[REG]: Introduce registry creation

.github/workflows/ci.yml

@@ -0,0 +1,46 @@
+name: Run Tests
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version:
+          - "3.10"
+          - "3.11"
+          - "3.12"
+          - "3.13"
+          - "3.14"
+
+    steps:
+      - uses: actions/checkout@v6
+      - name: Set up git-annex
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y git-annex
+      - name: Install Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install tox tox-gh-actions
+      - name: Configure Git for DataLad
+        run: |
+          git config --global user.email "julio-runner@github.com"
+          git config --global user.name "GitHub Runner"
+      - name: Test with tox
+        run: |
+          tox
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: true
+          flags: julio
+        if: success() && matrix.python-version == 3.13

CHANGELOG.md

@@ -1,3 +1,10 @@
+## [0.0.1](https://github.com/juaml/junifer-julio/tree/0.0.1) - 2025-12-11
+
+### Added
+
+- Introduce registry creation ([#2](https://github.com/juaml/juni-julio/issues/2))
+
+
 ## [0.0.0](https://github.com/juaml/junifer-julio/tree/0.0.0) - 2025-12-11
 
 ### Added

codecov.yml

@@ -0,0 +1,29 @@
+codecov:
+  notify: {}
+  require_ci_to_pass: false
+
+comment: # this is a top-level key
+  layout: "reach, diff, flags, files"
+  behavior: default
+  require_changes: false # if true: only post the comment if coverage changes
+  require_base: no # [yes :: must have a base report to post]
+
+coverage:
+  status:
+    project: off
+    patch: off
+
+flag_management:
+  default_rules:
+    carryforward: true
+  individual_flags:
+    - name: julio
+      paths:
+        - julio/
+      statuses:
+        - type: project
+          target: 90%
+          threshold: 1%
+        - type: patch
+          target: 95%
+          threshold: 1%

julio/__init__.pyi

@@ -0,0 +1,5 @@
+__all__ = [
+    "create",
+]
+
+from ._functions import create

julio/_cli.py

@@ -0,0 +1,154 @@
+"""CLI for julio."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import logging
+import logging.config
+import pathlib
+import sys
+
+import click
+import datalad
+import structlog
+
+from . import _functions as cli_func
+
+
+__all__ = ["cli", "create"]
+
+# Common processors for stdlib and structlog
+_timestamper = structlog.processors.TimeStamper(fmt="%Y-%m-%d %H:%M:%S")
+
+
+def _remove_datalad_message(_, __, event_dict):
+    """Clean datalad records."""
+    if "message" in event_dict:
+        event_dict.pop("message")
+    if "dlm_progress" in event_dict:
+        event_dict.pop("dlm_progress")
+    if "dlm_progress_noninteractive_level" in event_dict:
+        event_dict.pop("dlm_progress_noninteractive_level")
+    if "dlm_progress_update" in event_dict:
+        event_dict.pop("dlm_progress_update")
+    if "dlm_progress_label" in event_dict:
+        event_dict.pop("dlm_progress_label")
+    if "dlm_progress_unit" in event_dict:
+        event_dict.pop("dlm_progress_unit")
+    if "dlm_progress_total" in event_dict:
+        event_dict.pop("dlm_progress_total")
+    return event_dict
+
+
+_pre_chain = [
+    structlog.stdlib.add_log_level,
+    structlog.stdlib.add_logger_name,
+    structlog.stdlib.ExtraAdder(),
+    _timestamper,
+    _remove_datalad_message,
+]
+
+
+def _set_log_config(verbose: int) -> None:
+    """Set logging config.
+
+    Parameters
+    ----------
+    verbose : int
+        Verbosity.
+
+    """
+    # Configure logger based on verbosity
+    if verbose == 0:
+        level = logging.WARNING
+    elif verbose == 1:
+        level = logging.INFO
+    else:
+        level = logging.DEBUG
+    # Configure stdlib
+    logging.config.dictConfig(
+        {
+            "version": 1,
+            "disable_existing_loggers": False,
+            "formatters": {
+                "console": {
+                    "()": structlog.stdlib.ProcessorFormatter,
+                    "processors": [
+                        structlog.stdlib.add_logger_name,
+                        structlog.stdlib.ProcessorFormatter.remove_processors_meta,
+                        structlog.dev.ConsoleRenderer(
+                            colors=sys.stdout.isatty() and sys.stderr.isatty()
+                        ),
+                    ],
+                    "foreign_pre_chain": _pre_chain,
+                },
+            },
+            "handlers": {
+                "default": {
+                    "level": level,
+                    "class": "logging.StreamHandler",
+                    "formatter": "console",
+                },
+            },
+            "loggers": {
+                "": {
+                    "handlers": ["default"],
+                    "level": level,
+                    "propagate": True,
+                },
+            },
+        }
+    )
+    # Configure structlog
+    structlog.configure(
+        processors=[
+            structlog.stdlib.add_log_level,
+            structlog.stdlib.PositionalArgumentsFormatter(),
+            structlog.processors.TimeStamper(fmt="%Y-%m-%d %H:%M:%S"),
+            structlog.processors.StackInfoRenderer(),
+            structlog.processors.format_exc_info,
+            structlog.stdlib.ProcessorFormatter.wrap_for_formatter,
+        ],
+        logger_factory=structlog.stdlib.LoggerFactory(),
+        wrapper_class=structlog.make_filtering_bound_logger(level),
+        cache_logger_on_first_use=True,
+    )
+    # Remove datalad logger handlers to avoid duplicate logging
+    _datalad_lgr_hdlrs = datalad.log.lgr.handlers
+    for h in _datalad_lgr_hdlrs:
+        datalad.log.lgr.removeHandler(h)
+    datalad.log.lgr.setLevel(level)
+
+
+@click.group
+@click.version_option(prog_name="julio")
+@click.help_option()
+def cli() -> None:
+    """julio CLI."""  # noqa: D403
+
+
+@cli.command
+@click.argument(
+    "registry_path",
+    type=click.Path(
+        exists=False,
+        readable=True,
+        writable=True,
+        file_okay=False,
+        path_type=pathlib.Path,
+    ),
+    metavar="<registry>",
+)
+@click.option("-v", "--verbose", count=True, type=int)
+def create(
+    registry_path: click.Path,
+    verbose: int,
+) -> None:
+    """Create registry."""
+    _set_log_config(verbose)
+    try:
+        cli_func.create(registry_path)
+    except RuntimeError as err:
+        click.echo(f"{err}", err=True)
+    else:
+        click.echo("Success")

