pyannotators-patterns 0.5.123__tar.gz → 0.6.3__tar.gz

{pyannotators_patterns-0.5.123 → pyannotators_patterns-0.6.3}/.gitignore

@@ -129,3 +129,4 @@ dmypy.json
 .idea/
 .groovylintrc.json
 .emailNotif
+uv.lock

{pyannotators_patterns-0.5.123 → pyannotators_patterns-0.6.3}/.pre-commit-config.yaml

@@ -1,17 +1,14 @@
 repos:
--   repo: https://github.com/ambv/black
-    rev: 19.3b0
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.0
     hooks:
-    - id: black
-      language_version: python3.8
+    - id: ruff
+      args: [--fix]
+    - id: ruff-format
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.1.0
+    rev: v4.5.0
     hooks:
     - id: end-of-file-fixer
       exclude: '.bumpversion.cfg'
     - id: trailing-whitespace
       exclude: '.bumpversion.cfg'
--   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.7.9
-    hooks:
-    - id: flake8

{pyannotators_patterns-0.5.123 → pyannotators_patterns-0.6.3}/Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.8-slim-bookworm
+FROM python:3.12-slim-bookworm
 # Install prerequisites
 RUN apt-get update -y && \
     apt-get install -y \
@@ -11,9 +11,9 @@ RUN apt-get update -y && \
     apt-get update -y && \
     apt-get clean all -y
 
-# Enable Installing packages as root
-ENV FLIT_ROOT_INSTALL=1
+# Install uv
+RUN pip install uv
 
-# Add pyproject.toml + README.md for flit install
+# Add pyproject.toml + README.md for uv install
 ADD pyproject.toml pyproject.toml
 ADD README.md README.md

{pyannotators_patterns-0.5.123 → pyannotators_patterns-0.6.3}/Jenkinsfile

@@ -20,7 +20,7 @@ pipeline {
     JENKINS_UIDGID = '1004:1004'
 
     MAJOR_VERSION = '0'
-    MINOR_VERSION = '5'
+    MINOR_VERSION = '6'
   }
 
   stages {
@@ -58,7 +58,7 @@ pipeline {
         stage('Add credentials') {
           steps {
             script {
-              // Add password file for flit publishing
+              // Add password file for uv publishing
               sh "cp ${PATH_HOME}/.passwd-pypi .env"
             }
           }
@@ -73,6 +73,7 @@ pipeline {
               withCredentials([gitUsernamePassword(credentialsId: 'bitbucket-user', gitToolName: 'git-tool')]) {
                 sh 'git pull'
                 sh "echo '\"\"\"Annotator based on Presidio pattern recognizer\"\"\"' > src/pyannotators_patterns/__init__.py"
+                sh "echo '' >> src/pyannotators_patterns/__init__.py"
                 sh "echo '__version__ = \"${MAJOR_VERSION}.${MINOR_VERSION}.${BUILD_ID}\"' >> src/pyannotators_patterns/__init__.py"
                 sh 'git commit src/pyannotators_patterns/__init__.py -m "[Jenkins CI] Commit on version files" || echo "No changes to commit"'
                 sh 'git push'
@@ -103,13 +104,10 @@ pipeline {
       }
 
       stages {
-        stage('Install flit & flake8') {
+        stage('Install dependencies') {
           steps {
-            // remove any previous tox env
-            sh 'rm -rf .tox'
-            sh 'python -m pip install pip==22.0.3'
-            sh 'pip install --no-cache-dir flit==3.2.0 flake8==3.9.2 flakehell tox'
-            sh 'flit install'
+            sh 'pip install uv'
+            sh 'uv sync --extra test'
           }
         }
 
@@ -117,20 +115,20 @@ pipeline {
           steps {
             // remove any previous results.xml file
             sh "rm -f ${TEST_REPORT_DIR}/results.xml"
-            sh 'tox'
+            sh 'uv run ruff check .'
+            sh 'uv run ruff format --check .'
+            sh "uv run pytest --junit-xml=${TEST_REPORT_DIR}/results.xml"
           }
         }
 
