pyannotators-patterns 0.7.1__tar.gz → 1.6.27__tar.gz

{pyannotators_patterns-0.7.1 → pyannotators_patterns-1.6.27}/.gitignore

@@ -129,3 +129,9 @@ dmypy.json
 .idea/
 .groovylintrc.json
 .emailNotif
+uv.lock
+
+# SBOMs
+**/sbom*.json
+**/trivy*.html
+**/audit*.json

{pyannotators_patterns-0.7.1 → pyannotators_patterns-1.6.27}/.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-0.7.1 → pyannotators_patterns-1.6.27}/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-0.7.1 → pyannotators_patterns-1.6.27}/Jenkinsfile

@@ -6,6 +6,14 @@ pipeline {
 
   agent none
 
+  options {
+    throttleJobProperty(
+      categories: ['pyannotators'],
+      throttleEnabled: true,
+      throttleOption: 'category'
+    )
+  }
+
   triggers {
     upstream(upstreamProjects: 'pymultirole_plugins/' + BRANCH_NAME.replaceAll('/', '%2F'),\
                                 threshold: hudson.model.Result.SUCCESS)
@@ -18,16 +26,17 @@ pipeline {
     PYTHONPYCACHEPREFIX = '/tmp/.pytest_cache'
     PYTHONDONTWRITEBYTECODE = '1'
     JENKINS_UIDGID = '1004:1004'
+    SBOM_PROJECT_NAME = "sbom-${JOB_NAME.replaceAll('[^a-zA-Z0-9_.-]', '_')}"
 
-    MAJOR_VERSION = '0'
-    MINOR_VERSION = '7'
+    MAJOR_VERSION = "${MAJOR_VERSION_PY312}"
+    MINOR_VERSION = "${MINOR_VERSION_PY312}"
   }
 
   stages {
     stage('Catch build termination') {
       agent {
         node {
-          label 'built-in'
+          label 'pre-build'
           customWorkspace "${PATH_HOME}/${JOB_NAME}"
         }
       }
@@ -58,7 +67,7 @@ pipeline {
         stage('Add credentials') {
           steps {
             script {
-              // Add password file for flit publishing
+              // Add password file for uv publishing
               sh "cp ${PATH_HOME}/.passwd-pypi .env"
             }
           }
@@ -73,6 +82,7 @@ pipeline {
               withCredentials([gitUsernamePassword(credentialsId: 'bitbucket-user', gitToolName: 'git-tool')]) {
                 sh 'git pull'
                 sh "echo '\"\"\"Annotator based on Presidio pattern recognizer\"\"\"' > src/pyannotators_patterns/__init__.py"
+                sh "echo '' >> src/pyannotators_patterns/__init__.py"
                 sh "echo '__version__ = \"${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'
@@ -95,7 +105,7 @@ pipeline {
         //   - docker: /root/test-reports
         //   - host  : /tmp/_${JOB_NAME}/test-reports
         dockerfile {
-          label 'built-in'
+          label 'docker-build'
           customWorkspace "${PATH_HOME}/${JOB_NAME}"
           filename 'Dockerfile'
           args "-u root --privileged -v /tmp/_${JOB_NAME}/test-reports:${TEST_REPORT_DIR}"
@@ -103,13 +113,11 @@ 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 'rm -f uv.lock'
+            sh 'pip install uv'
+            sh 'uv sync --no-cache --extra test'
           }
         }
 
