From 075967de569d3ae42dc18cf7af06666dffa3ab80 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Mon, 11 Jul 2022 10:33:57 +0100 Subject: [PATCH 01/14] Update .gitmodules --- .gitmodules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitmodules b/.gitmodules index b9435cb704..a6e62b646d 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +1,3 @@ [submodule "src/pyne/pyne"] path = src/pyne/pyne - url = https://github.com/pyne/pyne + url = https://github.com/pyne/pyne.git From 033d1d30b838adf56972fe21f2aca6f1c5745592 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Mon, 11 Jul 2022 10:49:51 +0100 Subject: [PATCH 02/14] updated checkout action to v3 --- .github/workflows/docker_publish.yml | 12 ++++++------ .github/workflows/housekeeping.yml | 2 +- .github/workflows/linux_build_test.yml | 2 +- .github/workflows/mac_build_test.yml | 2 +- .github/workflows/windows_build_test.yml | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index ae4097a6a9..f33266fb43 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -22,7 +22,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Set up QEMU uses: docker/setup-qemu-action@v1 @@ -67,7 +67,7 @@ jobs: password: ${{ secrets.GITHUB_TOKEN }} - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Build and push Dockerfile_1_housekeeping uses: docker/build-push-action@v2 @@ -112,7 +112,7 @@ jobs: password: ${{ secrets.GITHUB_TOKEN }} - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Build and push Dockerfile_1_external_deps uses: docker/build-push-action@v2 @@ -182,7 +182,7 @@ jobs: password: ${{ secrets.GITHUB_TOKEN }} - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Build and push Dockerfile_3_moab uses: docker/build-push-action@v2 @@ -215,7 +215,7 @@ jobs: name: Running Housekeeping scrips steps: - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 with: submodules: recursive @@ -261,7 +261,7 @@ jobs: name: Installing and Testing DAGMC steps: - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 with: submodules: recursive diff --git a/.github/workflows/housekeeping.yml b/.github/workflows/housekeeping.yml index 376d4d9458..279ac75ad5 100644 --- a/.github/workflows/housekeeping.yml +++ b/.github/workflows/housekeeping.yml @@ -14,7 +14,7 @@ jobs: image: ghcr.io/svalinn/dagmc-ci-ubuntu-18.04-housekeeping:stable steps: - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Setup environment run: | diff --git a/.github/workflows/linux_build_test.yml b/.github/workflows/linux_build_test.yml index 862b1488e1..872155fff3 100644 --- a/.github/workflows/linux_build_test.yml +++ b/.github/workflows/linux_build_test.yml @@ -58,7 +58,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 with: submodules: recursive diff --git a/.github/workflows/mac_build_test.yml b/.github/workflows/mac_build_test.yml index 615ac57085..cd9e917dab 100644 --- a/.github/workflows/mac_build_test.yml +++ b/.github/workflows/mac_build_test.yml @@ -22,7 +22,7 @@ jobs: runs-on: macos-10.15 steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Initial setup shell: bash -l {0} diff --git a/.github/workflows/windows_build_test.yml b/.github/workflows/windows_build_test.yml index 2919511dcf..8a36af3dc9 100644 --- a/.github/workflows/windows_build_test.yml +++ b/.github/workflows/windows_build_test.yml @@ -63,7 +63,7 @@ jobs: cmake --build . --config Release cmake --install . --config Release - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: build DAGMC shell: bash -l {0} From 1c06011ce7eac73fbdb3e8a7811544cf2aedd3f5 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Mon, 11 Jul 2022 11:04:05 +0100 Subject: [PATCH 03/14] added dagmc as safe dir --- .github/workflows/docker_publish.