         stage('Publish on PyPI') {
           environment {
-            FLIT_USERNAME = getUserName '.env'
-            FLIT_PASSWORD = getUserPass '.env'
+            UV_PUBLISH_USERNAME = getUserName '.env'
+            UV_PUBLISH_PASSWORD = getUserPass '.env'
           }
           steps {
             // remove any previous folder dist
             sh 'rm -rf dist'
-            // create (as root) folder dist
-            sh 'mkdir dist'
             // pull recent updates of file __init__.py
             withCredentials([gitUsernamePassword(credentialsId: 'bitbucket-user', gitToolName: 'git-tool')]) {
               sh 'git config --global pull.rebase false'
@@ -143,18 +141,16 @@ pipeline {
             sh "chown ${JENKINS_UIDGID} src/pyannotators_patterns/__init__.py"
             // get git status
             sh 'git status'
-            // publish on PyPI
+            // build and publish on PyPI
             sh '''
                export COMMIT_VERSION=$( cat src/pyannotators_patterns/__init__.py|grep version|cut -d '"' -f2|tr -s '[:blank:]' )
                export BUILD_VERSION="${MAJOR_VERSION}"."${MINOR_VERSION}"."${BUILD_ID}"
-               if [ "${COMMIT_VERSION}" = "${BUILD_VERSION}" ] ; then flit publish ; fi
+               if [ "${COMMIT_VERSION}" = "${BUILD_VERSION}" ] ; then uv build && uv publish ; fi
                '''
             // remove current folder dist
             sh 'rm -rf dist'
             // remove current folder .hypothesis
             sh 'rm -rf .hypothesis'
-            // remove current folder .tox
-            sh 'rm -rf .tox'
           }
         }
       }
@@ -239,7 +235,7 @@ pipeline {
   }
 }
 
-// return FLIT_USERNAME from given file
+// return UV_PUBLISH_USERNAME from given file (reads FLIT_USERNAME key)
 def getUserName(path) {
   def USERNAME = sh(
                  script: "grep FLIT_USERNAME ${path}|cut -d '=' -f2",
@@ -248,7 +244,7 @@ def getUserName(path) {
   return USERNAME
 }
 
-// return FLIT_PASSWORD from given file
+// return UV_PUBLISH_PASSWORD from given file (reads FLIT_PASSWORD key)
 def getUserPass(path) {
   def USERPASS = sh(
                  script: "grep FLIT_PASSWORD ${path}|cut -d '=' -f2",

