From ae9e98bf3013b684cbd8c4e9081583f8e0fa18a4 Mon Sep 17 00:00:00 2001 From: Tim Band Date: Mon, 19 Jan 2026 11:16:33 +0000 Subject: [PATCH 01/16] New Overview page Mermaid diagrams can be embedded in docs Table CSS fixed --- .gitignore | 1 + docs/source/_static/custom.css | 5 + docs/source/conf.py | 4 + docs/source/index.rst | 2 + docs/source/introduction.rst | 18 +- docs/source/overview.rst | 256 ++++ poetry.lock | 2134 ++++++++++++++++++-------------- pyproject.toml | 11 +- 8 files changed, 1494 insertions(+), 937 deletions(-) create mode 100644 docs/source/_static/custom.css create mode 100644 docs/source/overview.rst diff --git a/.gitignore b/.gitignore index e35ed4f..09b9232 100644 --- a/.gitignore +++ b/.gitignore @@ -138,6 +138,7 @@ datafaker/config.ini # sphinx docs/build/* +docs/esbonio-build/* docs/temp/* # vim swap files diff --git a/docs/source/_static/custom.css b/docs/source/_static/custom.css new file mode 100644 index 0000000..9cd5016 --- /dev/null +++ b/docs/source/_static/custom.css @@ -0,0 +1,5 @@ +/* Fix for sphinx_rtd_theme's tables, which do not allow line breaks by default */ +.wy-table-responsive table td, +.wy-table-responsive table th { + white-space: normal; +} diff --git a/docs/source/conf.py b/docs/source/conf.py index 63233e5..2dd3fbd 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -29,6 +29,7 @@ "sphinx.ext.autosummary", "sphinx_rtd_theme", "sphinx.ext.napoleon", + "sphinxcontrib.mermaid", ] autodoc_mock_imports: list[str] = ["typer", "pydantic", "sqlalchemy"] @@ -41,3 +42,6 @@ html_theme = "sphinx_rtd_theme" # pylint: disable=C0103 html_static_path = ["_static"] + +def setup(app): + app.add_css_file("custom.css") diff --git a/docs/source/index.rst b/docs/source/index.rst index d2fc566..2ce1e0e 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -21,6 +21,7 @@ Contents: :glob: :maxdepth: 2 + overview installation docker quickstart @@ -29,6 +30,7 @@ Contents: loan_data health_data configuration + custom_generators api faq glossary diff --git a/docs/source/introduction.rst b/docs/source/introduction.rst index 8cf833a..2017628 100644 --- a/docs/source/introduction.rst +++ b/docs/source/introduction.rst @@ -210,18 +210,20 @@ So let us find these sections in ``config.yaml`` and change ``vocabulary_table: (deleting the other properties if you like): .. code-block:: yaml - category: - vocabulary_table: true - city: - vocabulary_table: true - country: - vocabulary_table: true + + category: + vocabulary_table: true + city: + vocabulary_table: true + country: + vocabulary_table: true and later (although it doesn't matter if you re-arrange the table blocks): .. code-block:: yaml - language: - vocabulary_table: true + + language: + vocabulary_table: true and now we take this file into the private network (or pretend to) and run (in the private network with ``SRC_DSN`` and ``SRC_SCHEMA`` set as above): diff --git a/docs/source/overview.rst b/docs/source/overview.rst new file mode 100644 index 0000000..cf1283e --- /dev/null +++ b/docs/source/overview.rst @@ -0,0 +1,256 @@ +================== +Datafaker Overview +================== + +Datafaker provides a way to create a fake version of sensitive data. + +Datafaker's workflow permits Information Governance oversight by design. + +Background +========== + +Conceptually, any faking of sensitive data achieves privacy through one or both of two mechanisms: +Reducing the real data down to summaries, and obfuscating the data by adding noise. + +After these privacy-preserving steps, reproducing a fake version of the full steps +involves adding noise to the summary data to turn it back into data with the +required structure and volume. We can call these stages Reduce, Obfuscate, +Repopulate. + +.. mermaid:: + :alt: Generic synthetic data flow + + block-beta + columns 1 + Source["Sensitive Data"] + block:Arrow1 + ArrowNote1(["Remove Personally\nIdentifiable Data\n/ summarize / other removal"]) + Summary<["Reduce"]>(down) + end + block:Intermediate1 + ReducedNote(["This data is less sensitive"]) + Reduced["Reduced data / summaries"] + end + block:Arrow2 + ArrowNote2(["Adding noise"]) + Obfuscation<["Obfuscate"]>(down) + end + block:Intermediate2 + ObfuscatedNote(["This data is even\nless sensitive"]) + Obfuscated("Obfuscated\nReduced data") + end + block:Arrow3 + ArrowNote3(["Replacing removed data\nbased on summaries"]) + Repopulation<["Repopulate"]>(down) + end + Destination["Synthetic Data"] + classDef nobox fill:#fff,stroke-width:0px; + class Intermediate1 nobox + class Intermediate2 nobox + class Arrow1 nobox + class Arrow2 nobox + class Arrow3 nobox + classDef note fill:#18c; + class ArrowNote1 note + class ArrowNote2 note + class ArrowNote3 note + class ReducedNote note + class ObfuscatedNote note + +In this diagram, Reduce and Obfuscate take place in a private environment such as +a Trusted Research Environment or some machine on a private network from which +the sensitive data can be read. Information Governance oversight happens at the end +of this process to decide if this obfucated summary can be released out of the private +network. + +The Repopulate process happens outside of the private network and outside of the remit +of Information Governance. This is important! The act of turning reduced +obfucated data into a larger quantity of randomized data is *not* a privacy-sheilding +process! By this time all the actual privacy-sheilding has already happened and +the Information Governance has already been applied. + +Reduction techniques +-------------------- + +Here are a few techniques