ibridges-servers-uu 0.1.0__tar.gz

ibridges_servers_uu-0.1.0/.github/workflows/python-package.yml

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+# This workflow contains actions for
+# - installing Python dependencies
+# - running tests
+# - linting with flake8, pylint
+# - checking docstrings with pydocstyle
+# - check if sphinx documentation builds correctly
+# - type checking with mypy
+#
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+# Replace packagename with your package name
+env:
+  PACKAGE_NAME: packagename
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
+
+#    When you want to test accross different OS replace lines 19-23 with the lines below
+#    runs-on: ${{ matrix.os }}-latest
+#    strategy:
+#      fail-fast: false
+#      matrix:
+#        os: [macos, ubuntu, windows]
+#        python-version: [3.8, 3.9, "3.10"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install ".[test]"
+
+    - name: Lint with Ruff
+      run: ruff check ibridgescontrib
+    - name: Check types with MyPy
+      run: mypy ibridgescontrib/uutemplate --namespace-packages --explicit-package-bases
+    - name: Check if templates are listed
+      run: |
+        ibridges setup --list
+        test $(ibridges setup --list | wc -l) -eq 11
+#    Uncomment the actions below depending on the linters and tests you want to do
+#    - name: Lint with flake8pip
+#      run: |
+#        python -m pip install flake8
+#        flake8 $PACKAGE_NAME
+#    - name: Lint with pylint
+#      run: |
+#        python -m pip install pylint
+#        pylint $PACKAGE_NAME
+#    - name: Check docstrings with pydocstyle
+#      run: |
+#        python -m pip install pydocstyle
+#        pydocstyle $PACKAGE_NAME --convention=numpy --add-select=D417 --add-ignore="D102,D105"
+#    - name: Test with pytest
+#      run: |
+#        python -m pip install pytest
+#        pytest tests
+#    - name: Test with MyPy
+#      run: |
+#        python -m pip install mypy
+#        mypy $PACKAGE_NAME
+#    - name: Check if documentation builds.
+#      run: |
+#        python -m pip install sphinx sphinx-rtd-theme sphinxcontrib-napoleon sphinx-autodoc-typehints
+#        cd docs; make html SPHINXOPTS="-W --keep-going"

ibridges_servers_uu-0.1.0/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#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: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

ibridges_servers_uu-0.1.0/.gitignore

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+ibridgescontrib/uutemplate/_version.py
+
+
+# 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/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+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/

ibridges_servers_uu-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Utrecht University
+
+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.

ibridges_servers_uu-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: ibridges-servers-uu
+Version: 0.1.0
+Summary: iRODS environments for connecting to Utrecht University YoDa servers
+Author-email: Raoul Schram <r.d.schram@uu.nl>
+License: MIT
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ibridges
+Provides-Extra: test
+Requires-Dist: ruff; extra == "test"
+Requires-Dist: mypy; extra == "test"
+
+# iRODS environments for Utrecht University YoDa servers
+
+This repository can be used to create an iRODS environment json that is needed to connect to the Utrecht University YoDa servers. 
+
+
+## Step 1: Install the plugin
+Type the following on the command line (in your virtual environment if you use one):
+
+```sh
+pip install git+https://github.com/UtrechtUniversity/ibridges-servers-uu.git
+```
+
+## Step 2: Find the right server
+
+On the command line run the following command:
+
+```sh
+ibridges setup --list
+```
+
+This shows you all the names of the YoDa servers available.
+
+## Step 3: Create your irods_environment.json
+
+In the following examples, we use the `uu-its` server, replace it with the server that is available to your faculty.
+
+```sh
+ibridges setup uu-its
+```
+
+This will ask for your email address. After filling it in, a file will be created in the default location for the irods environment file (`~/.irods/irods_environment.json` on Linux and MacOS). You can modify this location adding the `--output SOME_NEW_LOCATION` flag to the above command.
+
+## Step 4: Start using iBridges
+
+For the main documentation on how to use iBridges, see the iBridges main [repository](https://github.com/UtrechtUniversity/iBridges).
+
+```sh
+ibridges init
+```
+
+which will ask you for your data access password, which you can obtain through the YoDa portal.

