From d7f76fffd659082654c2b3dc27816587beec2e96 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 19:04:54 -0500 Subject: [PATCH 01/54] add template file for RLM license --- dockerfile | 1 + rlmcloud.in | 5 +++++ 2 files changed, 6 insertions(+) create mode 100644 rlmcloud.in diff --git a/dockerfile b/dockerfile index 1d0aa2cd..a099e481 100644 --- a/dockerfile +++ b/dockerfile @@ -36,6 +36,7 @@ RUN wget -O /cubit.deb https://f002.backblazeb2.com/file/cubit-downloads/Corefor # install cubit RUN dpkg -i cubit.deb ENV PYTHONPATH=/opt/Coreform-Cubit-2023.11/bin/ +COPY ./rlmcloud.in /opt/Coreform-Cubit-2023.11/bin/licenses # parastell env COPY ./environment.yml /environment.yml diff --git a/rlmcloud.in b/rlmcloud.in new file mode 100644 index 00000000..5aec1645 --- /dev/null +++ b/rlmcloud.in @@ -0,0 +1,5 @@ +# +# Ports 5053 and 5132 must be open in your firewall for outgoing connections. +# +CUSTOMER Wisc isv=csimsoft server=@SERVER@ port=5053 password=@PASSWORD@ + From ecc6dd61972fa8a658e334a9f8e9414b70cc0d46 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 19:22:23 -0500 Subject: [PATCH 02/54] first attempt at action --- .github/workflows/docker_publish.yml | 54 ++++++++++++++++++++++++++++ dockerfile => Dockerfile | 2 +- 2 files changed, 55 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/docker_publish.yml rename dockerfile => Dockerfile (96%) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml new file mode 100644 index 00000000..2efedc21 --- /dev/null +++ b/.github/workflows/docker_publish.yml @@ -0,0 +1,54 @@ +name: Build & Publish docker image for ParaStell CI + +on: + # allows us to run workflows manually + workflow_dispatch: + push: + paths: + - 'Dockefile' + - '.github/workflows/docker_publish.yml' + +jobs: + build-dependency-img: + runs-on: ubuntu-latest + + name: Installing Dependencies and ParaStell + steps: + - name: Log in to the Container registry + uses: docker/login-action@v2 + with: + registry: ghcr.io + username: ${{ github.repository_owner }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: Checkout repository + uses: actions/checkout@v4 + + - name: Build, Test, and Push ParaStell + id: build-parastell + uses: docker/build-push-action@v5 + with: + cache-from: type=registry,ref=ghcr.io/svalinn/parastell:ci-layer-cache + cache-to: type=registry,ref=ghcr.io/svalinn/parastell:ci-layer-cache,mode=max + file: Dockerfile + push: true + tags: ghcr.io/svalinn/parstell:ci-testing + + test-dependency-img: + runs-on: ghcr.io/svalinn/parastell:ci-testing + + name: Testing CI image + steps: + - name: populate environment + run: | + echo "rlmSERVER=${{ secrets.rlmSERVER }}" >> "$GITHUB_ENV" + echo "rlmPASSWD=${{ secrets.rlmPASSWORD}}" >> "$GITHUB_ENV" + + - name: test secrets + run: | + echo "${rlmSERVER}" + echo "${rlmPASSWORD}" + sed -e "s/@SERVER@/${rlmSERVER}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in + + + diff --git a/dockerfile b/Dockerfile similarity index 96% rename from dockerfile rename to Dockerfile index a099e481..593596a6 100644 --- a/dockerfile +++ b/Dockerfile @@ -36,7 +36,7 @@ RUN wget -O /cubit.deb https://f002.backblazeb2.com/file/cubit-downloads/Corefor # install cubit RUN dpkg -i cubit.deb ENV PYTHONPATH=/opt/Coreform-Cubit-2023.11/bin/ -COPY ./rlmcloud.in /opt/Coreform-Cubit-2023.11/bin/licenses +COPY ./rlmcloud.in /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in # parastell env COPY ./environment.yml /environment.yml From b0eeaa83295953ed075ed4f8443ce581643aedc2 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 19:24:30 -0500 Subject: [PATCH 03/54] setup buildx --- .github/workflows/docker_publish.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 2efedc21..e67507b3 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -24,6 +24,9 @@ jobs: - name: Checkout repository uses: actions/checkout@v4 + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + - name: Build, Test, and Push ParaStell id: build-parastell uses: docker/build-push-action@v5 From 79171a83544ceaca353eb1dc7898cb8c24ebd8f8 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 19:36:59 -0500 Subject: [PATCH 04/54] add job dependency and update login version --- .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 e67507b3..38123ea9 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -15,7 +15,7 @@ jobs: name: Installing Dependencies and ParaStell steps: - name: Log in to the Container registry - uses: docker/login-action@v2 + uses: docker/login-action@v3 with: registry: ghcr.io username: ${{ github.repository_owner }} @@ -38,6 +38,7 @@ jobs: tags: ghcr.io/svalinn/parstell:ci-testing test-dependency-img: + needs: build-dependency-img runs-on: ghcr.io/svalinn/parastell:ci-testing name: Testing CI image From 5e762171a75205f55e889ac1ed7c23d640b8757d Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 19:41:12 -0500 Subject: [PATCH 05/54] specify different tag --- .