Merge pull request #32 from Remi-Gau/cli

[ENH] add CLI

.github/workflows/testing.yml

@@ -14,25 +14,12 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  # Determine if tests should be run based on commit message.
-  check_skip:
-    runs-on: ubuntu-latest
-    outputs:
-      skip: ${{ steps.result_step.outputs.ci-skip }}
-    steps:
-    - id: result_step
-      uses: mstachniuk/ci-skip@master
-      with:
-        commit-filter: '[skip ci];[ci skip];[skip github];[no ci]'
-        commit-filter-separator: ;
 
   run_tests:
-    needs: check_skip
-    if: ${{ needs.check_skip.outputs.skip == 'false' }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ['3.8', '3.9', '3.10', '3.11']
     runs-on: ${{ matrix.os }}
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}

.github/workflows/testing_cli.yml

@@ -0,0 +1,53 @@
+---
+name: Run tests CLI
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - '*'
+
+concurrency:
+  group: environment-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  test_cli:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.11']
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+    - name: Set up python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Display Python version
+      shell: bash {0}
+      run: python -c "import sys; print(sys.version)"
+    - name: Install bids examples
+      run: git clone https://github.com/bids-standard/bids-examples.git
+    - name: Install pybids-reports
+      shell: bash {0}
+      run: pip install .
+    - name: Info CLI
+      shell: bash {0}
+      run: |
+        pybids_reports --version
+        pybids_reports --help
+    - name: Run test for CLI
+      shell: bash {0}
+      run: |
+        bash tools/run_on_examples.sh

.gitignore

@@ -1,3 +1,5 @@
+bids-examples
+
 # do not track _version.py for hatch
 bids/ext/reports/_version.py
 

bids/ext/reports/__init__.py

@@ -1,7 +1,7 @@
 """pybids-reports: A tool for building methods sections for BIDS datasets."""
 from __future__ import annotations
 
-from . import _version  # type: ignore
+from . import _version
 from . import parameters
 from . import parsing
 from . import report

bids/ext/reports/cli.py

@@ -0,0 +1,114 @@
+"""General parser for the cohort_creator package."""
+from __future__ import annotations
+
+import argparse
+import sys
+from pathlib import Path
+from typing import IO
+from typing import Sequence
+
+import rich
+from reports import BIDSReport
+
+from ._version import __version__
+from .logger import pybids_reports_logger
+from bids.layout import BIDSLayout
+
+# from bids.reports import BIDSReport
+LOGGER = pybids_reports_logger()
+
+
+class MuhParser(argparse.ArgumentParser):
+    def _print_message(self, message: str, file: IO[str] | None = None) -> None:
+        rich.print(message, file=file)
+
+
+def base_parser() -> MuhParser:
+    parser = MuhParser(
+        prog="pybids_reports",
+        description="Report generator for BIDS datasets.",
+        epilog="""
+        For a more readable version of this help section,
+        see the online doc https://cohort-creator.readthedocs.io/en/latest/
+        """,
+    )
+    parser.add_argument(
+        "bids_dir",
+        help="""
+        Path to BIDS dataset.
+        """,
+        nargs=1,
+    )
+    parser.add_argument(
+        "output_dir",
+        help="""
+        Output path.
+        """,
+        nargs=1,
+    )
+    parser.add_argument(
+        "--participant_label",
+        help="""
+        The label(s) of the participant(s) that should be used for the report.
+        The label corresponds to sub-<participant_label> from the BIDS spec
+        (so it does not include "sub-").
+
+        If this parameter is not provided, The first subject will be used.
+        Multiple participants can be specified with a space separated list.
+        """,
+        nargs="+",
+    )
+    parser.add_argument(
+        "-v",
+        "--version",
+        action="version",
+        version=f"{__version__}",
+    )
+    parser.add_argument(
+        "--verbosity",
+        help="""
+        Verbosity level.
+        """,
+        required=False,
+        choices=[0, 1, 2, 3],
+        default=2,
+        type=int,
+        nargs=1,
+    )
+    return parser
+
+
+def set_verbosity(verbosity: int | list[int]) -> None:
+    if isinstance(verbosity, list):
+        verbosity = verbosity[0]
+    if verbosity == 0:
+        LOGGER.setLevel("ERROR")
+    elif verbosity == 1:
+        LOGGER.setLevel("WARNING")
+    elif verbosity == 2:
+        LOGGER.setLevel("INFO")
+    elif verbosity == 3:
+        LOGGER.setLevel("DEBUG")
+
+
+def cli(argv: Sequence[str] = sys.argv) -> None:
+    """Entry point."""
+    parser = base_parser()
+
+    args, unknowns = parser.parse_known_args(argv[1:])
+
+    bids_dir = Path(args.bids_dir[0]).resolve()
+    # output_dir = Path(args.output_dir[0])
+    participant_label = args.participant_label or None
+
+    set_verbosity(args.verbosity)
+
+    LOGGER.debug(f"{bids_dir}")
+
+    layout = BIDSLayout(bids_dir)
+
+    report = BIDSReport(layout)
+    if participant_label:
+        report.generate(subject=participant_label)
+    else:
+        report.generate()

bids/ext/reports/logger.py

@@ -0,0 +1,19 @@
+"""General logger for the cohort_creator package."""
+from __future__ import annotations
+
+import logging
+
+from rich.logging import RichHandler
+
+
+def pybids_reports_logger(log_level: str = "INFO") -> logging.Logger:
+    FORMAT = "%(message)s"
+
+    logging.basicConfig(
+        level=log_level,
+        format=FORMAT,
+        datefmt="[%X]",
+        handlers=[RichHandler()],
+    )
+
+    return logging.getLogger("pybids_reports")