lara-django-data 0.2.91__tar.gz

lara_django_data-0.2.91/PKG-INFO

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+Metadata-Version: 2.3
+Name: lara_django_data
+Version: 0.2.91
+Summary: 
+Author: mark doerr
+Author-email: mark doerr <mark.doerr@uni-greifswald.de>
+License: GPLv3+
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Education
+Classifier: Operating System :: OS Independent
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: ==3.13.*
+Project-URL: Documentation, https://larasuite.gitlab.io/lara_django_data
+Project-URL: Source, https://gitlab.com/larasuite/lara_django_data
+Project-URL: Bug Tracker, https://gitlab.com/larasuite/lara_django_data/issues
+Project-URL: Changelog, https://gitlab.com/larasuite/lara_django_data/blob/main/CHANGELOG.md
+Description-Content-Type: text/markdown
+
+# LARA-django Data
+
+A LARA python-django app for generically managing experimental data in lab automation systems and scientific laboratories.
+
+## Installation
+
+In the active LARA-django environment, install
+
+    cd  lara_django_data
+    pip install .
+
+
+Add "my_new_app" to your INSTALLED_APPS setting like this:
+
+    INSTALLED_APPS = [
+        ...
+        ' lara_django_data',
+    ]
+
+Include the lara-django-app URLconf in your project urls.py like
+this:
+
+    path(' lara_django_data', include('my_new_app.urls')),
+
+Run 
+
+    python manage.py makemigrations  lara_django_data
+    python manage.py migrate 
+    
+to create the my_new_app database models.
+
+
+In case you like to test the app, please load the demo data:
+
+Start the development server 
+
+    lara-django-dev runserver
+
+and visit
+
+http://127.0.0.1:8000/admin/ 
+
+to create some entries (you'll need the Admin app enabled).
+
+
+## Environment variables
+
+for development, please set
+
+    export DJANGO_ALLOWED_HOSTS=localhost
+    export DJANGO_SETTINGS_MODULE=lara_django.settings.devel
+
+for production, please set 
+
+    export DJANGO_SETTINGS_MODULE=lara_django.settings.production
+
+if your media does not reside in the default media folder, please set
+environment variable to 
+
+    export DJANGO_MEDIA_PATH='path/to/my/media'
+
+to use user defined fixtures, please set: :: export
+    
+    DJANGO_FIXTURE_PATH='path/to/user/fixtures'
+
+
+Testing all applications
+
+## Basic Commands
+
+### Type checks
+
+Running type checks with mypy:
+
+    $ mypy lara_django_data
+
+### Test coverage
+
+To run the tests, check your test coverage, and generate an HTML coverage report:
+
+    $ coverage run -m pytest
+    $ coverage html
+    $ open htmlcov/index.html
+
+#### Running tests with pytest
+
+    $ pytest
+
+
+[![Built with Cookiecutter Django](https://img.shields.io/badge/built%20with-Cookiecutter%20Django-ff69b4.svg?logo=cookiecutter)](https://github.com/cookiecutter/cookiecutter-django/)
+[![Black code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
+
+License: GPLv3
+
+## Contributors ✨
+
+Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
+
+<!-- prettier-ignore-start -->
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- markdownlint-disable -->
+<!-- markdownlint-enable -->
+<!-- ALL-CONTRIBUTORS-LIST:END -->
+<!-- prettier-ignore-end -->
+
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!