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 38123ea9..b03d00e6 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -35,11 +35,11 @@ jobs: cache-to: type=registry,ref=ghcr.io/svalinn/parastell:ci-layer-cache,mode=max file: Dockerfile push: true - tags: ghcr.io/svalinn/parstell:ci-testing + tags: ghcr.io/svalinn/parstell-ci test-dependency-img: needs: build-dependency-img - runs-on: ghcr.io/svalinn/parastell:ci-testing + runs-on: ghcr.io/svalinn/parastell-ci name: Testing CI image steps: From 5e915db066246e148dabf331c4bb75869a63873a Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 19:48:30 -0500 Subject: [PATCH 06/54] try layer-cache --- .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 b03d00e6..3ccfe609 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -39,7 +39,7 @@ jobs: test-dependency-img: needs: build-dependency-img - runs-on: ghcr.io/svalinn/parastell-ci + runs-on: ghcr.io/svalinn/parastell:ci-layer-cache name: Testing CI image steps: From 4274e683f0b6706b45c27d0fb080c99e5edd0b4c Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 19:52:06 -0500 Subject: [PATCH 07/54] specifcy container instead of runner --- .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 3ccfe609..dca0048d 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -39,7 +39,8 @@ jobs: test-dependency-img: needs: build-dependency-img - runs-on: ghcr.io/svalinn/parastell:ci-layer-cache + runs-on: ubuntu-latest + container: ghcr.io/svalinn/parstell-ci name: Testing CI image steps: From 46f7ec71ae01bb733e25fe243d6f2857fcefbfb7 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 19:57:26 -0500 Subject: [PATCH 08/54] correct capitalization for secrets --- .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 dca0048d..02232313 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -46,8 +46,8 @@ jobs: steps: - name: populate environment run: | - echo "rlmSERVER=${{ secrets.rlmSERVER }}" >> "$GITHUB_ENV" - echo "rlmPASSWD=${{ secrets.rlmPASSWORD}}" >> "$GITHUB_ENV" + echo "rlmSERVER=${{ secrets.RLMSERVER }}" >> "$GITHUB_ENV" + echo "rlmPASSWD=${{ secrets.RLMPASSWORD}}" >> "$GITHUB_ENV" - name: test secrets run: | From 41b4369284ec17a806d9fd7a559f03c8ff2b6e0e Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 20:03:43 -0500 Subject: [PATCH 09/54] test cubit --- .github/workflows/docker_publish.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 02232313..cd9a00d9 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -52,8 +52,10 @@ jobs: - name: test secrets run: | echo "${rlmSERVER}" - echo "${rlmPASSWORD}" - sed -e "s/@SERVER@/${rlmSERVER}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in + echo "${rlmPASSWD}" + sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/$rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in + echo y | coreform_cubit -nographics + From a56769fc3f564985dd9581bec37333686fb269ba Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 20:07:40 -0500 Subject: [PATCH 10/54] save license file after sed --- .github/workflows/docker_publish.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index cd9a00d9..1f2e992d 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -53,9 +53,9 @@ jobs: run: | echo "${rlmSERVER}" echo "${rlmPASSWD}" - sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/$rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in + sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/$rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic echo y | coreform_cubit -nographics - + From 5f53575465079380bf6046a8afb16615b1bc3c28 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 20:13:59 -0500 Subject: [PATCH 11/54] look at license file --- .github/workflows/docker_publish.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 1f2e992d..d907d495 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -54,6 +54,7 @@ jobs: echo "${rlmSERVER}" echo "${rlmPASSWD}" sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/$rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic + cat /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic echo y | coreform_cubit -nographics From dd39a0d73a90b6ff906fb187a0151f47fb940d2a Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 20:42:32 -0500 Subject: [PATCH 12/54] env substitution typo --- .github/workflows/docker_publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index d907d495..aae81ebe 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -53,7 +53,7 @@ jobs: run: | echo "${rlmSERVER}" echo "${rlmPASSWD}" - sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/$rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic + sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic cat /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic echo y | coreform_cubit -nographics From 7e88b436e5c68dfd7f0e14b7fda9b96504e9085a Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 20:51:21 -0500 Subject: [PATCH 13/54] run pytest --- .github/workflows/docker_publish.