From 6625140362d24f81a14dbfea3d4e36afaa21a8e7 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Sat, 6 Apr 2024 12:37:27 +0000
Subject: [PATCH 01/23] bump dev 0.0.9_dev

---
 .pre-commit-config.yaml    | 2 +-
 src/nbmetaclean/version.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c686b53..ac9fcfc 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/ayasyrev/nbmetaclean
-  rev: 0.0.7
+  rev: 0.0.8
   hooks:
   -   id: nbclean
       name: nbclean
diff --git a/src/nbmetaclean/version.py b/src/nbmetaclean/version.py
index 0e12f90..eb14da7 100644
--- a/src/nbmetaclean/version.py
+++ b/src/nbmetaclean/version.py
@@ -1 +1 @@
-__version__ = "0.0.8"  # pragma: no cover
+__version__ = "0.0.9_dev"  # pragma: no cover

From e8a7fd929529067169cd973ae721102cd6db387b Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Wed, 10 Jul 2024 08:25:53 +0000
Subject: [PATCH 02/23] reguirements  rearrange

---
 requirements_dev.txt        |  2 ++
 requirements_test_extra.txt |  2 --
 setup.py                    | 30 ++++++++++++++++++------------
 3 files changed, 20 insertions(+), 14 deletions(-)
 delete mode 100644 requirements_test_extra.txt

diff --git a/requirements_dev.txt b/requirements_dev.txt
index 8778d84..d400fe5 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -1,7 +1,9 @@
 black
 black[jupyter]
+coverage[toml]
 flake8
 isort
 mypy
+nox
 pre-commit
 ruff
diff --git a/requirements_test_extra.txt b/requirements_test_extra.txt
deleted file mode 100644
index 16ac163..0000000
--- a/requirements_test_extra.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-coverage[toml]
-nox
diff --git a/setup.py b/setup.py
index f7abcb7..8c11aa0 100644
--- a/setup.py
+++ b/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(

From bda952788db09019c3d8cdd36a5df99a60e33bd6 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Wed, 10 Jul 2024 09:30:14 +0000
Subject: [PATCH 03/23] pre-commit update

---
 .pre-commit-config.yaml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ac9fcfc..a17a98f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
       entry: nbclean
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0
   hooks:
     - id: check-added-large-files
     - id: check-ast
@@ -34,7 +34,7 @@ repos:
     - id: requirements-txt-fixer
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.3.5
+  rev: v0.5.1
   hooks:
     # Run the linter.
     - id: ruff
@@ -47,5 +47,4 @@ 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

From f5ffb64a8d16dd7b1c44aa6d7295d5ebb607a536 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Tue, 16 Jul 2024 08:51:53 +0000
Subject: [PATCH 04/23] nox uv + ruff

---
 noxfile.py            | 5 ++---
 noxfile_conda.py      | 4 ++--
 noxfile_conda_lint.py | 6 +++---
 noxfile_lint.py       | 8 ++++----
 4 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index 770d95b..68b78e7 100644
--- a/noxfile.py
+++ b/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("-r", "requirements_test.txt")
-    session.install(".")
+    session.install(".[test]")
     session.run("pytest", *args)
diff --git a/noxfile_conda.py b/noxfile_conda.py
index 7ba7b37..ef4a184 100644
--- a/noxfile_conda.py
+++ b/noxfile_conda.py
@@ -4,6 +4,6 @@
 @nox.session(python=["3.8", "3.9", "3.10", "3.11", "3.12"], venv_backend="mamba")
 def conda_tests(session: nox.Session) -> None:
     args = session.posargs or ["--cov"]
-    session.conda_install("--file", "requirements_test.txt")
-    session.install(".")
+    session.conda_install("uv")
+    session.install(".[test]")
     session.run("pytest", *args)
diff --git a/noxfile_conda_lint.py b/noxfile_conda_lint.py
index f4052aa..88ab393 100644
--- a/noxfile_conda_lint.py
+++ b/noxfile_conda_lint.py
@@ -1,10 +1,10 @@
 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")
 def conda_lint(session: nox.Session) -> None:
     args = session.posargs or locations
-    session.conda_install("flake8")
-    session.run("flake8", *args)
+    session.conda_install("ruff")
+    session.run("ruff", "check", *args)
diff --git a/noxfile_lint.py b/noxfile_lint.py
index 84af18a..d2429a7 100644
--- a/noxfile_lint.py
+++ b/noxfile_lint.py
@@ -1,10 +1,10 @@
 import nox
 
