Fix config

.reuse/dep5

@@ -3,7 +3,7 @@ Upstream-Name: somesy
 Upstream-Contact: Mustafa Soylu <m.soylu@fz-juelich.de>
 Source: https://github.com/Materials-Data-Science-and-Informatics/somesy
 
-Files: .gitignore pyproject.toml poetry.lock .pre-commit-config.yaml .pre-commit-hooks.yaml .somesy.toml codemeta.json CITATION.cff README.md RELEASE_NOTES.md CHANGELOG.md CODE_OF_CONDUCT.md AUTHORS.md CONTRIBUTING.md .gitlab-ci.yml .gitlab/* .github/* mkdocs.yml docs/*
+Files: .gitignore pyproject.toml poetry.lock .pre-commit-config.yaml .pre-commit-hooks.yaml .sourcery.yaml .somesy.toml codemeta.json CITATION.cff README.md RELEASE_NOTES.md CHANGELOG.md CODE_OF_CONDUCT.md AUTHORS.md CONTRIBUTING.md .gitlab-ci.yml .gitlab/* .github/* mkdocs.yml docs/*
 Copyright: 2023 Forschungszentrum Jülich GmbH - Institute Materials Data Science and Informatics (IAS9) - Stefan Sandfeld (s.sandfeld@fz-juelich.de)
 License: CC0-1.0
 

.somesy.toml

@@ -42,7 +42,7 @@ contribution = "Valuable input concerning metadata standards and usability."
 contribution_begin = "2023-03-01"
 contribution_type = "ideas"
 
-[config.cli]
+[config]
 no_sync_cff = false
 cff_file = "CITATION.cff"
 no_sync_pyproject = false

.sourcery.yaml

@@ -0,0 +1,70 @@
+# 🪄 This is your project's Sourcery configuration file.
+
+# You can use it to get Sourcery working in the way you want, such as
+# ignoring specific refactorings, skipping directories in your project,
+# or writing custom rules.
+
+# 📚 For a complete reference to this file, see the documentation at
+# https://docs.sourcery.ai/Configuration/Project-Settings/
+
+# This file was auto-generated by Sourcery on 2023-07-19 at 10:22.
+
+version: '1'  # The schema version of this config file
+
+ignore: # A list of paths or files which Sourcery will ignore.
+- .git
+- venv
+- .venv
+- env
+- .env
+- .tox
+- node_modules
+- vendor
+
+rule_settings:
+  enable:
+  - default
+  disable: []  # A list of rule IDs Sourcery will never suggest.
+  rule_types:
+  - refactoring
+  - suggestion
+  - comment
+  python_version: '3.8' # A string specifying the lowest Python version your project supports. Sourcery will not suggest refactorings requiring a higher Python version.
+
+# rules:  # A list of custom rules Sourcery will include in its analysis.
+# - id: no-print-statements
+#   description: Do not use print statements in the test directory.
+#   pattern: print(...)
+#   language: python
+#   replacement:
+#   condition:
+#   explanation:
+#   paths:
+#     include:
+#     - test
+#     exclude:
+#     - conftest.py
+#   tests: []
+#   tags: []
+
+# rule_tags: {} # Additional rule tags.
+
+# metrics:
+#   quality_threshold: 25.0
+
+# github:
+#   labels: []
+#   ignore_labels:
+#   - sourcery-ignore
+#   request_review: author
+#   sourcery_branch: sourcery/{base_branch}
+
+# clone_detection:
+#   min_lines: 3
+#   min_duplicates: 2
+#   identical_clones_only: false
+
+# proxy:
+#   url:
+#   ssl_certs_file:
+#   no_ssl_verify: false

pyproject.toml

@@ -44,7 +44,8 @@ cffconvert = "^2.0.0"
 wrapt = "^1.15.0"
 packaging = "^23.1"
 rdflib = "^6.3.2"
-codemetapy = "^2.5.0"
+codemetapy = { git = "https://github.com/proycon/codemetapy.git" }
+# codemetapy = "^2.5.1" # TODO: use once released
 
 [tool.poetry.group.dev.dependencies]
 poethepoet = "^0.18.1"

src/somesy/cli/init.py

@@ -1,78 +1,71 @@
 """Set config files for somesy."""
 import logging
-import traceback
 from pathlib import Path
 
 import typer
 
 from somesy.commands import init_config
-from somesy.core.discover import discover_input
+from somesy.core.core import discover_input
 from somesy.core.log import SomesyLogLevel, set_log_level
 
+from .util import wrap_exceptions
+
 logger = logging.getLogger("somesy")
 app = typer.Typer()
 