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index aae81ebe..df627cbd 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -54,8 +54,10 @@ jobs: echo "${rlmSERVER}" echo "${rlmPASSWD}" sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic - cat /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic - echo y | coreform_cubit -nographics + cd /opt/parastell/tests + pytest -v . + + From c3727f0c23501e80a2b9742a0b7ae76fd300182e Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 20:51:36 -0500 Subject: [PATCH 14/54] checkout this brach during testing --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 593596a6..b78175bf 100644 --- a/Dockerfile +++ b/Dockerfile @@ -50,7 +50,8 @@ RUN git clone https://github.com/aaroncbader/pystell_uw.git ENV PYTHONPATH=$PYTHONPATH:/opt/pystell_uw # install parastell -RUN git clone https://github.com/svalinn/parastell.git +RUN git clone https://github.com/svalinn/parastell.git && + git checkout gh_action ENV PYTHONPATH=$PYTHONPATH:/opt/parastell WORKDIR / From 42a7b3d2728518909e7579a72e5a0fbf0091ef6a Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 20:52:32 -0500 Subject: [PATCH 15/54] newline --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index b78175bf..dc453e41 100644 --- a/Dockerfile +++ b/Dockerfile @@ -50,7 +50,7 @@ RUN git clone https://github.com/aaroncbader/pystell_uw.git ENV PYTHONPATH=$PYTHONPATH:/opt/pystell_uw # install parastell -RUN git clone https://github.com/svalinn/parastell.git && +RUN git clone https://github.com/svalinn/parastell.git && \ git checkout gh_action ENV PYTHONPATH=$PYTHONPATH:/opt/parastell From a86239c3835913826ea3e9993cb0df4070aefa2a Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 20:53:36 -0500 Subject: [PATCH 16/54] typo in trigger --- .github/workflows/docker_publish.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index df627cbd..f5026742 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -5,7 +5,7 @@ on: workflow_dispatch: push: paths: - - 'Dockefile' + - 'Dockerfile' - '.github/workflows/docker_publish.yml' jobs: @@ -56,7 +56,7 @@ jobs: sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic cd /opt/parastell/tests pytest -v . - + From 518b12acc7a5c501e36a8158549ed6806641af1d Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Tue, 9 Apr 2024 20:56:40 -0500 Subject: [PATCH 17/54] cd before checkout --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index dc453e41..4738bc1c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -51,6 +51,7 @@ ENV PYTHONPATH=$PYTHONPATH:/opt/pystell_uw # install parastell RUN git clone https://github.com/svalinn/parastell.git && \ + cd parastell && \ git checkout gh_action ENV PYTHONPATH=$PYTHONPATH:/opt/parastell From 65feedb03b169f270838b39dbd71cfc17d3ba162 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 14:37:44 -0500 Subject: [PATCH 18/54] pin older version of cad_to_dagmc --- environment.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index b482a26d..8f17e255 100644 --- a/environment.yml +++ b/environment.yml @@ -9,12 +9,14 @@ dependencies: - scikit-learn - cadquery - moab==5.5.0[build=nompi_tempest_*] - - cad_to_dagmc - ca-certificates - certifi - openssl - matplotlib + - gmsh + - python-gmsh - pip: + - cad_to_dagmc<0.6 - netcdf4 - pyyaml - pytest \ No newline at end of file From 5b93e3764ba6511a4fa74afa72b45c0e1f678525 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 14:37:58 -0500 Subject: [PATCH 19/54] force activation of conda env --- .github/workflows/docker_publish.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index f5026742..5a683433 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -51,6 +51,7 @@ jobs: - name: test secrets run: | + conda activate parastell_env echo "${rlmSERVER}" echo "${rlmPASSWD}" sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic From 6a20a4489012e26af8ddde083c03e3d3307119e9 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 15:49:25 -0500 Subject: [PATCH 20/54] create build targets --- Dockerfile | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 4738bc1c..e3b8db04 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM continuumio/miniconda3 +FROM continuumio/miniconda3 as parastell-deps ENV TZ=America/Chicago RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone @@ -49,11 +49,14 @@ WORKDIR /opt RUN git clone https://github.com/aaroncbader/pystell_uw.git ENV PYTHONPATH=$PYTHONPATH:/opt/pystell_uw +WORKDIR / + +from parastell-deps as parastell + # install parastell RUN git clone https://github.com/svalinn/parastell.git && \ cd parastell && \ git checkout gh_action ENV PYTHONPATH=$PYTHONPATH:/opt/parastell -WORKDIR / From fde91d4ea0565b640c56aae6a87b1fb75ae94593 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 15:50:36 -0500 Subject: [PATCH 21/54] build deps target and checkout for boostrap testing --- .github/workflows/docker_publish.yml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 