bam-masterdata 0.0.0__tar.gz

bam_masterdata-0.0.0/.coveragerc

@@ -0,0 +1,4 @@
+[run]
+omit =
+    bam_masterdata/_version.py
+    */__init__.py

bam_masterdata-0.0.0/.github/workflows/actions.yml

@@ -0,0 +1,72 @@
+name: Installing and Testing
+on: [push]
+
+# https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs
+# `contents` is for permission to the contents of the repository.
+# `pull-requests` is for permission to pull request
+permissions:
+  contents: write
+  checks: write
+  pull-requests: write
+
+env:
+  UV_SYSTEM_PYTHON: true
+
+jobs:
+  install-and-test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python_version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{matrix.python_version}}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{matrix.python_version}}
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        uv pip install -e '.[dev]'
+    - name: mypy
+      run: |
+        python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional --exclude dependencies bam_masterdata tests
+    - name: Test with pytest
+      run: |
+        python -m pytest -sv --ignore=bam_masterdata/dependencies tests
+  build-and-install:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Build the package
+      run: |
+        uv pip install build
+        python -m build --sdist
+    - name: Install the package
+      run: |
+        uv pip install dist/*.tar.gz
+  ruff-linting:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v4
+        - uses: chartboost/ruff-action@v1
+          with:
+            args: "check . --exclude bam_masterdata/dependencies"
+  ruff-formatting:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v4
+        - uses: chartboost/ruff-action@v1
+          with:
+            args: "format . --check --verbose --exclude bam_masterdata/dependencies"

bam_masterdata-0.0.0/.github/workflows/coveralls.yml

@@ -0,0 +1,44 @@
+name: Testing with coveralls Report
+on: [push]
+
+# https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs
+# `contents` is for permission to the contents of the repository.
+# `pull-requests` is for permission to pull request
+permissions:
+  contents: write
+  checks: write
+  pull-requests: write
+
+env:
+  UV_SYSTEM_PYTHON: true
+
+jobs:
+  coveralls-test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Install dependencies
+      run: |
+        uv pip install -e '.[dev]'
+        uv pip install coveralls
+    - name: Build coverage file
+      run: |
+        pytest --cov-config=.coveragerc --junitxml=pytest.xml --cov=bam_masterdata tests | tee pytest-coverage.txt
+    - name: Pytest coverage comment
+      uses: MishaKav/pytest-coverage-comment@main
+      with:
+        pytest-coverage-path: pytest-coverage.txt
+        junitxml-path: pytest.xml
+    - name: Submit to coveralls
+      continue-on-error: true
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        coveralls --service=github

bam_masterdata-0.0.0/.github/workflows/mkdocs-deploy.yml

@@ -0,0 +1,29 @@
+name: Deploy MkDocs Site
+
+on:
+  push:
+    branches:
+      - main # Triggers deployment on push to the main branch
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+      - name: Install Documentation Dependencies
+        run: |
+          pip install --upgrade pip
+          pip install .[docu]
+      - name: Deploy docs
+        uses: mhausenblas/mkdocs-deploy-gh-pages@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          CONFIG_FILE: mkdocs.yml

bam_masterdata-0.0.0/.github/workflows/publish.yml

@@ -0,0 +1,43 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Build and Publish Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+env:
+  UV_SYSTEM_PYTHON: true
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        uv pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

bam_masterdata-0.0.0/.gitignore

@@ -0,0 +1,177 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+_version.py
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+coverage.txt
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+.pyenv
+.testenv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# VSCode settings
+.vscode/launch.json
+
+# Ruff
+.ruff_cache
+
+# pytest coverage
+pytest.xml
+pytest-coverage.txt
+
+# artifacts
+artifacts

bam_masterdata-0.0.0/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "bam_masterdata/dependencies/openbisschema"]
+	path = bam_masterdata/dependencies/openbisschema
+	url = https://git.bam.de/bam-data-store/development/openbisschema.git

bam_masterdata-0.0.0/.vscode/settings.json

@@ -0,0 +1,85 @@
+{
+  "python.defaultInterpreterPath": "~/Miniconda3/python.exe",
+  "python.terminal.activateEnvInCurrentTerminal": true,
+  "editor.rulers": [90],
+  "editor.renderWhitespace": "all",
+  "editor.tabSize": 4,
+  "[javascript]": {
+      "editor.tabSize": 2
+  },
+  "files.trimTrailingWhitespace": true,
+  "files.watcherExclude": {
+      "${workspaceFolder}/.venv/**": true
+  },
+  "files.exclude": {
+      "\"**/*.pyc\": {\"when\": \"$(basename).py\"}": true,
+      "**/__pycache__": true,
+      "**/node_modules": true
+  },
+  "python.testing.pytestPath": "pytest",
+  "python.testing.pytestArgs": ["tests"],
+  "python.testing.unittestEnabled": false,
+  "editor.defaultFormatter": "charliermarsh.ruff",
+  "editor.formatOnSave": true,
+  "editor.codeActionsOnSave": {
+    "source.organizeImports.ruff": "always",
+    "source.fixAll.ruff": "always",
+  },
+  "launch": {
+    "version": "0.2.0",
+    "configurations": [
+      {
+        "name": "BM Python",
+        "type": "debugpy",
+        "request": "launch",
+        "console": "integratedTerminal",
+        "program": "${workspaceFolder}/bam_masterdata/metadata/entities.py",  // path to your entry point Python module
+      },
+      {
+        "name": "BM tests",
+        "type": "debugpy",
+        "request": "launch",
+        "console": "integratedTerminal",
+        "program": "${workspaceFolder}/.venv/bin/pytest",  // path to your virtual environment
+        "justMyCode": false,
+        "env": {
+        "_PYTEST_RAISE": "1"
+        },
+        "args": [
+            "-sv",
+            "${workspaceFolder}/tests/cli/test_cli.py"  // path to your testing module
+        ]
+      },
+      {
+        "name": "BM fill-masterdata",
+        "type": "debugpy",
+        "request": "launch",
+        "cwd": "${workspaceFolder}",
+        "program": "${workspaceFolder}/.venv/bin/bam_masterdata",
+        "justMyCode": false,
+        "args": [
+          "fill_masterdata",
+          // "--url=https://devel.datastore.bam.de/"
+        ]
+      },
+      {
+        "name": "BM export-to-json",
+        "type": "debugpy",
+        "request": "launch",
+        "cwd": "${workspaceFolder}",
+        "program": "${workspaceFolder}/.venv/bin/bam_masterdata",
+        "justMyCode": false,
+        "args": ["export_to_json"]
+      },
+      {
+        "name": "BM export-to-excel",
+        "type": "debugpy",
+        "request": "launch",
+        "cwd": "${workspaceFolder}",
+        "program": "${workspaceFolder}/.venv/bin/bam_masterdata",
+        "justMyCode": false,
+        "args": ["export_to_excel"]
+      },
+    ]
+  },
+}

bam_masterdata-0.0.0/PKG-INFO

@@ -0,0 +1,176 @@
+Metadata-Version: 2.2
+Name: bam-masterdata
+Version: 0.0.0
+Summary: The BAM Data Store utility tools and masterdata models wrapped in a Python package with a front-end web interface.
+Author-email: BAM Data Store <datastore@bam.de>
+Maintainer-email: "Jose M. Pizarro" <jose.pizarro-blanco@bam.de>
+Project-URL: Homepage, https://github.com/BAMresearch/bam-masterdata
+Project-URL: Bug Tracker, https://github.com/BAMresearch/bam-masterdata/issues
+Classifier: Natural Language :: English
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: pybis~=1.37.1rc4
+Requires-Dist: openpyxl
+Requires-Dist: click
+Requires-Dist: pydantic
+Provides-Extra: dev
+Requires-Dist: mypy==1.0.1; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-timeout; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: python-decouple; extra == "dev"
+Requires-Dist: structlog==24.4.0; extra == "dev"
+Provides-Extra: jupy
+Requires-Dist: jupyterlab; extra == "jupy"
+Requires-Dist: notebook; extra == "jupy"
+Requires-Dist: ipywidgets; extra == "jupy"
+Provides-Extra: docu
+Requires-Dist: mkdocs; extra == "docu"
+Requires-Dist: mkdocs-material; extra == "docu"
+Requires-Dist: pymdown-extensions; extra == "docu"
+Requires-Dist: mkdocs-click; extra == "docu"
+
+![test-and-build pipeline](https://github.com/BAMresearch/bam-masterdata/actions/workflows/actions.yml/badge.svg)
+
+# BAM Masterdata
+
+The BAM Masterdata is a repository containing all the masterdata schema defining in BAM, as well as some utility functions to handle the masterdata.
+
+<!--
+## Getting started
+
+ Add here installation instructions once the package is deployed -->
+
+## Development
+
+If you want to develop locally this package, clone the project and enter in the workspace folder:
+
+```sh
+git clone https://git.bam.de/bam-data-store/bam-masterdata.git
+cd bam-masterdata
+```
+
+Create a virtual environment (you can use Python>3.9) in your workspace:
+
+```sh
+python3 -m venv .venv
+source .venv/bin/activate
+```
+
+Run the following script:
+
+```sh
+./scripts/install_python_dependencies
+```
+
+### Run the tests
+
+You can locally run the tests by doing:
+
+```sh
+python -m pytest -sv tests
+```
+
+where the `-s` and `-v` options toggle the output verbosity.
+
+You can also generate a local coverage report:
+
+```sh
+python -m pytest --cov=src tests
+```
+
+### Run auto-formatting and linting
+
+We use [Ruff](https://docs.astral.sh/ruff/) for formatting and linting the code following the rules specified in the `pyproject.toml`. You can run locally:
+
+```sh
+ruff check .
+```
+
+This will produce an output with the specific issues found. In order to auto-fix them, run:
+
+```sh
+ruff format . --check
+```
+
+If some issues are not possible to fix automatically, you will need to visit the file and fix them by hand.
+
+### Run the local website
+
+**Under construction!**
+
+<!-- ### Debugging
+
+For interactive debugging of the tests, use `pytest` with the `--pdb` flag. We recommend using an IDE for debugging, e.g., _VSCode_. If that is the case, add the following snippet to your `.vscode/launch.json`:
+```json
+{
+  "configurations": [
+      {
+        "name": "<descriptive tag>",
+        "type": "debugpy",
+        "request": "launch",
+        "cwd": "${workspaceFolder}",
+        "program": "${workspaceFolder}/.pyenv/bin/pytest",
+        "justMyCode": true,
+        "env": {
+            "_PYTEST_RAISE": "1"
+        },
+        "args": [
+            "-sv",
+            "--pdb",
+            "<path-to-plugin-tests>",
+        ]
+    }
+  ]
+}
+```
+
+where `<path-to-plugin-tests>` must be changed to the local path to the test module to be debugged.
+
+The settings configuration file `.vscode/settings.json` automatically applies the linting and formatting upon saving the modified file. -->
+
+### Documentation on Github pages
+
+To view the documentation locally, make sure to have installed the extra packages (this is part of the `scripts/install_python_dependencies.sh`, so if you ran this script before, you don't need to do it again now):
+
+```sh
+uv pip install -e '[docu]'
+```
+
+The first time, build the server:
+
+```sh
+mkdocs build
+```
+
+Run the documentation server:
+
+```sh
+mkdocs serve
+```
+
+The output looks like:
+
+```sh
+INFO    -  Building documentation...
+INFO    -  Cleaning site directory
+INFO    -  [14:07:47] Watching paths for changes: 'docs', 'mkdocs.yml'
+INFO    -  [14:07:47] Serving on http://127.0.0.1:8000/
+```
+
+Simply click on `http://127.0.0.1:8000/`. The changes in the `md` files of the documentation are inmediately reflected when the files are saved (the local web will automatically refresh).
+
+## Main contributors
+
+| Name                | E-mail                                                       |
+| ------------------- | ------------------------------------------------------------ |
+| Carlos Madariaga    | [carlos.madariaga@bam.de](mailto:carlos.madariaga@bam.de)       |
+| Dr. Jose M. Pizarro | [jose.pizarro-blanco@bam.de](mailto:jose.pizarro-blanco@bam.de) |