lara_django_data-0.2.91/README.md

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+# LARA-django Data
+
+A LARA python-django app for generically managing experimental data in lab automation systems and scientific laboratories.
+
+## Installation
+
+In the active LARA-django environment, install
+
+    cd  lara_django_data
+    pip install .
+
+
+Add "my_new_app" to your INSTALLED_APPS setting like this:
+
+    INSTALLED_APPS = [
+        ...
+        ' lara_django_data',
+    ]
+
+Include the lara-django-app URLconf in your project urls.py like
+this:
+
+    path(' lara_django_data', include('my_new_app.urls')),
+
+Run 
+
+    python manage.py makemigrations  lara_django_data
+    python manage.py migrate 
+    
+to create the my_new_app database models.
+
+
+In case you like to test the app, please load the demo data:
+
+Start the development server 
+
+    lara-django-dev runserver
+
+and visit
+
+http://127.0.0.1:8000/admin/ 
+
+to create some entries (you'll need the Admin app enabled).
+
+
+## Environment variables
+
+for development, please set
+
+    export DJANGO_ALLOWED_HOSTS=localhost
+    export DJANGO_SETTINGS_MODULE=lara_django.settings.devel
+
+for production, please set 
+
+    export DJANGO_SETTINGS_MODULE=lara_django.settings.production
+
+if your media does not reside in the default media folder, please set
+environment variable to 
+
+    export DJANGO_MEDIA_PATH='path/to/my/media'
+
+to use user defined fixtures, please set: :: export
+    
+    DJANGO_FIXTURE_PATH='path/to/user/fixtures'
+
+
+Testing all applications
+
+## Basic Commands
+
+### Type checks
+
+Running type checks with mypy:
+
+    $ mypy lara_django_data
+
+### Test coverage
+
+To run the tests, check your test coverage, and generate an HTML coverage report:
+
+    $ coverage run -m pytest
+    $ coverage html
+    $ open htmlcov/index.html
+
+#### Running tests with pytest
+
+    $ pytest
+
+
+[![Built with Cookiecutter Django](https://img.shields.io/badge/built%20with-Cookiecutter%20Django-ff69b4.svg?logo=cookiecutter)](https://github.com/cookiecutter/cookiecutter-django/)
+[![Black code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
+
+License: GPLv3
+
+## Contributors ✨
+
+Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
+
+<!-- prettier-ignore-start -->
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- markdownlint-disable -->
+<!-- markdownlint-enable -->
+<!-- ALL-CONTRIBUTORS-LIST:END -->
+<!-- prettier-ignore-end -->
+
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!

