updating readme [skip ci]

.github/scripts/resolve_dockerfile.py

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+import sys
+import os
+import requests
+
+from ersilia_pack.parsers import DockerfileInstallParser, YAMLInstallParser
+
+REPO_PATH = os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../.."))
+PY_VERSION_MAP = {
+    '3.8': 'py38', 
+    '3.9': 'py39',
+    '3.10': 'py310',
+    '3.11': 'py311',
+    '3.12': 'py312'
+}
+model_id = sys.argv[1]
+def resolve_parser():
+    if os.path.exists(os.path.abspath(os.path.join(REPO_PATH, "Dockerfile"))):
+        return DockerfileInstallParser(file_dir=REPO_PATH)
+    elif os.path.exists(os.path.join(REPO_PATH, "install.yml")):
+        return YAMLInstallParser(file_dir=REPO_PATH)
+    else:
+        raise ValueError("No install file found")
+
+def resolve_python_version(parser):
+    return parser._get_python_version()
+
+def read_dockerfile(parser):
+    commands = parser._get_commands()
+    has_conda = parser._has_conda(commands)
+    if has_conda:
+        file_url = "https://raw.githubusercontent.com/ersilia-os/ersilia/master/dockerfiles/dockerize-ersiliapack/model/Dockerfile.conda"
+    else:
+        file_url = "https://raw.githubusercontent.com/ersilia-os/ersilia/master/dockerfiles/dockerize-ersiliapack/model/Dockerfile.pip"
+    response = requests.get(file_url)
+    return response.text
+
+def write_version_and_model_id(file_content, python_version):
+    python_version = PY_VERSION_MAP[python_version]
+    file_content = file_content.replace("eos_identifier", model_id)
+    lines = file_content.split("\n")
+    lines[0] = lines[0].replace("VERSION", python_version)
+    with open(os.path.join(REPO_PATH, "../", "Dockerfile"), "w") as f:
+        f.write("\n".join(lines))
+
+if __name__ == "__main__":
+    parser = resolve_parser()
+    python_version = resolve_python_version(parser)
+    dockerfile = read_dockerfile(parser)
+    write_version_and_model_id(dockerfile, python_version)

.github/scripts/verify_model_outcome.py

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+import csv
+
+def check_non_null_outcomes_in_output_csv(csv_file_path):
+    with open(csv_file_path, 'r') as csv_file:
+        csv_reader = csv.reader(csv_file)
+        header = next(csv_reader)
+        row = next(csv_reader)
+        for val in row[2:]: # Skip the first two columns (Inchikey and input)
+            if val not in ['', None]: # Returns if even one outcome is not null
+                return False
+    return True
+
+if __name__ == '__main__':
+    # Read file path from command line
+    import sys
+    if len(sys.argv) < 2:
+        print('Usage: python verify_model_output.py <output_csv_file>')
+        exit(1)
+
+    output_csv_file = sys.argv[1]
+
+    if check_non_null_outcomes_in_output_csv(output_csv_file):
+        # If there are null outcomes, exit with status code 1
+        print('All outcomes are null')
+    else:
+        print('Some outcomes are not null')
+

.github/workflows/json-check.yml

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+name: json syntax check
+
+on:
+  push:
+    paths:
+      - "**.json"
+  pull_request:
+
+jobs:
+  json-test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # pin@v3.5.2
+
+      - name: json syntax check
+        id: json-yaml-validate
+        uses: GrantBirki/json-yaml-validate@87b2d309a02f4942c5e602183eeea11008a640f9 # pin@v1.4.0

.github/workflows/post-model-upload.yml

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+name: Call Post Model Upload Actions
+
+on:
+  workflow_run:
+    workflows: ["Call Test Model Image"]
+    types:
+      - completed
+
+jobs:
+  call-post-upload-actions:
+    if: github.event.workflow_run.conclusion == 'success'
+    uses: ersilia-os/ersilia-model-workflows/.github/workflows/post-model-upload.yml@main
+    with:
+      repo_name: ${{ github.event.repository.name }}
+    secrets:
+      AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
+      AWS_ACCESS_KEY: ${{ secrets.AWS_ACCESS_KEY }}
+      AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}

.github/workflows/post2slack.yml

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+name: Send Slack message
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  slack:
+    runs-on: ubuntu-latest
+    steps:
+      - name: post slack
+        uses: slackapi/slack-github-action@v1.23.0
+        env:
+          SLACK_BOT_TOKEN: ${{ secrets.SLACK_TOKEN }}
+        with:
+          slack-message: |
+              "new issue: https://github.com/${{ github.repository }}/issues/${{ github.event.issue.number }} created."
+          channel-id: ${{ secrets.SLACK_CHANNEL_TESTER }}

.github/workflows/test-model-image.yml

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+name: Call Test Model Image
+
+on:
+  workflow_run:
+    workflows: ["Call Upload Model to Dockerhub"]
+    types:
+      - completed
+
+jobs:
+  test-model:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    uses: ersilia-os/ersilia-model-workflows/.github/workflows/test-model-image.yml@main
+    with:
+      repo_name: ${{ github.event.repository.name }}
+    secrets:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASSWORD: ${{ secrets.DOCKERHUB_PASSWORD }}