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index f33266fb43..3968cb167c 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -218,6 +218,8 @@ jobs: uses: actions/checkout@v3 with: submodules: recursive + set-safe-directory: 'DAGMC/DAGMC' + - name: Setup run: | From 9f5380de41d2940b7d173214162b28d95433ba74 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Mon, 11 Jul 2022 11:12:04 +0100 Subject: [PATCH 04/14] added abs path dagmc as safe dir --- .github/workflows/docker_publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 3968cb167c..0df4cf2e1e 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -218,7 +218,7 @@ jobs: uses: actions/checkout@v3 with: submodules: recursive - set-safe-directory: 'DAGMC/DAGMC' + set-safe-directory: '/__w/DAGMC/DAGMC' - name: Setup From fb93266ad2dce0eac56520758938b991d0091b8c Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Mon, 11 Jul 2022 11:40:39 +0100 Subject: [PATCH 05/14] added safe directory for dag install --- .github/workflows/docker_publish.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 0df4cf2e1e..68c5de9b9c 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -218,7 +218,7 @@ jobs: uses: actions/checkout@v3 with: submodules: recursive - set-safe-directory: '/__w/DAGMC/DAGMC' + set-safe-directory: "/__w/DAGMC/DAGMC" - name: Setup @@ -266,6 +266,7 @@ jobs: uses: actions/checkout@v3 with: submodules: recursive + set-safe-directory: "/__w/DAGMC/DAGMC" - name: Setup run: | From d9a2be157b1934a91c7daf2ac76bafcf21ea1f34 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Mon, 11 Jul 2022 11:47:46 +0100 Subject: [PATCH 06/14] added entry for safe dir PR --- doc/CHANGELOG.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/CHANGELOG.rst b/doc/CHANGELOG.rst index 0cbcc6a5e1..06d963b414 100644 --- a/doc/CHANGELOG.rst +++ b/doc/CHANGELOG.rst @@ -10,6 +10,7 @@ Next version **Changed:** * Using multi stage Dockerfile to reduce the number of Dockerfile (#813) + * Adding safe folder to allow CI to compile DAGMC (#814) v3.2.2 From 42bc8fa30054bf3d351f914f89ba158513c39a94 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Wed, 13 Jul 2022 21:09:19 +0100 Subject: [PATCH 07/14] Suggestions from PR review by @gonuke Co-authored-by: Paul Wilson --- .github/workflows/docker_publish.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 68c5de9b9c..12826c0626 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -218,7 +218,7 @@ jobs: uses: actions/checkout@v3 with: submodules: recursive - set-safe-directory: "/__w/DAGMC/DAGMC" + set-safe-directory: ${GITHUB_WORKSPACE} - name: Setup @@ -266,7 +266,7 @@ jobs: uses: actions/checkout@v3 with: submodules: recursive - set-safe-directory: "/__w/DAGMC/DAGMC" + set-safe-directory: ${GITHUB_WORKSPACE} - name: Setup run: | From 412f1404022e551a86d941f6a2bf714661dd9dc3 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Thu, 14 Jul 2022 18:39:11 +0100 Subject: [PATCH 08/14] replaced checkout safe dir with git config --- .github/workflows/docker_publish.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 12826c0626..71b05dff4f 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -218,11 +218,10 @@ jobs: uses: actions/checkout@v3 with: submodules: recursive - set-safe-directory: ${GITHUB_WORKSPACE} - - name: Setup run: | + git config --global --add safe.directory ${GITHUB_WORKSPACE} mkdir /root/build_dir/ echo "REPO_SLUG=${GITHUB_REPOSITORY}" >> $GITHUB_ENV echo "PULL_REQUEST=$(echo $GITHUB_REF | cut -d"/" -f3)" >> $GITHUB_ENV @@ -266,10 +265,10 @@ jobs: uses: actions/checkout@v3 with: submodules: recursive - set-safe-directory: ${GITHUB_WORKSPACE} - name: Setup run: | + git config --global --add safe.directory ${GITHUB_WORKSPACE} echo "MOAB_VERSION=${{ matrix.moab_versions }}" >> $GITHUB_ENV echo "COMPILER=${{ matrix.compiler }}" >> $GITHUB_ENV echo "HDF5_VERSION=${{ matrix.hdf5_versions }}" >> $GITHUB_ENV From e157c92583d169cb30d9c8783f17447995d72904 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Fri, 15 Jul 2022 10:13:46 +0100 Subject: [PATCH 09/14] added /github/home as safe dir --- .github/workflows/docker_publish.