that can be used to preserve privacy through data reduction. +Most Reduction techniques have a corresponding Repopulation technique +to add the missing data back into the synthetic data. + +.. list-table:: Reduction Techniques + :width: 100% + :widths: 10 30 20 + :header-rows: 1 + + * - Reduction technique + - Description + - Repopulation technique + * - Anonymization + - Removing Personally Identifiable Information (remembering what sort of information was removed and its format) + - Generation of Names/Addresses etcetera + * - Removal of unnecessary data + - Some data does not need to be supplied and so can be removed completely. + - None. + * - Summarization + - Extract the means, standard deviations and size of numeric data, the frequencies of categorical data, or other summary measures. + - Pick the new data from a suitable random distribution. + * - Low number suppression + - Removal of rare data, which could be used to infer the presence of certain individuals in the data set. + - None. + * - Grouping + - Gathering data into clusters and extracting summary data from each cluster. + - Picking new data by picking a cluster then picking from the appropriate random distribution. + +Each of these extracts less than the full information from the source, then +most of them replace the information left behind with generated information +(perhaps after an Obfuscation step). + +Differential Privacy +-------------------- + +One actual concrete method of faking data is to apply a process such as Differential +Privacy to the real data without summarizing. In such a case Information Governance +cannot be expected to examine the data for privacy breaches as there is the same +amount of data to examine as in the real database, and breaches are likely to be +more subtle than real names being produced; in this case Information Governance +would have to understand and trust the obfucation process. + +In the US, The National Institute for Science and Technology has some +`guidelines `_ +about the use of Differential Privacy but even that is at a loss to explain how to +understand its main parameter: + + Selecting privacy loss parameters, such as ε, is challenging, + and we offer no specific guidelines on their selection. + +So Differential Privacy can be useful, but it is very hard to quantify exactly +how much good it is doing to preserve privacy. + +Differential Privacy is an Obfuscation technique rather than a Reduction technique +because the same amount of data is output as was input. + +Datafaker's Operation +===================== + +Datafaker is based on the Alan Turing Institute's SqlSynthGen tool. +SqlSynthGen implements all three operations of Reduce, Obfuscate and Repopulate. + +Datafaker builds on SqlSynthGen by automating the specification of the Reduce +operation and making the dataflow clearer for Information Governance purposes +(amongst other improvements). Datafaker still retains SqlSynthGen's Obfuscation +by Differential Privacy functionality, but this has not yet been folded into the +automation and will not be described further here: we are relying on the +Reduce operation to provide privacy shielding. + +Datafaker has a number of phases of operation; below we describe how +these map to the Reduce, Obfuscate and Repopulate stages described above. + +.. mermaid:: + :alt: Simplified diagram of Datafaker's data flow + + block-beta + columns 1 + Source["Sensitive Data"] + block:Processing + columns 4 + Arrow1<["Extract\nstructure"]>(down) + Arrow2<["User guided\nconfiguration"]>(down) + Arrow3<["Extract\nsummary"]>(down) + Arrow4<["Extract\nvocabulary"]>(down) + Orm["orm.yaml\nstructure\ndefinition"] + Config["config.yaml\nconfiguration\nof summarization"] + SrcStats["src-stats.yaml\nSummary\nstatistics"] + Vocab["Vocabulary\ntable data"] + end + Arrow5<["Information Governance\npermits release"]>(down) + block:Release + columns 1 + Arrow6<["Repopulation"]>(down) + Destination["Synthetic Data"] + end + classDef nobox fill:#fff,stroke-width:0px; + class Processing nobox + classDef publicnet fill:#18c; + class Release publicnet + +Datafaker make-tables phase +--------------------------- + +``datafaker make-tables`` makes a file called ``orm.yaml`` that describes the structure of the source database. +This is part of the Reduce phase, but this file is used in every other Datafaker phase. +By describing the structure of the database, no private data is leaked. +However it is not impossible that, in describing the structure of some commercial +database, some commercially-sensitive information could be leaked. +In such a case, the file is alterable by hand as long as the YAML structure is maintained. + +Datafaker configuration phase +----------------------------- + +These commands are not really part of the Reduce phase, but allow the user to configure +what the Reduce phase will entail (and hence also what the Repopulate phase will entail). + +- ``datafaker configure-tables`` makes a file called ``config.yaml`` that describes what needs to happen to each table. +- ``datafaker configure-generators`` amends ``config.yaml`` with information on what happens to each column. +- ``datafaker configure-missingness`` optionally amends ``config.yaml`` with simple summary missingness information, + +Additional configuration can be applied by hand at this point to allow more sophisticated Repopulation to happen than the automated generation can manage. + +``config.yaml`` contains data that has been set by a user that has seen the contents of the database, +but should not