pyannotators_patterns-0.6.3/MIGRATION.md

@@ -0,0 +1,166 @@
+# Migration to Python 3.12, Pydantic v2, and uv tooling
+
+This document describes the migration steps to perform on this project according to past experience. Please apply all these changes if they make sense.
+
+## 0. Initial setup
+- create a py312 git branch and switch to it
+- change pyenv local to pymultirole312
+- reset version in __init__.py to 0.6.0
+
+## 1. Build system: flit → hatchling/uv
+
+The build system was migrated from **flit** to **hatchling** with **uv** as the package manager.
+
+- `pyproject.toml`: rewritten from flit legacy format (`[tool.flit.metadata]`) to PEP 621
+  with `hatchling` backend and `[project]` table
+- Version read dynamically from `src/pyconverters_pyword/__init__.py` via `[tool.hatch.version]`
+- Entry point `pyconverters.plugins` moved from `[tool.flit.entrypoints]` to `[project.entry-points]`
+- Replaced `flit` commands with `uv build` and `uv publish`
+- Jenkinsfile updated to use `uv sync` and `uv build`/`uv publish`
+- Dockerfile updated to install `uv` via `COPY --from=ghcr.io/astral-sh/uv:latest`
+
+## 2. Python version: 3.8+ → 3.12
+
+- `requires-python` set to `>=3.12` in `pyproject.toml`
+- `Dockerfile` base image changed from `python:3.8-slim-bookworm` to `python:3.12-slim-bookworm`
+- `FLIT_ROOT_INSTALL=1` env var removed from Dockerfile (no longer needed)
+- Classifiers updated from `Python :: 3.8` to `Python :: 3.12`
+
+## 3. Pydantic v1 → v2
+
+Replaced deprecated Pydantic v1 APIs in `pyword.py` and `tests/test_pyword.py`:
+
+- `.json(exclude_none=True, exclude_unset=True, indent=2)` → `.model_dump_json(...)` in tests
+- `DocumentList(__root__=docs)` → `DocumentList(root=docs)` (Pydantic v2 `RootModel` API)
+- `Field(extra="internal"/"advanced")` → `Field(json_schema_extra={"extra": "..."})` in `pyword.py`
+- `params.dict()` → `params.model_dump()` in `pyword.py`
+
+## 4. Python 3.12 type modernization
+
+Leveraged Python 3.12 builtins and modern syntax (enforced by ruff `UP` rules):
+
+- `typing.List[Document]` → `list[Document]` (method signatures in `pyword.py` and tests)
+- `typing.Type[BaseModel]` → `type[BaseModel]` (`get_model` return type in `pyword.py`)
+- Removed unused `typing` imports: `List`, `Type`
+
+## 5. Linter: black + flake8 → ruff
+
+- Removed `black`, `flake8`, `pytest-flake8`, `pytest-black`, `flakehell` dependencies
+- Added `ruff` to `[project.optional-dependencies].test`
+- Removed `[tool.flakehell]` configuration block from `pyproject.toml`
+- Configured `[tool.ruff]` in `pyproject.toml`:
+  - `line-length = 120`
+  - `target-version = "py312"`
+  - Lint rules: `E`, `W`, `F`, `I`, `B`, `C4`, `UP`, `ARG`, `SIM`
+  - Format: double quotes, space indent
+- Updated `.pre-commit-config.yaml`: replaced `black` and `flake8` hooks with `ruff` and `ruff-format`
+
+### Running the linter
+
+```
+uv run ruff check .
+uv run ruff format --check .
+```
+
+To auto-fix formatting:
+
+```
+uv run ruff format .
+```
+
+## 6. Test runner: tox → uv
+
+**tox** was removed entirely. The project now uses `uv run` to execute tests and linting directly.
+
+### What changed
+
+- Deleted `tox.ini`
+- Removed `tox`, `flake8`, `pytest-flake8`, `pytest-black` from test dependencies
+- Moved pytest configuration from `tox.ini` to `pyproject.toml`:
+
+```toml
+[tool.pytest.ini_options]
+addopts = "--durations=5"
+norecursedirs = ["docs"]
+```
+
+### Running tests
+
+```
+uv run pytest
+```
+
+### Why tox was unnecessary
+
+- The project targets a single Python version (3.12)
+- `uv run` provides virtual environment isolation without the extra layer
+
+## 7. Documentation generation
+
+Sphinx is used for documentation with the `docs` optional dependency group.
+
+### Fix: added `lxml_html_clean` dependency
+
+The `jupyter_sphinx` extension requires `lxml_html_clean` (split from `lxml` in recent versions).
+This was added to `[project.optional-dependencies].docs`.
+
+### Generating docs
+
+```
+uv run --extra docs sphinx-build docs docs/_build
+```
+
+## 8. Jenkinsfile updates
+
+- `__init__.py` generation now includes a blank line between the docstring and `__version__`
+  to comply with `ruff format`
+- Set `__version__ = "0.6.0"`
+- In Jenkinsfile, set `MINOR_VERSION = "6"`
+- Install step changed from `flit install` to `uv sync --extra test`
+- Lint step added: `uv run ruff check .` + `uv run ruff format --check .`
+- Test step changed from `tox` to `uv run pytest --junit-xml=...`
+- Build/publish pipeline uses `uv build && uv publish` instead of `flit publish`
+- Credentials: Jenkinsfile helper functions still read `FLIT_USERNAME` and `FLIT_PASSWORD`
+  from `.passwd-pypi`, but expose them as `UV_PUBLISH_USERNAME` and `UV_PUBLISH_PASSWORD`
+  for `uv publish`
+- Removed `.tox` cleanup steps
+
+## 9. .gitignore updates
+
+Added the following entry:
+- `uv.lock` — generated lock file, not committed
+
+(`docs/_build/` was already present.)
+
+## 10. Dependency cleanup and upgrades
+
+### Removed unused dependencies
+
+- None
+
+### Upgraded pinned dependencies
+
+- `pymultirole-plugins>=0.5.0,<0.6.0` → `pymultirole-plugins>=0.6.0,<0.7.0`
+- update dependencies to latest versions if possible
+
+## 11. Starlette `UploadFile` API change
+
+The `UploadFile` constructor signature changed in recent Starlette versions:
+
+**Before (old API):**
+```python
+UploadFile(filename, file, content_type)  # positional args
+```
+
+**After (new API):**
+```python
+UploadFile(file=..., filename=..., headers=Headers({"content-type": "..."}))
+```
+
+Updated in `tests/test_pyword.py` and added `Headers` import from `starlette.datastructures`.
+
+## 12. Additional unit tests
+
+- Analyze src directory and extended `tests/` with tests covering previously untested behaviour
+
+## 13. Update README.md