5a683433..9d3df7a1 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -35,6 +35,7 @@ jobs: cache-to: type=registry,ref=ghcr.io/svalinn/parastell:ci-layer-cache,mode=max file: Dockerfile push: true + target: parastell-deps tags: ghcr.io/svalinn/parstell-ci test-dependency-img: @@ -44,6 +45,9 @@ jobs: name: Testing CI image steps: + - name: Checkout repository + uses: actions/checkout@v4 + - name: populate environment run: | echo "rlmSERVER=${{ secrets.RLMSERVER }}" >> "$GITHUB_ENV" @@ -52,10 +56,8 @@ jobs: - name: test secrets run: | conda activate parastell_env - echo "${rlmSERVER}" - echo "${rlmPASSWD}" sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic - cd /opt/parastell/tests + cd tests pytest -v . From 270175bb77a19fb9dde9610da7a19f265854c137 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 16:56:59 -0500 Subject: [PATCH 22/54] env activate syntax --- .github/workflows/docker_publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 9d3df7a1..32d6b8a1 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -55,7 +55,7 @@ jobs: - name: test secrets run: | - conda activate parastell_env + source activate parastell_env sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic cd tests pytest -v . From dbb25faaf811d18e77ee897b0790ed55eb3e18f9 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 17:14:00 -0500 Subject: [PATCH 23/54] testing --- .github/workflows/docker_publish.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 32d6b8a1..9eda1ff9 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -52,10 +52,8 @@ jobs: run: | echo "rlmSERVER=${{ secrets.RLMSERVER }}" >> "$GITHUB_ENV" echo "rlmPASSWD=${{ secrets.RLMPASSWORD}}" >> "$GITHUB_ENV" - - - name: test secrets - run: | - source activate parastell_env + which conda + conda activate parastell_env sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic cd tests pytest -v . From d979369c1b700601bcd9db4662e3dd2775ecc6f1 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 17:18:16 -0500 Subject: [PATCH 24/54] run conda init --- .github/workflows/docker_publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 9eda1ff9..2c23a279 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -52,7 +52,7 @@ jobs: run: | echo "rlmSERVER=${{ secrets.RLMSERVER }}" >> "$GITHUB_ENV" echo "rlmPASSWD=${{ secrets.RLMPASSWORD}}" >> "$GITHUB_ENV" - which conda + conda init conda activate parastell_env sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic cd tests From b26ac57a91f39d65a14426c6f9fb4f105a5c235d Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 17:22:35 -0500 Subject: [PATCH 25/54] source bashrc --- .github/workflows/docker_publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 2c23a279..87b4346a 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -52,7 +52,7 @@ jobs: run: | echo "rlmSERVER=${{ secrets.RLMSERVER }}" >> "$GITHUB_ENV" echo "rlmPASSWD=${{ secrets.RLMPASSWORD}}" >> "$GITHUB_ENV" - conda init + . ${HOME}/.bashrc conda activate parastell_env sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic cd tests From ad362778c438d4bf49863f7c5933b1fbfa1c9a44 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 19:19:24 -0500 Subject: [PATCH 26/54] specify which bashrc b/c github --- .github/workflows/docker_publish.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 87b4346a..417cca51 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -52,8 +52,7 @@ jobs: run: | echo "rlmSERVER=${{ secrets.RLMSERVER }}" >> "$GITHUB_ENV" echo "rlmPASSWD=${{ secrets.RLMPASSWORD}}" >> "$GITHUB_ENV" - . ${HOME}/.bashrc - conda activate parastell_env + . /root/.bashrc sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic cd tests pytest -v . From a9089ea16831a64747370bff21d81f0c32100643 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 19:38:10 -0500 Subject: [PATCH 27/54] explicitly set HOME --- Dockerfile | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Dockerfile b/Dockerfile index e3b8db04..35c86a9e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -38,6 +38,9 @@ RUN dpkg -i cubit.deb ENV PYTHONPATH=/opt/Coreform-Cubit-2023.11/bin/ COPY ./rlmcloud.in /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in +RUN mkdir -p /github/home +ENV HOME /github/home + # parastell env COPY ./environment.yml /environment.yml RUN conda env create -f environment.yml From fb491c865ac4ed3cd76501af886c42bcb82fb670 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 19:48:07 -0500 Subject: [PATCH 28/54] call the right bashrc --- .github/workflows/docker_publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 417cca51..18041552 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -52,7 +52,7 @@ jobs: run: | echo "rlmSERVER=${{ secrets.RLMSERVER }}" >> "$GITHUB_ENV" echo "rlmPASSWD=${{ secrets.RLMPASSWORD}}" >> "$GITHUB_ENV" - . /root/.bashrc + . ${HOME}/.bashrc sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic cd tests pytest -v . From 5bd16573ea532eabbc7379305cc21c5c0397ddbb Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 19:57:43 -0500 Subject: [PATCH 29/54] try to do all the things --- .github/workflows/docker_publish.yml | 1 + Dockerfile | 1 + 2 files changed, 2 insertions(+) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 18041552..87b4346a 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -53,6 +53,7 @@ jobs: echo "rlmSERVER=${{ secrets.RLMSERVER }}" >> "$GITHUB_ENV" echo "rlmPASSWD=${{ secrets.RLMPASSWORD}}" >> "$GITHUB_ENV" . ${HOME}/.bashrc + conda activate parastell_env sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic cd tests pytest -v . diff --git a/Dockerfile b/Dockerfile index 35c86a9e..993b3aaa 100644 --- a/Dockerfile +++ b/Dockerfile @@ -40,6 +40,7 @@ COPY ./rlmcloud.in /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in RUN mkdir -p /github/home ENV HOME /github/home +RUN cp /root/.bashrc /github/home/.bashrc # parastell env COPY ./environment.yml /environment.yml From 5d5b58f75c7275d042f7bf632a39ccdae93e5d82 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 20:06:49 -0500 Subject: [PATCH 30/54] don't rely on HOME --- .github/workflows/docker_publish.yml | 2 +- Dockerfile | 7 +++---- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 87b4346a..9c02f154 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -52,7 +52,7 @@ jobs: run: | echo "rlmSERVER=${{ secrets.RLMSERVER }}" >> "$GITHUB_ENV" echo "rlmPASSWD=${{ secrets.RLMPASSWORD}}" >> "$GITHUB_ENV" - . ${HOME}/.bashrc + . /opt/etc/bashrc conda activate parastell_env sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic cd tests diff --git a/Dockerfile b/Dockerfile index 993b3aaa..f346916c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -38,14 +38,13 @@ RUN dpkg -i cubit.deb ENV PYTHONPATH=/opt/Coreform-Cubit-2023.11/bin/ COPY ./rlmcloud.in /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in -RUN mkdir -p /github/home -ENV HOME /github/home -RUN cp /root/.bashrc /github/home/.bashrc +RUN mkdir -p /opt/etc +RUN cp /root/.bashrc /opt/etc/bashrc # parastell env COPY ./environment.yml /environment.yml RUN conda env create -f environment.yml -RUN echo "source activate parastell_env" >> ~/.bashrc +RUN echo "source activate parastell_env" >> /opt/etc/bashrc WORKDIR /opt From 16893014feb0a61e821039c9546f4a86b8a5a623 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 20:14:16 -0500 Subject: [PATCH 31/54] activate syntax --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index f346916c..ebee5bd5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -44,7 +44,7 @@ RUN cp /root/.bashrc /opt/etc/bashrc # parastell env COPY ./environment.yml /environment.yml RUN conda env create -f environment.yml -RUN echo "source activate parastell_env" >> /opt/etc/bashrc +RUN echo "conda activate parastell_env" >> /opt/etc/bashrc WORKDIR /opt From d30f6ada164b3fe934989e9bf90f300372d65c80 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 20:27:07 -0500 Subject: [PATCH 32/54] put parasell on the pythonpath --- .github/workflows/docker_publish.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 9c02f154..f81c4381 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -55,6 +55,7 @@ jobs: . /opt/etc/bashrc conda activate parastell_env sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic + export PYTHONPATH=${PYTHONPATH}:`pwd`/parastell cd tests pytest -v . From d0b0ba6744924988c5a8b2dd6b39fbbbb2ec40b1 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 20:33:59 -0500 Subject: [PATCH 33/54] improve pythonpath --- .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 f81c4381..74712776 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -55,7 +55,7 @@ jobs: . /opt/etc/bashrc conda activate parastell_env sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic - export PYTHONPATH=${PYTHONPATH}:`pwd`/parastell + export PYTHONPATH=${PYTHONPATH}:`pwd` cd tests pytest -v . From 66f9931e01889509e930c7857c74c758360fd0c3 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 20:54:36 -0500 Subject: [PATCH 34/54] only ivb tests for now --- .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 74712776..657abe67 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -57,7 +57,7 @@ jobs: sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic export PYTHONPATH=${PYTHONPATH}:`pwd` cd tests - pytest -v . + pytest -v test_invessel_build.py From c029a3b427da1d9eae64642fdf9e295744adeb55 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 20:58:43 -0500 Subject: [PATCH 35/54] try source mesh tets --- .github/workflows/docker_publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 657abe67..ecc5a0c3 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -57,7 +57,7 @@ jobs: sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic export PYTHONPATH=${PYTHONPATH}:`pwd` cd tests - pytest -v test_invessel_build.py + pytest -v test_source_mesh.py From 7c1d8e2f3702c8f289a8fde9b4ca1cb250674da1 Mon Sep 17 00:00:00 2001 From: "Paul P.H. Wilson" Date: Wed, 10 Apr 2024 21:02:34 -0500 Subject: [PATCH 36/54] test only parastell --- .