contain any sensitive data as Datafaker has not written any of the data (or summaries thereof) +into the file. + +``config.yaml`` also contains human-readable descriptions of the summaries that will be produced, +but these will be copied into the summary file produced in the following stage, next to the actual summary data. + +Datafaker summary stats phase +----------------------------- + +``datafaker make-stats`` makes a file called ``src-stats.yaml``. This contains the summary data from the source database. + +Information Governance should be focused on ensuring that private data is not leaking out in this file. + +Obfuscation happens in this phase if it is configured; therefore this command represents +most of the Reduce and all of the Obfuscate phase. + +Once these files, ``orm.yaml``, ``config.yaml`` and ``make-stats.yaml`` have been examined and approved for release, +we can move to the next phase. + +Datafaker make-vocab phase +-------------------------- + +``datafaker make-vocab`` makes a whole set of ``.yaml`` or ``.yaml.gz`` files, +each of which represents the entire contents of one table in the source database. + +The idea is that some tables will never contain sensitive data, +they might describe, for example, all the care centres that +are referenced in the database, or all the set of all possible +deseases that might be diagnosed (not who has such a diagnosis +or even if anybody has). Such tables are referred to as +Vocabulary tables. + +Which tables are represented is configured by the ``configure-tables`` command, +so the user must be careful not to configure any tables containing sensitive +data as Vocabulary tables. + +Releasing the intermediate data +------------------------------- + +These files -- ``orm.yaml``, ``config.yaml``, the vocabulary files and especially +the ``src-stats.yaml`` file -- now need to have Information Governance +processes applied to them as it is these files that can be extracted from the +private network or Trusted Research Environment to allow the construction of +the synthetic data in a less sensitive computing environment, if required. + +The sensitive database is no longer required in Datafaker's operation. + +Datafaker Repopulate phase +-------------------------- + +- ``datafaker create-tables`` creates the structure of the destination database to match (as much as is requested) the structure of the source database +- ``datafaker create-generators`` creates Python code files that will actually generate the data (this phase might be removed in a future version of Datafaker) +- ``datafaker create-data`` writes fake data into the destination database. + +As these operations require no access to the sensitive data, this phase can be +distributed to anybody that wants to make their own fake data in their own +database should we want to allow that. This could allow them to make +larger or smaller similar databases, or tweak the generated data with +the results of their own simulations in order to test their own analyses. diff --git a/poetry.lock b/poetry.lock index d42dabf..f94e1f5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -34,13 +34,13 @@ files = [ [[package]] name = "astroid" -version = "3.3.10" +version = "3.3.11" description = "An abstract syntax tree for Python with inference support." optional = false python-versions = ">=3.9.0" files = [ - {file = "astroid-3.3.10-py3-none-any.whl", hash = "sha256:104fb9cb9b27ea95e847a94c003be03a9e039334a8ebca5ee27dafaf5c5711eb"}, - {file = "astroid-3.3.10.tar.gz", hash = "sha256:c332157953060c6deb9caa57303ae0d20b0fbdb2e59b4a4f2a6ba49d0a7961ce"}, + {file = "astroid-3.3.11-py3-none-any.whl", hash = "sha256:54c760ae8322ece1abd213057c4b5bba7c49818853fc901ef09719a60dbf9dec"}, + {file = "astroid-3.3.11.tar.gz", hash = "sha256:1e5a5011af2920c7c67a53f65d536d65bfa7116feeaf2354d8b94f29573bb0ce"}, ] [package.dependencies] @@ -125,23 +125,15 @@ test = ["distro (>=1.9.0,<1.10.0)", "flake8 (>=6.1,<7.0)", "flake8-pyi (>=24.1.0 [[package]] name = "attrs" -version = "25.3.0" +version = "25.4.0" description = "Classes Without Boilerplate" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "attrs-25.3.0-py3-none-any.whl", hash = "sha256:427318ce031701fea540783410126f03899a97ffc6f61596ad581ac2e40e3bc3"}, - {file = "attrs-25.3.0.tar.gz", hash = "sha256:75d7cefc7fb576747b2c81b4442d4d4a1ce0900973527c011d1030fd3bf4af1b"}, + {file = "attrs-25.4.0-py3-none-any.whl", hash = "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373"}, + {file = "attrs-25.4.0.tar.gz", hash = "sha256:16d5969b87f0859ef33a48b35d55ac1be6e42ae49d5e853b597db70c35c57e11"}, ] -[package.extras] -benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier"] -tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] - [[package]] name = "babel" version = "2.17.0" @@ -204,125 +196,146 @@ uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "certifi" -version = "2025.4.26" +version = "2026.1.4" description = "Python package for providing Mozilla's CA Bundle." optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "certifi-2025.4.26-py3-none-any.whl", hash = "sha256:30350364dfe371162649852c63336a15c70c6510c2ad5015b21c2345311805f3"}, - {file = "certifi-2025.4.26.tar.gz", hash = "sha256:0a816057ea3cdefcef70270d2c515e4506bbc954f417fa5ade2021213bb8f0c6"}, + {file = "certifi-2026.1.4-py3-none-any.whl", hash = "sha256:9943707519e4add1115f44c2bc244f782c0249876bf51b6599fee1ffbedd685c"}, + {file = "certifi-2026.1.4.tar.gz", hash = "sha256:ac726dd470482006e014ad384921ed6438c457018f4b3d204aea4281258b2120"}, ] [[package]] name = "cfgv" -version = "3.4.0" +version = "3.5.0" description = "Validate configuration and produce human readable error messages." optional = false -python-versions = ">=3.8" +python-versions = ">=3.10" files = [ - {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, - {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, + {file = "cfgv-3.5.0-py2.py3-none-any.whl", hash = "sha256:a8dc6b26ad22ff227d2634a65cb388215ce6cc96bbcc5cfde7641ae87e8dacc0"}, + {file = "cfgv-3.5.0.tar.gz", hash = "sha256:d5b1034354820651caa73ede66a6294d6e95c1b00acc5e9b098e917404669132"}, ] [[package]] name = "charset-normalizer" -version = "3.4.2" +version = "3.4.4" description = "The Real First Universal Charset Detector. 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true} smartnoise-sql = "^1" jinja2 = "^3.1.2" black = "^23.3.0" @@ -48,12 +46,15 @@ rstcheck-core = {extras = ["sphinx"], version = "^1.0.3"} json-schema-for-humans = "^1.3.4" pre-commit = "^3.3.3" testing-postgresql = "^1.3.0" +sphinx-rtd-theme = "^1.2.0" +sphinxcontrib-napoleon = "^0.7" +sphinxcontrib-mermaid = "^2.0.0" [tool.poetry.group.extras.dependencies] tqdm = "^4.65.0" [tool.poetry.extras] -docs = ["sphinx-rtd-theme", "sphinxcontrib-napoleon"] +docs = ["sphinx-rtd-theme", "sphinxcontrib-napoleon", "sphinxcontrib-mermaid"] [build-system] requires = ["poetry-core"] @@ -64,3 +65,7 @@ datafaker = "datafaker.main:app" [tool.isort] profile = "black" + +[tool.esbonio.sphinx] +buildCommand = ["sphinx-build", "-b", "html", "docs/source", "docs/esbonio-build"] +pythonCommand = ["poetry", "run", "python"] From a926d62cb161781888cb89f99946c479d1091833 Mon Sep 17 00:00:00 2001 From: Tim Band Date: Mon, 19 Jan 2026 13:20:48 +0000 Subject: [PATCH 02/16] First attempt at a documentation publishing workflow --- .github/workflows/docs.yml | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 .github/workflows/docs.yml diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..324d9e1 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,35 @@ +--- +name: publish documentation +on: {} +env: + PYTHON_VERSION: "3.12" +jobs: + docs: + runs-on: ubuntu-latest + steps: + - name: Checkout Code + uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + - name: Install poetry + shell: bash + run: | + sudo apt install python3-poetry + - name: Configure poetry + shell: bash + run: | + python -m poetry config virtualenvs.in-project true + - name: Install dependencies + shell: bash + run: | + python -m poetry install --all-extras + - name: Build documentation + shell: bash + run: | + python -m poetry run -C docs make html + - name: Publish docs on github Pages + uses: peaceiris/actions-gh-pages@v3 + with: + publish_branch: gh-pages + github_token: $${{ secrets.GITHUB_TOKEN }} + publish_dir: docs/build + force_orphan: true From a5da98cffc078725bf2d042ceed7d534473df44e Mon Sep 17 00:00:00 2001 From: Tim Band Date: Mon, 19 Jan 2026 13:25:58 +0000 Subject: [PATCH 03/16] Manual dispatch of documentation publish action --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 324d9e1..827c711 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -1,6 +1,6 @@ --- name: publish documentation -on: {} +on: workflow_dispatch env: PYTHON_VERSION: "3.12" jobs: From efd51cfc09684a9fbbad83e70605f8008e4971e8 Mon Sep 17 00:00:00 2001 From: Tim Band Date: Mon, 19 Jan 2026 15:15:47 +0000 Subject: [PATCH 04/16] Add Mermaid to the RST lint test --- tests/test_rst.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tests/test_rst.py b/tests/test_rst.py index 1a57ed6..969d063 100644 --- a/tests/test_rst.py +++ b/tests/test_rst.py @@ -1,7 +1,9 @@ """Run the .rst linter via a unit test. The CLI does not allow errors to be disabled, but we can ignore them here.""" +from docutils.parsers.rst import directives from pathlib import Path +from sphinxcontrib.mermaid import Mermaid from typing import Any from unittest import TestCase @@ -29,6 +31,7 @@ def test_dir(self) -> None: """Run the linter on the docs/ directory.""" docs_path = Path("docs/") rst_files = docs_path.glob("**/*.rst") + directives.register_directive("mermaid", Mermaid) all_errors = [] for rst_file in rst_files: From e1ca81fb8c35dc22bae7746f76d726cfbd575d4c Mon Sep 17 00:00:00 2001 From: Tim Band Date: Mon, 19 Jan 2026 16:38:18 +0000 Subject: [PATCH 05/16] Cleaned the pre-commit --- docs/source/conf.py | 6 +++++- tests/test_providers.py | 6 +++--- tests/test_rst.py | 4 ++-- tests/utils.py | 10 +++++++++- 4 files changed, 19 insertions(+), 7 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 2dd3fbd..fc2643a 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -11,6 +11,8 @@ import pathlib import sys +from sphinx.application import Sphinx + sys.path.insert(0, pathlib.Path(__file__).parents[2].resolve().as_posix()) sys.path.insert(0, os.path.abspath("../..")) @@ -43,5 +45,7 @@ html_theme = "sphinx_rtd_theme" # pylint: disable=C0103 html_static_path = ["_static"] -def setup(app): + +def setup(app: Sphinx) -> None: + """Include our own CSS in rendered pages.""" app.add_css_file("custom.css") diff --git a/tests/test_providers.py b/tests/test_providers.py index cd88007..eab3b1a 100644 --- a/tests/test_providers.py +++ b/tests/test_providers.py @@ -2,7 +2,7 @@ import datetime as dt from typing import Any -from sqlalchemy import Column, Integer, Text, insert +from sqlalchemy import Column, Integer, MetaData, Text, insert from sqlalchemy.ext.declarative import declarative_base from datafaker import providers @@ -11,7 +11,7 @@ # pylint: disable=invalid-name Base = declarative_base() # pylint: enable=invalid-name -metadata = Base.metadata +metadata: MetaData = Base.metadata class Person(Base): # type: ignore @@ -42,7 +42,7 @@ class ColumnValueProviderTestCase(RequiresDBTestCase): def setUp(self) -> None: """Pre-test setup.""" super().setUp() - metadata.create_all(self.engine) + metadata.create_all(self.sync_engine) def test_column_value_present(self) -> None: """Test the key method.""" diff --git a/tests/test_rst.py b/tests/test_rst.py index 969d063..ee89b5b 100644 --- a/tests/test_rst.py +++ b/tests/test_rst.py @@ -1,13 +1,13 @@ """Run the .rst linter via a unit test. The CLI does not allow errors to be disabled, but we can ignore them here.""" -from docutils.parsers.rst import directives from pathlib import Path -from sphinxcontrib.mermaid import Mermaid from typing import Any from unittest import TestCase +from docutils.parsers.rst import directives from restructuredtext_lint import lint_file +from sphinxcontrib.mermaid import Mermaid def _level_to_string(level: int) -> str: diff --git a/tests/utils.py b/tests/utils.py index db9a458..b9d28ab 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -13,7 +13,7 @@ import testing.postgresql import yaml -from sqlalchemy.schema import MetaData +from sqlalchemy import Engine, MetaData from datafaker import settings from datafaker.create import create_db_data_into @@ -21,6 +21,7 @@ from datafaker.make import make_src_stats, make_table_generators, make_tables_file from datafaker.remove import remove_db_data_from from datafaker.utils import ( + MaybeAsyncEngine, T, create_db_engine, get_sync_engine, @@ -137,6 +138,13 @@ class RequiresDBTestCase(DatafakerTestCase): database_name: str | None = None Postgresql = None + def __init__(self, *args: Any, **kwargs: Any) -> None: + """Declare the types.""" + super().__init__(*args, **kwargs) + self.engine: MaybeAsyncEngine + self.sync_engine: Engine + self.metadata: MetaData + @classmethod def setUpClass(cls) -> None: cls.Postgresql = testing.postgresql.PostgresqlFactory(cache_initialized_db=True) From 471cd048cfd01764c27bcceff54e4290763d879d Mon Sep 17 00:00:00 2001 From: Tim Band Date: Mon, 19 Jan 2026 17:16:43 +0000 Subject: [PATCH 06/16] bump docs workflow --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 827c711..f5e7949 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -1,5 +1,5 @@ --- -name: publish documentation +name: Publish Documentation on: workflow_dispatch env: PYTHON_VERSION: "3.12" From d6e590e376033e567d09288bc50663b08d7d19a6 Mon Sep 17 00:00:00 2001 From: Tim Band Date: Mon, 19 Jan 2026 17:20:55 +0000 Subject: [PATCH 07/16] Another attempt to bump docs workflow --- .github/workflows/{docs.yml => pubdocs.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{docs.yml => pubdocs.yml} (100%) diff --git a/.github/workflows/docs.yml b/.github/workflows/pubdocs.yml similarity index 100% rename from .github/workflows/docs.yml rename to .github/workflows/pubdocs.yml From e288b22c0d02294105ec57804b1026a3a6aaea84 Mon Sep 17 00:00:00 2001 From: Tim Band Date: Mon, 19 Jan 2026 17:22:14 +0000 Subject: [PATCH 08/16] temporarily make document publish "push" as well --- .github/workflows/pubdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pubdocs.yml b/.github/workflows/pubdocs.yml index f5e7949..c7d99e4 100644 --- a/.github/workflows/pubdocs.yml +++ b/.github/workflows/pubdocs.yml @@ -1,6 +1,6 @@ --- name: Publish Documentation -on: workflow_dispatch +on: [workflow_dispatch, push] env: PYTHON_VERSION: "3.12" jobs: From 3ab1a074a36533f944174a1f7b0b16c253fed0ee Mon Sep 17 00:00:00 2001 From: Tim Band Date: Mon, 19 Jan 2026 17:40:24 +0000 Subject: [PATCH 09/16] Fix working directory for docs build --- .github/workflows/{pubdocs.yml => docs.yml} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename .github/workflows/{pubdocs.yml => docs.yml} (92%) diff --git a/.github/workflows/pubdocs.yml b/.github/workflows/docs.yml similarity index 92% rename from .github/workflows/pubdocs.yml rename to .github/workflows/docs.yml index c7d99e4..81ff1ef 100644 --- a/.github/workflows/pubdocs.yml +++ b/.github/workflows/docs.yml @@ -24,8 +24,9 @@ jobs: python -m poetry install --all-extras - name: Build documentation shell: bash + working-directory: ./docs run: | - python -m poetry run -C docs make html + python -m poetry run make html - name: Publish docs on github Pages uses: peaceiris/actions-gh-pages@v3 with: From c7799abd6a2585deb49273dc1e814c3d210cc2ef Mon Sep 17 00:00:00 2001 From: Tim Band Date: Mon, 19 Jan 2026 17:43:41 +0000 Subject: [PATCH 10/16] Fix github token expansion --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 81ff1ef..d0099b8 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -31,6 +31,6 @@ jobs: uses: peaceiris/actions-gh-pages@v3 with: publish_branch: gh-pages - github_token: $${{ secrets.GITHUB_TOKEN }} + github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: docs/build force_orphan: true From 8f3604ba40ac1d1d9b570d9bcc08dadb995345cc Mon Sep 17 00:00:00 2001 From: Tim Band Date: Mon, 19 Jan 2026 18:05:29 +0000 Subject: [PATCH 11/16] Cleaned docs build --- datafaker/create.py | 8 +++--- datafaker/main.py | 4 +-- datafaker/make.py | 40 +++++++++++++--------------- datafaker/providers.py | 60 +++++++++++++++++++++--------------------- datafaker/remove.py | 4 +-- datafaker/utils.py | 4 +-- 6 files changed, 58 insertions(+), 62 deletions(-) diff --git a/datafaker/create.py b/datafaker/create.py index 5cddeb2..68c9255 100644 --- a/datafaker/create.py +++ b/datafaker/create.py @@ -130,11 +130,11 @@ def create_db_data_into( Populate the database. :param