Package without editable flag

.github/workflows/auth-ci.yml

@@ -37,7 +37,7 @@ jobs:
       working-directory: .
       run: |
         python -m pip install --upgrade pip
-        pip install -e cli/
+        pip install ./cli
         pip install -r cli/test-requirements.txt
         pip install -r server/requirements.txt
         pip install -r server/test-requirements.txt
@@ -48,7 +48,7 @@ jobs:
 
     - name: Run django server in background with generated certs
       working-directory: ./server
-      run: sh setup-dev-server.sh & sleep 6
+      run: sh setup-dev-server.sh -c cert.crt -k cert.key & sleep 6
 
     - name: Run server integration tests
       working-directory: ./server

.github/workflows/docker-ci.yml

@@ -38,7 +38,7 @@ jobs:
       working-directory: .
       run: |
         python -m pip install --upgrade pip
-        pip install -e cli/
+        pip install cli/
         pip install -r cli/test-requirements.txt
         pip install -r server/requirements.txt
         pip install -r server/test-requirements.txt
@@ -57,6 +57,12 @@ jobs:
         cp ../mock_tokens/tokens.json tokens.json
         docker build -t ${{ env.IMAGE_NAME }} -f Dockerfile.gha .
 
+    - name: Copy configurations for MedPerf client
+      working-directory: ./server
+      run: |
+        cp tokens.json ~/.medperf_dev/tokens.json
+        cp cert.crt ~/.medperf_dev/cert.crt
+
     - name: Run server in background
       working-directory: ./server
       run: PORT=8080 && docker run --name medperf_api -d -p 8000:${PORT} -e PORT=${PORT} -e SSL_FLAGS="--certfile=cert.crt --keyfile=cert.key" ${{ env.IMAGE_NAME }}

.github/workflows/local-ci.yml

@@ -38,7 +38,7 @@ jobs:
       working-directory: .
       run: |
         python -m pip install --upgrade pip
-        pip install -e cli/
+        pip install cli/
         pip install -r cli/test-requirements.txt
         pip install -r server/requirements.txt
         pip install -r server/test-requirements.txt
@@ -53,7 +53,7 @@ jobs:
 
     - name: Run server integration tests
       working-directory: ./server
-      run: python seed.py --cert cert.crt
+      run: python seed.py
 
     - name: Run chestxray demo
       working-directory: .

.github/workflows/unittests.yml

@@ -21,7 +21,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        if [ -f cli/requirements.txt ]; then pip install -e cli; fi
+        if [ -f cli/requirements.txt ]; then pip install ./cli; fi
         pip install -r server/requirements.txt
         pip install -r server/test-requirements.txt
     - name: Lint with flake8

cli/medperf/config.py

@@ -1,16 +1,13 @@
 from ._version import __version__
 from pathlib import Path
 
-BASE_DIR = Path(__file__).resolve().parent.parent.parent
-
 major_version, minor_version, patch_version = __version__.split(".")
 
 # MedPerf server
 server = "https://api.medperf.org"
 certificate = None
 
 local_server = "https://localhost:8000"
-local_certificate = str(BASE_DIR / "server" / "cert.crt")
 
 comms = "REST"
 
@@ -39,8 +36,6 @@
 access_token_storage_id = "medperf_access_token"
 refresh_token_storage_id = "medperf_refresh_token"
 
-local_tokens_path = BASE_DIR / "mock_tokens" / "tokens.json"
-
 # Storage config
 config_storage = Path.home().resolve() / ".medperf_config"
 logs_storage = Path.home().resolve() / ".medperf_logs"
@@ -49,6 +44,10 @@
 creds_folder = str(config_storage / ".tokens")
 tokens_db = str(config_storage / ".tokens_db")
 
+local_server_config_storage = Path.home().resolve() / ".medperf_dev"
+local_tokens_path = local_server_config_storage / "tokens.json"
+local_certificate = str(local_server_config_storage / "cert.crt")
+
 images_folder = ".images"
 trash_folder = ".trash"
 tmp_folder = ".tmp"

cli/medperf/utils.py

@@ -19,7 +19,7 @@
 from typing import List
 from colorama import Fore, Style
 from pexpect.exceptions import TIMEOUT
-from git import Repo, GitCommandError
+from git import Repo, GitCommandError, InvalidGitRepositoryError
 import medperf.config as config
 from medperf.exceptions import ExecutionError, MedperfException
 
