Dev #35 #36 #37 #38

.github/workflows/docs.yaml

@@ -5,10 +5,6 @@ on:
     branches:
       - main
     tags: ["*"]
-  pull_request:
-    branches:
-      - main
-    types: [opened, synchronize, reopened]
 
 concurrency:
   # Skip intermediate builds: always.

.github/workflows/tests.yaml

@@ -25,6 +25,7 @@ jobs:
 
       - name: Install package
         run: |
+          pip install uv
           pip install -e ".[test]"
 
       - name: Test with pytest

.gitignore

@@ -3,7 +3,7 @@ build
 coverage.xml
 *.egg-info
 dist
-.env
+.env*
 lcov.info
 __pycache__
 

.pre-commit-config.yaml

@@ -1,34 +1,37 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+default_install_hook_types:
+  - pre-commit
+  - commit-msg
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-json
       - id: check-yaml
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: v1.18.2
     hooks:
       - id: mypy
         additional_dependencies:
          - types-pyyaml
          - types-requests
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.0
+    rev: v0.14.3
     hooks:
-      - id: ruff  # Linter
-        args: [ --fix ]
+      - id: ruff-check  # Linter
+        args: [ --fix, --select, "I" ]
       - id: ruff-format  # Formatter
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         additional_dependencies:
           - tomli
   - repo: https://github.com/compilerla/conventional-pre-commit
-    rev: v3.6.0
+    rev: v4.3.0
     hooks:
       - id: conventional-pre-commit
         stages: [commit-msg]

Makefile

@@ -1,6 +1,6 @@
 install:
 	pip install -e ".[dev]"
-	pre-commit install -t pre-commit -t commit-msg
+	pre-commit install
 
 lint:
 	pre-commit run --all-files

docs/conf.py

@@ -2,9 +2,9 @@
 
 # -- Path setup --------------------------------------------------------------
 
-from datetime import datetime
 import os
 import sys
+from datetime import datetime
 
 import frame_cli
 

frame_cli/check.py

@@ -1,11 +1,11 @@
 """Check installation and API access."""
 
-from json import JSONDecodeError
 import shutil
+from json import JSONDecodeError
 
 import requests
 
-from .config import API_URL
+from .config import API_URL, REQUESTS_TIMEOUT
 
 
 def check() -> None:
@@ -20,7 +20,7 @@ def check_api() -> None:
 
     url = f"{API_URL}/healthz"
     try:
-        response = requests.get(url)
+        response = requests.get(url, timeout=REQUESTS_TIMEOUT)
     except Exception:
         print("API is not accessible. Check the API URL.")
         return

frame_cli/config.py

@@ -1,10 +1,12 @@
 """Configuration variables."""
 
+import contextlib
 import os
 
 from dotenv import load_dotenv
 
-load_dotenv()
+with contextlib.redirect_stdout(None), contextlib.redirect_stderr(None):
+    load_dotenv()
 
 LOGGING_LEVEL = os.getenv("FRAME_CLI_LOGGING_LEVEL", "INFO")
 API_URL = os.getenv("FRAME_CLI_API_URL", "https://frame-dev.epfl.ch/api/")
@@ -18,4 +20,7 @@
 FRAME_REPO_OWNER = "CHANGE-EPFL"
 FRAME_REPO_NAME = "frame-project"
 FRAME_REPO = f"{FRAME_REPO_OWNER}/{FRAME_REPO_NAME}"
-EXTERNAL_REFERENCES_PATH = os.path.join("backend", "api", "metadata_files", "external_references.yaml")
+FRAME_PYTHON_VERSION = "3.10"
+METADATA_DIR_PATH = os.path.join("backend", "api", "metadata_files")
+EXTERNAL_REFERENCES_PATH = os.path.join(METADATA_DIR_PATH, "external_references.yaml")
+REQUESTS_TIMEOUT = 10  # seconds

frame_cli/downloaders/zenodo.py

@@ -18,6 +18,7 @@
 )
 from rich.status import Status
 
+from ..config import REQUESTS_TIMEOUT
 from ..logging import logger
 from .downloader import Downloader
 
@@ -56,7 +57,7 @@ def download(
         url = f"https://{host}/api/records/{dataset_id}"
 