sorted_tables: The table names to populate, sorted so that foreign - keys' targets are populated before the foreign keys themselves. + keys' targets are populated before the foreign keys themselves. :param table_generator_dict: A mapping of table names to the generators - used to make data for them. + used to make data for them. :param story_generator_list: A list of story generators to be run after the - table generators on each pass. + table generators on each pass. :param num_passes: Number of passes to perform. :param db_dsn: Connection string for the destination database. :param schema_name: Destination schema name. @@ -196,7 +196,7 @@ def table_name(self) -> str | None: Get the name of the current table. :return: The table name, or None if there are no more stories - to process. + to process. """ return self._table_name diff --git a/datafaker/main.py b/datafaker/main.py index 47f0888..ee468d5 100644 --- a/datafaker/main.py +++ b/datafaker/main.py @@ -78,9 +78,9 @@ def load_metadata_config( :param orm_file_name: The name of the file to load. :param config: The ``config.yaml`` file object. Ignored tables will be - excluded from the output. + excluded from the output. :return: A dict representing the ``orm.yaml`` file, with the tables - the ``config`` says to ignore removed. + the ``config`` says to ignore removed. """ with open(orm_file_name, encoding="utf-8") as orm_fh: meta_dict = yaml.load(orm_fh, yaml.Loader) diff --git a/datafaker/make.py b/datafaker/make.py index c89a02b..371c620 100644 --- a/datafaker/make.py +++ b/datafaker/make.py @@ -6,7 +6,7 @@ from datetime import datetime from pathlib import Path from types import TracebackType -from typing import Any, Callable, Final, Mapping, Optional, Sequence, Tuple, Type +from typing import Any, Callable, Final, Mapping, Optional, Sequence, Tuple, Type, Union import pandas as pd import snsql @@ -90,8 +90,8 @@ def make_column_choices( :param table_config: The ``tables`` part of ``config.yaml``. :return: A list of ``ColumnChoice`` objects; that is, descriptions of - functions and their arguments to call to reveal a list of columns that - should have values generated for them. + functions and their arguments to call to reveal a list of columns that + should have values generated for them. """ return [ ColumnChoice( @@ -125,7 +125,7 @@ class TableGeneratorInfo: column_choices: list[ColumnChoice] rows_per_pass: int row_gens: list[RowGeneratorInfo] = field(default_factory=list) - unique_constraints: Sequence[UniqueConstraint | _PrimaryConstraint] = field( + unique_constraints: Sequence[Union[UniqueConstraint, _PrimaryConstraint]] = field( default_factory=list ) @@ -286,7 +286,7 @@ def _integer_generator(column: Column) -> tuple[str, dict[str, str]]: :param column: The column to get the generator for. :return: A pair consisting of the name of a generator and its - arguments. + arguments. """ if not column.primary_key: return ("generic.numeric.integer_number", {}) @@ -423,7 +423,7 @@ def _get_generator_and_arguments(column: Column) -> tuple[str | None, dict[str, Get the generator and its arguments from the column type. :return: A tuple of a string representing the generator callable and a dict of - keyword arguments to supply to it. + keyword arguments to supply to it. """ generator_function = _get_generator_for_column(type(column.type)) @@ -437,12 +437,10 @@ def _get_provider_for_column(column: Column) -> Tuple[list[str], str, dict[str, """ Get a default Mimesis provider and its arguments for a SQL column type. - Args: - column: SQLAlchemy column object + :param column: SQLAlchemy column object - Returns: - Tuple[str, str, list[str]]: Tuple containing the variable names to assign to, - generator function and any generator arguments. + :return: Tuple[str, str, list[str]]: Tuple containing the variable names + to assign to, generator function and any generator arguments. """ variable_names: list[str] = [column.name] @@ -589,19 +587,17 @@ def make_table_generators( # pylint: disable=too-many-locals The orm and vocabulary YAML files must already have been generated (by make-tables and make-vocab). - Args: - metadata: database ORM - config: Configuration to control the generator creation. - orm_filename: "orm.yaml" file path so that the generator - file can load the MetaData object - config_filename: "config.yaml" file path so that the generator - file can load the MetaData object - src_stats_filename: A filename for where to read src stats from. + :param metadata: database ORM + :param config: Configuration to control the generator creation. + :param orm_filename: "orm.yaml" file path so that the generator + file can load the MetaData object + :param config_filename: "config.yaml" file path so that the generator + file can load the MetaData object + :param src_stats_filename: A filename for where to read src stats from. Optional, if `None` this feature will be skipped - overwrite_files: Whether to overwrite pre-existing vocabulary files + :param overwrite_files: Whether to overwrite pre-existing vocabulary files - Returns: - A string that is a valid Python module, once written to file. + :return: A string that is a valid Python module, once written to file. """ row_generator_module_name: str = config.get("row_generators_module", None) story_generator_module_name = config.get("story_generators_module", None) diff --git a/datafaker/providers.py b/datafaker/providers.py index 39a9d9a..f791345 100644 --- a/datafaker/providers.py +++ b/datafaker/providers.py @@ -249,12 +249,12 @@ def merge_with_constants( Merge a list of items with other items that must be placed at certain indices. :param constants_at: A map of indices to objects that must be placed at - those indices. + those indices. :param xs: Items that fill in the gaps left by ``constants_at``. :return: ``xs`` with ``constants_at`` inserted at the appropriate - points. If there are not enough elements in ``xs`` to fill in the gaps - in ``constants_at``, the elements of ``constants_at`` after the gap - are dropped. + points. If there are not enough elements in ``xs`` to fill in the gaps + in ``constants_at``, the elements of ``constants_at`` after the gap + are dropped. """ outi = 0 xi = 0 @@ -344,7 +344,7 @@ def choice(self, a: list[Mapping[str, T]]) -> T | None: Choose a value with equal probability. :param a: The list of values to output. Each element is a mapping with - a key ``value`` and the key is the value to return. + a key ``value`` and the key is the value to return. :return: The chosen value. """ return self.choice_direct(a).get("value", None) @@ -371,8 +371,8 @@ def zipf_choice(self, a: list[Mapping[str, T]], n: int | None = None) -> T | Non 1/n times as frequently as the first value is chosen. :param a: The list of rows to choose between, most frequent first. - Each element is a mapping with a key ``value`` and the key is the - value to return. + Each element is a mapping with a key ``value`` and the key is the + value to return. :return: The chosen value. """ c = self.zipf_choice_direct(a, n) @@ -383,8 +383,8 @@ def weighted_choice(self, a: list[dict[str, Any]]) -> Any: Choice weighted by the count in the original dataset. :param a: a list of dicts, each with a ``value`` key - holding the value to be returned and a ``count`` key holding the - number of that value found in the original dataset + holding the value to be returned and a ``count`` key holding the + number of that value found in the original dataset :return: The chosen ``value``. """ vs = [] @@ -406,9 +406,9 @@ def multivariate_normal_np(self, cov: dict[str, Any]) -> np.typing.NDArray: Return an array of values chosen from the given covariates. :param cov: Keys are ``rank``: The number of values to output; - ``mN``: The mean of variable ``N`` (where ``N`` is between 0 and - one less than ``rank``). ``cN_M`` (where 0 < ``N`` <= ``M`` < ``rank``): - the covariance between the ``N``th and the ``M``th variables. + ``mN``: The mean of variable ``N`` (where ``N`` is between 0 and + one less than ``rank``). ``cN_M`` (where 0 < ``N`` <= ``M`` < ``rank``): + the covariance between the ``N``\th and the ``M``\th variables. :return: A numpy array of results. """ rank = int(cov["rank"]) @@ -473,10 +473,10 @@ def multivariate_normal(self, cov: dict[str, Any]) -> list[float]: Produce a list of values pulled from a multivariate distribution. :param cov: A dict with various keys: ``rank`` is the number of - output values, ``m0``, ``m1``, ... are the means of the - distributions (``rank`` of them). ``c0_0``, ``c0_1``, ``c1_1``, ... - are the covariates, ``cN_M`` is the covariate of the ``N``th and - ``M``th varaibles, with 0 <= ``N`` <= ``M`` < ``rank``. + output values, ``m0``, ``m1``, ... are the means of the + distributions (``rank`` of them). ``c0_0``, ``c0_1``, ``c1_1``, ... + are the covariates, ``cN_M`` is the covariate of the ``N``\th and + ``M``\th varaibles, with 0 <= ``N`` <= ``M`` < ``rank``. :return: list of ``rank`` floating point values """ out: list[float] = self.multivariate_normal_np(cov).tolist() @@ -487,11 +487,11 @@ def multivariate_lognormal(self, cov: dict[str, Any]) -> list[float]: Produce a list of values pulled from a multivariate distribution. :param cov: A dict with various keys: ``rank`` is the number of - output values, ``m0``, ``m1``, ... are the means of the - distributions (``rank`` of them). ``c0_0``, ``c0_1``, ``c1_1``, ... - are the covariates, ``cN_M`` is the covariate of the ``N``th and - ``M``th varaibles, with 0 <= ``N`` <= ``M`` < ``rank``. These - are all the means and covariants of the logs of the data. + output values, ``m0``, ``m1``, ... are the means of the + distributions (``rank`` of them). ``c0_0``, ``c0_1``, ``c1_1``, ... + are the covariates, ``cN_M`` is the covariate of the ``N``\th and + ``M``\th varaibles, with 0 <= ``N`` <= ``M`` < ``rank``. These + are all the means and covariants of the logs of the data. :return: list of ``rank`` floating point values """ out: list[Any] = np.exp(self.multivariate_normal_np(cov)).tolist() @@ -528,13 +528,13 @@ def alternatives( Pick between other generators. :param alternative_configs: List of alternative generators. - Each alternative has the following keys: "count" -- a weight for - how often to use this alternative; "name" -- which generator - for this partition, for example "composite"; "params" -- the - parameters for this alternative. + Each alternative has the following keys: "count" -- a weight for + how often to use this alternative; "name" -- which generator + for this partition, for example "composite"; "params" -- the + parameters for this alternative. :param counts: A list of weights for each alternative. If None, the - "count" value of each alternative is used. Each count is a dict - with a "count" key. + "count" value of each alternative is used. Each count is a dict + with a "count" key. :return: list of values """ if counts is not None: @@ -560,12 +560,12 @@ def with_constants_at( Insert constants into the results of a different generator. :param constants_at: A dictionary of positions and objects to insert - into the return list at those positions. + into the