 
 @app.command()
+@wrap_exceptions
 def config():
     """Set CLI configs for somesy."""
-    try:
-        # check if input file exists, if not, try to find it from default list
-        input_file_default = discover_input()
-
-        options = {}
-
-        # prompt for inputs
-        input_file = typer.prompt("Input file path", default=input_file_default)
-        input_file = Path(input_file)
-        options["input_file"] = input_file
-        options["no_sync_cff"] = not typer.confirm(
-            "Do you want to sync CFF file?", default=True
-        )
-
-        cff_file = typer.prompt("CFF file path", default="CITATION.cff")
-        if cff_file is not None or cff_file != "":
-            options["cff_file"] = cff_file
-
-        options["no_sync_pyproject"] = not typer.confirm(
-            "Do you want to sync pyproject.toml file?", default=True
-        )
-
-        pyproject_file = typer.prompt(
-            "pyproject.toml file path", default="pyproject.toml"
+    # check if input file exists, if not, try to find it from default list
+    input_file_default = discover_input()
+
+    # prompt for inputs
+    input_file = typer.prompt("Input file path", default=input_file_default)
+    input_file = Path(input_file)
+    options = {
+        "input_file": input_file,
+        "no_sync_cff": not typer.confirm(
+            "Do you want to sync to a CFF file?", default=True
+        ),
+    }
+    cff_file = typer.prompt("CFF file path", default="CITATION.cff")
+    if cff_file is not None or cff_file != "":
+        options["cff_file"] = cff_file
+
+    options["no_sync_pyproject"] = not typer.confirm(
+        "Do you want to sync to a pyproject.toml file?", default=True
+    )
+
+    pyproject_file = typer.prompt("pyproject.toml file path", default="pyproject.toml")
+    if pyproject_file is not None or pyproject_file != "":
+        options["pyproject_file"] = pyproject_file
+
+    options["no_sync_codemeta"] = not typer.confirm(
+        "Do you want to sync to a codemeta.json file?", default=True
+    )
+    codemeta_file = typer.prompt("codemeta.json file path", default="codemeta.json")
+    if codemeta_file is not None or codemeta_file != "":
+        options["codemeta_file"] = codemeta_file
+
+    options["show_info"] = typer.confirm(
+        "Do you want to show info about the sync process?"
+    )
+    options["verbose"] = typer.confirm("Do you want to show verbose logs?")
+    options["debug"] = typer.confirm("Do you want to show debug logs?")
+
+    set_log_level(
+        SomesyLogLevel.from_flags(
+            debug=options["debug"],
+            verbose=options["verbose"],
+            info=options["show_info"],
         )
-        if pyproject_file is not None or pyproject_file != "":
-            options["pyproject_file"] = pyproject_file
+    )
 
-        options["no_sync_codemeta"] = not typer.confirm(
-            "Do you want to sync codemeta.json file?", default=True
-        )
-        codemeta_file = typer.prompt("codemeta.json file path", default="codemeta.json")
-        if codemeta_file is not None or codemeta_file != "":
-            options["codemeta_file"] = codemeta_file
-
-        options["show_info"] = typer.confirm(
-            "Do you want to show info about the sync process?"
-        )
-        options["verbose"] = typer.confirm("Do you want to show verbose logs?")
-        options["debug"] = typer.confirm("Do you want to show debug logs?")
-
-        set_log_level(
-            SomesyLogLevel.from_flags(
-                debug=options["debug"],
-                verbose=options["verbose"],
-                info=options["show_info"],
-            )
-        )
-
-        logger.debug(f"CLI options entered: {options}")
-
-        init_config(input_file, options)
-        logger.info(
-            f"[bold green]Input file is updated/created at {input_file}[/bold green]"
-        )
+    logger.debug(f"CLI options entered: {options}")
 
-    except Exception as e:
-        logger.error(f"[bold red]Error: {e}[/bold red]")
-        logger.debug(f"[red]{traceback.format_exc()}[/red]")
-        raise typer.Exit(code=1)
+    init_config(input_file, options)
+    logger.info(
+        f"[bold green]Input file is updated/created at {input_file}[/bold green]"
+    )

src/somesy/cli/sync.py

@@ -1,24 +1,25 @@
 """Sync command for somesy."""
 import logging
-import traceback
 from pathlib import Path
 from typing import Optional
 
 import typer
 from rich.pretty import pretty_repr
 
 from somesy.commands import sync as sync_command
-from somesy.core.core import get_somesy_cli_config
-from somesy.core.discover import discover_input
+from somesy.core.core import discover_input
 from somesy.core.log import SomesyLogLevel, get_log_level, set_log_level
-from somesy.core.models import SomesyConfig
+from somesy.core.models import SomesyConfig, SomesyInput
+
+from .util import wrap_exceptions
 
 logger = logging.getLogger("somesy")
 
 app = typer.Typer()
 