.github/workflows/test-model-pr.yml

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+# This workflow only tests the model on PRs, not on every push to the main branch.
+# TODO(@dhanshree): Test ersilia in all supported Python versions
+name: Model Test on PR
+
+on:
+  pull_request:
+
+jobs:
+  test:
+    if: github.repository != 'ersilia-os/eos-template'
+    runs-on: ubuntu-latest
+    steps:
+      # This might stop working in the future, so we need to keep an eye on it
+      - 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
+
+      - uses: actions/checkout@v4.2.2
+        with:
+          lfs: true
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: "3.10.10"
+
+      - name: Install dependencies
+        run: |
+          conda install git-lfs -c conda-forge
+          git-lfs install
+          conda install gh -c conda-forge
+          python -m pip install 'ersilia[test]'
+
+      # TODO(@dhanshree) We can potentially restore the retries.
+      # TODO(@dhanshree) Correct the test command as needed
+      - name: Test model
+        env:
+          MODEL_ID: ${{ github.event.repository.name }}
+        run: |
+          ersilia -v test $MODEL_ID --shallow > test.log
+      
+      # Remove mock.txt if it exists
+      - name: Cleanup
+        run: |
+          if [ -f "mock.txt" ]; then
+            echo "Removing mock.txt file"
+            rm "mock.txt"
+          else
+            echo "mock.txt not found, skipping removal"
+          fi
+
+      # Upload EOS logs and test logs
+      - name: Upload log output
+        if: always()
+        uses: actions/upload-artifact@v4.5.0
+        with:
+          name: debug-logs
+          retention-days: 14
+          path: |
+            /home/runner/eos/*.log
+            ./*.log

.github/workflows/test-model-source.yml

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+name: Call Test Model Source
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  call-model-test:
+    if: github.repository != 'ersilia-os/eos-template'
+    uses: ersilia-os/ersilia-model-workflows/.github/workflows/test-model-source.yml@main
+    with:
+      branch: "main"
+      repo_name: ${{ github.event.repository.name }}
+    secrets:
+      AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
+      AWS_ACCESS_KEY: ${{ secrets.AWS_ACCESS_KEY }}
+      AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}

.github/workflows/upload-bentoml.yml

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+name: Call Upload Model to Dockerhub
+
+on:
+  workflow_run:
+    workflows: ["Call Test Model Source"]
+    types:
+      - completed
+
+jobs:
+  # Ersilia Pack Build
+  upload-ersilia-pack:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    uses: ersilia-os/ersilia-model-workflows/.github/workflows/upload-ersilia-pack.yml@main
+    with:
+      repo_name: ${{ github.event.repository.name }}
+    secrets:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASSWORD: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+  # BentoML Multistage Build (runs if Ersilia Pack fails)
+  upload-bentoml-multistage:
+    needs: upload-ersilia-pack
+    if: ${{ needs.upload-ersilia-pack.result == 'failure' }}
+    uses: ersilia-os/ersilia-model-workflows/.github/workflows/upload-bentoml.yml@main
+    with:
+      repo_name: ${{ github.event.repository.name }}
+      version: multistage-condapack
+    secrets:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASSWORD: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+  # BentoML Legacy Build (runs only if both previous jobs fail)
+  upload-bentoml-legacy:
+    needs: [upload-ersilia-pack, upload-bentoml-multistage]
+    if: ${{ needs.upload-ersilia-pack.result == 'failure' && needs.upload-bentoml-multistage.result == 'failure' }}
+    uses: ersilia-os/ersilia-model-workflows/.github/workflows/upload-bentoml.yml@main
+    with:
+      repo_name: ${{ github.event.repository.name }}
+      version: legacy
+    secrets:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASSWORD: ${{ secrets.DOCKERHUB_PASSWORD }}
+

.github/workflows/upload-ersilia-pack.yml

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+name: Call Upload Ersilia Pack Dockerized Model
+
+on:
+  workflow_run:
+    workflows: ["Call Upload Model to S3"]
+    types:
+      - completed
+
+jobs:
+  upload-model-to-dockerhub:
+    if: ${{ github.event.workflow_run.conclusion == 'failure' }}
+    uses: ersilia-os/ersilia-model-workflows/.github/workflows/upload-ersilia-pack.yml@main
+    with:
+      repo_name: ${{ github.event.repository.name }}
+    secrets:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASSWORD: ${{ secrets.DOCKERHUB_PASSWORD }}

.github/workflows/upload-model-to-s3.yml

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+name: Call Upload Model to S3
+
+on:
+  workflow_dispatch:
+  workflow_run:
+    workflows: ["Call Test Model Source"]
+    types:
+      - completed
+
+jobs:
+  upload:
+    if: ${{ github.event.workflow_run.conclusion == 'failure' }}
+    uses: ersilia-os/ersilia-model-workflows/.github/workflows/upload-model-to-s3.yml@main
+    with:
+      repo_name: ${{ github.event.repository.name }}
+    secrets:
+      AWS_ACCESS_KEY: ${{ secrets.AWS_ACCESS_KEY }}
+      AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+      AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}