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 71b05dff4f..9a0e841341 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -269,6 +269,7 @@ jobs: - name: Setup run: | git config --global --add safe.directory ${GITHUB_WORKSPACE} + git config --global --add safe.directory /github/home echo "MOAB_VERSION=${{ matrix.moab_versions }}" >> $GITHUB_ENV echo "COMPILER=${{ matrix.compiler }}" >> $GITHUB_ENV echo "HDF5_VERSION=${{ matrix.hdf5_versions }}" >> $GITHUB_ENV From 1b803013bc76c621874c6fad5d8f0a467c385fcc Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Fri, 15 Jul 2022 15:37:30 +0100 Subject: [PATCH 10/14] added more folders to safe dir --- .github/workflows/docker_publish.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 9a0e841341..c49762b7ef 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -269,7 +269,10 @@ jobs: - name: Setup run: | git config --global --add safe.directory ${GITHUB_WORKSPACE} - git config --global --add safe.directory /github/home + git config --global --add safe.directory /github/home/ + git config --global --add safe.directory /github/home/.cache + git config --global --add safe.directory /github/home/.cache/pip + git config --global --add safe.directory /github/home/.cache/pip/http echo "MOAB_VERSION=${{ matrix.moab_versions }}" >> $GITHUB_ENV echo "COMPILER=${{ matrix.compiler }}" >> $GITHUB_ENV echo "HDF5_VERSION=${{ matrix.hdf5_versions }}" >> $GITHUB_ENV From 751ab7951ce26aecb75f09ac203bf11d7769bcc2 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Thu, 21 Jul 2022 14:47:33 +0100 Subject: [PATCH 11/14] changed from 5.3.0 to 5.3.1 moab --- .github/workflows/docker_publish.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index c49762b7ef..fb4710c85d 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -8,7 +8,7 @@ on: - 'CI/?ocker**' - '.github/workflows/docker_publish.yml' - + jobs: build-base-img: runs-on: ubuntu-latest @@ -163,7 +163,7 @@ jobs: 1.10.4, ] moab_versions : [ - 5.3.0, + 5.3.1, develop, master, ] From 212025391838a7aff0cb1c73d7a5f015de2960a2 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Mon, 25 Jul 2022 21:46:00 +0100 Subject: [PATCH 12/14] updated to latest 5.4.0 moab --- .github/workflows/docker_publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index fb4710c85d..18c03c4576 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -163,7 +163,7 @@ jobs: 1.10.4, ] moab_versions : [ - 5.3.1, + 5.4.0, develop, master, ] From 880fc4e3941b7193ad0163932498ff840402916a Mon Sep 17 00:00:00 2001 From: Baptiste Mouginot <15145274+bam241@users.noreply.github.com> Date: Mon, 1 Aug 2022 22:21:18 +0200 Subject: [PATCH 13/14] update PYTHONPATH --- CI/Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CI/Dockerfile b/CI/Dockerfile index 2f25be054b..0bacbc7e76 100644 --- a/CI/Dockerfile +++ b/CI/Dockerfile @@ -80,6 +80,8 @@ RUN /root/etc/CI/docker/build_hdf5.sh FROM hdf5 AS moab +ENV PYTHONPATH=/root/build_dir/moab/bld/pymoab/lib/python3.6/site-packages + # Set MOAB env variable ENV moab_build_dir=${build_dir}/moab ENV moab_install_dir=${install_dir}/moab From 71075d730649aa53d53a23b32cafa68cbab568fc Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Thu, 4 Aug 2022 13:08:07 +0100 Subject: [PATCH 14/14] added pymoab import check --- CI/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/CI/Dockerfile b/CI/Dockerfile index 0bacbc7e76..3a1753b7ec 100644 --- a/CI/Dockerfile +++ b/CI/Dockerfile @@ -93,3 +93,4 @@ RUN if [ "${MOAB_VERSION}" != "master" ] && [ "${MOAB_VERSION}" != "develop" ]; /root/etc/CI/docker/build_moab.sh; \ fi; +RUN python -c "import pymoab"