-locations = "src/nbmetaclean", "tests", "noxfile.py"
+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("flake8")
-    session.run("flake8", *args)
+    session.install("ruff")
+    session.run("ruff", "check", *args)

From 67f0207bf3aec4d529df1d9b901fd051cbbadef2 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Tue, 16 Jul 2024 09:13:36 +0000
Subject: [PATCH 05/23] fix settings, nox files

---
 .flake8                 | 3 ---
 .pre-commit-config.yaml | 2 +-
 noxfile.py              | 2 +-
 noxfile_conda.py        | 2 +-
 pyproject.toml          | 2 +-
 5 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/.flake8 b/.flake8
index fe13e52..619d0e3 100644
--- a/.flake8
+++ b/.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
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a17a98f..76f3f7a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -34,7 +34,7 @@ repos:
     - id: requirements-txt-fixer
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.5.1
+  rev: v0.5.2
   hooks:
     # Run the linter.
     - id: ruff
diff --git a/noxfile.py b/noxfile.py
index 68b78e7..5819a1e 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -4,5 +4,5 @@
 @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(".[test]")
+    session.install("-e .[test]")
     session.run("pytest", *args)
diff --git a/noxfile_conda.py b/noxfile_conda.py
index ef4a184..305308c 100644
--- a/noxfile_conda.py
+++ b/noxfile_conda.py
@@ -5,5 +5,5 @@
 def conda_tests(session: nox.Session) -> None:
     args = session.posargs or ["--cov"]
     session.conda_install("uv")
-    session.install(".[test]")
+    session.install("uv", "pip", "install", "-e", ".[test]")
     session.run("pytest", *args)
diff --git a/pyproject.toml b/pyproject.toml
index a40cc44..aef05e2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [tool.coverage.paths]
-source = ["src", "*/site-packages"]
+source = ["src"]
 
 [tool.coverage.run]
 branch = true

From 89dad8b225d095da045e41fd4e860b7a9f9fc70a Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Tue, 16 Jul 2024 09:53:19 +0000
Subject: [PATCH 06/23] gh ci

---
 .github/workflows/lint.yml  | 17 +++++++++++++++++
 .github/workflows/tests.yml | 27 +++++++++++++++++++++++++++
 2 files changed, 44 insertions(+)
 create mode 100644 .github/workflows/lint.yml
 create mode 100644 .github/workflows/tests.yml

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 0000000..477534a
--- /dev/null
+++ b/.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 .
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
new file mode 100644
index 0000000..31b3345
--- /dev/null
+++ b/.github/workflows/tests.yml
@@ -0,0 +1,27 @@
+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]
+    - name: Tests
+      run: pytest

From 8ea5f3ae3790f7141dbb289f5e79dc0d8cb78042 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Fri, 26 Jul 2024 08:20:28 +0000
Subject: [PATCH 07/23] add codecov

---
 .github/workflows/tests.yml | 8 ++++++++
 README.md                   | 4 ++++
 2 files changed, 12 insertions(+)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 31b3345..4816688 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -23,5 +23,13 @@ jobs:
       run: |
         pip install uv
         uv pip install --system .[test]
+
     - name: Tests
       run: pytest
+
+    - name: CodeCov
+      if: ${{ matrix.python == '3.11' }}
+      uses: codecov/codecov-action@main
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: ayasyrev/nbmetaclean
diff --git a/README.md b/README.md
index 0b29f63..5dd4025 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,10 @@
 
 Pre-commit hook to clean Jupyter Notebooks metadata, execution_count and optionally output.
 
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/benchmark-utils)](https://pypi.org/project/nbmetaclean/)
+[![PyPI Status](https://badge.fury.io/py/nbmetaclean.svg)](https://badge.fury.io/py/nbmetaclean)
+[![Tests](https://github.com/ayasyrev/nbmetaclean/workflows/Tests/badge.svg)](https://github.com/ayasyrev/nbmetaclean/actions?workflow=Tests)  [![Codecov](https://codecov.io/gh/ayasyrev/nbmetaclean/branch/main/graph/badge.svg)](https://codecov.io/gh/ayasyrev/nbmetaclean)
+
 Pure Python, no dependencies.
 
 Can be used as a pre-commit hook or as a command line tool.

From 1987af01bd61fe87c383a89d0ff9b0964d96812a Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Fri, 26 Jul 2024 08:22:32 +0000
Subject: [PATCH 08/23] fix coverage gh ci

---
 .github/workflows/tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 4816688..e4220a4 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -22,10 +22,10 @@ jobs:
     - name: Install
       run: |
         pip install uv
-        uv pip install --system .[test]
+        uv pip install --system .[test] "coverage[toml]"
 
     - name: Tests
-      run: pytest
+      run: pytest --cov
 
     - name: CodeCov
       if: ${{ matrix.python == '3.11' }}

From e4c78db9f13ccd4181b11c6c48dd7d0a0d17a3b3 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Mon, 29 Jul 2024 13:42:35 +0000
Subject: [PATCH 09/23] add dry_run to clean_nb_file

---
 src/nbmetaclean/clean.py | 13 ++++++-------
 tests/test_clean.py      | 19 ++++++++++++++++++-
 2 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/src/nbmetaclean/clean.py b/src/nbmetaclean/clean.py
index cf69e55..559d35f 100644
--- a/src/nbmetaclean/clean.py
+++ b/src/nbmetaclean/clean.py
@@ -33,8 +33,9 @@ class CleanConfig:
             Preserve mask for notebook metadata. Defaults to None.
         cell_metadata_preserve_mask (Optional[tuple[str, ...]], optional):
             Preserve mask for cell metadata. Defaults to None.
-        mask_merge (bool, optional): Merge masks. Add new mask to default.
+        mask_merge (bool): Merge masks. Add new mask to default.
             If False - use new mask. Defaults to True.
+        dry_run (bool): perform a trial run, don't write results. Defaults to False.
     """
 
     clear_nb_metadata: bool = True
@@ -46,6 +47,7 @@ class CleanConfig:
     nb_metadata_preserve_mask: Optional[tuple[TupleStr, ...]] = None
     cell_metadata_preserve_mask: Optional[tuple[TupleStr, ...]] = None
     mask_merge: bool = True
+    dry_run: bool = False
 
 
 def filter_meta_mask(
@@ -175,12 +177,7 @@ def clean_nb_file(
 
     Args:
         path (Union[str, PosixPath]): Notebook filename or list of names.
-        clear_nb_metadata (bool): Clear notebook metadata. Defaults to True.
-        clear_cell_metadata (bool): Clear cell metadata. Defaults to False.
-        clear_outputs (bool): Clear outputs. Defaults to False.
-        preserve_timestamp (bool): Preserve timestamp. Defaults to True.
-        clear_execution_count (bool, optional): Clean execution count. Defaults to True.
-        silent (bool): Silent mode. Defaults to False.
+        cfg (CleanConfig, optional): Config for job, if None, used default settings. Default is None.
 
     Returns:
         tuple[List[Path], List[TuplePath]]: List of cleaned notebooks, list of notebooks with errors.
@@ -204,6 +201,8 @@ def clean_nb_file(
         )
         if result:
             cleaned.append(filename)
+            if cfg.dry_run:
+                continue
             if cfg.preserve_timestamp:
                 stat = filename.stat()
             write_nb(nb, filename)
diff --git a/tests/test_clean.py b/tests/test_clean.py
index 813f3e1..ab30826 100644
--- a/tests/test_clean.py
+++ b/tests/test_clean.py
@@ -255,7 +255,24 @@ def test_clean_nb_file(tmp_path: Path, capsys: CaptureFixture[str]):
     nb_clean = read_nb(path / "test_nb_2_clean.ipynb")
 
     # prepare temp test notebook
-    test_nb_path = write_nb(read_nb(path / nb_name), tmp_path / nb_name)
+    nb_source = read_nb(path / nb_name)
+    test_nb_path = write_nb(nb_source, tmp_path / nb_name)
+
+    # clean meta, leave execution_count
+    # first lets dry run
+    cleaned, errors = clean_nb_file(
+        test_nb_path,
+        cfg=CleanConfig(
+            clear_execution_count=False,
+            dry_run=True,
+        ),
+    )
+    assert len(cleaned) == 1
+    assert len(errors) == 0
+    nb = read_nb(cleaned[0])
+    assert nb["metadata"] == nb_source["metadata"]
+    assert nb["cells"][1]["execution_count"] == 1
+    assert nb["cells"][1]["outputs"][0]["execution_count"] == 1
 
     # clean meta, leave execution_count
     cleaned, errors = clean_nb_file(

From a01b03ec7e60224ea97e92085bae045949b371c2 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Mon, 29 Jul 2024 14:10:21 +0000
Subject: [PATCH 10/23] add dry run to app

---
 src/nbmetaclean/app.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/nbmetaclean/app.py b/src/nbmetaclean/app.py
index 68e969e..5131a7d 100644
--- a/src/nbmetaclean/app.py
+++ b/src/nbmetaclean/app.py
@@ -61,6 +61,11 @@
     action="store_true",
     help="Clean hidden notebooks.",
 )
+parser.add_argument(
+    "--dry_run",
+    action="store_true",
+    help="perform a trial run, don't write results",
+)
 
 
 def process_mask(mask: Union[list[str], None]) -> Union[tuple[TupleStr, ...], None]:

From de1c0dc48e7f13bf8717881c223adb64bebc933b Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Mon, 29 Jul 2024 14:17:36 +0000
Subject: [PATCH 11/23] rename typing to types

---
 src/nbmetaclean/clean.py                | 2 +-
 src/nbmetaclean/helpers.py              | 2 +-
 src/nbmetaclean/{typing.py => types.py} | 0
 3 files changed, 2 insertions(+), 2 deletions(-)
 rename src/nbmetaclean/{typing.py => types.py} (100%)

diff --git a/src/nbmetaclean/clean.py b/src/nbmetaclean/clean.py
index 559d35f..a0e0272 100644
--- a/src/nbmetaclean/clean.py
+++ b/src/nbmetaclean/clean.py
@@ -8,7 +8,7 @@
 
 from nbmetaclean.helpers import read_nb, write_nb
 
-from .typing import Cell, CodeCell, Metadata, Nb, Output
+from .types import Cell, CodeCell, Metadata, Nb, Output
 
 TupleStr = Tuple[str, ...]
 
diff --git a/src/nbmetaclean/helpers.py b/src/nbmetaclean/helpers.py
index b3f1c3a..90352f2 100644
--- a/src/nbmetaclean/helpers.py
+++ b/src/nbmetaclean/helpers.py
@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import Optional
 
-from .typing import Nb, PathOrStr
+from .types import Nb, PathOrStr
 
 
 def read_nb(path: PathOrStr) -> Nb:
diff --git a/src/nbmetaclean/typing.py b/src/nbmetaclean/types.py
similarity index 100%
rename from src/nbmetaclean/typing.py
rename to src/nbmetaclean/types.py

From c241df7f7884718424d52d85662668c626d31c0d Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Tue, 30 Jul 2024 18:04:58 +0000
Subject: [PATCH 12/23] fix app - dry run

---
 src/nbmetaclean/app.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/nbmetaclean/app.py b/src/nbmetaclean/app.py
index 5131a7d..15c291c 100644
--- a/src/nbmetaclean/app.py
+++ b/src/nbmetaclean/app.py
@@ -98,6 +98,7 @@ def app() -> None:
         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,
     )
     cleaned, errors = clean_nb_file(
         nb_files,

From b67d0e82b09bc03b4e2f48fc33ef1c170b540b51 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Thu, 8 Aug 2024 12:00:34 +0300
Subject: [PATCH 13/23] add -verbose argument, shorts flag for dry-run