         # Scan record
-        response = requests.get(url)
+        response = requests.get(url, timeout=REQUESTS_TIMEOUT)
         _check_request_response(response, f'getting Zenodo record "{dataset_id}"')
         record = response.json()
 

frame_cli/environment_managers/conda.py

@@ -0,0 +1,57 @@
+"""Module containing the CondaEnvironmentManager class."""
+
+import os
+import subprocess
+
+from rich.console import Console
+from rich.panel import Panel
+
+from .environment_manager import EnvironmentManager
+
+
+class CondaEnvironmentManager(EnvironmentManager):
+    """Environment manager for Conda."""
+
+    type = "conda"
+
+    def setup(self, destination: str, file_paths: list[str], *args, **kwargs) -> None:
+        """Set up the environment for the hybrid model.
+
+        Args:
+            destination (str): Hybrid model destination directory where the environment is set up.
+            file_paths (list[str]): List of paths to files that describe the environment.
+        """
+        os.chdir(destination)
+        console = Console()
+
+        conda_commands = ["conda", "mamba", "micromamba"]
+        conda_command = None
+
+        for conda_command in conda_commands:
+            try:
+                subprocess.run([conda_command, "--version"], check=True, capture_output=True)  # type: ignore
+                break
+            except (subprocess.CalledProcessError, FileNotFoundError):
+                conda_command = None
+
+        if conda_command is None:
+            console.print(
+                "No Conda (or equivalent) installation found. Please install Conda, Mamba, or Micromamba to create an environment for this model."
+            )
+            return
+
+        console.print("Setting up Conda environment...")
+        for file_path in file_paths:
+            if not os.path.isfile(file_path):
+                console.print(f"File {file_path} does not exist. Skipping...")
+                continue
+            if file_path.endswith((".yml", ".yaml")):
+                subprocess.run([conda_command, "env", "create", "-f", file_path, "--prefix", "./.venv", "-y"])
+                console.print(f"Conda environment setup from {file_path} complete. Skipping remaining files...")
+                break
+            else:
+                console.print(f"Unsupported file {file_path}. Skipping...")
+
+        console.print("Conda environment setup complete. Activate it from the model's root directory with")
+        activation_message = f"cd {destination}\n{conda_command} activate ./.venv"
+        console.print(Panel(activation_message))

frame_cli/environment_managers/environment_manager.py

@@ -1,5 +1,9 @@
 """Module containing the EnvironmentManager abstract base class."""
 
+import importlib
+import inspect
+import os
+import pkgutil
 from abc import ABC, abstractmethod
 
 
@@ -16,3 +20,38 @@ def setup(self, destination: str, file_paths: list[str], *args, **kwargs) -> Non
             destination (str): Hybrid model destination directory where the environment is set up.
             file_paths (list[str]): List of paths to files that describe the environment.
         """
+
+
+def _get_environment_manager_subclasses() -> dict[str, type[EnvironmentManager]]:
+    package_path = os.path.dirname(__file__)
+    subclasses = {}
+
+    for module_info in pkgutil.iter_modules([package_path]):
+        if module_info.ispkg:
+            continue
+
+        module = importlib.import_module(f"{__package__}.{module_info.name}")
+
+        for _, obj in inspect.getmembers(module):
+            if inspect.isclass(obj) and issubclass(obj, EnvironmentManager) and obj is not EnvironmentManager:
+                subclasses[obj.type] = obj
+
+    return subclasses
+
+
+_environment_manager_subclasses: dict | None = None
+
+
+def get_environment_manager(environment_type: str) -> EnvironmentManager | None:
+    """Get an instance of environment manager for the given type."""
+    global _environment_manager_subclasses
+
+    if _environment_manager_subclasses is None:
+        _environment_manager_subclasses = _get_environment_manager_subclasses()
+
+    manager_class = _environment_manager_subclasses.get(environment_type)
+
+    if manager_class is not None:
+        return manager_class()
+
+    return None

