Merge pull request #50 from ayasyrev/dev

ver 0.0.9

.flake8

@@ -6,6 +6,3 @@ extend-ignore = W503
 disable-noqa = True
 application-import-names = nbmetaclean, tests
 import-order-style = google
-per-file-ignores =
-    # imported but unused
-    __init__.py: F401

.github/workflows/lint.yml

@@ -0,0 +1,17 @@
+name: Lint
+on:
+  push:
+    branches:
+      - dev
+      - main
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@main
+    - uses: actions/setup-python@main
+      with:
+        python-version: "3.11"
+        architecture: x64
+    - run: pip install ruff
+    - run: ruff check .

.github/workflows/tests.yml

@@ -0,0 +1,35 @@
+name: Tests
+on:
+  push:
+    branches:
+      - dev
+      - main
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+    steps:
+    - name: Checkout
+      uses: actions/checkout@main
+    - name: Setup Python ${{ matrix.python }}
+      uses: actions/setup-python@main
+      with:
+        python-version: ${{ matrix.python }}
+        architecture: x64
+
+    - name: Install
+      run: |
+        pip install uv
+        uv pip install --system .[test] "coverage[toml]"
+
+    - name: Tests
+      run: pytest --cov
+
+    - name: CodeCov
+      if: ${{ matrix.python == '3.11' }}
+      uses: codecov/codecov-action@main
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: ayasyrev/nbmetaclean

.pre-commit-config.yaml

@@ -1,10 +1,13 @@
 repos:
-- repo: https://github.com/ayasyrev/nbmetaclean
-  rev: 0.0.8
+- repo: local
+
   hooks:
-  -   id: nbclean
-      name: nbclean
+    # local version for testing
+    - id: nbclean
+      name: nbclean local
       entry: nbclean
+      language: system
+      files: \.ipynb
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.6.0
@@ -34,7 +37,8 @@ repos:
     - id: requirements-txt-fixer
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.5.1
+  rev: v0.5.7
+
   hooks:
     # Run the linter.
     - id: ruff
@@ -47,5 +51,4 @@ repos:
     - id: python-check-mock-methods
     - id: python-use-type-annotations
     - id: python-check-blanket-noqa
-    - id: python-use-type-annotations
     - id: text-unicode-replacement-char

noxfile.py

@@ -1,9 +1,8 @@
 import nox
 
 
-@nox.session(python=["3.8", "3.9", "3.10", "3.11", "3.12"])
+@nox.session(python=["3.8", "3.9", "3.10", "3.11", "3.12"], venv_backend="uv")
 def tests(session: nox.Session) -> None:
     args = session.posargs or ["--cov"]
-    session.install("uv")
-    session.run("uv", "pip", "install", ".[test]")
+    session.install("-e .[test]")
     session.run("pytest", *args)

noxfile_conda.py

@@ -5,5 +5,5 @@
 def conda_tests(session: nox.Session) -> None:
     args = session.posargs or ["--cov"]
     session.conda_install("uv")
-    session.run("uv", "pip", "install", ".[test]")
+    session.install("uv", "pip", "install", "-e", ".[test]")
     session.run("pytest", *args)

noxfile_conda_lint.py

@@ -1,6 +1,6 @@
 import nox
 
-locations = "src/nbmetaclean", "tests", "noxfile.py"
+locations = "."
 
 
 @nox.session(python=["3.8", "3.9", "3.10", "3.11", "3.12"], venv_backend="mamba")

noxfile_lint.py

@@ -3,7 +3,7 @@
 locations = "."
 
 
-@nox.session(python=["3.8", "3.9", "3.10", "3.11", "3.12"])
+@nox.session(python=["3.8", "3.9", "3.10", "3.11", "3.12"], venv_backend="uv")
 def lint(session: nox.Session) -> None:
     args = session.posargs or locations
     session.install("ruff")

pyproject.toml

@@ -1,9 +1,22 @@
 [tool.coverage.paths]
-source = ["src", "*/site-packages"]
+source = ["src"]
 
 [tool.coverage.run]
 branch = true
 source = ["nbmetaclean"]
 
 [tool.coverage.report]
 show_missing = true
+
+[tool.ruff]
+extend-include = ["*.ipynb"]
+indent-width = 4
+
+[tool.ruff.lint]
+explicit-preview-rules = true
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"

requirements_dev.txt

@@ -1,7 +1,9 @@
 black
 black[jupyter]
+coverage[toml]
 flake8
 isort
 mypy
+nox
 pre-commit
 ruff

setup.py

@@ -1,24 +1,30 @@
 from setuptools import setup
 
+
 REQUIREMENTS_FILENAME = "requirements.txt"
 REQUIREMENTS_TEST_FILENAME = "requirements_test.txt"
+REQUIREMENTS_DEV_FILENAME = "requirements_dev.txt"
+
+
+def load_requirements(filename: str) -> list[str]:
+    """Load requirements from file"""
+    try:
+        with open(filename, encoding="utf-8") as fh:
+            return fh.read().splitlines()
+    except FileNotFoundError:
+        return []
 