ibridges_servers_uu-0.1.0/README.md

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+# iRODS environments for Utrecht University YoDa servers
+
+This repository can be used to create an iRODS environment json that is needed to connect to the Utrecht University YoDa servers. 
+
+
+## Step 1: Install the plugin
+Type the following on the command line (in your virtual environment if you use one):
+
+```sh
+pip install git+https://github.com/UtrechtUniversity/ibridges-servers-uu.git
+```
+
+## Step 2: Find the right server
+
+On the command line run the following command:
+
+```sh
+ibridges setup --list
+```
+
+This shows you all the names of the YoDa servers available.
+
+## Step 3: Create your irods_environment.json
+
+In the following examples, we use the `uu-its` server, replace it with the server that is available to your faculty.
+
+```sh
+ibridges setup uu-its
+```
+
+This will ask for your email address. After filling it in, a file will be created in the default location for the irods environment file (`~/.irods/irods_environment.json` on Linux and MacOS). You can modify this location adding the `--output SOME_NEW_LOCATION` flag to the above command.
+
+## Step 4: Start using iBridges
+
+For the main documentation on how to use iBridges, see the iBridges main [repository](https://github.com/UtrechtUniversity/iBridges).
+
+```sh
+ibridges init
+```
+
+which will ask you for your data access password, which you can obtain through the YoDa portal.

ibridges_servers_uu-0.1.0/ibridges_servers_uu.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: ibridges-servers-uu
+Version: 0.1.0
+Summary: iRODS environments for connecting to Utrecht University YoDa servers
+Author-email: Raoul Schram <r.d.schram@uu.nl>
+License: MIT
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ibridges
+Provides-Extra: test
+Requires-Dist: ruff; extra == "test"
+Requires-Dist: mypy; extra == "test"
+
+# iRODS environments for Utrecht University YoDa servers
+
+This repository can be used to create an iRODS environment json that is needed to connect to the Utrecht University YoDa servers. 
+
+
+## Step 1: Install the plugin
+Type the following on the command line (in your virtual environment if you use one):
+
+```sh
+pip install git+https://github.com/UtrechtUniversity/ibridges-servers-uu.git
+```
+
+## Step 2: Find the right server
+
+On the command line run the following command:
+
+```sh
+ibridges setup --list
+```
+
+This shows you all the names of the YoDa servers available.
+
+## Step 3: Create your irods_environment.json
+
+In the following examples, we use the `uu-its` server, replace it with the server that is available to your faculty.
+
+```sh
+ibridges setup uu-its
+```
+
+This will ask for your email address. After filling it in, a file will be created in the default location for the irods environment file (`~/.irods/irods_environment.json` on Linux and MacOS). You can modify this location adding the `--output SOME_NEW_LOCATION` flag to the above command.
+
+## Step 4: Start using iBridges
+
+For the main documentation on how to use iBridges, see the iBridges main [repository](https://github.com/UtrechtUniversity/iBridges).
+
+```sh
+ibridges init
+```
+
+which will ask you for your data access password, which you can obtain through the YoDa portal.

ibridges_servers_uu-0.1.0/ibridges_servers_uu.egg-info/SOURCES.txt

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+.gitignore
+LICENSE
+README.md
+pyproject.toml
+.github/workflows/python-package.yml
+.github/workflows/python-publish.yml
+ibridges_servers_uu.egg-info/PKG-INFO
+ibridges_servers_uu.egg-info/SOURCES.txt
+ibridges_servers_uu.egg-info/dependency_links.txt
+ibridges_servers_uu.egg-info/entry_points.txt
+ibridges_servers_uu.egg-info/requires.txt
+ibridges_servers_uu.egg-info/top_level.txt
+ibridgescontrib/uutemplate/__init__.py
+ibridgescontrib/uutemplate/templates.py

ibridges_servers_uu-0.1.0/ibridges_servers_uu.egg-info/dependency_links.txt

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+

ibridges_servers_uu-0.1.0/ibridges_servers_uu.egg-info/entry_points.txt

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+[ibridges_server_template]
+uu = ibridgescontrib.uutemplate.templates:IBridgesUUTemplates

ibridges_servers_uu-0.1.0/ibridges_servers_uu.egg-info/requires.txt

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+ibridges
+
+[test]
+ruff
+mypy