@@ -430,7 +430,12 @@ def filter_latest_associations(associations, entity_key):
 
 def check_for_updates() -> None:
     """Check if the current branch is up-to-date with its remote counterpart using GitPython."""
-    repo = Repo(config.BASE_DIR)
+    repo_root_dir = Path(__file__).resolve().parent.parent.parent
+    try:
+        repo = Repo(repo_root_dir)
+    except InvalidGitRepositoryError:  # package is installed not in -e mode from git repo
+        return
+
     if repo.bare:
         logging.debug("Repo is bare")
         return

cli/setup.py

@@ -1,4 +1,4 @@
-from setuptools import setup
+from setuptools import setup, find_packages
 from medperf._version import __version__
 
 with open("requirements.txt", "r") as f:
@@ -15,10 +15,12 @@
     name="medperf",
     version=__version__,
     description="CLI Tool for federated benchmarking on medical private data",
-    url="https://github.com/aristizabal95/medperf",
+    long_description=open('../README.md').read(),
+    long_description_content_type='text/markdown',
+    url="https://github.com/mlcommons/medperf",
     author="MLCommons",
     license="Apache 2.0",
-    packages=["medperf"],
+    packages=find_packages(where="."),
     install_requires=requires,
     python_requires=">=3.6",
     entry_points="""

docs/getting_started/installation.md

@@ -62,7 +62,7 @@ If using Docker, make sure [you can run Docker as a non-root user.](https://docs
 3. Install MedPerf from source:
 
     ```bash
-    pip install -e ./cli
+    pip install ./cli
     ```
 
 4. Verify the installation:

docs/mlcubes/shared/build.md

@@ -13,7 +13,7 @@ MedPerf provides some cookiecutter templates for all the related MLCubes. Additi
 
 2. Install the MedPerf CLI:
     ```bash
-    pip install -e cli
+    pip install ./cli
     ```
 
 3. If you have not done so, create a folder for keeping all MLCubes created in this tutorial:

server/seed.py

@@ -11,8 +11,10 @@
 from seed_utils import Server, set_user_as_admin, create_benchmark, create_model
 from auth_provider_token import auth_provider_token
 from pathlib import Path
+import shutil
 import json
 
+DEV_CONFIG_DIR = Path.home() / ".medperf_dev"
 REPO_BASE_DIR = Path(__file__).resolve().parent.parent
 
 
@@ -46,8 +48,9 @@ def seed(args):
 
 
 if __name__ == "__main__":
-    default_cert_file = str(REPO_BASE_DIR / "server" / "cert.crt")
-    default_tokens_file = str(REPO_BASE_DIR / "mock_tokens" / "tokens.json")
+    default_cert_file = str(DEV_CONFIG_DIR / "cert.crt")
+    local_tokens_file = str(REPO_BASE_DIR / "mock_tokens" / "tokens.json")
+    dest_tokens_file = str(DEV_CONFIG_DIR / "tokens.json")
 
     parser = argparse.ArgumentParser(description="Seed the db with demo entries")
     parser.add_argument(
@@ -78,9 +81,13 @@ def seed(args):
         "--tokens",
         type=str,
         help="Path to local tokens file",
-        default=default_tokens_file,
+        default=local_tokens_file,
     )
     args = parser.parse_args()
     if args.cert.lower() == "none":
         args.cert = None
+    DEV_CONFIG_DIR.mkdir(parents=True, exist_ok=True)
+    print('config folder:', DEV_CONFIG_DIR, DEV_CONFIG_DIR.exists())
+    shutil.copy(args.tokens, dest_tokens_file)  # for usage by medperf client
+    print('token file:', dest_tokens_file, Path(dest_tokens_file).exists())
     seed(args)

server/setup-dev-server.sh

@@ -9,19 +9,21 @@ do
     esac
 done
 
+CONFIG_PATH=$HOME/.medperf_dev
 DEPLOY="${DEPLOY:-1}"
 CERT_GENERATE="${CERT_GENERATE:-1}"
-CERT_FILE="${CERT_FILE:-cert.crt}"
-KEY_FILE="${KEY_FILE:-cert.key}"
+CERT_FILE="${CERT_FILE:-$CONFIG_PATH/cert.crt}"
+KEY_FILE="${KEY_FILE:-$CONFIG_PATH/cert.key}"
 RESET_DB="${RESET_DB:-0}"
 
 echo $CERT_FILE
 echo $KEY_FILE
 echo $DEPLOY
 echo $CERT_GENERATE
-echo $CERT_PATH
 echo $RESET_DB
+echo $CONFIG_PATH
 
+mkdir -p $CONFIG_PATH
 
 if [ -z "$CERT_FILE" ]
 then