pkg-infra 0.0.1__tar.gz

pkg_infra-0.0.1/.bumpversion.cfg

@@ -0,0 +1,7 @@
+[bumpversion]
+current_version = 0.0.1
+commit = True
+tag = True
+files = pyproject.toml pkg_infra/_metadata.py
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
+serialize = {major}.{minor}.{patch}

pkg_infra-0.0.1/.codecov.yaml

@@ -0,0 +1,17 @@
+# Based on pydata/xarray
+codecov:
+    require_ci_to_pass: no
+
+coverage:
+    status:
+        project:
+            default:
+                # Require 1% coverage, i.e., always succeed
+                target: 1
+        patch: false
+        changes: false
+
+comment:
+    layout: diff, flags, files
+    behavior: once
+    require_base: no

pkg_infra-0.0.1/.cruft.json

@@ -0,0 +1,75 @@
+{
+  "template": "https://github.com/saezlab/python-project.git",
+  "commit": "9994d74de08e6c13ae1c82fd47675347f1e3a79f",
+  "checkout": "master",
+  "context": {
+    "cookiecutter": {
+      "project_name": "pkg_infra",
+      "project_slug": "pkg_infra",
+      "package_name": "pkg_infra",
+      "short_description": "This is session handler, configuration and logging handler for Saezlab packages and applications.",
+      "readme": "This is session handler, configuration and logging handler for Saezlab packages and applications.",
+      "author_full_name": "Edwin Carreño",
+      "author_email": "ecarrenolozano@gmail.com",
+      "github_organization": "saezlab",
+      "project_repo": "https://github.com/saezlab/pkg_infra",
+      "license": "MIT License",
+      "_license": {
+        "MIT License": {
+          "license_short": "MIT",
+          "license_classifiers": "MIT License",
+          "license_spdx": "MIT"
+        },
+        "BSD 2-Clause License": {
+          "license_short": "BSD-2-Clause",
+          "license_classifiers": "BSD License",
+          "license_spdx": "BSD-2-Clause"
+        },
+        "BSD 3-Clause License": {
+          "license_short": "BSD-3-Clause",
+          "license_classifiers": "BSD License",
+          "license_spdx": "BSD-3-Clause"
+        },
+        "Apache License Version 2.0": {
+          "license_short": "Apache-2.0",
+          "license_classifiers": "Apache Software License",
+          "license_spdx": "Apache-2.0"
+        },
+        "GNU General Public License Version 3": {
+          "license_short": "GPL-3.0-or-later",
+          "license_classifiers": "GNU General Public License v3 (GPLv3)",
+          "license_spdx": "GPL-3.0-or-later"
+        },
+        "GNU Lesser General Public License Version 3": {
+          "license_short": "LGPL-3.0-or-later",
+          "license_classifiers": "GNU Lesser General Public License v3 (LGPLv3)",
+          "license_spdx": "LGPL-3.0-or-later"
+        },
+        "ISC License": {
+          "license_short": "ISC",
+          "license_classifiers": "ISC License (ISCL)",
+          "license_spdx": "ISC"
+        },
+        "Unlicense": {
+          "license_short": "Unlicense",
+          "license_classifiers": "The Unlicense (Unlicense)",
+          "license_spdx": "Unlicense"
+        }
+      },
+      "python_version": "3.10",
+      "copyright_holder": "Heidelberg University Hospital",
+      "__year": "2025",
+      "_extensions": [
+        "cookiecutter.extensions.TimeExtension"
+      ],
+      "_copy_without_render": [
+        ".github/workflows/*.yml",
+        ".github/workflows/**.yaml",
+        ".github/actions/*"
+      ],
+      "_template": "https://github.com/saezlab/python-project.git",
+      "_commit": "9994d74de08e6c13ae1c82fd47675347f1e3a79f"
+    }
+  },
+  "directory": null
+}

pkg_infra-0.0.1/.editorconfig

@@ -0,0 +1,12 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[Makefile]
+indent_style = tab

pkg_infra-0.0.1/.github/ISSUE_TEMPLATE/user-story.md

@@ -0,0 +1,17 @@
+---
+name: User Story
+about: This template is for creating user stories
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**As a** [role]
+**I need** [function]
+**So that** [benefit]
+
+### Details and Assumptions
+* [document what you know]
+   
+### Acceptance Criteria

pkg_infra-0.0.1/.github/actions/setup/action.yml

@@ -0,0 +1,21 @@
+name: Setup Python and Install Dependencies
+description: Sets up Python and installs dependencies using uv
+runs:
+    using: composite
+    steps:
+    -   uses: actions/setup-python@v5
+        with:
+            python-version: ${{ inputs.python-version }}
+    -   name: Install uv
+        shell: bash
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+    -   name: Create virtualenv and install dependencies
+        shell: bash
+        run: |
+            uv venv .venv
+            source .venv/bin/activate
+            uv pip install ".[dev,tests,docs]"
+inputs:
+    python-version:
+        required: true
+        description: Python version to use in the matrix.