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 ecc5a0c3..70e90c9f 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -57,7 +57,7 @@ jobs: sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic export PYTHONPATH=${PYTHONPATH}:`pwd` cd tests - pytest -v test_source_mesh.py + pytest -v test_parastell.py From 60323273bc1e73a2d312af4aae15ff7e24634fd9 Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 11:50:10 -0500 Subject: [PATCH 37/54] Update CAD-to-DAGMC conda installation --- environment.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/environment.yml b/environment.yml index 8f17e255..b482a26d 100644 --- a/environment.yml +++ b/environment.yml @@ -9,14 +9,12 @@ dependencies: - scikit-learn - cadquery - moab==5.5.0[build=nompi_tempest_*] + - cad_to_dagmc - ca-certificates - certifi - openssl - matplotlib - - gmsh - - python-gmsh - pip: - - cad_to_dagmc<0.6 - netcdf4 - pyyaml - pytest \ No newline at end of file From af16fe12abc9894ef87a46f3079429a55815cddf Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 12:06:58 -0500 Subject: [PATCH 38/54] Run --- .github/workflows/docker_publish.yml | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 70e90c9f..5afb728b 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -57,10 +57,4 @@ jobs: sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic export PYTHONPATH=${PYTHONPATH}:`pwd` cd tests - pytest -v test_parastell.py - - - - - - + pytest -v test_invessel_build.py From ec7d53391683730ff758d544a9c698b8cd1eda3b Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 12:12:33 -0500 Subject: [PATCH 39/54] Revert to running test_parastell.py --- .github/workflows/docker_publish.yml | 2 +- Dockerfile | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 5afb728b..8ae4902a 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -57,4 +57,4 @@ jobs: sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic export PYTHONPATH=${PYTHONPATH}:`pwd` cd tests - pytest -v test_invessel_build.py + pytest -v test_parastell.py diff --git a/Dockerfile b/Dockerfile index ebee5bd5..300ca853 100644 --- a/Dockerfile +++ b/Dockerfile @@ -61,5 +61,3 @@ RUN git clone https://github.com/svalinn/parastell.git && \ cd parastell && \ git checkout gh_action ENV PYTHONPATH=$PYTHONPATH:/opt/parastell - - From 623f0c20c17c29014bea9125ba869b9fd6debf97 Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 12:16:04 -0500 Subject: [PATCH 40/54] Change ParaStell branch in Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 300ca853..ca2aef70 100644 --- a/Dockerfile +++ b/Dockerfile @@ -59,5 +59,5 @@ from parastell-deps as parastell # install parastell RUN git clone https://github.com/svalinn/parastell.git && \ cd parastell && \ - git checkout gh_action + git checkout gh-action ENV PYTHONPATH=$PYTHONPATH:/opt/parastell From 56490d95e1ad43db45fb0bb6258056c11abcc1e2 Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 12:39:56 -0500 Subject: [PATCH 41/54] Check that correct branch is checked out --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index ca2aef70..2b21d5e4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -60,4 +60,5 @@ from parastell-deps as parastell RUN git clone https://github.com/svalinn/parastell.git && \ cd parastell && \ git checkout gh-action +RUN ls /opt/parastell/ ENV PYTHONPATH=$PYTHONPATH:/opt/parastell From 585b5493d5dbd6dac0144e39dbfcd67271e2def5 Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 12:56:01 -0500 Subject: [PATCH 42/54] Check that license file is properly modified --- .github/workflows/docker_publish.yml | 1 + Dockerfile | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 8ae4902a..0e4ed448 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -55,6 +55,7 @@ jobs: . /opt/etc/bashrc conda activate parastell_env sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic + cat /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic export PYTHONPATH=${PYTHONPATH}:`pwd` cd tests pytest -v test_parastell.py diff --git a/Dockerfile b/Dockerfile index 2b21d5e4..ca2aef70 100644 --- a/Dockerfile +++ b/Dockerfile @@ -60,5 +60,4 @@ from parastell-deps as parastell RUN git clone https://github.com/svalinn/parastell.git && \ cd parastell && \ git checkout gh-action -RUN ls /opt/parastell/ ENV PYTHONPATH=$PYTHONPATH:/opt/parastell From f11291dd4f7a04735aeba6c3038fff4d40b6da0a Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 13:23:33 -0500 Subject: [PATCH 43/54] Check environment --- .