frame_cli/environment_managers/julia.py

@@ -0,0 +1,39 @@
+"""Module containing the JuliaEnvironmentManager class."""
+
+import os
+import subprocess
+
+from rich.console import Console
+from rich.panel import Panel
+
+from .environment_manager import EnvironmentManager
+
+
+class JuliaEnvironmentManager(EnvironmentManager):
+    """Environment manager for Julia."""
+
+    type = "julia"
+
+    def setup(self, destination: str, file_paths: list[str], *args, **kwargs) -> None:
+        """Set up the environment for the hybrid model.
+
+        Args:
+            destination (str): Hybrid model destination directory where the environment is set up.
+            file_paths (list[str]): List of paths to files that describe the environment.
+        """
+        os.chdir(destination)
+        console = Console()
+        console.print("Setting up Julia environment...")
+
+        try:
+            subprocess.run(["julia", "--version"], check=True, capture_output=True)
+        except (subprocess.CalledProcessError, FileNotFoundError):
+            console.print("Julia installation not found. Please install Julia to create an environment for this model.")
+            return
+
+        console.print("Setting up Julia environment using Project.toml...")
+        subprocess.run(["julia", "-e", 'using Pkg; Pkg.activate("."); Pkg.instantiate()'])
+
+        console.print("Julia environment setup complete. Use it from the model's root directory with")
+        activation_message = f"cd {destination}\njulia --project=."
+        console.print(Panel(activation_message))

frame_cli/environment_managers/python_requirements.py → frame_cli/environment_managers/python.py

@@ -1,4 +1,4 @@
-"""Module containing the PythonRequirementsEnvironmentManager class."""
+"""Module containing the PythonEnvironmentManager class."""
 
 import os
 import subprocess
@@ -10,10 +10,10 @@
 from .environment_manager import EnvironmentManager
 
 
-class PythonRequirementsEnvironmentManager(EnvironmentManager):
-    """Environment manager for Python requirements."""
+class PythonEnvironmentManager(EnvironmentManager):
+    """Environment manager for Python."""
 
-    type = "python_requirements"
+    type = "python"
 
     def setup(self, destination: str, file_paths: list[str], *args, **kwargs) -> None:
         """Set up the environment for the hybrid model.
@@ -27,8 +27,17 @@ def setup(self, destination: str, file_paths: list[str], *args, **kwargs) -> Non
         console.print("Setting up Python environment...")
         subprocess.run(["uv", "venv"])
         subprocess.run(["uv", "pip", "install", "pip"])
-        for requirement_path in file_paths:
-            subprocess.run(["uv", "pip", "install", "-r", requirement_path])
+
+        for file_path in file_paths:
+            if not os.path.isfile(file_path):
+                console.print(f"File {file_path} does not exist. Skipping...")
+                continue
+            if file_path == "pyproject.toml":
+                subprocess.run(["uv", "pip", "install", "-e", "."])
+            elif file_path.endswith(".txt"):
+                subprocess.run(["uv", "pip", "install", "-r", file_path])
+            else:
+                console.print(f"Unsupported file {file_path}. Skipping...")
 
         console.print("Python environment setup complete. Activate it from the model's root directory with")
         activation_message = f"cd {destination}\n"

frame_cli/info.py

@@ -5,7 +5,7 @@
 import yaml
 
 from .config import FRAME_DIR_NAME, INFO_FILE_NAME
-from .metadata import get_model_name, get_model_url, get_metadata_file_path
+from .metadata import get_metadata_file_path, get_model_name, get_model_url
 
 
 def get_home_info_path() -> str:
@@ -160,7 +160,9 @@ def get_github_token(use_new_token: bool = False) -> str:
     global_info = get_global_info()
 
     if "github_token" not in global_info or use_new_token:
-        print("Create a GitHub token with `repo` scope: https://github.com/settings/tokens/new")
+        print(
+            "Use the following link to create a classical GitHub token with `repo` and `workflow` scopes: https://github.com/settings/tokens/new"
+        )
         github_token = input("GitHub token: ")
         global_info["github_token"] = github_token
         set_global_info(global_info)

frame_cli/init.py

@@ -2,10 +2,10 @@
 
 from .config import FRAME_METADATA_FILE_NAME
 from .metadata import (
-    create_metadata_file,
-    NotInsideGitRepositoryError,
     MetadataFileAlreadyExistsError,
     MetadataTemplateFetchError,
+    NotInsideGitRepositoryError,
+    create_metadata_file,
 )