pkg_infra-0.0.1/.github/workflows/ci-docs.yml

@@ -0,0 +1,30 @@
+name: Build MkDocs documentation
+
+on:
+    push:
+        branches: [main, master]
+
+permissions:
+    contents: write
+
+jobs:
+    build-documentation:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   name: Configure Git Credentials
+            run: |
+                git config user.name github-actions[bot]
+                git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+        -   uses: ./.github/actions/setup
+            with:
+                python-version: '3.12'
+        -   name: configure mkdocs-material cache
+            uses: actions/cache@v4
+            with:
+                key: mkdocs-material-${{ github.run_id }}
+                path: .cache
+                restore-keys: |
+                    mkdocs-material-
+        -   name: Build documentation with mkdocs
+            run: .venv/bin/mkdocs gh-deploy --force

pkg_infra-0.0.1/.github/workflows/ci-linting.yml

@@ -0,0 +1,16 @@
+name: Linting
+
+on: [push, pull_request]
+
+jobs:
+    linting:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: ./.github/actions/setup
+            with:
+                python-version: '3.13'
+        -   name: Run Ruff (lint + formatting + import order)
+            run: .venv/bin/ruff check .
+        -   name: Run Ruff format check (like Black)
+            run: .venv/bin/ruff format --check .

pkg_infra-0.0.1/.github/workflows/ci-security.yml

@@ -0,0 +1,16 @@
+name: Security Scan
+
+on: [push, pull_request]
+
+jobs:
+    security-check:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: actions/setup-python@v5
+            with:
+                python-version: '3.12'
+        -   name: Install Bandit
+            run: pip install bandit
+        -   name: Run Bandit
+            run: bandit -r . --exclude venv,.venv,.tox,tests --skip B101

pkg_infra-0.0.1/.github/workflows/ci-testing-unit.yml

@@ -0,0 +1,36 @@
+name: CI testing [unit testing]
+
+on: [push, pull_request]
+
+jobs:
+    lint:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: ./.github/actions/setup
+            with:
+                python-version: '3.13'
+        -   name: Run Ruff (lint + formatting + import order)
+            run: .venv/bin/ruff check .
+        -   name: Run Ruff format check (like Black)
+            run: .venv/bin/ruff format --check .
+
+    test:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version: ['3.10', '3.11', '3.12', '3.13']
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: ./.github/actions/setup
+            with:
+                python-version: ${{ matrix.python-version }}
+        -   name: Run tests with coverage
+            run: |
+                source .venv/bin/activate
+                pytest --cov=pkg_infra tests/
+        -   name: Upload coverage report
+            uses: actions/upload-artifact@v4
+            with:
+                name: coverage-report
+                path: .coverage*

pkg_infra-0.0.1/.github/workflows/publish-pypi.yml

@@ -0,0 +1,34 @@
+name: Publish to PyPI
+
+on:
+    release:
+        types: [published]
+    workflow_dispatch:
+
+permissions:
+    contents: read
+    id-token: write
+
+jobs:
+    build-and-publish:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+
+        -   uses: actions/setup-python@v5
+            with:
+                python-version: '3.12'
+
+        -   name: Install uv
+            uses: astral-sh/setup-uv@v5
+
+        -   name: Build distributions
+            run: uv build
+
+        -   name: Check package metadata
+            run: |
+                python -m pip install twine
+                twine check dist/*
+
+        -   name: Publish to PyPI
+            uses: pypa/gh-action-pypi-publish@release/v1

pkg_infra-0.0.1/.github/workflows/publish-testpypi.yml

@@ -0,0 +1,34 @@
+name: Publish to TestPyPI
+
+on:
+    workflow_dispatch:
+
+permissions:
+    contents: read
+    id-token: write
+
+jobs:
+    build-and-publish:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+
+        -   uses: actions/setup-python@v5
+            with:
+                python-version: '3.12'
+
+        -   name: Install uv
+            uses: astral-sh/setup-uv@v5
+
+        -   name: Build distributions
+            run: uv build
+
+        -   name: Check package metadata
+            run: |
+                python -m pip install twine
+                twine check dist/*
+
+        -   name: Publish to TestPyPI
+            uses: pypa/gh-action-pypi-publish@release/v1
+            with:
+                repository-url: https://test.pypi.org/legacy/

pkg_infra-0.0.1/.gitignore

@@ -0,0 +1,27 @@
+*~
+__pycache__/
+/build/
+/docs/_build/
+/docs/generated/
+.DS_Store
+/.vscode/
+/*.egg-info/
+*.egg
+*.prof
+*.coverage
+*.pickle
+/out/
+*.log
+/dist/
+*.pye
+*.pyc
+*.kate-swp
+/.tox/
+/.idea/
+/.pytest_cache/
+/.cache/
+/data/
+
+
+#Other
+demo/*

pkg_infra-0.0.1/.pre-commit-config.yaml

@@ -0,0 +1,89 @@
+# pre-commit-config.yaml
+# See https://pre-commit.com for docs and https://pre-commit.com/hooks.html for available hooks
+
+# ======================================================
+# =======        pre-commit configuration       ========
+# ======================================================
+fail_fast: false
+minimum_pre_commit_version: 3.0.0
+default_language_version:
+    python: python3
+default_stages:
+-   pre-commit
+-   pre-push
+
+# ======================================================
+# =======            repository hooks           ========
+# ======================================================
+# UPDATE all the hooks regularly by running in the
+# terminal:
+#   pre-commit autoupdate
+
+repos:
+    # Fast Python linter and formatter with auto-fix support
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.8
+    hooks:
+    -   id: ruff
+        args: [--fix, --show-fixes]
+        stages: [pre-commit]
+        files: \.py$
+    -   id: ruff-format
+        stages: [pre-commit]
+        files: \.py$
+
+    # Official pre-commit-hooks for general checks
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0    # Check for updates regularly
+    hooks:
+    -   id: check-added-large-files
+        stages: [pre-commit, pre-push]
+    -   id: check-ast
+        stages: [pre-commit]
+    -   id: check-case-conflict
+        stages: [pre-commit]
+    -   id: check-merge-conflict
+        stages: [pre-commit, pre-push]
+    -   id: check-symlinks
+        stages: [pre-commit]
+    -   id: check-yaml
+        args: [--unsafe]
+        stages: [pre-commit]
+        files: \.ya?ml$
+    -   id: detect-private-key
+        stages: [pre-commit]
+    -   id: end-of-file-fixer
+        stages: [pre-commit]
+    -   id: mixed-line-ending
+        args: [--fix=lf]
+        exclude: ^docs/make.bat$
+        stages: [pre-commit]
+    -   id: requirements-txt-fixer
+        stages: [pre-commit]
+
+    # Format code blocks in documentation files
+-   repo: https://github.com/asottile/blacken-docs
+    rev: 1.20.0
+    hooks:
+    -   id: blacken-docs
+        stages: [pre-commit]
+        files: \.(md|rst)$
+
+  # Format TOML and YAML files with pretty-format hooks
+-   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.16.0
+    hooks:
+    -   id: pretty-format-toml
+        args:
+        -   --autofix
+        -   --indent
+        -   '4'
+        stages: [pre-commit]
+        files: \.toml$
+    -   id: pretty-format-yaml
+        args:
+        -   --autofix
+        -   --indent
+        -   '4'
+        stages: [pre-commit]
+        files: \.ya?ml$

pkg_infra-0.0.1/.python-version

@@ -0,0 +1 @@
+>=3.10

pkg_infra-0.0.1/04_workdir.yaml

@@ -0,0 +1,8 @@
+logging:
+    formatters:
+        supersimple:
+            format: '%(message)s'
+    handlers:
+        file:
+            filename: logs/myapp.log
+            formatter: default

pkg_infra-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025, Edwin Carreño
+
+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.

pkg_infra-0.0.1/PKG-INFO

@@ -0,0 +1,164 @@
+Metadata-Version: 2.4
+Name: pkg_infra
+Version: 0.0.1
+Summary: This is session handler, configuration and logging handler for Saezlab packages and applications.
+Project-URL: Documentation, https://saezlab.github.io/pkg_infra
+Project-URL: Homepage, https://github.com/saezlab/pkg_infra
+Project-URL: Issues, https://github.com/saezlab/pkg_infra/issues
+Project-URL: Repository, https://github.com/saezlab/pkg_infra
+Author-email: Edwin Carreño <ecarrenolozano@gmail.com>
+Maintainer-email: Edwin Carreño <ecarrenolozano@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Requires-Dist: numpy>=2.2.6
+Requires-Dist: omegaconf>=2.3.0
+Requires-Dist: pandas>=2.3.3
+Requires-Dist: platformdirs>=4.5.0
+Requires-Dist: pydantic>=2.12.5
+Requires-Dist: python-json-logger>=4.0.0
+Requires-Dist: pyyaml>=6.0.3
+Requires-Dist: toml
+Provides-Extra: dev
+Requires-Dist: bump2version; extra == 'dev'
+Requires-Dist: distlib; extra == 'dev'
+Requires-Dist: ipykernel; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: twine; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.6.14; extra == 'docs'
+Requires-Dist: mkdocs<2,>=1.6; extra == 'docs'
+Requires-Dist: mkdocstrings[python]<0.30,>=0.29.1; extra == 'docs'
+Requires-Dist: pymdown-extensions>=10.15; extra == 'docs'
+Provides-Extra: security
+Requires-Dist: bandit; extra == 'security'
+Provides-Extra: semantic
+Requires-Dist: rdflib>=6.0.0; extra == 'semantic'
+Provides-Extra: tests
+Requires-Dist: codecov-cli>=10.2.0; extra == 'tests'
+Requires-Dist: coverage>=6.0; extra == 'tests'
+Requires-Dist: diff-cover; extra == 'tests'
+Requires-Dist: pytest-cov; extra == 'tests'
+Requires-Dist: pytest>=6.0; extra == 'tests'
+Requires-Dist: ruff; extra == 'tests'
+Requires-Dist: tox-gh>=1.5.0; extra == 'tests'
+Requires-Dist: tox>=3.20.1; extra == 'tests'
+Description-Content-Type: text/markdown
+
+![project-banner](https://raw.githubusercontent.com/saezlab/pkg_infra/main/docs/assets/project-banner-readme.png)
+
+---
+
+
+[![Tests](https://img.shields.io/github/actions/workflow/status/saezlab/pkg_infra/ci-testing-unit.yml?branch=main)](https://github.com/saezlab/pkg_infra/actions/workflows/ci-testing-unit.yml)
+[![Docs](https://img.shields.io/badge/docs-MkDocs-blue)](https://saezlab.github.io/pkg_infra/)
+![Pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)
+[![PyPI](https://img.shields.io/pypi/v/pkg_infra)](https://pypi.org/project/pkg_infra/)
+[![Python](https://img.shields.io/pypi/pyversions/pkg_infra)](https://pypi.org/project/pkg_infra/)
+[![PyPI](https://img.shields.io/pypi/v/pkg_infra)](https://pypi.org/project/pkg_infra/)
+[![Python](https://img.shields.io/pypi/pyversions/pkg_infra)](https://pypi.org/project/pkg_infra/)
+![License](https://img.shields.io/github/license/saezlab/pkg_infra)
+![Issues](https://img.shields.io/github/issues/saezlab/pkg_infra)
+![Last Commit](https://img.shields.io/github/last-commit/saezlab/pkg_infra)
+
+`pkg_infra` provides shared infrastructure for Saezlab Python packages. It
+standardizes three pieces of runtime behavior that are often reimplemented
+ad hoc across projects:
+
+- Session metadata for reproducible runs and workspace-aware execution
+- Layered YAML configuration with validation and predictable precedence
+- Centralized logging based on Python's standard `logging` module
+
+
+
+## What it includes
+
+- `pkg_infra.get_session(...)` as the main entrypoint for initializing runtime
+  state
+- Config loading from ecosystem, package default, user, working directory,
+  environment variable, and optional custom file sources
+- Pydantic-based validation for the merged settings model
+- Logging configuration generation with support for file handlers, JSON output,
+  package groups, and async queue-based logging
+- A packaged baseline configuration in
+  `src/pkg_infra/data/default_settings.yaml`
+
+## Installation
+
+Install the package from PyPI:
+
+```bash
+pip install pkg_infra
+```
+
+Install it from a local checkout with docs or test extras when developing:
+
+```bash
+pip install -e ".[docs,tests]"
+```
+
+## Quick Example
+
+```python
+from pathlib import Path
+
+from pkg_infra import get_session
+
+session = get_session(
+    workspace=Path("."),
+    include_location=False,
+)
+
+print(session)
+print(session.get_config_dict())
+
+corneto_settings = session.get_conf("corneto")
+print(corneto_settings)
+```
+
+## Configuration Precedence
+
+`pkg_infra` merges configuration sources in this order, where later sources
+override earlier ones:
+
+1. Ecosystem config
+2. Packaged default config
+3. User config
+4. Working-directory config
+5. Config file pointed to by `PKG_INFRA_CONFIG`
+6. Explicit custom config path passed by the caller
+
+## Documentation
+
+The full documentation is published at
+<https://saezlab.github.io/pkg_infra/>.
+
+To serve the docs locally without the current upstream Material warning banner:
+
+```bash
+source .venv/bin/activate
+export NO_MKDOCS_2_WARNING=1
+PYTHONPATH=src mkdocs serve
+```
+
+Recommended starting points:
+
+- Installation: `docs/installation.md`
+- Quickstart: `docs/learn/tutorials/quickstart.md`
+- Project context and rationale: `docs/pkg_infra-project/`
+
+## Contributing
+
+Contributions are welcome. The repository includes dedicated guides for
+documentation and code contributions in `docs/community/`.
+
+## License
+
+This project is distributed under the MIT License. See `LICENSE` for details.