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 0e4ed448..f9be17ef 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -54,8 +54,11 @@ jobs: echo "rlmPASSWD=${{ secrets.RLMPASSWORD}}" >> "$GITHUB_ENV" . /opt/etc/bashrc conda activate parastell_env + printenv sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic - cat /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic export PYTHONPATH=${PYTHONPATH}:`pwd` + + - name: test environment + run: | cd tests pytest -v test_parastell.py From fa4e1df6dfadc45a8025e60ea2b699eafae7a251 Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 13:34:52 -0500 Subject: [PATCH 44/54] Try alternative way of setting environment variables from secrets --- .github/workflows/docker_publish.yml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index f9be17ef..5927952a 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -50,15 +50,12 @@ jobs: - name: populate environment run: | - echo "rlmSERVER=${{ secrets.RLMSERVER }}" >> "$GITHUB_ENV" - echo "rlmPASSWD=${{ secrets.RLMPASSWORD}}" >> "$GITHUB_ENV" . /opt/etc/bashrc conda activate parastell_env - printenv sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic export PYTHONPATH=${PYTHONPATH}:`pwd` - - - name: test environment - run: | cd tests pytest -v test_parastell.py + env: + rlmSERVER: ${{ secrets.RLMSERVER }} + rlmPASSWD: ${{ secrets.RLMPASSWORD}} From cc96d1e15a337bedc65e3ac452bc2833ff849261 Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 13:40:38 -0500 Subject: [PATCH 45/54] Include all ParaStell scripts --- .github/workflows/docker_publish.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 5927952a..5493480e 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -55,7 +55,7 @@ jobs: sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic export PYTHONPATH=${PYTHONPATH}:`pwd` cd tests - pytest -v test_parastell.py + pytest -v . env: rlmSERVER: ${{ secrets.RLMSERVER }} - rlmPASSWD: ${{ secrets.RLMPASSWORD}} + rlmPASSWD: ${{ secrets.RLMPASSWORD }} From 198b88e57f9c4c8dd03859c3784eceb05b2aa3d3 Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 17:09:10 -0500 Subject: [PATCH 46/54] Implement suggestions --- .github/workflows/docker_publish.yml | 6 +++--- Dockerfile | 5 ++--- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 5493480e..03c31843 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -36,12 +36,12 @@ jobs: file: Dockerfile push: true target: parastell-deps - tags: ghcr.io/svalinn/parstell-ci + tags: ghcr.io/svalinn/parastell-ci test-dependency-img: needs: build-dependency-img runs-on: ubuntu-latest - container: ghcr.io/svalinn/parstell-ci + container: ghcr.io/svalinn/parastell-ci name: Testing CI image steps: @@ -51,9 +51,9 @@ jobs: - name: populate environment run: | . /opt/etc/bashrc - conda activate parastell_env sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic export PYTHONPATH=${PYTHONPATH}:`pwd` + git checkout gh-action cd tests pytest -v . env: diff --git a/Dockerfile b/Dockerfile index ca2aef70..05be8a5b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -57,7 +57,6 @@ WORKDIR / from parastell-deps as parastell # install parastell -RUN git clone https://github.com/svalinn/parastell.git && \ - cd parastell && \ - git checkout gh-action +RUN mkdir parastell +COPY . parastell/ ENV PYTHONPATH=$PYTHONPATH:/opt/parastell From 1b6d136c5eb055415caaa776e10c9a4354050cdb Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 17:14:37 -0500 Subject: [PATCH 47/54] Modify copying of ParaStell in Dockerfile --- Dockerfile | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/Dockerfile b/Dockerfile index 05be8a5b..5d2db9c5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,7 +5,7 @@ RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone RUN apt-get update -y RUN apt-get upgrade -y -# install dependencies +# Install dependencies RUN apt-get install -y libgl1-mesa-glx \ libgl1-mesa-dev \ libglu1-mesa-dev \ @@ -30,10 +30,10 @@ RUN apt-get install -y libgl1-mesa-glx \ libxcursor1 \ libxinerama1 -# download cubit +# Download Coreform Cubit RUN wget -O /cubit.deb https://f002.backblazeb2.com/file/cubit-downloads/Coreform-Cubit/Releases/Linux/Coreform-Cubit-2023.11%2B43088-Lin64.deb -# install cubit +# Install Cubit RUN dpkg -i cubit.deb ENV PYTHONPATH=/opt/Coreform-Cubit-2023.11/bin/ COPY ./rlmcloud.in /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in @@ -41,14 +41,14 @@ COPY ./rlmcloud.in /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in RUN mkdir -p /opt/etc RUN cp /root/.bashrc /opt/etc/bashrc -# parastell env +# Install Python dependencies in parastell env conda environment COPY ./environment.yml /environment.yml RUN conda env create -f environment.yml RUN echo "conda activate parastell_env" >> /opt/etc/bashrc WORKDIR /opt -# install pystell_uw +# Install PyStell-UW RUN git clone https://github.com/aaroncbader/pystell_uw.git ENV PYTHONPATH=$PYTHONPATH:/opt/pystell_uw @@ -56,7 +56,6 @@ WORKDIR / from parastell-deps as parastell -# install parastell -RUN mkdir parastell -COPY . parastell/ +# Install ParaStell +COPY . parastell ENV PYTHONPATH=$PYTHONPATH:/opt/parastell From