WIP: new implementation of the labware ontology based on owlready2 / EMMOntopy

.bumpversion.cfg

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+[bumpversion]
+current_version = 0.0.1
+commit = True
+tag = True
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:labop_labware/__init__.py]
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"

.editorconfig

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+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

.flake8

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+[flake8]
+ignore = E203, W503
+select = B,B9,C,E,F,W
+max-complexity = 10
+max-line-length = 120
+per-file-ignores =
+    test/*:S101

.gitattributes

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+# this file is used by git large file support (git-lfs) to move 
+# large / binary files to a special location / database 
+*.jar filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.ZIP filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.tar.bz2 filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.PNG filter=lfs diff=lfs merge=lfs -text
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.JPG filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
+*.JPEG filter=lfs diff=lfs merge=lfs -text
+*.pdf filter=lfs diff=lfs merge=lfs -text
+*.PDF filter=lfs diff=lfs merge=lfs -text
+*.mp3 filter=lfs diff=lfs merge=lfs -text
+*.MP3 filter=lfs diff=lfs merge=lfs -text
+*.wav filter=lfs diff=lfs merge=lfs -text
+*.WAV filter=lfs diff=lfs merge=lfs -text
+*.mp4 filter=lfs diff=lfs merge=lfs -text
+*.mov filter=lfs diff=lfs merge=lfs -text
+*.ods filter=lfs diff=lfs merge=lfs -text
+*.xls filter=lfs diff=lfs merge=lfs -text
+*.xlsx filter=lfs diff=lfs merge=lfs -text
+*.odt filter=lfs diff=lfs merge=lfs -text
+*.doc filter=lfs diff=lfs merge=lfs -text
+*.docx filter=lfs diff=lfs merge=lfs -text
+

.gitignore

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+# this file is used by git to ignore certain files or directories
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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
+
+# sqlite database
+*.sqlite
+*.sqlite3
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/source/
+_build
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IntelliJ Idea family of suites
+.idea/
+*.iml
+
+# IDE settings - Visual Stuido code
+.vscode/
+
+# PyCharm
 .idea
+
+# Mac stuff
 .DS_Store
-__pycache__
-.ipynb_checkpoints
-*.out
-README.html
-build
-*.egg-info
+
+# Generated files
+bin/
+.build_*
+
+# owlready
+catalog-*.xml

AUTHORS.md

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+
+# Acknowledgements and Credits
+
+The OSO labware project thanks
+
+
+Contributors
+------------
+
+* Mickey Kim <[email protected]>  ! Thanks for the phantastic cookiecutter template !
+
+
+Development Lead
+----------------
+
+* mark doerr <[email protected]>

DEVELOPMENT.md

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+.. highlight:: shell
+
+Development
+===========
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `labop_labware` for local development.
+
+#. Clone the `labop_labware` repo from GitLab::
+
+    $ git clone [email protected]:https://gitlab.com/opensourcelab/scientificdata/ontologies/openscienceontology/labware.git
+
+#. Ensure `poetry is installed`_.
+#. Install dependencies and start your virtualenv::
+
+    $ poetry install
+    $ poetry shell
+
+#. Create a branch for local development::
+
+    $ git checkout -b feature/IssueNumber_name-of-your-bugfix-or-feature
+
+    # please do not use the '#' in branch names !
+
+Now you can make your changes locally.
+
+#. When you're done making changes, check that your changes pass the
+   tests, including testing other Python versions, with tox::
+
+    $ tox
+
+#. Commit your changes and push your branch to GitLab::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin feature/IssueNumber_name-of-your-bugfix-or-feature
+
+#. Submit a merge request through GitLab
+
+.. _poetry is installed: https://python-poetry.org/docs/
+
+Merge Request Guidelines
+-------------------------
+
+Before you submit a merge request, check that it meets these guidelines:
+
+1. The merge request should only include changes relating to one ticket.
+2. The merge request should include tests to cover any added changes and 
+   check that all existing and new tests pass.
+3. If the merge request adds functionality, the docs should be updated.
+   Put your new functionality into a function with a docstring, and add
+   the feature to the list in README.rst.
+4. The team should be informed of any impactful changes.
+
+Documentation
+--------------
+
+The Sphinx Documentation Sytem is used, 
+
+markdown is supported via the mystparser ( https://cerodell.github.io/sphinx-quickstart-guide/build/html/markdown.html )
+
+To build the documentation, run
+
+    $ invoke docs
+
+Tips
+----
+
+#. To run a subset of tests::
+
+    $ pytest tests.test_labop_labware
+
+Deploying to PyPI
+-----------------
+
+For every release:
+
+#. Update HISTORY.rst
+
+#. Update version number (can also be patch or major)::
+
+    bump2version minor
+
+#. Run the static analysis and tests::
+
+    tox
+
+#. Commit the changes::
+
+    git add HISTORY.rst
+    git commit -m "Changelog for upcoming release <#.#.#>"
+
+#. Push the commit::
+
+    git push
+
+#. Add the release tag (version) on GitLab: https://gitlab.com/https://gitlab.com/opensourcelab/scientificdata/ontologies/openscienceontology/labware/-/tags
+
+The GitLab CI pipeline will then deploy to PyPI if tests pass.

HISTORY.md

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+
+# History  of labop_labware 
+
+
+* 0.0.1 (2022-12-11)
+
+
+* First release ....

LICENSE

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+MIT License
+
+Copyright (c) 2022, mark doerr
+
+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 NON-INFRINGEMENT. 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.