pyannotators_patterns-0.6.3/PKG-INFO

@@ -0,0 +1,129 @@
+Metadata-Version: 2.4
+Name: pyannotators-patterns
+Version: 0.6.3
+Summary: Annotator based on Presidio pattern recognizer
+Project-URL: Homepage, https://github.com/oterrier/pyannotators_patterns/
+Author-email: Olivier Terrier <olivier.terrier@kairntech.com>
+License: The MIT License (MIT)
+        
+        Copyright (c) 2021 Olivier Terrier
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in
+        all copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+        THE SOFTWARE.
+License-File: AUTHORS.md
+License-File: LICENSE
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Information Technology
+Classifier: Intended Audience :: System Administrators
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development :: Libraries :: Application Frameworks
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.12
+Requires-Dist: collections-extended
+Requires-Dist: log-with-context
+Requires-Dist: presidio-analyzer>=2.2.354
+Requires-Dist: pymultirole-plugins<0.7.0,>=0.6.0
+Requires-Dist: spacy[lookups]>=3.7.0
+Requires-Dist: tldextract>=5.1.2
+Requires-Dist: unidecode
+Provides-Extra: dev
+Requires-Dist: bump2version; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: jupyter-sphinx; extra == 'docs'
+Requires-Dist: lxml-html-clean; extra == 'docs'
+Requires-Dist: m2r2; extra == 'docs'
+Requires-Dist: sphinx; extra == 'docs'
+Requires-Dist: sphinx-rtd-theme; extra == 'docs'
+Requires-Dist: sphinxcontrib-apidoc; extra == 'docs'
+Provides-Extra: test
+Requires-Dist: dirty-equals; extra == 'test'
+Requires-Dist: pip; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-check; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: ruff; extra == 'test'
+Description-Content-Type: text/markdown
+
+# pyannotators_patterns
+
+[![license](https://img.shields.io/github/license/oterrier/pyannotators_patterns)](https://github.com/oterrier/pyannotators_patterns/blob/master/LICENSE)
+[![tests](https://github.com/oterrier/pyannotators_patterns/workflows/tests/badge.svg)](https://github.com/oterrier/pyannotators_patterns/actions?query=workflow%3Atests)
+[![codecov](https://img.shields.io/codecov/c/github/oterrier/pyannotators_patterns)](https://codecov.io/gh/oterrier/pyannotators_patterns)
+[![docs](https://img.shields.io/readthedocs/pyannotators_patterns)](https://pyannotators_patterns.readthedocs.io)
+[![version](https://img.shields.io/pypi/v/pyannotators_patterns)](https://pypi.org/project/pyannotators_patterns/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyannotators_patterns)](https://pypi.org/project/pyannotators_patterns/)
+
+Annotator based on Presidio regex pattern recognizers.
+
+## Installation
+
+```
+pip install pyannotators-patterns
+```
+
+## Developing
+
+### Prerequisites
+
+You will need [uv](https://github.com/astral-sh/uv) (package manager) and Python 3.12+.
+
+Clone the repository:
+
+```
+git clone https://github.com/oterrier/pyannotators_patterns
+cd pyannotators_patterns
+```
+
+Install dependencies (including test extras):
+
+```
+uv sync --extra test
+```
+
+### Running the test suite
+
+```
+uv run pytest
+```
+
+### Linting and formatting
+
+```
+uv run ruff check .
+uv run ruff format --check .
+```
+
+To auto-fix formatting:
+
+```
+uv run ruff format .
+```
+
+### Building the documentation
+
+```
+uv run --extra docs sphinx-build docs docs/_build
+```
+
+The built documentation is available at `docs/_build/index.html`.

{pyannotators_patterns-0.5.123 → pyannotators_patterns-0.6.3}/README.md

@@ -7,42 +7,56 @@
 [![version](https://img.shields.io/pypi/v/pyannotators_patterns)](https://pypi.org/project/pyannotators_patterns/)
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyannotators_patterns)](https://pypi.org/project/pyannotators_patterns/)
 
-Annotator based on Facebook's Patterns
+Annotator based on Presidio regex pattern recognizers.
 