 
 @app.callback(invoke_without_command=True)
+@wrap_exceptions
 def sync(
     input_file: Path = typer.Option(
         None,
@@ -88,68 +89,46 @@ def sync(
     ),
 ):
     """Sync project metadata input with metadata files."""
-    try:
-        # ---------------
-        # config assembly
-
-        # cli_log_level is None if the user did not pass a log level (-> "default")
-        cli_log_level: Optional[SomesyLogLevel] = get_log_level()
-
-        # config from CLI (merged with possibly set CLI flags for logging)
-        curr_log_level: SomesyLogLevel = cli_log_level or SomesyLogLevel.SILENT
-        passed_cli_args = {
-            k: v
-            for k, v in dict(
-                no_sync_cff=no_sync_cff,
-                cff_file=cff_file,
-                no_sync_pyproject=no_sync_pyproject,
-                pyproject_file=pyproject_file,
-                no_sync_codemeta=no_sync_codemeta,
-                codemeta_file=codemeta_file,
-                show_info=curr_log_level == SomesyLogLevel.INFO,
-                verbose=curr_log_level == SomesyLogLevel.VERBOSE,
-                debug=curr_log_level == SomesyLogLevel.DEBUG,
-            ).items()
-            if v is not None
-        }
-        cli_conf = SomesyConfig(**passed_cli_args)
-        cli_conf = cli_conf.dict()
-        logger.debug(f"CLI config (excluding defaults):\n{pretty_repr(cli_conf)}")
-
-        # ----
-        # now try to get config from a config file
-        # check if input file exists, if not, try to find it from default list
-        somesy_conf_file: Path = discover_input(input_file)
-        file_conf = get_somesy_cli_config(somesy_conf_file)
-
-        # convert logging flags into somesy log level (for comparison)
-        config_log_level = SomesyLogLevel.from_flags(
-            info=file_conf.show_info, verbose=file_conf.verbose, debug=file_conf.debug
-        )
-        # convert into dict
-        file_conf = file_conf.dict()
-        logger.debug(f"File config (excluding defaults):\n{pretty_repr(file_conf)}")
-
-        # prioritized combination of config settings (cli overrides config file)
-        conf = SomesyConfig(**{**file_conf, **cli_conf})
-
-        # if the log level was not initialized using a common CLI flag yet,
-        # set it according to the loaded configuration
-        if cli_log_level is None:
-            set_log_level(config_log_level)
-
-        logger.debug(f"Combined config (Defaults + File + CLI):\n{pretty_repr(conf)}")
-        # --------
-        run_sync(conf)
-
-    except Exception as e:
-        logger.error(f"[bold red]Error: {e}[/bold red]")
-        logger.debug(f"[red]{traceback.format_exc()}[/red]")
-        raise typer.Exit(code=1)
-
-
-def run_sync(conf: SomesyConfig):
+    # ---------------
+    # config from CLI (merged with possibly set CLI flags for logging)
+    passed_cli_args = {
+        k: v
+        for k, v in dict(
+            input_file=discover_input(input_file),
+            no_sync_cff=no_sync_cff,
+            cff_file=cff_file,
+            no_sync_pyproject=no_sync_pyproject,
+            pyproject_file=pyproject_file,
+            no_sync_codemeta=no_sync_codemeta,
+            codemeta_file=codemeta_file,
+        ).items()
+        if v is not None
+    }
+    somesy_conf = SomesyConfig(**passed_cli_args)
+
+    # cli_log_level is None if the user did not pass a log level (-> "default")
+    cli_log_level: Optional[SomesyLogLevel] = get_log_level()
+
+    if cli_log_level is not None:
+        # update log level flags if cli log level was set
+        somesy_conf.update_log_level(cli_log_level)
+
+    somesy_input: SomesyInput = somesy_conf.get_input()
+
+    if cli_log_level is None:
+        # no cli log level -> set it according to the loaded configuration
+        set_log_level(somesy_input.config.log_level())
+
+    logger.debug(
+        f"Combined config (Defaults + File + CLI):\n{pretty_repr(somesy_input.config)}"
+    )
+    # --------
+    run_sync(somesy_input)
+
+
+def run_sync(somesy_input: SomesyInput):
     """Write log messages and run synchronization based on passed config."""
+    conf = somesy_input.config
     logger.info("[bold green]Synchronizing project metadata...[/bold green]")
     logger.info("Files to sync:")
     if not conf.no_sync_pyproject:
@@ -163,6 +142,6 @@ def run_sync(conf: SomesyConfig):
             f"  - [italic]codemeta.json[/italic]:\t[grey]{conf.codemeta_file}[/grey]\n"
         )
     # ----
-    sync_command(conf)
+    sync_command(somesy_input)
     # ----
     logger.info("[bold green]Metadata synchronization completed.[/bold green]")

src/somesy/cli/util.py

@@ -0,0 +1,20 @@
+"""Utility functions for CLI commands."""
+import logging
+import traceback
+
+import typer
+import wrapt
+
+logger = logging.getLogger("somesy")
+
+
+@wrapt.decorator
+def wrap_exceptions(wrapped, instance, args, kwargs):
+    """Format and log exceptions for cli commands."""
+    try:
+        return wrapped(*args, **kwargs)
+
+    except Exception as e:
+        logger.error(f"[bold red]Error: {e}[/bold red]")
+        logger.debug(f"[red]{traceback.format_exc()}[/red]")
+        raise typer.Exit(code=1) from e