---
 src/nbmetaclean/app.py   | 10 ++++++++++
 src/nbmetaclean/clean.py |  2 ++
 2 files changed, 12 insertions(+)

diff --git a/src/nbmetaclean/app.py b/src/nbmetaclean/app.py
index 15c291c..2310fee 100644
--- a/src/nbmetaclean/app.py
+++ b/src/nbmetaclean/app.py
@@ -62,10 +62,17 @@
     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="Print more info - cleaned notebooks.",
+)
 
 
 def process_mask(mask: Union[list[str], None]) -> Union[tuple[TupleStr, ...], None]:
@@ -106,6 +113,9 @@ def app() -> None:
     )
     if not cfg.silent:
         print(f"cleaned nbs: {len(cleaned)}")
+        if cfg.verbose:
+            for nb in cleaned:
+                print("- ", nb)
         if errors:
             print(f"with errors: {len(errors)}")
             for nb, exc in errors:
diff --git a/src/nbmetaclean/clean.py b/src/nbmetaclean/clean.py
index a0e0272..2bfccf2 100644
--- a/src/nbmetaclean/clean.py
+++ b/src/nbmetaclean/clean.py
@@ -36,6 +36,7 @@ class CleanConfig:
         mask_merge (bool): Merge masks. Add new mask to default.
             If False - use new mask. Defaults to True.
         dry_run (bool): perform a trial run, don't write results. Defaults to False.
+        verbose (bool): Print more info - cleaned notebooks. Defaults to False.
     """
 
     clear_nb_metadata: bool = True
@@ -48,6 +49,7 @@ class CleanConfig:
     cell_metadata_preserve_mask: Optional[tuple[TupleStr, ...]] = None
     mask_merge: bool = True
     dry_run: bool = False
+    verbose: bool = False
 
 
 def filter_meta_mask(

From 4cdee5779eb90ce730f06f9de7400bffa4de2a61 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Thu, 8 Aug 2024 13:07:41 +0300
Subject: [PATCH 14/23] cfg to one line

---
 src/nbmetaclean/clean.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/nbmetaclean/clean.py b/src/nbmetaclean/clean.py
index 2bfccf2..7a066e4 100644
--- a/src/nbmetaclean/clean.py
+++ b/src/nbmetaclean/clean.py
@@ -184,8 +184,7 @@ def clean_nb_file(
     Returns:
         tuple[List[Path], List[TuplePath]]: List of cleaned notebooks, list of notebooks with errors.
     """
-    if cfg is None:
-        cfg = CleanConfig()
+    cfg = cfg or CleanConfig()
     if not isinstance(path, list):
         path = [path]
     cleaned: list[Path] = []

From 6fc083bbdeb2e476a6eb21831dab6fd491eb8606 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Thu, 8 Aug 2024 16:54:08 +0300
Subject: [PATCH 15/23] remove verbose, remove print from `clean_nb_file`

---
 src/nbmetaclean/app.py   | 11 ++---------
 src/nbmetaclean/clean.py |  8 ++------
 tests/test_clean.py      | 14 --------------
 3 files changed, 4 insertions(+), 29 deletions(-)

diff --git a/src/nbmetaclean/app.py b/src/nbmetaclean/app.py
index 2310fee..3d1dd8a 100644
--- a/src/nbmetaclean/app.py
+++ b/src/nbmetaclean/app.py
@@ -67,12 +67,6 @@
     action="store_true",
     help="perform a trial run, don't write results",
 )
-parser.add_argument(
-    "-V",
-    "--verbose",
-    action="store_true",
-    help="Print more info - cleaned notebooks.",
-)
 
 
 def process_mask(mask: Union[list[str], None]) -> Union[tuple[TupleStr, ...], None]:
@@ -113,9 +107,8 @@ def app() -> None:
     )
     if not cfg.silent:
         print(f"cleaned nbs: {len(cleaned)}")
-        if cfg.verbose:
-            for nb in cleaned:
-                print("- ", nb)
+        for nb in cleaned:
+            print("- ", nb)
         if errors:
             print(f"with errors: {len(errors)}")
             for nb, exc in errors:
diff --git a/src/nbmetaclean/clean.py b/src/nbmetaclean/clean.py
index 7a066e4..b889021 100644
--- a/src/nbmetaclean/clean.py
+++ b/src/nbmetaclean/clean.py
@@ -36,7 +36,6 @@ class CleanConfig:
         mask_merge (bool): Merge masks. Add new mask to default.
             If False - use new mask. Defaults to True.
         dry_run (bool): perform a trial run, don't write results. Defaults to False.
-        verbose (bool): Print more info - cleaned notebooks. Defaults to False.
     """
 
     clear_nb_metadata: bool = True
@@ -49,7 +48,6 @@ class CleanConfig:
     cell_metadata_preserve_mask: Optional[tuple[TupleStr, ...]] = None
     mask_merge: bool = True
     dry_run: bool = False
-    verbose: bool = False
 
 
 def filter_meta_mask(
@@ -189,8 +187,7 @@ def clean_nb_file(
         path = [path]
     cleaned: list[Path] = []
     errors: list[tuple[Path, Exception]] = []
-    to_clean = len(path)
-    for num, filename in enumerate(path):
+    for filename in path:
         try:
             nb = read_nb(filename)
         except Exception as ex:
@@ -209,6 +206,5 @@ def clean_nb_file(
             write_nb(nb, filename)
             if cfg.preserve_timestamp:
                 os.utime(filename, (stat.st_atime, stat.st_mtime))
-            if not cfg.silent:
-                print(f"done {num + 1} of {to_clean}: {filename}")
+
     return cleaned, errors
diff --git a/tests/test_clean.py b/tests/test_clean.py
index ab30826..465df66 100644
--- a/tests/test_clean.py
+++ b/tests/test_clean.py
@@ -289,10 +289,6 @@ def test_clean_nb_file(tmp_path: Path, capsys: CaptureFixture[str]):
     # clean meta, execution_count
     # path as list
     cleaned, errors = clean_nb_file([test_nb_path], CleanConfig())
-    captured = capsys.readouterr()
-    out = captured.out
-    assert out.startswith("done")
-    assert "test_clean_nb_file0/.test_nb_2_meta.ipynb" in out
     assert len(cleaned) == 1
     nb = read_nb(cleaned[0])
     assert nb == nb_clean
@@ -300,17 +296,7 @@ def test_clean_nb_file(tmp_path: Path, capsys: CaptureFixture[str]):
     # try clean cleaned
     cleaned, errors = clean_nb_file(test_nb_path, CleanConfig())
     assert len(cleaned) == 0
-    captured = capsys.readouterr()
-    out = captured.out
-    assert not out.strip()
-
-    # silent
-    test_nb_path = write_nb(read_nb(path / nb_name), tmp_path / nb_name)
-    cleaned, errors = clean_nb_file(test_nb_path, CleanConfig(silent=True))
-    assert len(cleaned) == 1
     assert len(errors) == 0
-    captured = capsys.readouterr()
-    assert not captured.out.strip()
 
 
 def test_clean_nb_file_errors(capsys: CaptureFixture[str], tmp_path: Path):

From 2cbb4acf2505150ccce4a268c3af50bb29f0f0d2 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Fri, 9 Aug 2024 11:11:31 +0300
Subject: [PATCH 16/23] set timestamp at write_nb

---
 src/nbmetaclean/clean.py   | 8 ++++----
 src/nbmetaclean/helpers.py | 7 ++++++-
 tests/test_read_write.py   | 7 +++++++
 3 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/src/nbmetaclean/clean.py b/src/nbmetaclean/clean.py
index b889021..4675d2f 100644
--- a/src/nbmetaclean/clean.py
+++ b/src/nbmetaclean/clean.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import copy
-import os
 from dataclasses import dataclass
 from pathlib import Path
 from typing import Optional, Tuple, Union
@@ -203,8 +202,9 @@ def clean_nb_file(
                 continue
             if cfg.preserve_timestamp:
                 stat = filename.stat()
-            write_nb(nb, filename)
-            if cfg.preserve_timestamp:
-                os.utime(filename, (stat.st_atime, stat.st_mtime))
+                timestamp = (stat.st_atime, stat.st_mtime)
+            else:
+                timestamp = None
+            write_nb(nb, filename, timestamp)
 
     return cleaned, errors
diff --git a/src/nbmetaclean/helpers.py b/src/nbmetaclean/helpers.py
index 90352f2..ff0d181 100644
--- a/src/nbmetaclean/helpers.py
+++ b/src/nbmetaclean/helpers.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import json
+import os
 from pathlib import Path
 from typing import Optional
 
@@ -22,12 +23,14 @@ def read_nb(path: PathOrStr) -> Nb:
 def write_nb(
     nb: Nb,
     path: PathOrStr,
+    timestamp: Optional[tuple[float, float]] = None,
 ) -> Path:
-    """Write notebook to file
+    """Write notebook to file, optionally set timestamp.
 
     Args:
         nb (Notebook): Notebook to write
         path (Union[str, PosixPath]): filename to write
+        timestamp (Optional[tuple[float, float]]): timestamp to set, (st_atime, st_mtime) defaults to None
     Returns:
         Path: Filename of written notebook.
     """
@@ -45,6 +48,8 @@ def write_nb(
             )
             + "\n",
         )
+    if timestamp is not None:
+        os.utime(filename, timestamp)
     return filename
 
 
diff --git a/tests/test_read_write.py b/tests/test_read_write.py
index 0a7e301..b2b94b5 100644
--- a/tests/test_read_write.py
+++ b/tests/test_read_write.py
@@ -41,3 +41,10 @@ def test_write_nb(tmp_path: Path):
     # write with name w/o suffix
     result = write_nb(nb, tmp_path / "test_nb_1")
     assert result == tmp_path / "test_nb_1.ipynb"
+
+    # write with stat
+    stat = file.stat()
+    timestamp = (stat.st_atime, stat.st_mtime)
+    result = write_nb(nb, tmp_path / "test_nb_1", timestamp=timestamp)
+    res_stat = result.stat()
+    assert timestamp == (res_stat.st_atime, res_stat.st_mtime)

From 08e6351083c8fa8d277acb962c0022bd623cd86a Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Mon, 12 Aug 2024 15:37:09 +0300
Subject: [PATCH 17/23] update pre-commit

---
 .pre-commit-config.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 76f3f7a..927b2fb 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,8 +3,6 @@ repos:
   rev: 0.0.8
   hooks:
   -   id: nbclean
-      name: nbclean
-      entry: nbclean
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.6.0
@@ -34,7 +32,7 @@ repos:
     - id: requirements-txt-fixer
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.5.2
+  rev: v0.5.7
   hooks:
     # Run the linter.
     - id: ruff

From f89d03f2e645513020e811ff46dd46ff2b3e571d Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Mon, 12 Aug 2024 18:34:53 +0300
Subject: [PATCH 18/23] add ruff settings and make pre-commit nbclean local

---
 .pre-commit-config.yaml | 10 +++++++---
 pyproject.toml          | 13 +++++++++++++
 2 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 927b2fb..b176598 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,8 +1,12 @@
 repos:
-- repo: https://github.com/ayasyrev/nbmetaclean
-  rev: 0.0.8
+- repo: local
   hooks:
-  -   id: 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
diff --git a/pyproject.toml b/pyproject.toml
index aef05e2..b4abb8e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,3 +7,16 @@ 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"

From d3da28bca3185e1b650334b6b6a9e4f3306e4829 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Mon, 12 Aug 2024 19:09:22 +0300
Subject: [PATCH 19/23] Add verbose mode to CLI, app function, and CleanConfig
 class.

---
 src/nbmetaclean/app.py   | 29 ++++++++++++++++++-----------
 src/nbmetaclean/clean.py |  2 ++
 2 files changed, 20 insertions(+), 11 deletions(-)

diff --git a/src/nbmetaclean/app.py b/src/nbmetaclean/app.py
index 3d1dd8a..f74a096 100644
--- a/src/nbmetaclean/app.py
+++ b/src/nbmetaclean/app.py
@@ -67,6 +67,12 @@
     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]:
@@ -78,17 +84,6 @@ def process_mask(mask: Union[list[str], None]) -> Union[tuple[TupleStr, ...], No
 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,
@@ -100,7 +95,19 @@ def app() -> None:
         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] = []
+    if clean_config.verbose:
+        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 clean_config.verbose:
+        print(f"notebooks to check: {len(nb_files)} ")
     cleaned, errors = clean_nb_file(
         nb_files,
         clean_config,
diff --git a/src/nbmetaclean/clean.py b/src/nbmetaclean/clean.py
index 4675d2f..f4efa26 100644
--- a/src/nbmetaclean/clean.py
+++ b/src/nbmetaclean/clean.py
@@ -35,6 +35,7 @@ class CleanConfig:
         mask_merge (bool): Merge masks. Add new mask to default.
             If False - use new mask. Defaults to True.
         dry_run (bool): perform a trial run, don't write results. Defaults to False.
+        verbose (bool): Verbose mode. Print extra information. Defaults to False.
     """
 
     clear_nb_metadata: bool = True
@@ -47,6 +48,7 @@ class CleanConfig:
     cell_metadata_preserve_mask: Optional[tuple[TupleStr, ...]] = None
     mask_merge: bool = True
     dry_run: bool = False
+    verbose: bool = False
 
 
 def filter_meta_mask(

From ce955c0005bfbf76016e7f77f2cf3ccb8b0226af Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Tue, 13 Aug 2024 13:50:33 +0300
Subject: [PATCH 20/23] clean app output

---
 src/nbmetaclean/app.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/nbmetaclean/app.py b/src/nbmetaclean/app.py
index f74a096..33eaacf 100644
--- a/src/nbmetaclean/app.py
+++ b/src/nbmetaclean/app.py
@@ -113,9 +113,13 @@ def app() -> None:
         clean_config,
     )
     if not cfg.silent:
-        print(f"cleaned nbs: {len(cleaned)}")
-        for nb in cleaned:
-            print("- ", nb)
+        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:

From 024e6bd44eaf84ec2911319a495ff4d49af834e1 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Tue, 13 Aug 2024 14:20:59 +0300
Subject: [PATCH 21/23] Add print_result function and refactor app function to
 use it for output.

---
 src/nbmetaclean/app.py | 48 +++++++++++++++++++++++++++---------------
 1 file changed, 31 insertions(+), 17 deletions(-)

diff --git a/src/nbmetaclean/app.py b/src/nbmetaclean/app.py
index 33eaacf..d3c26ca 100644
--- a/src/nbmetaclean/app.py
+++ b/src/nbmetaclean/app.py
@@ -81,6 +81,31 @@ 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()
@@ -99,31 +124,20 @@ def app() -> None:
     )
     path_list = cfg.path if isinstance(cfg.path, list) else [cfg.path]
     nb_files: list[Path] = []
-    if clean_config.verbose:
-        print(f"Path: {', '.join(cfg.path)}, preserve timestamp: {not cfg.not_pt}")
     for path in path_list:
-        try:
+        path = Path(path)
+        if path.exists():
             nb_files.extend(get_nb_names(path, hidden=cfg.clean_hidden_nbs))
-        except FileNotFoundError:
+        else:
             print(f"{path} not exists!")
-    if clean_config.verbose:
-        print(f"notebooks to check: {len(nb_files)} ")
+
     cleaned, errors = clean_nb_file(
         nb_files,
         clean_config,
     )
+
     if not cfg.silent:
-        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}")
+        print_result(cleaned, errors, clean_config, path_list, len(nb_files))
 
 
 if __name__ == "__main__":

From 6905efe8a8132e9ff80a6b28164895df7112ead2 Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Thu, 15 Aug 2024 11:48:05 +0300
Subject: [PATCH 22/23] app argument `not_ec` - preserve execution count

---
 src/nbmetaclean/app.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/nbmetaclean/app.py b/src/nbmetaclean/app.py
index d3c26ca..fba439d 100644
--- a/src/nbmetaclean/app.py
+++ b/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",
@@ -112,7 +117,7 @@ def app() -> None:
     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,

From ce6c7bcae36638580d86c95c6c21f6f518281fff Mon Sep 17 00:00:00 2001
From: ayasyrev <a.yasyrev@gmail.com>
Date: Thu, 15 Aug 2024 13:26:39 +0300
Subject: [PATCH 23/23] bump version 0.0.9

---
 src/nbmetaclean/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/nbmetaclean/version.py b/src/nbmetaclean/version.py
index eb14da7..00ec2dc 100644
--- a/src/nbmetaclean/version.py
+++ b/src/nbmetaclean/version.py
@@ -1 +1 @@
-__version__ = "0.0.9_dev"  # pragma: no cover
+__version__ = "0.0.9"