Merge branch 'MHubAI:main' into m-gc-node21-baseline

.github/scripts/mhub_check.py

@@ -0,0 +1,63 @@
+import utils
+import os, sys, json
+
+# introduction
+print()
+print("------------------------------------------------")
+print("MHub Compliance Checks started.")
+print("We will check for a correct folder setup, Dockerfile and meta.json compliance.")
+print()
+
+# print event path variable
+PR = os.environ['PR_NUMBER']
+print("Pull request:    ", PR)
+
+# get the first argument to this script which should be the list of modified files from an earlyer step
+modified_files = json.loads(os.environ['MODIFIED_FILES']) 
+print("Modified files:  ", "\n                  ".join(modified_files))
+
+# modified models list
+modified_models = list(set(fp.split("/")[1] for fp in modified_files))
+print("Modified models: ", ", ".join(modified_models))
+
+# we allow modifications only to a single file for now
+# TODO: iterate model list (we can outsource model checks and then call a check_model script with the model name as argument)
+if len(modified_models) != 1:
+    print("CHECK FAILED: ", "Exactly one model must be modified in a pull request.")
+    sys.exit(1)
+
+# model name
+model_name = modified_models[0]
+
+# run compliance checks
+try:
+    # check folder structure
+    utils.validateModelFolder(base='models', model_name=model_name)
+
+    # check meta.json
+    utils.validateModelMetaJson(model_meta_json_file=os.path.join('models', model_name, 'meta.json'))
+
+    # validate dockerfile
+    utils.validateDockerfile(base='models', model_name=model_name)
+
+except utils.MHubComplianceError as e:
+    print()
+    print("---------------- CHECK FAILED ----------------")
+    print("This PR violates one or more MHub compliance rules:")
+    print(str(e))
+    print()
+    sys.exit(1)
+
+except Exception as e:
+    print()
+    print("---------------- CHECK FAILED ----------------")
+    print("An unexpected error occured during compliance checks.")
+    print()
+    sys.exit(1)
+
+# all checks passed
+print()
+print("---------------- CHECK PASSED ----------------")
+print("All compliance checks passed.")
+print("Note: compliance checks are a beta feature. Passing all automated compliance checks does not guarantee that your model is compliant with the MHub standard. We will now perform a manual review of your model. Testing your model on a public dataset is obligatory.")
+print()