return list at those positions. :param subgen: The name of the function to call to get the results - that will have the constants inserted into. + that will have the constants inserted into. :param params: Keyword arguments to the ``subgen`` function. :return: A list of results from calling ``subgen(**params)`` - with ``constants_at`` inserted in at the appropriate indices. + with ``constants_at`` inserted in at the appropriate indices. """ if subgen not in self.PERMITTED_SUBGENS: logger.error( diff --git a/datafaker/remove.py b/datafaker/remove.py index 3924cda..540a729 100644 --- a/datafaker/remove.py +++ b/datafaker/remove.py @@ -1,5 +1,5 @@ """Functions and classes to undo the operations in create.py.""" -from typing import Any, Mapping +from typing import Any, Mapping, Optional from sqlalchemy import MetaData, delete @@ -56,7 +56,7 @@ def remove_db_vocab( reinstate_vocab_foreign_key_constraints(metadata, meta_dict, config, dst_conn) -def remove_db_tables(metadata: MetaData | None) -> None: +def remove_db_tables(metadata: Optional[MetaData]) -> None: """Drop the tables in the destination schema.""" settings = get_settings() assert settings.dst_dsn, "Missing destination database settings" diff --git a/datafaker/utils.py b/datafaker/utils.py index 8bd21a7..01f9e24 100644 --- a/datafaker/utils.py +++ b/datafaker/utils.py @@ -488,7 +488,7 @@ def make_foreign_key_name(table_name: str, col_name: str) -> str: def remove_vocab_foreign_key_constraints( metadata: MetaData, config: Mapping[str, Any], - dst_engine: Connection | Engine, + dst_engine: Union[Connection, Engine], ) -> None: """ Remove the foreign key constraints from vocabulary tables. @@ -532,7 +532,7 @@ def reinstate_vocab_foreign_key_constraints( metadata: MetaData, meta_dict: Mapping[str, Any], config: Mapping[str, Any], - dst_engine: Connection | Engine, + dst_engine: Union[Connection, Engine], ) -> None: """ Put the removed foreign keys back into the destination database. From e253367cf282f730e903bd643e1cd64a070d8226 Mon Sep 17 00:00:00 2001 From: Tim Band Date: Tue, 20 Jan 2026 11:15:30 +0000 Subject: [PATCH 12/16] Fixed backslashes in docstrings --- datafaker/providers.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/datafaker/providers.py b/datafaker/providers.py index f791345..775a9f6 100644 --- a/datafaker/providers.py +++ b/datafaker/providers.py @@ -402,7 +402,7 @@ def constant(self, value: T) -> T: return value def multivariate_normal_np(self, cov: dict[str, Any]) -> np.typing.NDArray: - """ + r""" Return an array of values chosen from the given covariates. :param cov: Keys are ``rank``: The number of values to output; @@ -469,7 +469,7 @@ def _find_constants(self, result: dict[str, Any]) -> dict[int, Any]: } def multivariate_normal(self, cov: dict[str, Any]) -> list[float]: - """ + r""" Produce a list of values pulled from a multivariate distribution. :param cov: A dict with various keys: ``rank`` is the number of @@ -483,7 +483,7 @@ def multivariate_normal(self, cov: dict[str, Any]) -> list[float]: return out def multivariate_lognormal(self, cov: dict[str, Any]) -> list[float]: - """ + r""" Produce a list of values pulled from a multivariate distribution. :param cov: A dict with various keys: ``rank`` is the number of From e591a6449f57316da58cd3d7d7ce12e0e0cb30bf Mon Sep 17 00:00:00 2001 From: Tim Band Date: Tue, 20 Jan 2026 12:00:18 +0000 Subject: [PATCH 13/16] Docs publish warning removed --- .github/workflows/docs.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index d0099b8..c9bfbbc 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -10,6 +10,8 @@ jobs: - name: Checkout Code uses: actions/checkout@v4 - uses: actions/setup-python@v5 + with: + python-version: "${{ env.PYTHON_VERSION }}" - name: Install poetry shell: bash run: | From 647cb962b0bc2ef0a320a2db6b2ecdc09d250edd Mon Sep 17 00:00:00 2001 From: Tim Band Date: Tue, 20 Jan 2026 12:02:20 +0000 Subject: [PATCH 14/16] looks like Python shouldn't be invoked as a module --- .github/workflows/docs.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index c9bfbbc..72dde50 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -19,16 +19,16 @@ jobs: - name: Configure poetry shell: bash run: | - python -m poetry config virtualenvs.in-project true + poetry config virtualenvs.in-project true - name: Install dependencies shell: bash run: | - python -m poetry install --all-extras + poetry install --all-extras - name: Build documentation shell: bash working-directory: ./docs run: | - python -m poetry run make html + poetry run make html - name: Publish docs on github Pages uses: peaceiris/actions-gh-pages@v3 with: From cbd009782ad3058d7809428adedf863c9f03ceaf Mon Sep 17 00:00:00 2001 From: Tim Band Date: Tue, 20 Jan 2026 12:15:45 +0000 Subject: [PATCH 15/16] Deploy the built html dir --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 72dde50..ada5b87 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -34,5 +34,5 @@ jobs: with: publish_branch: gh-pages github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: docs/build + publish_dir: docs/build/html force_orphan: true From 821aa6c23fdf89ac1636dac3e2a75595f3a6a989 Mon Sep 17 00:00:00 2001 From: Tim Band Date: Tue, 20 Jan 2026 12:25:09 +0000 Subject: [PATCH 16/16] Not on push, only on workflow_dispatch Does this work? --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index ada5b87..5932112 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -1,6 +1,6 @@ --- name: Publish Documentation -on: [workflow_dispatch, push] +on: workflow_dispatch env: PYTHON_VERSION: "3.12" jobs: