From 1fabae6155883c87b998a534efa2d371a2ee433d Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Tue, 12 Sep 2023 11:55:37 +0200 Subject: [PATCH 01/14] ensure databooks runs under pydanticv2 --- databooks/data_models/base.py | 10 +- databooks/data_models/cell.py | 43 +- databooks/data_models/notebook.py | 36 +- poetry.lock | 1281 ++++++++++++----------- pyproject.toml | 2 +- tests/test_cli.py | 71 +- tests/test_conflicts.py | 4 +- tests/test_data_models/test_notebook.py | 32 +- tests/test_git_utils.py | 4 +- tests/test_metadata.py | 2 +- 10 files changed, 817 insertions(+), 668 deletions(-) diff --git a/databooks/data_models/base.py b/databooks/data_models/base.py index 8173596e..e65b4b4e 100644 --- a/databooks/data_models/base.py +++ b/databooks/data_models/base.py @@ -5,7 +5,7 @@ from collections import UserList from typing import Any, Dict, Generic, Iterable, List, TypeVar, cast, overload -from pydantic import BaseModel, Extra, create_model +from pydantic import ConfigDict, BaseModel, create_model from typing_extensions import Protocol, runtime_checkable T = TypeVar("T") @@ -88,11 +88,7 @@ def resolve( class DatabooksBase(BaseModel): """Base Pydantic class with extras on managing fields.""" - - class Config: - """Default configuration for base class.""" - - extra = Extra.allow + model_config = ConfigDict(extra="allow") def remove_fields( self, @@ -158,7 +154,7 @@ def __sub__(self, other: DatabooksBase) -> DiffModel: "Diff" + type(self).__name__, __base__=type(self), resolve=resolve, - is_diff=True, + is_diff=(bool, True), **fields_d, ) return cast(DiffModel, DiffInstance()) # it'll be filled in with the defaults diff --git a/databooks/data_models/cell.py b/databooks/data_models/cell.py index 7e20f2d6..a806165a 100644 --- a/databooks/data_models/cell.py +++ b/databooks/data_models/cell.py @@ -3,7 +3,7 @@ from typing import Any, Callable, Dict, Iterable, List, Optional, Sequence, Union -from pydantic import PositiveInt, validator +from pydantic import field_validator, PositiveInt from rich.console import Console, ConsoleOptions, ConsoleRenderable, RenderResult from rich.markdown import Markdown from rich.panel import Panel @@ -63,7 +63,7 @@ def remove_fields( if self.cell_type == "code": self.outputs: CellOutputs = ( - CellOutputs(__root__=[]) + CellOutputs([]) if "outputs" not in dict(self) else self.outputs ) @@ -118,14 +118,16 @@ def __rich__( """Rich display of cell stream outputs.""" return Text("".join(self.text)) - @validator("output_type") + @field_validator("output_type") + @classmethod def output_type_must_be_stream(cls, v: str) -> str: """Check if stream has `stream` type.""" if v != "stream": raise ValueError(f"Invalid output type. Expected `stream`, got {v}.") return v - @validator("name") + @field_validator("name") + @classmethod def stream_name_must_match(cls, v: str) -> str: """Check if stream name is either `stdout` or `stderr`.""" valid_names = ("stdout", "stderr") @@ -178,7 +180,8 @@ def __rich_console__( """Rich display of data display outputs.""" yield from self.rich_output - @validator("output_type") + @field_validator("output_type") + @classmethod def output_type_must_match(cls, v: str) -> str: """Check if stream has `display_data` type.""" if v != "display_data": @@ -198,7 +201,8 @@ def __rich_console__( yield Text(f"Out [{self.execution_count or ' '}]:", style="out_count") yield from self.rich_output - @validator("output_type") + @field_validator("output_type") + @classmethod def output_type_must_match(cls, v: str) -> str: """Check if stream has `execute_result` type.""" if v != "execute_result": @@ -222,7 +226,8 @@ def __rich__( """Rich display of error outputs.""" return Text.from_ansi("\n".join(self.traceback)) - @validator("output_type") + @field_validator("output_type") + @classmethod def output_type_must_match(cls, v: str) -> str: """Check if stream has `error` type.""" if v != "error": @@ -234,11 +239,12 @@ def output_type_must_match(cls, v: str) -> str: CellStreamOutput, CellDisplayDataOutput, CellExecuteResultOutput, CellErrorOutput ] +from pydantic import RootModel -class CellOutputs(DatabooksBase): +class CellOutputs(DatabooksBase, RootModel): """Outputs of notebook code cells.""" - __root__: List[CellOutputType] + root: List[CellOutputType] def __rich_console__( self, console: Console, options: ConsoleOptions @@ -250,9 +256,13 @@ def __rich_console__( def values( self, ) -> List[CellOutputType]: - """Alias `__root__` with outputs for easy referencing.""" - return self.__root__ - + """Alias `root` with outputs for easy referencing.""" + return self.root + + # shouldn't need this, since BaseModel should implement equality on all fields, something's not working i.e. root eq works fine, model_config eq works fine, but whole class eq doesn't work... + # but maybe because of multi inheritance it doesn't work anymore :shrug: + def __eq__(self: CellOutputs, other: CellOutputs) -> bool: + return self.root == other.root and self.model_config == other.model_config class CodeCell(BaseCell): """Cell of type `code` - defined for rich displaying in terminal.""" @@ -273,7 +283,8 @@ def __rich_console__( ) yield self.outputs - @validator("cell_type") + @field_validator("cell_type") + @classmethod def cell_has_code_type(cls, v: str) -> str: """Extract the list values from the __root__ attribute of `CellOutputs`.""" if v != "code": @@ -292,7 +303,8 @@ def __rich__( """Rich display of markdown cells.""" return Panel(Markdown("".join(self.source))) - @validator("cell_type") + @field_validator("cell_type") + @classmethod def cell_has_md_type(cls, v: str) -> str: """Extract the list values from the __root__ attribute of `CellOutputs`.""" if v != "markdown": @@ -311,7 +323,8 @@ def __rich__( """Rich display of raw cells.""" return Panel(Text("".join(self.source))) - @validator("cell_type") + @field_validator("cell_type") + @classmethod def cell_has_md_type(cls, v: str) -> str: """Extract the list values from the __root__ attribute of `CellOutputs`.""" if v != "raw": diff --git a/databooks/data_models/notebook.py b/databooks/data_models/notebook.py index 0891ab30..94e2130c 100644 --- a/databooks/data_models/notebook.py +++ b/databooks/data_models/notebook.py @@ -20,8 +20,8 @@ cast, ) -from pydantic import Extra, validate_model -from pydantic.generics import GenericModel +from pydantic import BaseModel, Extra +# from pydantic.v1 import validate_model from rich import box from rich.columns import Columns from rich.console import Console, ConsoleOptions, Group, RenderableType, RenderResult @@ -38,20 +38,32 @@ CellsPair = Tuple[List[Cell], List[Cell]] T = TypeVar("T", Cell, CellsPair) +from pydantic import RootModel -class Cells(GenericModel, BaseCells[T]): +class Cells(RootModel[T], BaseCells[T]): """Similar to `list`, with `-` operator using `difflib.SequenceMatcher`.""" - __root__: Sequence[T] = () + root: Sequence[T] - def __init__(self, elements: Sequence[T] = ()) -> None: - """Allow passing data as a positional argument when instantiating class.""" - super(Cells, self).__init__(__root__=elements) + + # shouldn't need this, since BaseModel should implement equality on all fields, something's not working i.e. root eq works fine, model_config eq works fine, but whole class eq doesn't work... + # but maybe because of multi inheritance it doesn't work anymore :shrug: + def __eq__(self: Cells, other: Cells) -> bool: + return self.root == other.root + + # def __init__(self, elements: Sequence[T] = ()) -> None: + # """Allow passing data as a positional argument when instantiating class.""" + # # super(Cells, self).__init__(elements) @property def data(self) -> List[T]: # type: ignore """Define property `data` required for `collections.UserList` class.""" - return list(self.__root__) + return list(self.root) + + @data.setter + def data(self, value): # type: ignore + """Define property `data` required for `collections.UserList` class.""" + self._data = value def __iter__(self) -> Generator[Any, None, None]: """Use list property as iterable.""" @@ -265,9 +277,11 @@ def write( f"File exists at {path} exists. Specify `overwrite = True`." ) - _, _, validation_error = validate_model(self.__class__, self.dict()) - if validation_error: - raise validation_error + self.__class__.model_validate(self.dict()) + + # import pdb + # pdb.set_trace() + with path.open("w") as f: json.dump(self.dict(), fp=f, **json_kwargs) diff --git a/poetry.lock b/poetry.lock index 093dacf7..810bbab4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,29 @@ +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.5.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.7" +files = [ + {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"}, + {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"}, +] + +[package.dependencies] +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} + [[package]] name = "astunparse" version = "1.6.3" description = "An AST unparser for Python" -category = "dev" optional = false python-versions = "*" +files = [ + {file = "astunparse-1.6.3-py2.py3-none-any.whl", hash = "sha256:c2652417f2c8b5bb325c885ae329bdf3f86424075c4fd1a128674bc6fba4b8e8"}, + {file = "astunparse-1.6.3.tar.gz", hash = "sha256:5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872"}, +] [package.dependencies] six = ">=1.6.1,<2.0" @@ -14,41 +33,129 @@ wheel = ">=0.23.0,<1.0" name = "cached-property" version = "1.5.2" description = "A decorator for caching properties in classes." -category = "dev" optional = false python-versions = "*" +files = [ + {file = "cached-property-1.5.2.tar.gz", hash = "sha256:9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130"}, + {file = "cached_property-1.5.2-py2.py3-none-any.whl", hash = "sha256:df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0"}, +] [[package]] name = "certifi" -version = "2023.5.7" +version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." -category = "dev" optional = false python-versions = ">=3.6" +files = [ + {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"}, + {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, +] [[package]] name = "cfgv" version = "3.3.1" description = "Validate configuration and produce human readable error messages." -category = "dev" optional = false python-versions = ">=3.6.1" +files = [ + {file = "cfgv-3.3.1-py2.py3-none-any.whl", hash = "sha256:c6a0883f3917a037485059700b9e75da2464e6c27051014ad85ba6aaa5884426"}, + {file = "cfgv-3.3.1.tar.gz", hash = "sha256:f5a830efb9ce7a445376bb66ec94c638a9787422f96264c98edc6bdeed8ab736"}, +] [[package]] name = "charset-normalizer" -version = "3.1.0" +version = "3.2.0" description = "The Real First Universal Charset Detector. 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"sphinx-lint"] +testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] + +[metadata] +lock-version = "2.0" +python-versions = "^3.7" +content-hash = "7e9705ff65f29eb0690cd7e9e87e952821b4e62702e37b1d992b85ce476716bb" diff --git a/pyproject.toml b/pyproject.toml index f5bdfd2b..d339021e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ databooks = "databooks.cli:app" python = "^3.7" typer = ">=0.4.0,<1.0.0" rich = "^12.6.0" -pydantic = "^1.8.2" +pydantic = "2.0.*" GitPython = "^3.1.24" tomli = "^2.0.1" typing-extensions = "^4.0.1" diff --git a/tests/test_cli.py b/tests/test_cli.py index d5b0371c..534c3b8a 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -98,11 +98,28 @@ def test_meta__check(tmp_path: Path, caplog: LogCaptureFixture) -> None: assert nb_read == nb_write assert logs[0].message == "Found unwanted metadata in 1 out of 1 files." + # import pdb + # pdb.set_trace() + # Clean notebook and check again - runner.invoke(app, ["meta", str(read_path), "--yes"]) + result_clean = runner.invoke(app, ["meta", str(read_path), "--yes"]) + + + # import pdb + # pdb.set_trace() + + result = runner.invoke(app, ["meta", str(read_path), "--check"]) + + + # import pdb + # pdb.set_trace() logs = list(caplog.records) + + # import pdb + # pdb.set_trace() + assert result.exit_code == 0 assert len(logs) == 4 assert logs[-1].message == "No unwanted metadata!" @@ -123,7 +140,7 @@ def test_meta__config(tmp_path: Path) -> None: assert result.exit_code == 0 assert nb_read != nb_write, "Notebook was not overwritten" - assert all(c.outputs == CellOutputs(__root__=[]) for c in nb_write.cells) + assert all(c.outputs == CellOutputs([]) for c in nb_write.cells) assert all(c.execution_count is not None for c in nb_write.cells) # Override config file arguments @@ -229,6 +246,8 @@ def test_assert__config(caplog: LogCaptureFixture) -> None: ) +from databooks.data_models.cell import RawCell, MarkdownCell + def test_fix(tmp_path: Path) -> None: """Fix notebook conflicts.""" # Setup @@ -244,11 +263,11 @@ def test_fix(tmp_path: Path) -> None: another_field_to_remove="another field", ) - extra_cell = BaseCell( - cell_type="raw", + extra_cell = RawCell( metadata=CellMetadata(random_meta=["meta"]), source="extra", ) + notebook_2.cells = notebook_2.cells + [extra_cell] notebook_2.nbformat += 1 notebook_2.nbformat_minor += 1 @@ -259,8 +278,9 @@ def test_fix(tmp_path: Path) -> None: contents_main=notebook_1.json(), contents_other=notebook_2.json(), commit_message_main="Notebook from main", - commit_message_other="Notebook from other", + commit_message_other="Notebook from other" ) + with raises(GitCommandError): git_repo.git.merge("other") # merge fails and raises error due to conflict @@ -286,18 +306,18 @@ def test_fix(tmp_path: Path) -> None: assert fixed_notebook.nbformat == notebook_1.nbformat assert fixed_notebook.nbformat_minor == notebook_1.nbformat_minor assert fixed_notebook.cells == notebook_1.cells + [ - BaseCell( + MarkdownCell( metadata=CellMetadata(git_hash=id_main), source=[f"`<<<<<<< {id_main}`"], cell_type="markdown", ), - BaseCell( + MarkdownCell( source=["`=======`"], cell_type="markdown", metadata=CellMetadata(), ), extra_cell, - BaseCell( + MarkdownCell( metadata=CellMetadata(git_hash=id_other), source=[f"`>>>>>>> {id_other}`"], cell_type="markdown", @@ -320,12 +340,18 @@ def test_fix__config(tmp_path: Path) -> None: another_field_to_remove="another field", ) - extra_cell = BaseCell( - cell_type="raw", + from typing import cast + from databooks.data_models.cell import RawCell, MarkdownCell + + # ok so since notebook requires its cells to be more specific than BaseCells, we cannot pass BaseCell, since the class might depend on child class methods the base class doesn't possess + # contravariance? + extra_cell = RawCell( metadata=CellMetadata(random_meta=["meta"]), source="extra", ) + notebook_2.cells = notebook_2.cells + [extra_cell] + notebook_2.nbformat += 1 notebook_2.nbformat_minor += 1 @@ -350,6 +376,10 @@ def test_fix__config(tmp_path: Path) -> None: result = runner.invoke( app, ["fix", str(tmp_path), "--config", str(config_path)] ) + + # import pdb + # pdb.set_trace() + fixed_notebook = JupyterNotebook.parse_file(path=tmp_path / nb_path) assert len(conflict_files) == 1 @@ -365,25 +395,31 @@ def test_fix__config(tmp_path: Path) -> None: assert fixed_notebook.metadata == NotebookMetadata(**expected_metadata) assert fixed_notebook.nbformat == notebook_2.nbformat assert fixed_notebook.nbformat_minor == notebook_2.nbformat_minor - assert fixed_notebook.cells == notebook_1.cells + [ - BaseCell( + + expected = notebook_1.cells + [ + MarkdownCell( metadata=CellMetadata(git_hash=id_main), source=[f"`<<<<<<< {id_main}`"], cell_type="markdown", ), - BaseCell( + MarkdownCell( source=["`=======`"], cell_type="markdown", metadata=CellMetadata(), ), extra_cell, - BaseCell( + MarkdownCell( metadata=CellMetadata(git_hash=id_other), source=[f"`>>>>>>> {id_other}`"], cell_type="markdown", ), ] + # import pdb + # pdb.set_trace() + + # something's wrong with root models, they are not equal + assert fixed_notebook.cells == expected def test_show() -> None: """Show notebook in terminal.""" @@ -474,6 +510,7 @@ def test_show_no_multiple() -> None: result = runner.invoke(app, ["show", dirpath]) assert result.exit_code == 1 +from databooks.data_models.cell import RawCell def test_diff(tmp_path: Path) -> None: """Show rich diffs of notebooks.""" @@ -489,8 +526,7 @@ def test_diff(tmp_path: Path) -> None: another_field_to_remove="another field", ) - extra_cell = BaseCell( - cell_type="raw", + extra_cell = RawCell( metadata=CellMetadata(random_meta=["meta"]), source="extra", ) @@ -577,8 +613,7 @@ def test_diff_svg(tmp_path: Path) -> None: another_field_to_remove="another field", ) - extra_cell = BaseCell( - cell_type="raw", + extra_cell = RawCell( metadata=CellMetadata(random_meta=["meta"]), source="extra", ) diff --git a/tests/test_conflicts.py b/tests/test_conflicts.py index 28452252..dba689ee 100644 --- a/tests/test_conflicts.py +++ b/tests/test_conflicts.py @@ -9,6 +9,7 @@ from tests.test_data_models.test_notebook import TestJupyterNotebook from tests.test_git_utils import ConflictFile, init_repo_diff +from databooks.data_models.cell import RawCell def test_path2diff(tmp_path: Path) -> None: """Return a DiffFile based on a path and git conflicts.""" @@ -22,8 +23,7 @@ def test_path2diff(tmp_path: Path) -> None: field_to_remove=["Field to remove"], another_field_to_remove="another field", ) - extra_cell = BaseCell( - cell_type="raw", + extra_cell = RawCell( metadata=CellMetadata(random_meta=["meta"]), source="extra", ) diff --git a/tests/test_data_models/test_notebook.py b/tests/test_data_models/test_notebook.py index 7dc88d7d..5be5acae 100644 --- a/tests/test_data_models/test_notebook.py +++ b/tests/test_data_models/test_notebook.py @@ -19,6 +19,7 @@ from databooks.data_models.notebook import ( Cell, Cells, + CellsPair, JupyterNotebook, NotebookMetadata, ) @@ -113,7 +114,7 @@ def test_clear(self, caplog: LogCaptureFixture) -> None: assert cell == CodeCell( cell_type="code", metadata=CellMetadata(), - outputs=CellOutputs(__root__=[]), + outputs=CellOutputs([]), source=["test_source"], execution_count=None, ) @@ -131,10 +132,13 @@ def test_cells_sub(self) -> None: assert type(dl1) == type(dl2) == Cells[Cell] assert type(diff) == Cells[Tuple[List[Cell], List[Cell]]] - assert diff == Cells( # type: ignore + + expected = Cells[CellsPair]( # type: ignore [([self.cell], [self.cell]), ([], [self.cell])] ) + assert diff == expected + def test_cell_remove_fields(self, caplog: LogCaptureFixture) -> None: """Test remove fields with logs.""" caplog.set_level(logging.DEBUG) @@ -144,7 +148,7 @@ def test_cell_remove_fields(self, caplog: LogCaptureFixture) -> None: assert cell.dict() == dict( cell_type="code", - metadata=self.cell_metadata, + metadata=self.cell_metadata.dict(), source=["test_source"], execution_count=1, outputs=[], @@ -179,7 +183,7 @@ def test_clear_metadata(self) -> None: assert all(cell.metadata == CellMetadata() for cell in notebook.cells) assert all( - cell.outputs == CellOutputs(__root__=[]) + cell.outputs == CellOutputs([]) for cell in notebook.cells if cell.cell_type == "code" ) @@ -198,6 +202,10 @@ def test_notebook_sub(self) -> None: """ notebook_1 = deepcopy(self.jupyter_notebook) notebook_2 = deepcopy(self.jupyter_notebook) + + # import pdb + # pdb.set_trace() + notebook_1.metadata = NotebookMetadata( kernelspec=dict( display_name="different_kernel_display_name", name="kernel_name" @@ -211,7 +219,7 @@ def test_notebook_sub(self) -> None: source="extra", ) notebook_2.cells = notebook_2.cells + [extra_cell] - + diff = notebook_1 - notebook_2 notebook = deepcopy(notebook_1) @@ -220,6 +228,10 @@ def test_notebook_sub(self) -> None: **notebook_1.metadata.dict(), **{"tags": []} ) + # import pdb + # pdb.set_trace() + + # TODO - without .dict(), they're not equal, not sure why... assert diff.resolve(keep_first_cells=True) == notebook notebook.cells = notebook_2.cells @@ -243,7 +255,7 @@ def test_notebook_sub(self) -> None: cell_type="markdown", ), ] - assert diff.resolve(keep_first_cells=None) == notebook + assert diff.resolve(keep_first_cells=None).dict() == notebook.dict() def test_parse_file() -> None: @@ -275,7 +287,8 @@ def test_parse_file() -> None: "toc-autonumbering": False, }, ) - assert notebook.cells == Cells( + + expected_cells = Cells[Cell]( [ MarkdownCell( metadata=CellMetadata(tags=[]), @@ -351,6 +364,11 @@ def test_parse_file() -> None: ] ) + # import pdb + # pdb.set_trace() + + assert notebook.cells == expected_cells + def test_write_file(tmp_path: Path) -> None: """Check that serialization and deserialization are valid.""" diff --git a/tests/test_git_utils.py b/tests/test_git_utils.py index d4bca362..c4f12031 100644 --- a/tests/test_git_utils.py +++ b/tests/test_git_utils.py @@ -99,6 +99,7 @@ def test_get_conflict_blobs(tmp_path: Path) -> None: assert conflict.first_contents == b"HELLO EVERYONE!" assert conflict.last_contents == b"hello world" +from databooks.data_models.cell import RawCell def test_get_nb_diffs(tmp_path: Path) -> None: """Get the diffs for notebooks.""" @@ -112,8 +113,7 @@ def test_get_nb_diffs(tmp_path: Path) -> None: field_to_remove=["Field to remove"], another_field_to_remove="another field", ) - extra_cell = BaseCell( - cell_type="raw", + extra_cell = RawCell( metadata=CellMetadata(random_meta=["meta"]), source="extra", ) diff --git a/tests/test_metadata.py b/tests/test_metadata.py index d99c9d11..81f8a901 100644 --- a/tests/test_metadata.py +++ b/tests/test_metadata.py @@ -60,7 +60,7 @@ def test_metadata_clear(tmp_path: Path) -> None: assert all( cell.outputs == CellOutputs( - __root__=[ + [ {"name": "stdout", "output_type": "stream", "text": ["test text\n"]} ] ) From 2e6c30f53bc89f0fced4649e071327b62ddf0cfc Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Tue, 12 Sep 2023 13:22:12 +0200 Subject: [PATCH 02/14] bump pydantic to highest possible version, without introducing additional migration changes --- poetry.lock | 223 +++++++++++++++++++++++++------------------------ pyproject.toml | 2 +- 2 files changed, 114 insertions(+), 111 deletions(-) diff --git a/poetry.lock b/poetry.lock index 810bbab4..6d320595 100644 --- a/poetry.lock +++ b/poetry.lock @@ -334,19 +334,22 @@ smmap = ">=3.0.1,<6" [[package]] name = "gitpython" -version = "3.1.35" +version = "3.1.36" description = "GitPython is a Python library used to interact with Git repositories" optional = false python-versions = ">=3.7" files = [ - {file = "GitPython-3.1.35-py3-none-any.whl", hash = "sha256:c19b4292d7a1d3c0f653858db273ff8a6614100d1eb1528b014ec97286193c09"}, - {file = "GitPython-3.1.35.tar.gz", hash = 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"^12.6.0" -pydantic = "2.0.*" +pydantic = "2.1.*" GitPython = "^3.1.24" tomli = "^2.0.1" typing-extensions = "^4.0.1" From f1d39e1356dff5dafc61b1803959adad65191b93 Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Tue, 12 Sep 2023 15:31:32 +0200 Subject: [PATCH 03/14] typing fixes --- .pre-commit-config.yaml | 8 ++++---- databooks/data_models/base.py | 3 ++- databooks/data_models/cell.py | 20 +++++++++--------- databooks/data_models/notebook.py | 27 ++++++++----------------- tests/test_cli.py | 24 +++++++--------------- tests/test_conflicts.py | 3 +-- tests/test_data_models/test_notebook.py | 2 +- tests/test_git_utils.py | 3 +-- tests/test_metadata.py | 4 +--- 9 files changed, 35 insertions(+), 59 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 126e93d5..e59ecfb1 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -33,9 +33,9 @@ repos: - types-all==1.0.0 - typer==0.3.2 - rich==10.16.2 - - pydantic==1.9.0 + - pydantic==2.2.* - GitPython==3.1.26 - - typing-extensions==4.0.1 + - typing-extensions==4.6.* - tomli==2.0.1 - repo: https://github.com/codespell-project/codespell rev: v2.2.4 @@ -55,7 +55,7 @@ repos: - typer-cli==0.0.12 - typer==0.3.2 - rich==10.16.2 - - pydantic==1.9.0 + - pydantic==2.2 - GitPython==3.1.26 - - typing-extensions==4.0.1 + - typing-extensions==4.6.* - tomli==2.0.1 diff --git a/databooks/data_models/base.py b/databooks/data_models/base.py index e65b4b4e..03ac00c3 100644 --- a/databooks/data_models/base.py +++ b/databooks/data_models/base.py @@ -5,7 +5,7 @@ from collections import UserList from typing import Any, Dict, Generic, Iterable, List, TypeVar, cast, overload -from pydantic import ConfigDict, BaseModel, create_model +from pydantic import BaseModel, ConfigDict, create_model from typing_extensions import Protocol, runtime_checkable T = TypeVar("T") @@ -88,6 +88,7 @@ def resolve( class DatabooksBase(BaseModel): """Base Pydantic class with extras on managing fields.""" + model_config = ConfigDict(extra="allow") def remove_fields( diff --git a/databooks/data_models/cell.py b/databooks/data_models/cell.py index a806165a..98d40446 100644 --- a/databooks/data_models/cell.py +++ b/databooks/data_models/cell.py @@ -3,7 +3,7 @@ from typing import Any, Callable, Dict, Iterable, List, Optional, Sequence, Union -from pydantic import field_validator, PositiveInt +from pydantic import PositiveInt, RootModel, field_validator from rich.console import Console, ConsoleOptions, ConsoleRenderable, RenderResult from rich.markdown import Markdown from rich.panel import Panel @@ -63,9 +63,7 @@ def remove_fields( if self.cell_type == "code": self.outputs: CellOutputs = ( - CellOutputs([]) - if "outputs" not in dict(self) - else self.outputs + CellOutputs([]) if "outputs" not in dict(self) else self.outputs ) self.execution_count: Optional[PositiveInt] = ( None if "execution_count" not in dict(self) else self.execution_count @@ -239,7 +237,6 @@ def output_type_must_match(cls, v: str) -> str: CellStreamOutput, CellDisplayDataOutput, CellExecuteResultOutput, CellErrorOutput ] -from pydantic import RootModel class CellOutputs(DatabooksBase, RootModel): """Outputs of notebook code cells.""" @@ -258,11 +255,14 @@ def values( ) -> List[CellOutputType]: """Alias `root` with outputs for easy referencing.""" return self.root - - # shouldn't need this, since BaseModel should implement equality on all fields, something's not working i.e. root eq works fine, model_config eq works fine, but whole class eq doesn't work... - # but maybe because of multi inheritance it doesn't work anymore :shrug: - def __eq__(self: CellOutputs, other: CellOutputs) -> bool: - return self.root == other.root and self.model_config == other.model_config + + # Before CellOutputs inherited from RootModel + # eq worked well (suppose covered by DatabooksBase, + # which inherits from Pydantic's BaseModel) + def __eq__(self: CellOutputs, other: object) -> bool: + """Comparison of different CellOutputs.""" + return type(other) == CellOutputs and self.root == other.root and self.model_config == other.model_config + class CodeCell(BaseCell): """Cell of type `code` - defined for rich displaying in terminal.""" diff --git a/databooks/data_models/notebook.py b/databooks/data_models/notebook.py index 94e2130c..9c2a4053 100644 --- a/databooks/data_models/notebook.py +++ b/databooks/data_models/notebook.py @@ -20,8 +20,7 @@ cast, ) -from pydantic import BaseModel, Extra -# from pydantic.v1 import validate_model +from pydantic import Extra, RootModel from rich import box from rich.columns import Columns from rich.console import Console, ConsoleOptions, Group, RenderableType, RenderResult @@ -38,33 +37,21 @@ CellsPair = Tuple[List[Cell], List[Cell]] T = TypeVar("T", Cell, CellsPair) -from pydantic import RootModel -class Cells(RootModel[T], BaseCells[T]): +class Cells(RootModel[Sequence[T]], BaseCells[T]): """Similar to `list`, with `-` operator using `difflib.SequenceMatcher`.""" root: Sequence[T] - - # shouldn't need this, since BaseModel should implement equality on all fields, something's not working i.e. root eq works fine, model_config eq works fine, but whole class eq doesn't work... - # but maybe because of multi inheritance it doesn't work anymore :shrug: - def __eq__(self: Cells, other: Cells) -> bool: - return self.root == other.root - - # def __init__(self, elements: Sequence[T] = ()) -> None: - # """Allow passing data as a positional argument when instantiating class.""" - # # super(Cells, self).__init__(elements) + def __eq__(self: Cells, other: object) -> bool: + """Compare different Cells.""" + return type(other) == Cells and self.root == other.root @property def data(self) -> List[T]: # type: ignore """Define property `data` required for `collections.UserList` class.""" return list(self.root) - @data.setter - def data(self, value): # type: ignore - """Define property `data` required for `collections.UserList` class.""" - self._data = value - def __iter__(self) -> Generator[Any, None, None]: """Use list property as iterable.""" return (el for el in self.data) @@ -93,6 +80,8 @@ def __sub__(self: Cells[Cell], other: Cells[Cell]) -> Cells[CellsPair]: f" {n_context} for {len(self)} and {len(other)} cells in" " notebooks." ) + + # weird, root is Sequence type, but mypy doesn't see this, only its element type... return Cells[CellsPair]( [ # https://github.com/python/mypy/issues/9459 @@ -100,7 +89,7 @@ def __sub__(self: Cells[Cell], other: Cells[Cell]) -> Cells[CellsPair]: for _, i1, j1, i2, j2 in chain.from_iterable(diff_opcodes) ] ) - + def __rich_console__( self, console: Console, options: ConsoleOptions ) -> RenderResult: diff --git a/tests/test_cli.py b/tests/test_cli.py index 534c3b8a..617befa0 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -12,7 +12,7 @@ from typer.testing import CliRunner from databooks.cli import _config_callback, _parse_paths, app -from databooks.data_models.cell import BaseCell, CellMetadata, CellOutputs +from databooks.data_models.cell import CellMetadata, CellOutputs, MarkdownCell, RawCell from databooks.data_models.notebook import JupyterNotebook, NotebookMetadata from databooks.git_utils import get_conflict_blobs from databooks.version import __version__ @@ -102,15 +102,12 @@ def test_meta__check(tmp_path: Path, caplog: LogCaptureFixture) -> None: # pdb.set_trace() # Clean notebook and check again - result_clean = runner.invoke(app, ["meta", str(read_path), "--yes"]) - + runner.invoke(app, ["meta", str(read_path), "--yes"]) # import pdb # pdb.set_trace() - result = runner.invoke(app, ["meta", str(read_path), "--check"]) - # import pdb # pdb.set_trace() @@ -246,8 +243,6 @@ def test_assert__config(caplog: LogCaptureFixture) -> None: ) -from databooks.data_models.cell import RawCell, MarkdownCell - def test_fix(tmp_path: Path) -> None: """Fix notebook conflicts.""" # Setup @@ -278,7 +273,7 @@ def test_fix(tmp_path: Path) -> None: contents_main=notebook_1.json(), contents_other=notebook_2.json(), commit_message_main="Notebook from main", - commit_message_other="Notebook from other" + commit_message_other="Notebook from other", ) with raises(GitCommandError): @@ -340,16 +335,11 @@ def test_fix__config(tmp_path: Path) -> None: another_field_to_remove="another field", ) - from typing import cast - from databooks.data_models.cell import RawCell, MarkdownCell - - # ok so since notebook requires its cells to be more specific than BaseCells, we cannot pass BaseCell, since the class might depend on child class methods the base class doesn't possess - # contravariance? extra_cell = RawCell( metadata=CellMetadata(random_meta=["meta"]), source="extra", ) - + notebook_2.cells = notebook_2.cells + [extra_cell] notebook_2.nbformat += 1 @@ -379,7 +369,7 @@ def test_fix__config(tmp_path: Path) -> None: # import pdb # pdb.set_trace() - + fixed_notebook = JupyterNotebook.parse_file(path=tmp_path / nb_path) assert len(conflict_files) == 1 @@ -417,10 +407,11 @@ def test_fix__config(tmp_path: Path) -> None: # import pdb # pdb.set_trace() - + # something's wrong with root models, they are not equal assert fixed_notebook.cells == expected + def test_show() -> None: """Show notebook in terminal.""" with resources.path("tests.files", "tui-demo.ipynb") as nb_path: @@ -510,7 +501,6 @@ def test_show_no_multiple() -> None: result = runner.invoke(app, ["show", dirpath]) assert result.exit_code == 1 -from