.github/scripts/utils.py

@@ -0,0 +1,187 @@
+from typing import List, Union
+from enum import Enum
+import requests, os
+import json
+import jsonschema
+
+# NOTE: all file path operations are relative to the repository root.
+
+# references for documentation
+class DocuRef(Enum):
+    MODEL_FOLDER_STRUCTURE = "https://github.com/MHubAI/documentation/blob/main/documentation/mhub_models/model_folder_structure.md"
+    DOCKERFILE = "https://github.com/MHubAI/documentation/blob/main/documentation/mhub_models/the_mhub_dockerfile.md"
+    CONFIG = "https://github.com/MHubAI/documentation/blob/main/documentation/mhubio/the_mhubio_config_file.md"
+    MHUBIO_MODULES = "https://github.com/MHubAI/documentation/blob/main/documentation/mhubio/mhubio_modules.md"
+    MODEL_META_JSON = "https://github.com/MHubAI/documentation/blob/main/documentation/mhub_models/model_json.md"
+
+class MHubComplianceError(Exception):
+    """Raised when a model is not compliant with MHub standards"""
+
+    def __init__(self, message: str, docu_ref: Union[DocuRef, List[DocuRef]]):
+        if isinstance(docu_ref, list):
+            msg = f"{message} (see {', '.join([d.value for d in docu_ref])})"
+        else:
+            msg = f"{message} ( see {docu_ref.value} for more information)"
+
+        super().__init__(msg)
+
+def get_modified_files_from_PR(prid, repo = 'models') -> List[str]:
+
+    # GitHub API URL to list files modified in the PR
+    api_url = f"https://api.github.com/repos/MHubAI/{repo}/pulls/{prid}/files"
+
+    # Send a GET request to the GitHub API
+    response = requests.get(api_url)
+
+    if response.status_code != 200:
+        raise Exception(f"Failed to fetch modified files: {response.status_code}")
+
+    # Parse the JSON response and extract the file paths
+    modified_files = [file["filename"] for file in response.json()]
+
+    # return list of modified files
+    return modified_files
+
+def get_modified_models_from_modified_files(modified_files: List[str]) -> List[str]:
+    modified_models = []
+
+    # Parse the JSON response and extract the file paths
+    for file in modified_files:
+
+        # get the model name (/models/<model_name>/...)
+        model_name = file.split("/")[1]
+        modified_models.append(model_name)
+
+    # remove duplicates
+    modified_models = list(set(modified_models))
+
+    return modified_models
+
+def validateModelFolder(base: str, model_name: str):
+
+    model_path = os.path.join(base, model_name)
+
+    # check if the model folder exists
+    if not os.path.isdir(model_path):
+        raise MHubComplianceError(f"Model folder {model_path} does not exist", DocuRef.MODEL_FOLDER_STRUCTURE)
+
+    # check if the model folder contains the following and no additional ressources
+    # - /dockerfiles/Dockerfile
+    # - /config/default.yml
+    # - /utils
+    # - /meta.json
+
+    # check if the model folder contains a Dockerfile
+    dockerfile_path = os.path.join(model_path, "dockerfiles", "Dockerfile")
+    if not os.path.isfile(dockerfile_path):
+        raise MHubComplianceError(f"Model folder {model_path} does not contain a Dockerfile", [DocuRef.MODEL_FOLDER_STRUCTURE, DocuRef.DOCKERFILE])
+
+    # check if the model folder contains a default config
+    config_path = os.path.join(model_path, "config", "default.yml")
+    if not os.path.isfile(config_path):
+        raise MHubComplianceError(f"Model folder {model_path} does not contain a default workflow configuration", [DocuRef.MODEL_FOLDER_STRUCTURE, DocuRef.CONFIG])
+
+    # check if the model folder contains a utils folder
+    # NOTE: utils is not mandatory, however, all MHub-IO modules must be inside the utils folder if they exist.
+    #       we can check modified files for any *.py and demand they're inside the utils folder.
+    #utils_path = os.path.join(model_path, "utils")
+    #if not os.path.isdir(utils_path):
+    #    raise MHubComplianceError(f"Model folder {model_path} does not contain a utils folder")
+
+    # check if the model folder contains a model.json
+    model_json_path = os.path.join(model_path, "meta.json")
+    if not os.path.isfile(model_json_path):
+        raise MHubComplianceError(f"Model folder {model_path} does not contain a meta.json", [DocuRef.MODEL_FOLDER_STRUCTURE, DocuRef.MODEL_META_JSON])
