fae9..60e723a8a8c 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -285,7 +285,7 @@ jobs: shell: bash run: | if [ "${{ matrix.wheels }}" == "false" ]; then - INSTALL_FLAGS="--no-binary -v" + INSTALL_FLAGS="--no-binary -vvv" fi pip install ${INSTALL_FLAGS} mdanalysis mdanalysistests pytest-xdist pytest-timeout "gsd<3.0" From f0efe47d266adb9767c7069fa32f2304b96ce007 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Tue, 15 Aug 2023 02:02:33 +0100 Subject: [PATCH 3/6] change flag order, no binary has to be just before mdanalysis --- .github/workflows/gh-ci-cron.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 60e723a8a8c..42956bfe4de 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -285,7 +285,7 @@ jobs: shell: bash run: | if [ "${{ matrix.wheels }}" == "false" ]; then - INSTALL_FLAGS="--no-binary -vvv" + INSTALL_FLAGS="-vvv --no-binary" fi pip install ${INSTALL_FLAGS} mdanalysis mdanalysistests pytest-xdist pytest-timeout "gsd<3.0" From adef56b882cf893e790b4ebf9aa49a1b11fc0b5f Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Tue, 15 Aug 2023 19:50:23 +0100 Subject: [PATCH 4/6] some comments --- .github/workflows/gh-ci-cron.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 42956bfe4de..7f6d7e7f3ad 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -270,8 +270,10 @@ jobs: python-version: ["3.9", "3.10", "3.11"] wheels: ['true', 'false'] steps: + # Checkout to have access to local actions (i.e. setup-os) - uses: actions/checkout@v3 + # We need this here in order to make sure we assign the correct compiler (i.e. clang for macos) - name: setup_os uses: ./.github/actions/setup-os with: @@ -284,6 +286,8 @@ jobs: - name: install_mdanalysis shell: bash run: | + # If wheels is False we build directly from source so we use the --no-binary flag + # to avoid pulling down wheels for MDAnalysis (which are already precompiled) if [ "${{ matrix.wheels }}" == "false" ]; then INSTALL_FLAGS="-vvv --no-binary" fi From a8950c7d8d678ee6d756df5006e522f02eb13d59 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Wed, 16 Aug 2023 15:36:32 +0100 Subject: [PATCH 5/6] Update gh-ci-cron.yaml --- .github/workflows/gh-ci-cron.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 7f6d7e7f3ad..f0d6ef1bb7c 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -3,9 +3,6 @@ on: schedule: # 3 am Tuesdays and Fridays - cron: "0 3 * * 2,5" - pull_request: - branches: - - develop concurrency: # Probably overly cautious group naming. From 4254151c25310024d9069971551295924ccd1e52 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 28 Aug 2023 10:26:56 +0100 Subject: [PATCH 6/6] Update gh-ci-cron.yaml --- .github/workflows/gh-ci-cron.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index f0d6ef1bb7c..58ea166bf62 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -288,7 +288,7 @@ jobs: if [ "${{ matrix.wheels }}" == "false" ]; then INSTALL_FLAGS="-vvv --no-binary" fi - pip install ${INSTALL_FLAGS} mdanalysis mdanalysistests pytest-xdist pytest-timeout "gsd<3.0" + pip install ${INSTALL_FLAGS} mdanalysis mdanalysistests pytest-xdist pytest-timeout - name: run_tests shell: bash