julio/_functions.py

@@ -0,0 +1,56 @@
+"""Functions for julio."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from pathlib import Path
+
+import datalad.api as dl
+import structlog
+from datalad.support.exceptions import IncompleteResultsError
+
+
+__all__ = ["create"]
+
+
+logger = structlog.get_logger()
+
+
+def create(registry_path: Path):
+    """Create a registry at `registry_path`.
+
+    Parameters
+    ----------
+    registry_path : pathlib.Path
+        Path to the registry.
+
+    Raises
+    ------
+    RuntimeError
+        If there is a problem creating the registry.
+
+    """
+    try:
+        ds = dl.create(
+            path=registry_path,
+            cfg_proc="text2git",
+            on_failure="stop",
+            result_renderer="disabled",
+        )
+    except IncompleteResultsError as e:
+        raise RuntimeError(f"Failed to create dataset: {e.failed}") from e
+    else:
+        logger.debug(
+            "Registry created successfully",
+            cmd="create",
+            path=str(registry_path.resolve()),
+        )
+    # Add config file
+    conf_path = Path(ds.path) / "registry-config.yml"
+    conf_path.touch()
+    ds.save(
+        conf_path,
+        message="[julio] add registry configuration",
+        on_failure="stop",
+        result_renderer="disabled",
+    )

julio/tests/test_functions.py

@@ -0,0 +1,29 @@
+"""Test for functions."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import shutil
+from pathlib import Path
+
+import pytest
+
+from julio import create
+
+
+def test_create(tmp_path: Path) -> None:
+    """Test registry creation.
+
+    Parameters
+    ----------
+    tmp_path : Path
+        Pytest fixture that provides a temporary directory.
+
+    """
+    registry_path = tmp_path / "test_registry"
+    create(registry_path)
+    config_path = registry_path / "registry-config.yml"
+    assert config_path.is_file()
+    with pytest.raises(RuntimeError):
+        create(registry_path)
+    shutil.rmtree(registry_path)

pyproject.toml

@@ -38,6 +38,7 @@ dependencies = [
     "click>=8.1.3,<8.2",
     "datalad>=1.0.0,<1.3.0",
     "lazy_loader==0.4",
+    "structlog>=25.0.0,<26.0.0",
 ]
 dynamic = ["version"]
 
@@ -123,12 +124,13 @@ known-first-party = ["julio"]
 known-third-party =[
     "click",
     "datalad",
+    "structlog",
     "pytest",
 ]
 
 [tool.pytest.ini_options]
 minversion = "7.0"
-testpaths = "tests"
+testpaths = "julio"
 log_cli_level = "INFO"
 xfail_strict = true
 addopts = [
@@ -176,3 +178,29 @@ showcontent = true
 directory = "fixed"
 name = "Fixed"
 showcontent = true
+
+[tool.coverage.paths]
+source = [
+    "julio",
+    "*/site-packages/julio",
+]
+
+[tool.coverage.run]
+branch = true
+omit = [
+    "*/__init__.py",
+    "*/_version.py",
+    "*/_cli.py",
+    "*/tests/*",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    # Have to re-enable the standard pragma
+    "pragma: no cover",
+    # Type checking if statements should not be considered
+    "if TYPE_CHECKING:",
+    # Don't complain if non-runnable code isn't run:
+    "if __name__ == .__main__.:",
+]
+precision = 2