lara_django_data-0.2.91/pyproject.toml

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+[build-system]
+requires = ["uv_build>=0.9.0,<=0.10.0"]
+build-backend = "uv_build"
+
+[project]
+name = "lara_django_data"
+version = "0.2.91"
+description = ""
+readme = "README.md"
+license = {text = "GPLv3+"}
+authors =[{name = "mark doerr", email = "mark.doerr@uni-greifswald.de"}] 
+
+requires-python = "==3.13.*"
+classifiers = [
+    'Development Status :: 3 - Alpha',
+    'Intended Audience :: Developers',
+    'Intended Audience :: Science/Research',
+    'Intended Audience :: Education',
+    'Operating System :: OS Independent',
+    'Natural Language :: English',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.13',
+    'Topic :: Scientific/Engineering',
+    'Topic :: Scientific/Engineering :: Information Analysis',
+    'Topic :: Scientific/Engineering :: Visualization',
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
+    'Topic :: Scientific/Engineering :: Chemistry',
+]
+
+dependencies = []
+
+[project.urls]
+Documentation = "https://larasuite.gitlab.io/lara_django_data"
+Source =  "https://gitlab.com/larasuite/lara_django_data"
+"Bug Tracker" = "https://gitlab.com/larasuite/lara_django_data/issues"
+Changelog = "https://gitlab.com/larasuite/lara_django_data/blob/main/CHANGELOG.md"
+
+
+[dependency-groups]
+dev = [
+  "django-mcp-server>=0.5",
+  "grpcio>=1.73.0",
+  "grpcio-tools>=1.73.0",
+  "pytest>=8,<9",
+  "pytest-cov>=6,<7",
+  "pytest-xdist>=3.3",
+  "pytest-asyncio>=1.0.0",
+  "git-changelog>=2.4",
+  "dotenv>=0.9",
+  "pre-commit>=4.0",
+  "python-semantic-release>=9.21",
+  "ruff>=0.11.0",
+]
+docs = [
+  "myst-parser>=0.16; python_version >= '3.11'",
+  "sphinx>=8.2; python_version >= '3.11'",
+  "sphinx-autobuild>=2024.10.3",
+  "python-docs-theme>=2025.5",
+  # alternative theme: 
+  "furo>=2024.6.0",
+]
+
+[tool.ruff]
+target-version = "py313"
+line-length = 120
+extend-exclude = [
+    "*/migrations/*.py",
+    "*/tests/*.py",
+    "tests/*.py",
+    #"staticfiles/*",
+    #"lara_django_vue3/lara_vue3_projects1/grpc/*.py",
+    #"api/grpc/python/lara_vue3_projects1_grpc/v1/*",
+    "jupyter/*.ipynb",
+]
+lint.select = [
+  "B",   # flake8-bugbear
+  "D",   # flake8-docstrings
+  "C4",  # flake8-comprehensions
+  "S",   # flake8-bandit
+  "F",   # pyflake
+  "E",   # pycodestyle
+  "W",   # pycodestyle
+  "UP",  # pyupgrade
+  "I",   # isort
+  "RUF", # ruff specific
+]
+lint.ignore = [
+  "D203", # 1 blank line required before class docstring
+  "D212", # Multi-line docstring summary should start at the first line
+  "D100", # Missing docstring in public module
+  "D104", # Missing docstring in public package
+  "D107", # Missing docstring in `__init__`
+  "D401", # First line of docstring should be in imperative mood
+]
+lint.per-file-ignores."conftest.py" = [ "D100" ]
+lint.per-file-ignores."docs/conf.py" = [ "D100" ]
+lint.per-file-ignores."setup.py" = [ "D100" ]
+lint.per-file-ignores."tests/**/*" = [
+  "D100",
+  "D101",
+  "D102",
+  "D103",
+  "D104",
+  "S101",
+]
+lint.isort.known-first-party = [ "lara_django_data", "tests" ]
+
+[tool.pytest.ini_options]
+addopts = """\
+    -v
+    -Wdefault
+    --cov=src/lara_django_data
+    --cov-report=term-missing
+    --cov-report=term
+    --cov-report=xml
+    """
+
+[tool.coverage.run]
+branch = true
+
+
+[tool.coverage.report]
+# Regexes for lines to exclude from consideration
+exclude_lines = [
+    # Have to re-enable the standard pragma
+    "pragma: no cover",
+    "@overload",
+    # Don't complain about missing debug-only code:
+    "def __repr__",
+    "def __repr__(self):",
+    "if self.debug",
+    "if TYPE_CHECKING",
+    # Don't complain if tests don't hit defensive assertion code:
+    "raise AssertionError",
+    "raise NotImplementedError",
+    # Don't complain if non-runnable code isn't run:
+    "if 0:",
+    "if __name__ == .__main__.:",
+    # Don't complain about abstract methods, they aren't run:
+    "@abstractmethod",
+    "@abc.abstractmethod",
+]
+ignore_errors = true
+skip_empty = true
+precision = 2
+omit = [
+    "setup.py",
+    # auto-generated by grpcio_tools.protoc
+    "*_pb2.py",
+    # will be copied to the server, so this source code is never executed
+]
+
+[tool.mypy]
+check_untyped_defs = true
+disallow_any_generics = true
+disallow_incomplete_defs = true
+disallow_untyped_defs = true
+mypy_path = "src/"
+no_implicit_optional = true
+show_error_codes = true
+warn_unreachable = true
+warn_unused_ignores = true
+exclude = [
+  'docs/.*',
+  'setup.py',
+]
+
+[[tool.mypy.overrides]]
+module = "tests.*"
+# allow_untyped_defs = true
+ignore_errors = true
+
+[[tool.mypy.overrides]]
+module = "docs.*"
+ignore_errors = true
+
+[tool.semantic_release]
+version_toml = [ "pyproject.toml:project.version", 
+                 "api/grpc/pyproject.toml:project.version" ]
+version_variables = [
+  "docs/conf.py:release",
+]
+build_command = """
+uv lock
+git add uv.lock
+uv build
+"""
+
+[tool.semantic_release.changelog]
+exclude_commit_patterns = [
+  '''chore(?:\([^)]*?\))?: .+''',
+  '''ci(?:\([^)]*?\))?: .+''',
+  '''refactor(?:\([^)]*?\))?: .+''',
+  '''style(?:\([^)]*?\))?: .+''',
+  '''test(?:\([^)]*?\))?: .+''',
+  '''build\((?!deps\): .+)''',
+  '''Merged? .*''',
+  '''Initial [Cc]ommit.*''', # codespell:ignore
+]
+
+[tool.semantic_release.changelog.environment]
+keep_trailing_newline = true
+
+[tool.semantic_release.branches.main]
+match = "main"
+
+[tool.semantic_release.branches.noop]
+match = "(?!main$)"
+prerelease = true
+
+[tool.semantic_release.remote]
+name = "origin"
+type = "gitlab"
+ignore_token_for_push = false
+insecure = false
+
+[tool.semantic_release.publish]
+upload_to_vcs_release = false

lara_django_data-0.2.91/src/lara_django_data/__init__.py

@@ -0,0 +1,8 @@
+from importlib.metadata import version as get_version
+
+__version__ = get_version(__package__)
+
+__version_info__ = tuple(
+    int(num) if num.isdigit() else num
+    for num in __version__.replace("-", ".", 1).split(".")
+)