+
+
+def validateModelMetaJson(model_meta_json_file: str):
+
+    # load schema
+    with open(os.path.join('.github', 'schemas', 'meta.schema.json'), "r") as f:
+        schema = json.load(f)
+
+    # load model meta json
+    with open(model_meta_json_file, "r") as f:
+        model_meta_json = json.load(f)
+
+    # validate
+    try: 
+        jsonschema.validate(instance=model_meta_json, schema=schema)
+    except jsonschema.ValidationError as e:
+        raise MHubComplianceError(f"Model meta json is not compliant with the schema: {e.message}", DocuRef.MODEL_META_JSON)
+
+def validateDockerfile(base: str, model_name: str):
+
+    # get dockerfile path
+    model_dockerfile = os.path.join(base, model_name, "dockerfiles", "Dockerfile")
+
+    # read dockerfile
+    with open(model_dockerfile, "r") as f:
+        dockerfile = f.read()
+
+    # split dockerfile into lines
+    lines = dockerfile.split("\n")
+
+    # remove empty lines
+    lines = [line for line in lines if line.strip() != ""]
+
+    # check that the dockerfile contains only a single FROM command which 
+    # is the first line of the file and is `FROM mhubai/base:latest`
+    if not lines[0].strip() == "FROM mhubai/base:latest":
+        raise MHubComplianceError(f"Dockerfile does not contain the correct FROM command: {lines[0]}", DocuRef.DOCKERFILE)
+
+    # some status variables from parsing the dockerfile
+    dockerfile_defines_arg_mhub_models_repo = False
+    dockerfile_contains_mhubio_import = False
+
+    # check that dockerfile contains no ADD or COPY commands
+    # We also don't allow changing the WORKDIR which is set to /app in the base and must be consistent across all models
+    #  so no new line is allowed to start with ADD, COPY, WORKDIR, .. 
+    for i, line in enumerate(lines):
+
+        # forbidden keywords
+
+        if line.startswith("WORKDIR"):
+            raise MHubComplianceError(f"WORKDIR must not be set to any other than `/app` as defined in our base image. {line}", DocuRef.DOCKERFILE)
+
+        if line.startswith("ADD") or line.startswith("COPY"):
+            raise MHubComplianceError(f"Dockerfile contains ADD or COPY command: {line}", DocuRef.DOCKERFILE)
+
+        if line.startswith("FROM") and i > 0:
+            raise MHubComplianceError(f"Dockerfile contains FROM command not at the beginning of the file: {line}", DocuRef.DOCKERFILE)
+
+        # required keywords & status variables
+
+        if line == "ARG MHUB_MODELS_REPO":
+            dockerfile_defines_arg_mhub_models_repo = True
+
+        if line == f"RUN buildutils/import_mhub_model.sh {model_name} ${{MHUB_MODELS_REPO}}":
+           dockerfile_contains_mhubio_import = True
+
+    # check if the dockerfile contains the required ARG MHUB_MODELS_REPO and model import
+    if not dockerfile_defines_arg_mhub_models_repo:
+        raise MHubComplianceError(f"Dockerfile does not define 'ARG MHUB_MODELS_REPO'", DocuRef.DOCKERFILE)
+
+    if not dockerfile_contains_mhubio_import:
+        raise MHubComplianceError(f"Dockerfile does not contain the required mhubio import command: 'RUN buildutils/import_mhub_model.sh {model_name} ${{MHUB_MODELS_REPO}}'.", DocuRef.DOCKERFILE)
+
+    # check that the entrypoint of the dockerfile matches
+    #  ENTRYPOINT ["mhub.run"]  |  ENTRYPOINT ["python", "-m", "mhubio.run"]
+    if not lines[-2].strip() in ['ENTRYPOINT ["mhub.run"]', 'ENTRYPOINT ["python3", "-m", "mhubio.run"]']:
+        raise MHubComplianceError(f"Dockerfile does not contain the correct entrypoint: {lines[-2]}", DocuRef.DOCKERFILE)
+
+    #  CMD ["--workflow", "default"] | CMD ["--config", "/app/models/$model_name/config/default.yml"]
+    if not lines[-1].strip() in ['CMD ["--workflow", "default"]', f'CMD ["--config", "/app/models/{model_name}/config/default.yml"]']:
+        raise MHubComplianceError(f"Dockerfile does not contain the correct entrypoint: {lines[-1]}", DocuRef.DOCKERFILE)
+
+
+def get_model_configuration_files(base: str, model_name: str) -> List[str]:
+
+    # get config path
+    model_config_dir = os.path.join(base, model_name, "config")
+
+    # get workflow files
+    model_workflows = [cf[:-4] for cf in os.listdir(model_config_dir) if cf.endswith(".yml")]
+
+    # return list of configuration files
+    return model_workflows

