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Adding safe folder to allow CI to compile DAGMC #816

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merged 16 commits into from Aug 18, 2022
Merged

Adding safe folder to allow CI to compile DAGMC #816

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075967d
Update .gitmodules
shimwell Jul 11, 2022
033d1d3
updated checkout action to v3
shimwell Jul 11, 2022
1c06011
added dagmc as safe dir
shimwell Jul 11, 2022
9f5380d
added abs path dagmc as safe dir
shimwell Jul 11, 2022
fb93266
added safe directory for dag install
shimwell Jul 11, 2022
d9a2be1
added entry for safe dir PR
shimwell Jul 11, 2022
42bc8fa
Suggestions from PR review by @gonuke
shimwell Jul 13, 2022
412f140
replaced checkout safe dir with git config
shimwell Jul 14, 2022
e157c92
added /github/home as safe dir
shimwell Jul 15, 2022
1b80301
added more folders to safe dir
shimwell Jul 15, 2022
058b1de
Merge branch 'develop' into fixing_docker_publish_ci-2
shimwell Jul 18, 2022
751ab79
changed from 5.3.0 to 5.3.1 moab
shimwell Jul 21, 2022
2120253
updated to latest 5.4.0 moab
shimwell Jul 25, 2022
880fc4e
update PYTHONPATH
bam241 Aug 1, 2022
90e277f
Merge pull request #3 from bam241/fixing_docker_publish_ci-2
shimwell Aug 2, 2022
71075d7
added pymoab import check
shimwell Aug 4, 2022
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22 changes: 14 additions & 8 deletions .github/workflows/docker_publish.yml
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Expand Up @@ -8,7 +8,7 @@ on:
- 'CI/?ocker**'
- '.github/workflows/docker_publish.yml'


jobs:
build-base-img:
runs-on: ubuntu-latest
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -163,7 +163,7 @@ jobs:
1.10.4,
]
moab_versions : [
5.3.0,
5.4.0,
develop,
master,
]
Expand All @@ -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
Expand Down Expand Up @@ -215,12 +215,13 @@ jobs:
name: Running Housekeeping scrips
steps:
- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
submodules: recursive

- 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
Expand Down Expand Up @@ -261,12 +262,17 @@ jobs:
name: Installing and Testing DAGMC
steps:
- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
submodules: recursive

- name: Setup
run: |
git config --global --add safe.directory ${GITHUB_WORKSPACE}
git config --global --add safe.directory /github/home/
git config --global --add safe.directory /github/home/.cache
git config --global --add safe.directory /github/home/.cache/pip
git config --global --add safe.directory /github/home/.cache/pip/http
echo "MOAB_VERSION=${{ matrix.moab_versions }}" >> $GITHUB_ENV
echo "COMPILER=${{ matrix.compiler }}" >> $GITHUB_ENV
echo "HDF5_VERSION=${{ matrix.hdf5_versions }}" >> $GITHUB_ENV
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/housekeeping.yml
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Expand Up @@ -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: |
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/linux_build_test.yml
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Expand Up @@ -58,7 +58,7 @@ jobs:

steps:
- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
submodules: recursive

Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/mac_build_test.yml
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Expand Up @@ -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}
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/windows_build_test.yml
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Expand Up @@ -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}
Expand Down
2 changes: 1 addition & 1 deletion .gitmodules
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@@ -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
2 changes: 2 additions & 0 deletions CI/Dockerfile
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Expand Up @@ -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
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This makes me wonder if we are installing MOAB in the wrong place? Or not installing it at all? Or we are installing it in the right place and we should reference that place here instead?

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we could add a python import command to the dockerfile to see if it is found by python if that helps check it it was installed

python -c "import pymoab"

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@bam241 bam241 Aug 2, 2022 •
edited

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The problem does not come from us.
It comes from Moab.
when they build and install pymoab they install it locally with pip -e for testing purposes
The problem is this is prevented because /root/build_dir/moab/bld/pymoab/lib/python3.6/site-packages is not in our PYTHONPATH

see:
here in pymoab CMakelist.txt

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Hmmm… maybe the problem is that line 91 in the pymoab CMake is commented out?!?

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Looks like @pshriwise commented this out in 2018 🤣

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Wow that survived a long time


# Set MOAB env variable
ENV moab_build_dir=${build_dir}/moab
ENV moab_install_dir=${install_dir}/moab
Expand Down
1 change: 1 addition & 0 deletions doc/CHANGELOG.rst
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Expand Up @@ -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)
* Correction to CMake variable name in OpenMC install instructions (#817)


Expand Down