init

.github/workflows/deploy-pypi.yml

@@ -0,0 +1,31 @@
+name: Publish rich-click to PyPI
+on:
+  release:
+    types: [published]
+
+jobs:
+  build-n-publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        name: Check out source-code repository
+
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.8"
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel build
+          pip install .
+
+      - name: Build the distribution
+        run: python setup.py sdist bdist_wheel
+
+      - name: Publish to PyPI
+        if: github.repository == 'qbicpkgs/omero-bifrost'
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 Phil Ewels
+
+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.

README.md

@@ -1 +1,15 @@
-# omero-bifrost
+## OMERO-Bifroest
+
+---
+
+# Dev notes
+
+To install packages in `requirements.txt` in the current conda env.:
+
+`pip install -r requirements.txt`
+
+To test package, install using pip:
+
+`pip install -e .`
+
+---

bifrost_conda_env.yaml

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+name: omero-bifrost
+channels:
+  - ome
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python=3.8
+  - zeroc-ice36-python=3.6.5
+  - omero-py=5.15.0
+  - pip:
+    - typer==0.9.0
+    - rich==13.5.2

requirements.txt

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+typer==0.9.0
+rich==13.5.2
+zeroc-ice==3.6.5
+omero-py==5.15.0

setup.cfg

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+[metadata]
+name = omero-bifrost
+version = attr: omero_bifrost.__version__
+url = https://github.com/luiskuhn/
+author = Luis Kuhn Cuellar
+author_email = luis.kuhn@gmail.com
+description = Bifrost bridge for large-scale transfer of OMERO-stored bioimage data
+license = MIT
+license_files = LICENSE
+long_description = file: README.md
+long_description_content_type = text/markdown
+classifiers =
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+    Programming Language :: Python :: 3
+
+[options]
+packages = find:
+package_dir =
+    =src
+python_requires = >= 3.8
+install_requires = file: requirements.txt
+
+[options.entry_points]
+console_scripts =
+    omero-bifrost = omero_bifrost.cli:app
+
+[options.packages.find]
+where = src

setup.py

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+from setuptools import setup
+
+setup()

src/omero_bifrost/__init__.py

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+"""Top-level package for bifrost."""
+
+__author__ = """Luis Kuhn Cuellar"""
+__version__ = '0.0.1dev'