databooks.data_models.cell import RawCell def test_diff(tmp_path: Path) -> None: """Show rich diffs of notebooks.""" diff --git a/tests/test_conflicts.py b/tests/test_conflicts.py index dba689ee..e81e110e 100644 --- a/tests/test_conflicts.py +++ b/tests/test_conflicts.py @@ -4,12 +4,11 @@ from pytest import raises from databooks.conflicts import path2conflicts -from databooks.data_models.cell import BaseCell, CellMetadata +from databooks.data_models.cell import CellMetadata, RawCell from databooks.data_models.notebook import NotebookMetadata from tests.test_data_models.test_notebook import TestJupyterNotebook from tests.test_git_utils import ConflictFile, init_repo_diff -from databooks.data_models.cell import RawCell def test_path2diff(tmp_path: Path) -> None: """Return a DiffFile based on a path and git conflicts.""" diff --git a/tests/test_data_models/test_notebook.py b/tests/test_data_models/test_notebook.py index 5be5acae..162ba263 100644 --- a/tests/test_data_models/test_notebook.py +++ b/tests/test_data_models/test_notebook.py @@ -219,7 +219,7 @@ def test_notebook_sub(self) -> None: source="extra", ) notebook_2.cells = notebook_2.cells + [extra_cell] - + diff = notebook_1 - notebook_2 notebook = deepcopy(notebook_1) diff --git a/tests/test_git_utils.py b/tests/test_git_utils.py index c4f12031..005f398e 100644 --- a/tests/test_git_utils.py +++ b/tests/test_git_utils.py @@ -3,7 +3,7 @@ from git import GitCommandError, Repo from pytest import raises -from databooks.data_models.cell import BaseCell, CellMetadata +from databooks.data_models.cell import CellMetadata, RawCell from databooks.data_models.notebook import NotebookMetadata from databooks.git_utils import ( ChangeType, @@ -99,7 +99,6 @@ def test_get_conflict_blobs(tmp_path: Path) -> None: assert conflict.first_contents == b"HELLO EVERYONE!" assert conflict.last_contents == b"hello world" -from databooks.data_models.cell import RawCell def test_get_nb_diffs(tmp_path: Path) -> None: """Get the diffs for notebooks.""" diff --git a/tests/test_metadata.py b/tests/test_metadata.py index 81f8a901..eee2f27a 100644 --- a/tests/test_metadata.py +++ b/tests/test_metadata.py @@ -60,9 +60,7 @@ def test_metadata_clear(tmp_path: Path) -> None: assert all( cell.outputs == CellOutputs( - [ - {"name": "stdout", "output_type": "stream", "text": ["test text\n"]} - ] + [{"name": "stdout", "output_type": "stream", "text": ["test text\n"]}] ) for cell in nb_write.cells if cell.cell_type == "code" From 875b740e8868add63320da77d3d5977e34728a2e Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Tue, 12 Sep 2023 15:39:30 +0200 Subject: [PATCH 04/14] fix some minor typing issues --- databooks/data_models/cell.py | 6 +++++- databooks/data_models/notebook.py | 9 ++++----- tests/test_data_models/test_notebook.py | 3 +++ 3 files changed, 12 insertions(+), 6 deletions(-) diff --git a/databooks/data_models/cell.py b/databooks/data_models/cell.py index 98d40446..d02943f8 100644 --- a/databooks/data_models/cell.py +++ b/databooks/data_models/cell.py @@ -261,7 +261,11 @@ def values( # which inherits from Pydantic's BaseModel) def __eq__(self: CellOutputs, other: object) -> bool: """Comparison of different CellOutputs.""" - return type(other) == CellOutputs and self.root == other.root and self.model_config == other.model_config + return ( + type(other) == CellOutputs + and self.root == other.root + and self.model_config == other.model_config + ) class CodeCell(BaseCell): diff --git a/databooks/data_models/notebook.py b/databooks/data_models/notebook.py index 9c2a4053..9266ad56 100644 --- a/databooks/data_models/notebook.py +++ b/databooks/data_models/notebook.py @@ -43,15 +43,15 @@ class Cells(RootModel[Sequence[T]], BaseCells[T]): root: Sequence[T] - def __eq__(self: Cells, other: object) -> bool: + def __eq__(self: Cells[T], other: object) -> bool: """Compare different Cells.""" - return type(other) == Cells and self.root == other.root + return isinstance(other, Cells) and self.root == other.root @property def data(self) -> List[T]: # type: ignore """Define property `data` required for `collections.UserList` class.""" return list(self.root) - + def __iter__(self) -> Generator[Any, None, None]: """Use list property as iterable.""" return (el for el in self.data) @@ -81,7 +81,6 @@ def __sub__(self: Cells[Cell], other: Cells[Cell]) -> Cells[CellsPair]: " notebooks." ) - # weird, root is Sequence type, but mypy doesn't see this, only its element type... return Cells[CellsPair]( [ # https://github.com/python/mypy/issues/9459 @@ -89,7 +88,7 @@ def __sub__(self: Cells[Cell], other: Cells[Cell]) -> Cells[CellsPair]: for _, i1, j1, i2, j2 in chain.from_iterable(diff_opcodes) ] ) - + def __rich_console__( self, console: Console, options: ConsoleOptions ) -> RenderResult: diff --git a/tests/test_data_models/test_notebook.py b/tests/test_data_models/test_notebook.py index 162ba263..bf2413ed 100644 --- a/tests/test_data_models/test_notebook.py +++ b/tests/test_data_models/test_notebook.py @@ -137,6 +137,9 @@ def test_cells_sub(self) -> None: [([self.cell], [self.cell]), ([], [self.cell])] ) + # import pdb + # pdb.set_trace() + assert diff == expected def test_cell_remove_fields(self, caplog: LogCaptureFixture) -> None: From 4f967eff5f1f6315d6158c05f2e62f3f2d973b06 Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Wed, 13 Sep 2023 09:42:48 +0200 Subject: [PATCH 05/14] unify poetry and precommit versions --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e59ecfb1..c5e1391a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -33,7 +33,7 @@ repos: - types-all==1.0.0 - typer==0.3.2 - rich==10.16.2 - - pydantic==2.2.* + - pydantic==2.1.* - GitPython==3.1.26 - typing-extensions==4.6.* - tomli==2.0.1 @@ -55,7 +55,7 @@ repos: - typer-cli==0.0.12 - typer==0.3.2 - rich==10.16.2 - - pydantic==2.2 + - pydantic==2.1 - GitPython==3.1.26 - typing-extensions==4.6.* - tomli==2.0.1 From c8c1089a0e194e5a133b5c0d0ded43f5eb7ede14 Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Wed, 13 Sep 2023 09:44:11 +0200 Subject: [PATCH 06/14] remove unused debugging code pieces --- databooks/data_models/notebook.py | 3 --- tests/test_cli.py | 19 ------------------- tests/test_data_models/test_notebook.py | 13 ------------- 3 files changed, 35 deletions(-) diff --git a/databooks/data_models/notebook.py b/databooks/data_models/notebook.py index 9266ad56..60a3f554 100644 --- a/databooks/data_models/notebook.py +++ b/databooks/data_models/notebook.py @@ -267,9 +267,6 @@ def write( self.__class__.model_validate(self.dict()) - # import pdb - # pdb.set_trace() - with path.open("w") as f: json.dump(self.dict(), fp=f, **json_kwargs) diff --git a/tests/test_cli.py b/tests/test_cli.py index 617befa0..c433a768 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -98,25 +98,13 @@ def test_meta__check(tmp_path: Path, caplog: LogCaptureFixture) -> None: assert nb_read == nb_write assert logs[0].message == "Found unwanted metadata in 1 out of 1 files." - # import pdb - # pdb.set_trace() - # Clean notebook and check again runner.invoke(app, ["meta", str(read_path), "--yes"]) - # import pdb - # pdb.set_trace() - result = runner.invoke(app, ["meta", str(read_path), "--check"]) - # import pdb - # pdb.set_trace() - logs = list(caplog.records) - # import pdb - # pdb.set_trace() - assert result.exit_code == 0 assert len(logs) == 4 assert logs[-1].message == "No unwanted metadata!" @@ -367,9 +355,6 @@ def test_fix__config(tmp_path: Path) -> None: app, ["fix", str(tmp_path), "--config", str(config_path)] ) - # import pdb - # pdb.set_trace() - fixed_notebook = JupyterNotebook.parse_file(path=tmp_path / nb_path) assert len(conflict_files) == 1 @@ -405,10 +390,6 @@ def test_fix__config(tmp_path: Path) -> None: ), ] - # import pdb - # pdb.set_trace() - - # something's wrong with root models, they are not equal assert fixed_notebook.cells == expected diff --git a/tests/test_data_models/test_notebook.py b/tests/test_data_models/test_notebook.py index bf2413ed..9a3a9120 100644 --- a/tests/test_data_models/test_notebook.py +++ b/tests/test_data_models/test_notebook.py @@ -137,9 +137,6 @@ def test_cells_sub(self) -> None: [([self.cell], [self.cell]), ([], [self.cell])] ) - # import pdb - # pdb.set_trace() - assert diff == expected def test_cell_remove_fields(self, caplog: LogCaptureFixture) -> None: @@ -206,9 +203,6 @@ def test_notebook_sub(self) -> None: notebook_1 = deepcopy(self.jupyter_notebook) notebook_2 = deepcopy(self.jupyter_notebook) - # import pdb - # pdb.set_trace() - notebook_1.metadata = NotebookMetadata( kernelspec=dict( display_name="different_kernel_display_name", name="kernel_name" @@ -231,10 +225,6 @@ def test_notebook_sub(self) -> None: **notebook_1.metadata.dict(), **{"tags": []} ) - # import pdb - # pdb.set_trace() - - # TODO - without .dict(), they're not equal, not sure why... assert diff.resolve(keep_first_cells=True) == notebook notebook.cells = notebook_2.cells @@ -367,9 +357,6 @@ def test_parse_file() -> None: ] ) - # import pdb - # pdb.set_trace() - assert notebook.cells == expected_cells From 347349fbc42eb6800ab8e280ac62b7be28775632 Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Fri, 15 Sep 2023 09:35:31 +0200 Subject: [PATCH 07/14] fix - compare databooks directly in test vs. their inner dicts --- tests/test_data_models/test_notebook.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_data_models/test_notebook.py b/tests/test_data_models/test_notebook.py index 9a3a9120..35e730ac 100644 --- a/tests/test_data_models/test_notebook.py +++ b/tests/test_data_models/test_notebook.py @@ -248,7 +248,7 @@ def test_notebook_sub(self) -> None: cell_type="markdown", ), ] - assert diff.resolve(keep_first_cells=None).dict() == notebook.dict() + assert diff.resolve(keep_first_cells=None) == notebook def test_parse_file() -> None: From 1d9be3b5254eb2d1543038bf6260aefd4afa3054 Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Fri, 15 Sep 2023 09:37:03 +0200 Subject: [PATCH 08/14] remove unnecessary type ignore, lint --- tests/test_data_models/test_notebook.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/tests/test_data_models/test_notebook.py b/tests/test_data_models/test_notebook.py index 35e730ac..6bf17475 100644 --- a/tests/test_data_models/test_notebook.py +++ b/tests/test_data_models/test_notebook.py @@ -133,9 +133,7 @@ def test_cells_sub(self) -> None: assert type(dl1) == type(dl2) == Cells[Cell] assert type(diff) == Cells[Tuple[List[Cell], List[Cell]]] - expected = Cells[CellsPair]( # type: ignore - [([self.cell], [self.cell]), ([], [self.cell])] - ) + expected = Cells[CellsPair]([([self.cell], [self.cell]), ([], [self.cell])]) assert diff == expected From f30f0c7fc24f758f108325b25e85b44ffa97124f Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Fri, 15 Sep 2023 13:20:04 +0200 Subject: [PATCH 09/14] remove unnecessary arguments, since subclasses already define these --- databooks/data_models/notebook.py | 3 --- tests/test_cli.py | 6 ------ tests/test_data_models/test_notebook.py | 12 ------------ 3 files changed, 21 deletions(-) diff --git a/databooks/data_models/notebook.py b/databooks/data_models/notebook.py index 60a3f554..d4c63dc3 100644 --- a/databooks/data_models/notebook.py +++ b/databooks/data_models/notebook.py @@ -141,19 +141,16 @@ def wrap_git( MarkdownCell( metadata=CellMetadata(git_hash=hash_first), source=[f"`<<<<<<< {hash_first}`"], - cell_type="markdown", ), *first_cells, MarkdownCell( source=["`=======`"], - cell_type="markdown", metadata=CellMetadata(), ), *last_cells, MarkdownCell( metadata=CellMetadata(git_hash=hash_last), source=[f"`>>>>>>> {hash_last}`"], - cell_type="markdown", ), ] diff --git a/tests/test_cli.py b/tests/test_cli.py index c433a768..240d6ae1 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -292,18 +292,15 @@ def test_fix(tmp_path: Path) -> None: MarkdownCell( metadata=CellMetadata(git_hash=id_main), source=[f"`<<<<<<< {id_main}`"], - cell_type="markdown", ), MarkdownCell( source=["`=======`"], - cell_type="markdown", metadata=CellMetadata(), ), extra_cell, MarkdownCell( metadata=CellMetadata(git_hash=id_other), source=[f"`>>>>>>> {id_other}`"], - cell_type="markdown", ), ] @@ -375,18 +372,15 @@ def test_fix__config(tmp_path: Path) -> None: MarkdownCell( metadata=CellMetadata(git_hash=id_main), source=[f"`<<<<<<< {id_main}`"], - cell_type="markdown", ), MarkdownCell( source=["`=======`"], - cell_type="markdown", metadata=CellMetadata(), ), extra_cell, MarkdownCell( metadata=CellMetadata(git_hash=id_other), source=[f"`>>>>>>> {id_other}`"], - cell_type="markdown", ), ] diff --git a/tests/test_data_models/test_notebook.py b/tests/test_data_models/test_notebook.py index 6bf17475..e7a5839c 100644 --- a/tests/test_data_models/test_notebook.py +++ b/tests/test_data_models/test_notebook.py @@ -78,7 +78,6 @@ def cell_metadata(self) -> CellMetadata: def cell(self) -> CodeCell: """`CodeCell` property to test on.""" return CodeCell( - cell_type="code", metadata=self.cell_metadata, source=["test_source"], execution_count=1, @@ -112,7 +111,6 @@ def test_clear(self, caplog: LogCaptureFixture) -> None: logs = list(caplog.records) assert cell == CodeCell( - cell_type="code", metadata=CellMetadata(), outputs=CellOutputs([]), source=["test_source"], @@ -209,7 +207,6 @@ def test_notebook_sub(self) -> None: another_field_to_remove="another field", ) extra_cell = RawCell( - cell_type="raw", metadata=CellMetadata(random_meta=["meta"]), source="extra", ) @@ -232,18 +229,15 @@ def test_notebook_sub(self) -> None: MarkdownCell( metadata=CellMetadata(git_hash=None), source=["`<<<<<<< None`"], - cell_type="markdown", ), MarkdownCell( source=["`=======`"], - cell_type="markdown", metadata=CellMetadata(), ), extra_cell, MarkdownCell( metadata=CellMetadata(git_hash=None), source=["`>>>>>>> None`"], - cell_type="markdown", ), ] assert diff.resolve(keep_first_cells=None) == notebook @@ -284,13 +278,11 @@ def test_parse_file() -> None: MarkdownCell( metadata=CellMetadata(tags=[]), source=["# `databooks` demo!"], - cell_type="markdown", id="9adc7c77-95f1-4cb9-b987-1411e28f2976", ), CodeCell( metadata=CellMetadata(tags=["random-tag"]), source=["from random import random # cell with tags"], - cell_type="code", outputs=[], execution_count=1, id="6a6eafec-a799-455b-8c1b-fd43a0a1f3ca", @@ -298,7 +290,6 @@ def test_parse_file() -> None: CodeCell( metadata=CellMetadata(tags=[]), source=["random()"], - cell_type="code", outputs=[ { "data": {"text/plain": ["0.9995123767309688"]}, @@ -313,7 +304,6 @@ def test_parse_file() -> None: CodeCell( metadata=CellMetadata(), source=['print("notebooks + git ❤️")'], - cell_type="code", outputs=[ { "name": "stdout", @@ -327,7 +317,6 @@ def test_parse_file() -> None: CodeCell( metadata=CellMetadata(), source=["throw error"], - cell_type="code", outputs=[ { "ename": "SyntaxError", @@ -349,7 +338,6 @@ def test_parse_file() -> None: RawCell( metadata=CellMetadata(), source=["This is a raw cell! 🚀"], - cell_type="raw", id="b2cf154d-0d1d-44d1-9ab8-7ee4b3d37f12", ), ] From 9d3224c4aaf646a9f39e558a95a9714449a5325b Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Mon, 18 Sep 2023 13:19:30 +0200 Subject: [PATCH 10/14] Bump pydantic to latest version. Solve migration issues. Remove lots of custom code. --- .pre-commit-config.yaml | 4 +- databooks/data_models/base.py | 9 + databooks/data_models/cell.py | 13 +- databooks/data_models/notebook.py | 18 +- databooks/metadata.py | 3 + poetry.lock | 227 ++++++++++++------------ pyproject.toml | 2 +- tests/test_cli.py | 15 +- tests/test_data_models/test_notebook.py | 7 +- tests/test_metadata.py | 5 +- tests/test_tui.py | 1 + 11 files changed, 167 insertions(+), 137 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c5e1391a..6c62e791 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -33,7 +33,7 @@ repos: - types-all==1.0.0 - typer==0.3.2 - rich==10.16.2 - - pydantic==2.1.* + - pydantic==2.3.* - GitPython==3.1.26 - typing-extensions==4.6.* - tomli==2.0.1 @@ -55,7 +55,7 @@ repos: - typer-cli==0.0.12 - typer==0.3.2 - rich==10.16.2 - - pydantic==2.1 + - pydantic==2.3.* - GitPython==3.1.26 - typing-extensions==4.6.* - tomli==2.0.1 diff --git a/databooks/data_models/base.py b/databooks/data_models/base.py index 03ac00c3..4e48309a 100644 --- a/databooks/data_models/base.py +++ b/databooks/data_models/base.py @@ -113,8 +113,13 @@ def remove_fields( if recursive and isinstance(field_val, DatabooksBase): field_val.remove_fields(fields) elif field in d_model: + # import pdb + # pdb.set_trace() delattr(self, field) + # import pdb + # pdb.set_trace() + def __str__(self) -> str: """Return outputs of __repr__.""" return repr(self) @@ -136,6 +141,9 @@ def __sub__(self, other: DatabooksBase) -> DiffModel: self_d = dict(self) other_d = dict(other) + # import pdb + # pdb.set_trace() + # Build dict with {field: (type, value)} for each field fields_d: Dict[str, Any] = {} for name in self_d.keys() | other_d.keys(): @@ -158,4 +166,5 @@ def __sub__(self, other: DatabooksBase) -> DiffModel: is_diff=(bool, True), **fields_d, ) + return cast(DiffModel, DiffInstance()) # it'll be filled in with the defaults diff --git a/databooks/data_models/cell.py b/databooks/data_models/cell.py index d02943f8..91e4726a 100644 --- a/databooks/data_models/cell.py +++ b/databooks/data_models/cell.py @@ -238,7 +238,7 @@ def output_type_must_match(cls, v: str) -> str: ] -class CellOutputs(DatabooksBase, RootModel): +class CellOutputs(RootModel): """Outputs of notebook code cells.""" root: List[CellOutputType] @@ -256,17 +256,6 @@ def values( """Alias `root` with outputs for easy referencing.""" return self.root - # Before CellOutputs inherited from RootModel - # eq worked well (suppose covered by DatabooksBase, - # which inherits from Pydantic's BaseModel) - def __eq__(self: CellOutputs, other: object) -> bool: - """Comparison of different CellOutputs.""" - return ( - type(other) == CellOutputs - and self.root == other.root - and self.model_config == other.model_config - ) - class CodeCell(BaseCell): """Cell of type `code` - defined for rich displaying in terminal.""" diff --git a/databooks/data_models/notebook.py b/databooks/data_models/notebook.py index d4c63dc3..71fd0772 100644 --- a/databooks/data_models/notebook.py +++ b/databooks/data_models/notebook.py @@ -43,10 +43,6 @@ class Cells(RootModel[Sequence[T]], BaseCells[T]): root: Sequence[T] - def __eq__(self: Cells[T], other: object) -> bool: - """Compare different Cells.""" - return isinstance(other, Cells) and self.root == other.root - @property def data(self) -> List[T]: # type: ignore """Define property `data` required for `collections.UserList` class.""" @@ -81,6 +77,9 @@ def __sub__(self: Cells[Cell], other: Cells[Cell]) -> Cells[CellsPair]: " notebooks." ) + # import pdb + # pdb.set_trace() + return Cells[CellsPair]( [ # https://github.com/python/mypy/issues/9459 @@ -247,9 +246,14 @@ def parse_file(cls, path: Path | str, **parse_kwargs: Any) -> JupyterNotebook: raise ValueError( f"Value of `content_type` must be `json` (default), got `{content_arg}`" ) - return super(JupyterNotebook, cls).parse_file( - path=path, content_type="json", **parse_kwargs - ) + + with open(path, "r+") as file: + raw_json = file.read() + + # import pdb + # pdb.set_trace() + + return JupyterNotebook.model_validate_json(json_data=raw_json) def write( self, path: Path | str, overwrite: bool = False, **json_kwargs: Any diff --git a/databooks/metadata.py b/databooks/metadata.py index 514b9b40..98ca4b2a 100644 --- a/databooks/metadata.py +++ b/databooks/metadata.py @@ -60,6 +60,9 @@ def clear( ) nb_equals = notebook == JupyterNotebook.parse_file(read_path) + # import pdb + # pdb.set_trace() + if nb_equals or check: msg = ( "no metadata to remove." diff --git a/poetry.lock b/poetry.lock index 6d320595..95a9a790 100644 --- a/poetry.lock +++ b/poetry.lock @@ -737,18 +737,18 @@ virtualenv = ">=20.10.0" [[package]] name = "pydantic" -version = "2.1.1" +version = "2.3.0" description = "Data validation using Python type hints" optional = false python-versions = ">=3.7" files = [ - {file = "pydantic-2.1.1-py3-none-any.whl", hash = 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typing-extensions = "^4.0.1" diff --git a/tests/test_cli.py b/tests/test_cli.py index 240d6ae1..d536da37 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -92,6 +92,9 @@ def test_meta__check(tmp_path: Path, caplog: LogCaptureFixture) -> None: result = runner.invoke(app, ["meta", str(read_path), "--check"]) nb_write = JupyterNotebook.parse_file(path=read_path) + # import pdb + # pdb.set_trace() + logs = list(caplog.records) assert result.exit_code == 1 assert len(logs) == 1 @@ -105,7 +108,14 @@ def test_meta__check(tmp_path: Path, caplog: LogCaptureFixture) -> None: logs = list(caplog.records) + # import pdb + # pdb.set_trace() + assert result.exit_code == 0 + + # import pdb + # pdb.set_trace() + assert len(logs) == 4 assert logs[-1].message == "No unwanted metadata!" @@ -125,7 +135,7 @@ def test_meta__config(tmp_path: Path) -> None: assert result.exit_code == 0 assert nb_read != nb_write, "Notebook was not overwritten" - assert all(c.outputs == CellOutputs([]) for c in nb_write.cells) + assert all(c.outputs == CellOutputs(root=[]) for c in nb_write.cells) assert all(c.execution_count is not None for c in nb_write.cells) # Override config file arguments @@ -384,6 +394,9 @@ def test_fix__config(tmp_path: Path) -> None: ), ] + # import pdb + # pdb.set_trace() + assert fixed_notebook.cells == expected diff --git a/tests/test_data_models/test_notebook.py b/tests/test_data_models/test_notebook.py index e7a5839c..e896cddc 100644 --- a/tests/test_data_models/test_notebook.py +++ b/tests/test_data_models/test_notebook.py @@ -112,7 +112,7 @@ def test_clear(self, caplog: LogCaptureFixture) -> None: assert cell == CodeCell( metadata=CellMetadata(), - outputs=CellOutputs([]), + outputs=CellOutputs(root=[]), source=["test_source"], execution_count=None, ) @@ -179,7 +179,7 @@ def test_clear_metadata(self) -> None: assert all(cell.metadata == CellMetadata() for cell in notebook.cells) assert all( - cell.outputs == CellOutputs([]) + cell.outputs == CellOutputs(root=[]) for cell in notebook.cells if cell.cell_type == "code" ) @@ -220,6 +220,9 @@ def test_notebook_sub(self) -> None: **notebook_1.metadata.dict(), **{"tags": []} ) + # import pdb + # pdb.set_trace() + assert diff.resolve(keep_first_cells=True) == notebook notebook.cells = notebook_2.cells diff --git a/tests/test_metadata.py b/tests/test_metadata.py index eee2f27a..a94badb1 100644 --- a/tests/test_metadata.py +++ b/tests/test_metadata.py @@ -27,6 +27,9 @@ def test_metadata_clear__check_verbose( ) logs = list(caplog.records) + # import pdb + # pdb.set_trace() + assert ( JupyterNotebook.parse_file(path=read_path) == TestJupyterNotebook().jupyter_notebook @@ -60,7 +63,7 @@ def test_metadata_clear(tmp_path: Path) -> None: assert all( cell.outputs == CellOutputs( - [{"name": "stdout", "output_type": "stream", "text": ["test text\n"]}] + root=[{"name": "stdout", "output_type": "stream", "text": ["test text\n"]}] ) for cell in nb_write.cells if cell.cell_type == "code" diff --git a/tests/test_tui.py b/tests/test_tui.py index 706c7c1d..87a6f676 100644 --- a/tests/test_tui.py +++ b/tests/test_tui.py @@ -252,6 +252,7 @@ def test_multiple_diff_nb() -> None: notebook_2.cells = notebook_2.cells + [extra_cell, extra_cell, extra_cell] diff = notebook_1 - notebook_2 + assert render(diff) == dedent( """\ kernel_display_name another_kernel From bdc0fa5956f6eb68f12fc8a456aa55fd185ffcd1 Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Mon, 18 Sep 2023 13:20:41 +0200 Subject: [PATCH 11/14] cleanup --- databooks/data_models/base.py | 8 -------- databooks/data_models/notebook.py | 6 ------ databooks/metadata.py | 3 --- tests/test_cli.py | 13 ------------- tests/test_data_models/test_notebook.py | 3 --- tests/test_metadata.py | 3 --- 6 files changed, 36 deletions(-) diff --git a/databooks/data_models/base.py b/databooks/data_models/base.py index 4e48309a..ae362cef 100644 --- a/databooks/data_models/base.py +++ b/databooks/data_models/base.py @@ -113,13 +113,8 @@ def remove_fields( if recursive and isinstance(field_val, DatabooksBase): field_val.remove_fields(fields) elif field in d_model: - # import pdb - # pdb.set_trace() delattr(self, field) - # import pdb - # pdb.set_trace() - def __str__(self) -> str: """Return outputs of __repr__.""" return repr(self) @@ -141,9 +136,6 @@ def __sub__(self, other: DatabooksBase) -> DiffModel: self_d = dict(self) other_d = dict(other) - # import pdb - # pdb.set_trace() - # Build dict with {field: (type, value)} for each field fields_d: Dict[str, Any] = {} for name in self_d.keys() | other_d.keys(): diff --git a/databooks/data_models/notebook.py b/databooks/data_models/notebook.py index 71fd0772..495f2c35 100644 --- a/databooks/data_models/notebook.py +++ b/databooks/data_models/notebook.py @@ -77,9 +77,6 @@ def __sub__(self: Cells[Cell], other: Cells[Cell]) -> Cells[CellsPair]: " notebooks." ) - # import pdb - # pdb.set_trace() - return Cells[CellsPair]( [ # https://github.com/python/mypy/issues/9459 @@ -250,9 +247,6 @@ def parse_file(cls, path: Path | str, **parse_kwargs: Any) -> JupyterNotebook: with open(path, "r+") as file: raw_json = file.read() - # import pdb - # pdb.set_trace() - return JupyterNotebook.model_validate_json(json_data=raw_json) def write( diff --git a/databooks/metadata.py b/databooks/metadata.py index 98ca4b2a..514b9b40 100644 --- a/databooks/metadata.py +++ b/databooks/metadata.py @@ -60,9 +60,6 @@ def clear( ) nb_equals = notebook == JupyterNotebook.parse_file(read_path) - # import pdb - # pdb.set_trace() - if nb_equals or check: msg = ( "no metadata to remove." diff --git a/tests/test_cli.py b/tests/test_cli.py index d536da37..433e9154 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -92,9 +92,6 @@ def test_meta__check(tmp_path: Path, caplog: LogCaptureFixture) -> None: result = runner.invoke(app, ["meta", str(read_path), "--check"]) nb_write = JupyterNotebook.parse_file(path=read_path) - # import pdb - # pdb.set_trace() - logs = list(caplog.records) assert result.exit_code == 1 assert len(logs) == 1 @@ -108,14 +105,7 @@ def test_meta__check(tmp_path: Path, caplog: LogCaptureFixture) -> None: logs = list(caplog.records) - # import pdb - # pdb.set_trace() - assert result.exit_code == 0 - - # import pdb - # pdb.set_trace() - assert len(logs) == 4 assert logs[-1].message == "No unwanted metadata!" @@ -394,9 +384,6 @@ def test_fix__config(tmp_path: Path) -> None: ), ] - # import pdb - # pdb.set_trace() - assert fixed_notebook.cells == expected diff --git a/tests/test_data_models/test_notebook.py b/tests/test_data_models/test_notebook.py index e896cddc..7632e04a 100644 --- a/tests/test_data_models/test_notebook.py +++ b/tests/test_data_models/test_notebook.py @@ -220,9 +220,6 @@ def test_notebook_sub(self) -> None: **notebook_1.metadata.dict(), **{"tags": []} ) - # import pdb - # pdb.set_trace() - assert diff.resolve(keep_first_cells=True) == notebook notebook.cells = notebook_2.cells diff --git a/tests/test_metadata.py b/tests/test_metadata.py index a94badb1..15b7e0b6 100644 --- a/tests/test_metadata.py +++ b/tests/test_metadata.py @@ -27,9 +27,6 @@ def test_metadata_clear__check_verbose( ) logs = list(caplog.records) - # import pdb - # pdb.set_trace() - assert ( JupyterNotebook.parse_file(path=read_path) == TestJupyterNotebook().jupyter_notebook From 9eb4956ea4067abb769aabd1dc57f6c6402ac833 Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Mon, 18 Sep 2023 13:21:52 +0200 Subject: [PATCH 12/14] remove explicit root argument mentioning, not needed for root models --- tests/test_cli.py | 2 +- tests/test_data_models/test_notebook.py | 4 ++-- tests/test_metadata.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_cli.py b/tests/test_cli.py index 433e9154..240d6ae1 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -125,7 +125,7 @@ def test_meta__config(tmp_path: Path) -> None: assert result.exit_code == 0 assert nb_read != nb_write, "Notebook was not overwritten" - assert all(c.outputs == CellOutputs(root=[]) for c in nb_write.cells) + assert all(c.outputs == CellOutputs([]) for c in nb_write.cells) assert all(c.execution_count is not None for c in nb_write.cells) # Override config file arguments diff --git a/tests/test_data_models/test_notebook.py b/tests/test_data_models/test_notebook.py index 7632e04a..e7a5839c 100644 --- a/tests/test_data_models/test_notebook.py +++ b/tests/test_data_models/test_notebook.py @@ -112,7 +112,7 @@ def test_clear(self, caplog: LogCaptureFixture) -> None: assert cell == CodeCell( metadata=CellMetadata(), - outputs=CellOutputs(root=[]), + outputs=CellOutputs([]), source=["test_source"], execution_count=None, ) @@ -179,7 +179,7 @@ def test_clear_metadata(self) -> None: assert all(cell.metadata == CellMetadata() for cell in notebook.cells) assert all( - cell.outputs == CellOutputs(root=[]) + cell.outputs == CellOutputs([]) for cell in notebook.cells if cell.cell_type == "code" ) diff --git a/tests/test_metadata.py b/tests/test_metadata.py index 15b7e0b6..eee2f27a 100644 --- a/tests/test_metadata.py +++ b/tests/test_metadata.py @@ -60,7 +60,7 @@ def test_metadata_clear(tmp_path: Path) -> None: assert all( cell.outputs == CellOutputs( - root=[{"name": "stdout", "output_type": "stream", "text": ["test text\n"]}] + [{"name": "stdout", "output_type": "stream", "text": ["test text\n"]}] ) for cell in nb_write.cells if cell.cell_type == "code" From 87e9e1cee1f067193acadb389d2371a75819f70f Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Mon, 18 Sep 2023 14:52:44 +0200 Subject: [PATCH 13/14] change pydantic to latest available version --- poetry.lock | 2 +- pyproject.toml | 2 +- tests/test_tui.py | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 95a9a790..3ce9968b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1295,4 +1295,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more [metadata] lock-version = "2.0" python-versions = "^3.7" -content-hash = "35d4397ac75605b366a39e9e2dcb5919f54c295ace439b8b3f0dd14247953f1c" +content-hash = "5cf684ae46bd56de0cd75b5d65497068cdc950df1a0477450f71f26e7e035ffd" diff --git a/pyproject.toml b/pyproject.toml index 928c7451..aba22e30 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ databooks = "databooks.cli:app" python = "^3.7" typer = ">=0.4.0,<1.0.0" rich = "^12.6.0" -pydantic = "^2.2" +pydantic = "^2.3" GitPython = "^3.1.24" tomli = "^2.0.1" typing-extensions = "^4.0.1" diff --git a/tests/test_tui.py b/tests/test_tui.py index 87a6f676..706c7c1d 100644 --- a/tests/test_tui.py +++ b/tests/test_tui.py @@ -252,7 +252,6 @@ def test_multiple_diff_nb() -> None: notebook_2.cells = notebook_2.cells + [extra_cell, extra_cell, extra_cell] diff = notebook_1 - notebook_2 - assert render(diff) == dedent( """\ kernel_display_name another_kernel From 7aa698b794ebb111f8d10246b630ac2dbc3b3311 Mon Sep 17 00:00:00 2001 From: Lukas Valatka Date: Tue, 19 Sep 2023 13:14:27 +0200 Subject: [PATCH 14/14] use path for ingesting file contents for conciseness --- databooks/data_models/notebook.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/databooks/data_models/notebook.py b/databooks/data_models/notebook.py index 495f2c35..d9c4cdf3 100644 --- a/databooks/data_models/notebook.py +++ b/databooks/data_models/notebook.py @@ -244,10 +244,8 @@ def parse_file(cls, path: Path | str, **parse_kwargs: Any) -> JupyterNotebook: f"Value of `content_type` must be `json` (default), got `{content_arg}`" ) - with open(path, "r+") as file: - raw_json = file.read() - - return JupyterNotebook.model_validate_json(json_data=raw_json) + path = Path(path) if not isinstance(path, Path) else path + return JupyterNotebook.model_validate_json(json_data=path.read_text()) def write( self, path: Path | str, overwrite: bool = False, **json_kwargs: Any