adc8225bba262199c3fba7995557c6a767f70f7b Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 17:25:19 -0500 Subject: [PATCH 48/54] Modify ParaStell installation --- Dockerfile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 5d2db9c5..fbee6f9a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -54,8 +54,10 @@ ENV PYTHONPATH=$PYTHONPATH:/opt/pystell_uw WORKDIR / -from parastell-deps as parastell +FROM parastell-deps as parastell # Install ParaStell -COPY . parastell +RUN mkdir /opt/parastell +WORKDIR /opt +COPY . parastell/ ENV PYTHONPATH=$PYTHONPATH:/opt/parastell From 65adeb591a5d5e62a3df3799ae30c51aa7310004 Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 17:30:28 -0500 Subject: [PATCH 49/54] Modify location of branch checkout --- .github/workflows/docker_publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 03c31843..b7c4d735 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -37,6 +37,7 @@ jobs: push: true target: parastell-deps tags: ghcr.io/svalinn/parastell-ci + run: git checkout gh-action test-dependency-img: needs: build-dependency-img @@ -53,7 +54,6 @@ jobs: . /opt/etc/bashrc sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic export PYTHONPATH=${PYTHONPATH}:`pwd` - git checkout gh-action cd tests pytest -v . env: From c8317d83fae1de8a62bd6b4d0859b5a88314a42a Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 17:40:44 -0500 Subject: [PATCH 50/54] Remove branch change in CI test job --- .github/workflows/docker_publish.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index b7c4d735..0fb644bf 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -37,7 +37,6 @@ jobs: push: true target: parastell-deps tags: ghcr.io/svalinn/parastell-ci - run: git checkout gh-action test-dependency-img: needs: build-dependency-img From 399fb2a8934b6ead1e10e335ccf7b1f5549510a3 Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 17:50:37 -0500 Subject: [PATCH 51/54] Try removing ParaStell installation --- Dockerfile | 6 ------ 1 file changed, 6 deletions(-) diff --git a/Dockerfile b/Dockerfile index fbee6f9a..0d8f7ccc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -55,9 +55,3 @@ ENV PYTHONPATH=$PYTHONPATH:/opt/pystell_uw WORKDIR / FROM parastell-deps as parastell - -# Install ParaStell -RUN mkdir /opt/parastell -WORKDIR /opt -COPY . parastell/ -ENV PYTHONPATH=$PYTHONPATH:/opt/parastell From 548b14fceafe01cc821e0d80d3c58b411651c0e9 Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 17:52:47 -0500 Subject: [PATCH 52/54] Remove ParaStell build stage from Dockerfile --- Dockerfile | 2 -- 1 file changed, 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 0d8f7ccc..f230815b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -53,5 +53,3 @@ RUN git clone https://github.com/aaroncbader/pystell_uw.git ENV PYTHONPATH=$PYTHONPATH:/opt/pystell_uw WORKDIR / - -FROM parastell-deps as parastell From b2e0ce52f8463f4d3a70b6a02a8ca0fb45397d80 Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 18:07:49 -0500 Subject: [PATCH 53/54] Clean up GitHub action --- .github/workflows/docker_publish.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 0fb644bf..642bedd6 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -1,4 +1,4 @@ -name: Build & Publish docker image for ParaStell CI +name: Build & publish Docker image for ParaStell CI on: # allows us to run workflows manually @@ -12,22 +12,22 @@ jobs: build-dependency-img: runs-on: ubuntu-latest - name: Installing Dependencies and ParaStell + name: Install Dependencies steps: - - name: Log in to the Container registry - uses: docker/login-action@v3 - with: - registry: ghcr.io - username: ${{ github.repository_owner }} - password: ${{ secrets.GITHUB_TOKEN }} - - name: Checkout repository uses: actions/checkout@v4 - name: Set up Docker Buildx uses: docker/setup-buildx-action@v3 - - name: Build, Test, and Push ParaStell + - name: Log into GitHub Container Registry + uses: docker/login-action@v3 + with: + registry: ghcr.io + username: ${{ github.repository_owner }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: Build and push ParaStell Docker image id: build-parastell uses: docker/build-push-action@v5 with: @@ -43,7 +43,7 @@ jobs: runs-on: ubuntu-latest container: ghcr.io/svalinn/parastell-ci - name: Testing CI image + name: Test CI Image steps: - name: Checkout repository uses: actions/checkout@v4 From 4482f625cd69b5411d972258db145594d645373a Mon Sep 17 00:00:00 2001 From: Connor Moreno Date: Thu, 25 Apr 2024 18:11:45 -0500 Subject: [PATCH 54/54] Modify job step names --- .github/workflows/docker_publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml index 642bedd6..7e777ae5 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker_publish.yml @@ -48,7 +48,7 @@ jobs: - name: Checkout repository uses: actions/checkout@v4 - - name: populate environment + - name: Populate environment and run tests run: | . /opt/etc/bashrc sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic