Merge branch 'v1_feature_branch' into hextof-lab-loader

Author: zain-sohail

.cspell/custom-dictionary.txt

@@ -82,6 +82,7 @@ datestring
 ddir
 delaxes
 delayeds
+delenv
 Desy
 Deutsches
 dfield

.github/workflows/documentation.yml

@@ -107,12 +107,21 @@ jobs:
         run: |
           if [[ $GITHUB_REF == refs/tags/* ]]; then
             VERSION=${GITHUB_REF#refs/tags/}
-            echo "folder=sed/$VERSION" >> $GITHUB_OUTPUT
-            rm docs-repo/sed/stable
-            ln -s -r docs-repo/sed/$VERSION docs-repo/sed/stable
+              echo "folder=sed/$VERSION" >> $GITHUB_OUTPUT
+            if [[ $VERSION == *a* ]]; then
+              rm -rf docs-repo/sed/latest
+              ln -s -r docs-repo/sed/$VERSION docs-repo/sed/latest
+            else
+              rm -rf docs-repo/sed/stable
+              rm -rf docs-repo/sed/latest
+              ln -s -r docs-repo/sed/$VERSION docs-repo/sed/stable
+              ln -s -r docs-repo/sed/$VERSION docs-repo/sed/latest
+            fi
           elif [[ $GITHUB_REF == refs/heads/main ]]; then
+            rm -rf docs-repo/sed/latest
             echo "folder=sed/latest" >> $GITHUB_OUTPUT
           else
+            rm -rf docs-repo/sed/develop
             echo "folder=sed/develop" >> $GITHUB_OUTPUT
           fi
 

README.md

@@ -1,4 +1,4 @@
-[![Documentation Status](https://github.com/OpenCOMPES/sed/actions/workflows/documentation.yml/badge.svg)]([https://opencompes.github.io/sed/](https://opencompes.github.io/docs/sed/latest/))
+[![Documentation Status](https://github.com/OpenCOMPES/sed/actions/workflows/documentation.yml/badge.svg)](https://opencompes.github.io/docs/sed/stable/)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 ![](https://github.com/OpenCOMPES/sed/actions/workflows/linting.yml/badge.svg?branch=main)
 ![](https://github.com/OpenCOMPES/sed/actions/workflows/testing_multiversion.yml/badge.svg?branch=main)
@@ -58,11 +58,11 @@ pip install sed-processor
 
 # Documentation
 Comprehensive documentation including several workflow examples can be found here:
-https://opencompes.github.io/docs/sed/latest/
+https://opencompes.github.io/docs/sed/stable/
 
 
 # Contributing
-Users are welcome to contribute to the development of **sed-processor**. Information how to contribute, including how to install developer versions can be found in the [documentation](https://opencompes.github.io/docs/sed/latest/misc/contribution.html)
+Users are welcome to contribute to the development of **sed-processor**. Information how to contribute, including how to install developer versions can be found in the [documentation](https://opencompes.github.io/docs/sed/stable/misc/contribution.html)
 
 We would like to thank our contributors!
 

docs/user_guide/config.md

@@ -4,8 +4,8 @@ The config module contains a mechanism to collect configuration parameters from
 It will load an (optional) provided config file, or alternatively use a passed python dictionary as initial config dictionary, and subsequently look for the following additional config files to load:
 
 * ``folder_config``: A config file of name :file:`sed_config.yaml` in the current working directory. This is mostly intended to pass calibration parameters of the workflow between different notebook instances.
-* ``user_config``: A config file provided by the user, stored as :file:`.sed/config.yaml` in the current user's home directly. This is intended to give a user the option for individual configuration modifications of system settings.
-* ``system_config``: A config file provided by the system administrator, stored as :file:`/etc/sed/config.yaml` on Linux-based systems, and :file:`%ALLUSERSPROFILE%/sed/config.yaml` on Windows. This should provide all necessary default parameters for using the sed processor with a given setup. For an example for an mpes setup, see :ref:`example_config`
+* ``user_config``: A config file provided by the user, stored as :file:`.config/sed/config_v1.yaml` in the current user's home directly. This is intended to give a user the option for individual configuration modifications of system settings.
+* ``system_config``: A config file provided by the system administrator, stored as :file:`/etc/sed/config_v1.yaml` on Linux-based systems, and :file:`%ALLUSERSPROFILE%/sed/config_v1.yaml` on Windows. This should provide all necessary default parameters for using the sed processor with a given setup. For an example for an mpes setup, see :ref:`example_config`
 * ``default_config``: The default configuration shipped with the package. Typically, all parameters here should be overwritten by any of the other configuration files.
 