@@ -117,20 +125,22 @@ 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'
+            // remove any previous files used for sbom
+            sh 'rm -f sbom*.json trivy*.html syft trivy'
             // pull recent updates of file __init__.py
             withCredentials([gitUsernamePassword(credentialsId: 'bitbucket-user', gitToolName: 'git-tool')]) {
               sh 'git config --global pull.rebase false'
@@ -143,18 +153,90 @@ 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}" = "${BUILD_VERSION}" ] ; then uv build && uv publish ; fi
                '''
             // remove current folder dist
             sh 'rm -rf dist'
             // remove current folder .hypothesis
             sh 'rm -rf .hypothesis'
-            // remove current folder .tox
-            sh 'rm -rf .tox'
+          }
+        }
+      }
+    }
+
+    stage('Prepare SBOM') {
+      when {
+        beforeAgent true
+        environment name: 'SKIP_JOB', value: '0'
+      }
+      options {
+        timeout(time: 120, unit: 'SECONDS')
+      }
+
+      agent {
+        docker {
+          image 'alpine:3.19'
+          label 'docker-build'
+          customWorkspace "${PATH_HOME}/${JOB_NAME}"
+          args "-u 0 -v ${PATH_HOME}/.cache/trivy:/root/.cache/trivy"
+        }
+      }
+
+      stages {
+        stage('Generate SBOM') {
+          steps {
+            sh """
+               apk add --no-cache curl
+
+               curl -sSfL https://raw.githubusercontent.com/anchore/syft/main/install.sh | sh -s -- -b . v${SYFT_VERSION}
+
+               ./syft . \
+                --exclude '**/syft' \
+                --exclude '**/.pytest_cache' \
+                --exclude '**/.ruff_cache' \
+                --exclude '**/sbom.cdx.json' \
+                --exclude '**/sbom.spdx.json' \
+                --source-name "${JOB_NAME}" \
+                --source-version "${BUILD_NUMBER}" \
+                -o cyclonedx-json=${SBOM_PROJECT_NAME}.cdx.json \
+                -o spdx-json=${SBOM_PROJECT_NAME}.spdx.json
+
+               rm -f ./syft
+               """
+          }
+        }
+
+        stage('Analyse SBOM') {
+          steps {
+            sh """
+               curl -sfL https://raw.githubusercontent.com/aquasecurity/trivy/main/contrib/install.sh | sh -s -- -b . v${TRIVY_VERSION}
+               if [ ! -f trivy-html-template.tpl ]; then
+                 curl -L https://raw.githubusercontent.com/aquasecurity/trivy/main/contrib/html.tpl -o trivy-html-template.tpl
+               fi
+
+               ./trivy sbom ${SBOM_PROJECT_NAME}.cdx.json \
+                --cache-dir "/root/.cache/trivy" \
+                --severity HIGH,CRITICAL \
+                --exit-code 1 \
+                --no-progress \
+                --format template \
+                --template "@trivy-html-template.tpl" \
+                -o trivy-report-${SBOM_PROJECT_NAME}.html || EXIT_CODE=\$?
+
+               rm -f ./trivy
+
+               exit \${EXIT_CODE:-0}
+               """
+          }
+        }
+
+        stage('Archive SBOM & analysis') {
+          steps {
+            archiveArtifacts artifacts: 'sbom*.json, trivy*.html', excludes: 'sbom.cdx.json, sbom.spdx.json', fingerprint: true
           }
         }
       }
@@ -239,7 +321,7 @@ 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 +330,7 @@ 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",
@@ -409,6 +491,6 @@ def analyseBuildCause() {
     println 'Skipping build because last commit has been done by CI'
     env.SKIP_JOB = '1'
     switchEmailNotif(false, 0)
-    //currentBuild.result = 'NOT_BUILT'
+    currentBuild.result = 'NOT_BUILT'
   }
 }

pyannotators_patterns-1.6.27/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-1.6.27/PKG-INFO

@@ -0,0 +1,157 @@
+Metadata-Version: 2.4
+Name: pyannotators-patterns
+Version: 1.6.27
+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: 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: sbom
+Requires-Dist: cyclonedx-bom; extra == 'sbom'
+Requires-Dist: pip-audit; extra == 'sbom'
+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`.
+
+## SBOM & vulnerability check
+
+Install the SBOM dependencies:
+
+```
+uv sync --extra sbom
+```
+
+Generate a CycloneDX SBOM from the current environment:
+
+```
+uv run cyclonedx-py environment -o sbom.cdx.json --output-format json
+```
+
+Audit dependencies for known vulnerabilities:
+
+```
+uv run pip-audit --format json --output audit-report.json
+```
+
+To fail on any known vulnerability (useful in CI):
+
+```
+uv run pip-audit --strict
+```