lara_django_data-0.2.91/src/lara_django_data/admin.py

@@ -0,0 +1,101 @@
+"""_____________________________________________________________________
+
+:PROJECT: LARAsuite
+
+*lara_django_data admin *
+
+:details: lara_django_data admin module admin backend configuration.
+         - 
+:authors: mark doerr <mark.doerr@uni-greifswald.de>
+
+.. note:: -
+.. todo:: - run "lara-django-dev admin_generator lara_django_data >> admin.py" to update this file
+________________________________________________________________________
+"""
+
+# -*- coding: utf-8 -*-
+from django.contrib import admin
+
+from .models import ExtraData, Visualisation, Data, Evaluation
+
+
+@admin.register(ExtraData)
+class ExtraDataAdmin(admin.ModelAdmin):
+    list_display = (
+        "name_full",
+        "namespace",
+        "data_type",
+        "description",
+        "media_type",
+        "file",
+        "image",
+        "extradata_id",
+    )
+    list_filter = ("data_type", "namespace", "media_type")
+
+
+@admin.register(Visualisation)
+class VisualisationAdmin(admin.ModelAdmin):
+    list_display = (
+        "name",
+        "namespace",
+        "version",
+        "data_type",
+        "description",
+        "visualisation_id",
+    )
+    list_filter = (
+        "namespace",
+        "data_type",
+        "plotting_method_instance",
+        "plotting_procedure_instance",
+    )
+    raw_id_fields = ("tags",)
+    search_fields = ()
+
+
+@admin.register(Data)
+class DataAdmin(admin.ModelAdmin):
+    list_display = (
+        "name_full",
+        "name",
+        "namespace",
+        "data_type",
+        "version",
+        "datetime_created",
+        "file",
+        "description",
+        "data_id",
+    )
+    list_filter = (
+        "data_type",
+        "media_type",
+        "namespace",
+        "datetime_created",
+        "process_instance",
+    )
+    raw_id_fields = ("visualisations", "tags", "users", "groups", "data_extra")
+    search_fields = ()
+
+
+@admin.register(Evaluation)
+class EvaluationAdmin(admin.ModelAdmin):
+    list_display = (
+        "namespace",
+        "name",
+        "version",
+        "eval_method_instance",
+        "eval_procedure_instance",
+        "caption",
+        "description",
+        "evaluation_id",
+    )
+    list_filter = ("namespace", "eval_method_instance", "eval_procedure_instance")
+    raw_id_fields = (
+        "parent_evals",
+        "data_eval",
+        "data_results",
+        "visualisations",
+        "tags",
+    )
+    search_fields = ()

lara_django_data-0.2.91/src/lara_django_data/apps.py

@@ -0,0 +1,63 @@
+"""_____________________________________________________________________
+
+:PROJECT: LARAsuite
+
+*lara_django_data app *
+
+:details: lara_django_data app configuration. 
+         This provides a generic django app configuration mechanism.
+         For more details see:
+         https://docs.djangoproject.com/en/4.0/ref/applications/
+         - 
+:authors: mark doerr <mark.doerr@uni-greifswald.de>
+
+.. note:: -
+.. todo:: - 
+________________________________________________________________________
+"""
+
+from django.apps import AppConfig
+
+from django.db.models.signals import pre_save, post_save
+
+
+class LaraDjangoDataConfig(AppConfig):
+    name = 'lara_django_data'
+    url_path = 'data/'
+    # enter a verbose name for your app: lara_django_data here - this will be used in the admin interface
+    verbose_name = 'LARA-django Data'
+    # lara_app_icon = 'lara_django_data_icon.svg'  # this will be used to display an icon, e.g. in the main LARA menu.
+    lara_app_color = 'sky'  # this will be used to highlight the app in the main LARA sidebar and app page
+    lara_app_icon = "lara_data_icon.svg"
+    verbose_name_short = "Data"
+    lara_app_description = "Data and Evaluations"
+    lara_class_apps = [
+        {
+            "name": "Data",
+            "path":  "lara_django_data:data-list", # "/projects/project/list",
+            "icon": "lara_projects_icon.svg",
+            "color": lara_app_color,
+        },
+        {
+            "name": "Evaluations",
+            "path": "lara_django_data:data-list",
+            "icon": "lara_experiments_icon.svg",
+            "color": lara_app_color,
+        }
+    ]
+    lara_instance_apps = []
+
+    def ready(self):
+        from . import signals
+
+        pre_save.connect(signals.pre_save_handler,  dispatch_uid='lara_django_data.post_save' )
+
+        # add urlpatterns 
+        from django.urls import path, include
+        from lara_django.urls import urlpatterns
+
+        urlpatterns += [ 
+            path(self.url_path, include('lara_django_data.urls', namespace='lara_django_data')),
+        ]
+
+