 The config mechanism returns the combined dictionary, and reports the loaded configuration files. In order to disable or overwrite any of the configuration files, they can be also given as optional parameters (path to a file, or python dictionary).

pyproject.toml

@@ -18,8 +18,16 @@ authors = [
 ]
 readme = "README.md"
 keywords = ["sed", "mpes", "flash", "arpes"]
-license = {text = "MIT"}
+license = { file = "LICENSE" }
 requires-python = ">=3.9,<3.13"
+classifiers = [
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
 dependencies = [
     "bokeh>=2.4.2",
     "dask>=2021.12.0,<2024.8",

src/sed/core/config.py

@@ -11,13 +11,20 @@
 
 import yaml
 from platformdirs import user_config_path
+from pydantic import ValidationError
 
 from sed.core.config_model import ConfigModel
 from sed.core.logging import setup_logging
 
 package_dir = os.path.dirname(find_spec("sed").origin)
 
 USER_CONFIG_PATH = user_config_path(appname="sed", appauthor="OpenCOMPES", ensure_exists=True)
+SYSTEM_CONFIG_PATH = (
+    Path(os.environ["ALLUSERSPROFILE"]).joinpath("sed")
+    if platform.system() == "Windows"
+    else Path("/etc/").joinpath("sed")
+)
+ENV_DIR = Path(".env")
 
 # Configure logging
 logger = setup_logging("config")
@@ -48,11 +55,11 @@ def parse_config(
         user_config (dict | str, optional): user-based config dictionary
             or file path. The loaded dictionary is completed with the user-based values,
             taking preference over system and default values.
-            Defaults to the file ".sed/config.yaml" in the current user's home directory.
+            Defaults to the file ".config/sed/config_v1.yaml" in the current user's home directory.
         system_config (dict | str, optional): system-wide config dictionary
             or file path. The loaded dictionary is completed with the system-wide values,
-            taking preference over default values. Defaults to the file "/etc/sed/config.yaml"
-            on linux, and "%ALLUSERSPROFILE%/sed/config.yaml" on windows.
+            taking preference over default values. Defaults to the file "/etc/sed/config_v1.yaml"
+            on linux, and "%ALLUSERSPROFILE%/sed/config_v1.yaml" on windows.
         default_config (dict | str, optional): default config dictionary
             or file path. The loaded dictionary is completed with the default values.
             Defaults to *package_dir*/config/default.yaml".
@@ -61,6 +68,7 @@ def parse_config(
     Raises:
         TypeError: Raised if the provided file is neither *json* nor *yaml*.
         FileNotFoundError: Raised if the provided file is not found.
+        ValueError: Raised if there is a validation error in the config file.
 
     Returns:
         dict: Loaded and completed config dict, possibly verified by pydantic config model.
@@ -91,9 +99,7 @@ def parse_config(
         user_dict = copy.deepcopy(user_config)
     else:
         if user_config is None:
-            user_config = str(
-                Path.home().joinpath(".sed").joinpath("config.yaml"),
-            )
+            user_config = str(USER_CONFIG_PATH.joinpath("config_v1.yaml"))
         if Path(user_config).exists():
             user_dict = load_config(user_config)
             if verbose:
@@ -104,14 +110,7 @@ def parse_config(
         system_dict = copy.deepcopy(system_config)
     else:
         if system_config is None:
-            if platform.system() in ["Linux", "Darwin"]:
-                system_config = str(
-                    Path("/etc/").joinpath("sed").joinpath("config.yaml"),
-                )
-            elif platform.system() == "Windows":
-                system_config = str(
-                    Path(os.environ["ALLUSERSPROFILE"]).joinpath("sed").joinpath("config.yaml"),
-                )
+            system_config = str(SYSTEM_CONFIG_PATH.joinpath("config_v1.yaml"))
         if Path(system_config).exists():
             system_dict = load_config(system_config)
             if verbose:
@@ -146,9 +145,19 @@ def parse_config(
 
     if not verify_config:
         return config_dict
-    # Run the config through the ConfigModel to ensure it is valid
-    config_model = ConfigModel(**config_dict)
-    return config_model.model_dump(exclude_unset=True, exclude_none=True)
+
+    try:
+        # Run the config through the ConfigModel to ensure it is valid
+        config_model = ConfigModel(**config_dict)
+        return config_model.model_dump(exclude_unset=True, exclude_none=True)
+    except ValidationError as e:
+        error_msg = (
+            "Invalid configuration file detected. The following validation errors were found:\n"
+        )
+        for error in e.errors():
+            error_msg += f"\n- {' -> '.join(str(loc) for loc in error['loc'])}: {error['msg']}"
+        logger.error(error_msg)
+        raise ValueError(error_msg) from e
 
 
 def load_config(config_path: str) -> dict:
@@ -269,31 +278,38 @@ def read_env_var(var_name: str) -> str | None:
     1. OS environment variables
     2. .env file in current directory
     3. .env file in user config directory
+    4. .env file in system config directory
 
     Args:
         var_name (str): Name of the environment variable to read
 
     Returns:
         str | None: Value of the environment variable or None if not found
     """
-    # First check OS environment variables
+    # 1. check OS environment variables
     value = os.getenv(var_name)
     if value is not None:
         logger.debug(f"Found {var_name} in OS environment variables")
         return value
 
-    # Then check .env in current directory
-    local_vars = _parse_env_file(Path(".env"))
+    # 2. check .env in current directory
+    local_vars = _parse_env_file(ENV_DIR)
     if var_name in local_vars:
         logger.debug(f"Found {var_name} in ./.env file")
         return local_vars[var_name]
 
-    # Finally check .env in user config directory
+    # 3. check .env in user config directory
     user_vars = _parse_env_file(USER_CONFIG_PATH / ".env")
     if var_name in user_vars:
         logger.debug(f"Found {var_name} in user config .env file")
         return user_vars[var_name]
 
+    # 4. check .env in system config directory
+    system_vars = _parse_env_file(SYSTEM_CONFIG_PATH / ".env")
+    if var_name in system_vars:
+        logger.debug(f"Found {var_name} in system config .env file")
+        return system_vars[var_name]
+
     logger.debug(f"Environment variable {var_name} not found in any location")
     return None