 
-# Requirements
-try:
-    with open(REQUIREMENTS_FILENAME, encoding="utf-8") as fh:
-        REQUIRED = fh.read().split("\n")
-except FileNotFoundError:
-    REQUIRED = []
+REQUIRED = load_requirements(REQUIREMENTS_FILENAME)
+TEST_REQUIRED = load_requirements(REQUIREMENTS_TEST_FILENAME)
+DEV_REQUIRED = load_requirements(REQUIREMENTS_DEV_FILENAME)
 
-try:
-    with open(REQUIREMENTS_TEST_FILENAME, encoding="utf-8") as fh:
-        TEST_REQUIRED = fh.read().split("\n")
-except FileNotFoundError:
-    TEST_REQUIRED = []
 
 # What packages are optional?
-EXTRAS = {"test": TEST_REQUIRED}
+EXTRAS = {
+    "test": TEST_REQUIRED,
+    "dev": DEV_REQUIRED + TEST_REQUIRED,
+}
 
 
 setup(

src/nbmetaclean/app.py

@@ -21,6 +21,11 @@
     action="store_true",
     help="Silent mode.",
 )
+parser.add_argument(
+    "--not_ec",
+    action="store_false",
+    help="Do not clear execution_count.",
+)
 parser.add_argument(
     "--not-pt",
     action="store_true",
@@ -61,6 +66,18 @@
     action="store_true",
     help="Clean hidden notebooks.",
 )
+parser.add_argument(
+    "-D",
+    "--dry_run",
+    action="store_true",
+    help="perform a trial run, don't write results",
+)
+parser.add_argument(
+    "-V",
+    "--verbose",
+    action="store_true",
+    help="Verbose mode. Print extra information.",
+)
 
 
 def process_mask(mask: Union[list[str], None]) -> Union[tuple[TupleStr, ...], None]:
@@ -69,41 +86,63 @@ def process_mask(mask: Union[list[str], None]) -> Union[tuple[TupleStr, ...], No
     return tuple(tuple(item.split(".")) for item in mask)
 
 
+def print_result(
+    cleaned: list[Path],
+    errors: list[tuple[Path, Exception]],
+    clean_config: CleanConfig,
+    path: list[Path],
+    num_nbs: int,
+) -> None:
+    if clean_config.verbose:
+        print(
+            f"Path: {', '.join(path)}, preserve timestamp: {clean_config.preserve_timestamp}"
+        )
+        print(f"checked: {num_nbs} notebooks")
+    if cleaned:
+        if len(cleaned) == 1:
+            print(f"cleaned: {cleaned[0]}")
+        else:
+            print(f"cleaned: {len(cleaned)} notebooks")
+            for nb in cleaned:
+                print("- ", nb)
+    if errors:
+        print(f"with errors: {len(errors)}")
+        for nb, exc in errors:
+            print(f"{nb}: {exc}")
+
+
 def app() -> None:
     """Clean metadata and execution_count from Jupyter notebook."""
     cfg = parser.parse_args()
-    path_list = cfg.path if isinstance(cfg.path, list) else [cfg.path]
-    nb_files: list[Path] = []
-    if not cfg.silent:
-        print(f"Path: {', '.join(cfg.path)}, preserve timestamp: {not cfg.not_pt}")
-    for path in path_list:
-        try:
-            nb_files.extend(get_nb_names(path, hidden=cfg.clean_hidden_nbs))
-        except FileNotFoundError:
-            print(f"{path} not exists!")
-    if not cfg.silent:
-        print(f"notebooks to check: {len(nb_files)} ")
     clean_config = CleanConfig(
         clear_nb_metadata=not cfg.dont_clear_nb_metadata,
         clear_cell_metadata=cfg.clear_cell_metadata,
-        clear_execution_count=True,
+        clear_execution_count=cfg.not_ec,
         clear_outputs=cfg.clear_outputs,
         preserve_timestamp=not cfg.not_pt,
         silent=cfg.silent,
         nb_metadata_preserve_mask=process_mask(cfg.nb_metadata_preserve_mask),
         cell_metadata_preserve_mask=process_mask(cfg.cell_metadata_preserve_mask),
         mask_merge=not cfg.dont_merge_masks,
+        dry_run=cfg.dry_run,
+        verbose=cfg.verbose if not cfg.silent else False,
     )
+    path_list = cfg.path if isinstance(cfg.path, list) else [cfg.path]
+    nb_files: list[Path] = []
+    for path in path_list:
+        path = Path(path)
+        if path.exists():
+            nb_files.extend(get_nb_names(path, hidden=cfg.clean_hidden_nbs))
+        else:
+            print(f"{path} not exists!")
+
     cleaned, errors = clean_nb_file(
         nb_files,
         clean_config,
     )
+
     if not cfg.silent:
-        print(f"cleaned nbs: {len(cleaned)}")
-        if errors:
-            print(f"with errors: {len(errors)}")
-            for nb, exc in errors:
-                print(f"{nb}: {exc}")
+        print_result(cleaned, errors, clean_config, path_list, len(nb_files))
 
 
 if __name__ == "__main__":