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updating readme [skip ci]
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@ersilia-bot
ersilia-bot committed Apr 9, 2024
1 parent cea60a6 commit 2e40a24
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109 changes: 77 additions & 32 deletions .github/workflows/upload-model-to-dockerhub.yml
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Expand Up @@ -14,12 +14,12 @@ jobs:
steps:
# https://github.com/docker/setup-qemu-action
- name: Set up QEMU
uses: docker/setup-qemu-action@v1
uses: docker/setup-qemu-action@v3

# https://github.com/docker/setup-buildx-action
- name: Set up Docker Buildx
id: buildx
uses: docker/setup-buildx-action@v1
uses: docker/setup-buildx-action@v3

# log in to dockerhub
- name: Login to Docker Hub
Expand All @@ -35,7 +35,22 @@ jobs:
persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
lfs: 'true'

- name: Free Disk Space (Ubuntu)
uses: jlumbroso/free-disk-space@main
with:
# this might remove tools that are actually needed,
# if set to "true" but frees about 6 GB
tool-cache: true

# all of these default to true, but feel free to set to
# "false" if necessary for your workflow
android: true
dotnet: true
haskell: true
large-packages: true
swap-storage: true

- name: Generate the Dockerfile
id: generate-dockerfile
env:
Expand All @@ -44,11 +59,67 @@ jobs:
wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/place_a_dockerfile_in_current_eos_repo.py
python -m pip install requests
python place_a_dockerfile_in_current_eos_repo.py $REPO_NAME
# We cannot tag it as anything other than latest because
# ersilia cli only looks for the 'latest' tag
- name: Build only AMD64 Image for Testing
id: buildForTest
uses: docker/build-push-action@v5
with:
context: .
load: true
tags: ersiliaos/${{ github.event.repository.name }}:latest

- name: Add conda to system path
run: echo $CONDA/bin >> $GITHUB_PATH

- name: Source conda
run: source $CONDA/etc/profile.d/conda.sh

- name: Set Python to 3.10.10
run:
conda install -y python=3.10.10

- name: Install dependencies
run: |
source activate
conda init
conda install git-lfs -c conda-forge
git-lfs install
conda install gh -c conda-forge
- name: Install ersilia
run: |
source activate
python --version
echo "After conda init"
conda init
python -m pip install git+https://github.com/ersilia-os/ersilia.git
# TODO This is very hacky, maybe we want to use the ersilia test command in the future for this
- name: Test Built Image
id: testBuiltImage
run: |
ersilia -v fetch ${{ github.event.repository.name }} --from_dockerhub
ersilia -v serve ${{ github.event.repository.name }}
ersilia -v run -i "CCCC" -o "output.json"
expected=$(jq '.[0].output.outcome[]' output.json | wc -l)
result=$(jq '.[0].output.outcome[] | select(. != null)' output.json | wc -l)
echo "Expected correct outcomes $expected"
echo "Returned correct outcomes $result"
if [ $expected -ne $result ]
then
echo "Error in model output, aborting build and push"
exit 1
fi
env:
PULL_IMAGE: n

- name: Build and push
id: buildMultiple
continue-on-error: true
uses: docker/build-push-action@v2
uses: docker/build-push-action@v5
timeout-minutes: 45
with:
context: .
platforms: linux/amd64,linux/arm64
Expand All @@ -69,15 +140,15 @@ jobs:
- name: Build only for Linux/amd64
id: buildSingle
if: steps.buildCheck.outputs.failed == 'true'
uses: docker/build-push-action@v2
uses: docker/build-push-action@v5
with:
context: .
platforms: linux/amd64
push: ${{ github.event_name != 'pull_request' }}
tags: ersiliaos/${{ github.event.repository.name }}:latest

- name: Update Metadata JSON file with DockerHub info
id: UpdateMetadata
id: updateMetadata
run: |
mv Dockerfile_legacy Dockerfile
python3 -c "
Expand Down Expand Up @@ -106,32 +177,6 @@ jobs:
github_token: ${{ secrets.GITHUB_TOKEN }}
amend: true
force: true

- name: Add conda to system path
run: echo $CONDA/bin >> $GITHUB_PATH

- name: Source conda
run: source $CONDA/etc/profile.d/conda.sh

- name: Set Python to 3.10.10
run:
conda install -y python=3.10.10

- name: Install dependencies
run: |
source activate
conda init
conda install git-lfs -c conda-forge
git-lfs install
conda install gh -c conda-forge
- name: Install ersilia
run: |
source activate
python --version
echo "After conda init"
conda init
python -m pip install git+https://github.com/ersilia-os/ersilia.git

- name: Update metadata to AirTable
id: update-metadata-to-airtable
Expand Down
113 changes: 113 additions & 0 deletions output.json
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@@ -0,0 +1,113 @@
[
{
"input": {
"key": "IJDNQMDRQITEOD-UHFFFAOYSA-N",
"input": "CCCC",
"text": "CCCC"
},
"output": {
"outcome": [
"CCCC",
"CCCCC",
"CCCP",
"CCCBr",
"CCCN",
"[CH2-]CCC",
"[CH2]CCC",
"CCCF",
"CCCCl",
"CCCO",
"CCCI",
"CCCS",
"CCCSC",
"CC[Si]CC",
"CC[CH-]CC",
"CC[SiH2]CC",
"CCNCC",
"CCSCC",
"CCCNC",
"CCC[SiH2]C",
"CC[SnH4+2]CC",
"CCOCC",
"CC[CH]CC",
"C[CH-]CCC",
"CCBCC",
"CCPCC",
"CCCOC",
"C[CH]CCC",
"CCCPC",
"CC[Sn]CC",
"[CH2-]CCCC",
"CCCCI",
"C#CCCC",
"CCCCN",
"CCCC#N",
"CCCC[Sn+2]",
"CCCC[SiH2]",
"CCCC[SnH]",
"CCCCO",
"[C-]#[N+]CCC",
"CCCC[SiH3]",
"CCCC[SnH3]",
"CCCCP",
"[CH2]CCCC",
"CCCC=O",
"CCCCBr",
"CCCC[SnH6+3]",
"CCCCF",
"CCCCCl",
"C=CCCC",
"CCCCS",
"CCOC",
"CCSC",
"C[CH-]CC",
"C[CH]CC",
"CCNC",
"CCC(C)C",
"CC[C@@H](C)S",
"CCC(C)=O",
"C=C(C)CC",
"CC[C@@H](C)I",
"CC[C@H](C)O",
"CC[C@H](C)Br",
"CC[C@@H](C)Br",
"CCC(C)=S",
"CC[C-](C)C",
"CC[C@H](C)Cl",
"CC[C@H](C)S",
"CC[C@@H](C)N",
"CC[C@H](C)I",
"CC[C@@H](C)F",
"CC[C@@H](C)O",
"CC[C@H](C)N",
"CC[C@@H](C)Cl",
"CC[C@H](C)F",
"C/C=C/CC",
"C/C=C\\CC",
"CC=CCC",
"CC#[N+]CC",
"CC#CCC",
"C#CCC",
"C=CCC",
"C/C=C/C",
"CC#CC",
"C/C=C\\C",
"C[CH]C(C)C",
"[CH2]CCCCl",
"[CH2-]CCCF",
"[CH2]CCCO",
"CC1CC1",
"C[C@@H]1CCO1",
"C[C@@H]1CCN1",
"CC1CCC1",
"[CH]1CCC1",
"[CH2-]C1CC1",
"BrC1CCC1",
"[CH-]1CCC1",
"C1CCCC1",
"C1CCC1",
"C1C2CC12"
]
}
}
]

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