.github/workflows/model_compliance.yml

@@ -0,0 +1,49 @@
+name: MHub Contribution Check
+
+on:
+  pull_request:
+    branches:
+      - "main"
+
+env:
+  PR_NUMBER: ${{ github.event.number }}
+
+jobs:
+  test:
+    name: Setup Compliance
+    runs-on: ubuntu-latest
+
+    steps:
+
+      # Checkout the latest code from the repo
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      # Setup which version of Python to use
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+            python-version: 3.8
+
+      # Display the Python version being used
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      # Install Python dependencies
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install requests jsonschema
+
+      # Get the list of files modified in the PR
+      - name: Get files modified in PR
+        id: modified_files
+        uses: Ana06/[email protected]
+        with:
+          format: json
+
+      # Run check script
+      - name: Run MHub compliance test
+        run: python .github/scripts/mhub_check.py 
+        env: 
+          MODIFIED_FILES: ${{ steps.modified_files.outputs.all }}

base/buildutils/import_mhub_model.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+
+# Script to import the MHub model definition from GitHub.
+# provide the name of the model as a parameter.
+# Usage: utils/import_mhub_model.sh <model_name> <(repo_url=https://github.com/MHubAI/models.git::main)> <(branch=main)>
+
+# parameters extraction
+MODEL_NAME=$1
+REPO_AND_BRANCH=${2:-https://github.com/MHubAI/models.git::main}
+REPO_URL=$(echo $REPO_AND_BRANCH | awk -F :: '{print $1}')
+REPO_BRANCH=$(echo $REPO_AND_BRANCH | awk -F :: '{print $2}')
+REPO_BRANCH=${REPO_BRANCH:-$3}
+REPO_BRANCH=${REPO_BRANCH:-main}
+
+# printout paramaters (this happens during the docker build...)
+echo "Importing model definition from MHub models repository."
+echo "├── MODEL NAME ..... ${MODEL_NAME}"
+echo "├── REPOSITORY ..... ${REPO_URL}"
+echo "└── BRANCH ......... ${REPO_BRANCH}"
+echo 
+
+# fail if model name is empty
+if [ -z "$MODEL_NAME" ]; then
+    echo "Error: no model name provided."
+    exit 1
+fi
+
+# print a warning that the model definition is not from the 
+# the official MHub Models repository and therefore only 
+# suitable for development
+if [ "$REPO_URL@$REPO_BRANCH" != "https://github.com/MHubAI/models.git@main" ]; then
+    echo 
+    echo "Warning: the model definition is not from the official MHub Models repository and therefore only suitable for development."
+    echo 
+fi
+
+# perform a sparse checkout of the model definition folder 
+# (models/<model_name>) from the referenced repository and branch
+git init
+git fetch ${REPO_URL} ${REPO_BRANCH}
+git merge FETCH_HEAD
+git sparse-checkout set "models/${MODEL_NAME}"
+rm -r .git

base/dockerfiles/Dockerfile

@@ -58,13 +58,14 @@ RUN pip3 install --upgrade pip && pip3 install --no-cache-dir \
 RUN pip3 install git+https://github.com/MHubAI/mhubio.git \
   && pip3 install git+https://github.com/MHubAI/segdb.git \
   && git init \
-  && git sparse-checkout set "base/utils" "base/bin" \
+  && git sparse-checkout set "base/buildutils" "base/bin" \
   && git fetch https://github.com/MHubAI/models.git main \
   && git merge FETCH_HEAD \
-  && mv base/utils . \
+  && mv base/buildutils . \
   && chmod +x base/bin/* \
   && cp base/bin/* /usr/bin/ \
-  && rm -r base
+  && rm -r base \
+  && rm -r .git
 
 # Install DCMQI by pulling the latest release from GitHub (via GitHub API)
 # Run everything in a single RUN command to avoid creating intermediate layers (and allowing environment variables to be used)