ibridges_servers_uu-0.1.0/ibridges_servers_uu.egg-info/top_level.txt

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+ibridgescontrib

ibridges_servers_uu-0.1.0/ibridgescontrib/uutemplate/__init__.py

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+"""Package to create irods_environment.json for Utrecht University servers."""
+from ibridgescontrib.uutemplate.templates import IBridgesUUTemplates
+
+__all__ = ["IBridgesUUTemplates"]

ibridges_servers_uu-0.1.0/ibridgescontrib/uutemplate/templates.py

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+"""Templates for irods_environment.json for Utrecht University servers."""
+from __future__ import annotations
+
+from string import Template
+
+_SERVERS_TO_ZONE = {
+    "uu-youth": "nluu1p",
+    "uu-geo": "nluu11p",
+    "uu-i-lab": "nluu5p",
+    "uu-dgk": "nluu9ot",
+    "uu-science": "nluu6p",
+    "uu-fsw": "nluu10p",
+    "uu-its": "nluu12p"
+}
+
+
+_BASE_TEMPLATE = """{
+    "irods_host": "${host}.data.uu.nl",
+    "irods_port": 1247,
+    "irods_home": "/${zone}/home",
+    "irods_user_name": "${email_address}",
+    "irods_default_resource": "${resc}",
+    "irods_zone_name": "${zone}",
+    "irods_authentication_scheme": "pam",
+    "irods_encryption_algorithm": "AES-256-CBC",
+    "irods_encryption_key_size": 32,
+    "irods_encryption_num_hash_rounds": 16,
+    "irods_encryption_salt_size": 8,
+    "irods_client_server_policy": "CS_NEG_REQUIRE",
+    "irods_client_server_negotiation": "request_server_negotiation"
+}
+"""
+
+
+class IBridgesUUTemplates:
+    """Template for creating iRODS environment json files at Utrecht University."""
+
+    name = "Utrecht University templates"
+    questions = ["email_address"]
+    descriptions = {
+        "uu-youth": "YOUth Cohort Study",
+        "uu-geo": "Geosciences",
+        "uu-i-lab": "Humanities, Law, Economics, Governance, Open Societies",
+        "uu-dgk": "Veterinary Medicine, Medicine",
+        "uu-science": "Science",
+        "uu-fsw": "Social and Behavioral Sciences",
+        "uu-its": "University Corporate Offices"
+    }
+
+    @staticmethod
+    def list_templates() -> list[str]:
+        """List all templates for servers that are available."""
+        return list(_SERVERS_TO_ZONE)
+
+    @staticmethod
+    def contains(template_name: str) -> bool:
+        """Whether a template name is provided by this template."""
+        return template_name in _SERVERS_TO_ZONE
+
+    @staticmethod
+    def environment_json(template_name: str, email_address: str) -> str:
+        """Create a valid environment.json with the given inputs."""
+        host = template_name[3:]
+        zone = _SERVERS_TO_ZONE[template_name]
+        template = Template(_BASE_TEMPLATE)
+        resc = "irodsResc2" if template_name in ["uu-dgk", "uu-youth"] else "irodsResc"
+        return template.substitute({"zone": zone, "email_address": email_address,
+                                    "host": host, "resc": resc})

ibridges_servers_uu-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ibridges-servers-uu"
+description = "iRODS environments for connecting to Utrecht University YoDa servers"
+authors = [
+    {name = "Raoul Schram", email = "r.d.schram@uu.nl"},
+]
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "MIT"}
+classifiers = [
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "License :: OSI Approved :: MIT License",
+]
+dynamic = ["version"]
+dependencies = [
+    "ibridges"
+]
+
+[project.optional-dependencies]
+test = ["ruff", "mypy"]
+
+[project.entry-points."ibridges_server_template"]
+uu = "ibridgescontrib.uutemplate.templates:IBridgesUUTemplates"
+
+[tool.setuptools]
+packages = ["ibridgescontrib"]
+
+[tool.setuptools_scm]
+write_to = "ibridgescontrib/uutemplate/_version.py"
+
+[tool.ruff]
+line-length = 100
+target-version = "py311"
+
+[tool.ruff.lint]
+select = ["C", "D", "E", "F", "UP", "B", "SIM", "I", "N", "W"]
+ignore = ["D203", "D213", "D206", "UP007"]

ibridges_servers_uu-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+