 ## Installation
 
-You can simply `pip install pyannotators_patterns`.
+```
+pip install pyannotators-patterns
+```
 
 ## Developing
 
-### Pre-requesites
+### Prerequisites
 
-You will need to install `flit` (for building the package) and `tox` (for orchestrating testing and documentation building):
+You will need [uv](https://github.com/astral-sh/uv) (package manager) and Python 3.12+.
+
+Clone the repository:
 
 ```
-python3 -m pip install flit tox
+git clone https://github.com/oterrier/pyannotators_patterns
+cd pyannotators_patterns
 ```
 
-Clone the repository:
+Install dependencies (including test extras):
 
 ```
-git clone https://github.com/oterrier/pyannotators_patterns
+uv sync --extra test
 ```
 
 ### Running the test suite
 
-You can run the full test suite against all supported versions of Python (3.8) with:
+```
+uv run pytest
+```
+
+### Linting and formatting
 
 ```
-tox
+uv run ruff check .
+uv run ruff format --check .
 ```
 
-### Building the documentation
+To auto-fix formatting:
 
-You can build the HTML documentation with:
+```
+uv run ruff format .
+```
+
+### Building the documentation
 
 ```
-tox -e docs
+uv run --extra docs sphinx-build docs docs/_build
 ```
 
-The built documentation is available at `docs/_build/index.html.
+The built documentation is available at `docs/_build/index.html`.

{pyannotators_patterns-0.5.123 → pyannotators_patterns-0.6.3}/docs/conf.py

@@ -18,7 +18,6 @@ import os
 
 import pyannotators_patterns
 
-
 # -- Project information -----------------------------------------------------
 
 project = "pyannotators_patterns"

pyannotators_patterns-0.6.3/pyproject.toml

@@ -0,0 +1,87 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "pyannotators-patterns"
+dynamic = ["version"]
+description = "Annotator based on Presidio pattern recognizer"
+readme = "README.md"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Olivier Terrier", email = "olivier.terrier@kairntech.com"},
+]
+keywords = []
+classifiers = [
+    "Intended Audience :: Information Technology",
+    "Intended Audience :: Developers",
+    "Intended Audience :: System Administrators",
+    "Operating System :: OS Independent",
+    "Topic :: Software Development :: Libraries :: Application Frameworks",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Software Development :: Libraries",
+    "Topic :: Software Development",
+    "License :: OSI Approved :: MIT License",
+    "Development Status :: 4 - Beta",
+    "Programming Language :: Python :: 3.12",
+]
+requires-python = ">=3.12"
+dependencies = [
+    "pymultirole-plugins>=0.6.0,<0.7.0",
+    "tldextract>=5.1.2",
+    "spacy[lookups]>=3.7.0",
+    "log-with-context",
+    "collections_extended",
+    "unidecode",
+    "presidio-analyzer>=2.2.354",
+]
+
+[project.urls]
+Homepage = "https://github.com/oterrier/pyannotators_patterns/"
+
+[project.entry-points."pyannotators.plugins"]
+patterns = "pyannotators_patterns.patterns:PatternsAnnotator"
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-cov",
+    "ruff",
+    "pip",
+    "dirty-equals",
+    "pytest-check",
+]
+docs = [
+    "sphinx",
+    "sphinx-rtd-theme",
+    "m2r2",
+    "sphinxcontrib.apidoc",
+    "jupyter_sphinx",
+    "lxml_html_clean",
+]
+dev = [
+    "pre-commit",
+    "bump2version",
+]
+
+[tool.hatch.version]
+path = "src/pyannotators_patterns/__init__.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/pyannotators_patterns"]
+
+[tool.pytest.ini_options]
+addopts = "--durations=5"
+norecursedirs = ["docs"]
+
+[tool.ruff]
+line-length = 120
+target-version = "py312"
+
+[tool.ruff.lint]
+select = ["E", "W", "F", "I", "B", "C4", "UP", "ARG", "SIM"]
+ignore = ["E501"]
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"

{pyannotators_patterns-0.5.123 → pyannotators_patterns-0.6.3}/src/pyannotators_patterns/__init__.py

@@ -1,2 +1,3 @@
 """Annotator based on Presidio pattern recognizer"""
-__version__ = "0.5.123"
+
+__version__ = "0.6.3"