careamics 0.0.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Potentially problematic release.
This version of careamics might be problematic. Click here for more details.
- careamics-0.0.1/.github/ISSUE_TEMPLATE.md +15 -0
- careamics-0.0.1/.github/TEST_FAIL_TEMPLATE.md +12 -0
- careamics-0.0.1/.github/dependabot.yml +10 -0
- careamics-0.0.1/.github/workflows/ci.yml +108 -0
- careamics-0.0.1/.gitignore +111 -0
- careamics-0.0.1/.pre-commit-config.yaml +34 -0
- careamics-0.0.1/LICENSE +28 -0
- careamics-0.0.1/PKG-INFO +46 -0
- careamics-0.0.1/README.md +18 -0
- careamics-0.0.1/pyproject.toml +144 -0
- careamics-0.0.1/src/careamics/__init__.py +8 -0
- careamics-0.0.1/src/careamics/py.typed +5 -0
- careamics-0.0.1/tests/test_careamics.py +2 -0
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* careamics version:
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* Python version:
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* Operating System:
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### Description
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Describe what you were trying to get done.
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Tell us what happened, what went wrong, and what you expected to happen.
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### What I Did
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```
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Paste the command(s) you ran and the output.
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If there was a crash, please include the traceback here.
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```
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---
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title: "{{ env.TITLE }}"
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labels: [bug]
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---
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The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
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The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
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with commit: {{ sha }}
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Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
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(This post will be updated if another test fails, as long as this issue remains open.)
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# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
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version: 2
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updates:
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directory: "/"
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schedule:
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interval: "weekly"
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commit-message:
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prefix: "ci(dependabot):"
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name: CI
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on:
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push:
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branches:
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- main
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tags:
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- "v*"
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pull_request:
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workflow_dispatch:
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schedule:
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# run every week (for --pre release tests)
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jobs:
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check-manifest:
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# check-manifest is a tool that checks that all files in version control are
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# included in the sdist (unless explicitly excluded)
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runs-on: ubuntu-latest
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steps:
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- run: pipx run check-manifest
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test:
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name: ${{ matrix.platform }} (${{ matrix.python-version }})
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runs-on: ${{ matrix.platform }}
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11"]
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platform: [ubuntu-latest, macos-latest, windows-latest]
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steps:
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- name: ๐ Cancel Previous Runs
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uses: styfle/cancel-workflow-action@0.11.0
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with:
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access_token: ${{ github.token }}
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- name: ๐ Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache-dependency-path: "pyproject.toml"
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cache: "pip"
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run: |
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python -m pip install -U pip
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python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || '' }}
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- name: ๐งช Run Tests
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run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
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if: failure() && github.event_name == 'schedule'
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uses: JasonEtco/create-an-issue@v2
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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PLATFORM: ${{ matrix.platform }}
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PYTHON: ${{ matrix.python-version }}
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RUN_ID: ${{ github.run_id }}
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TITLE: "[test-bot] pip install --pre is failing"
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with:
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filename: .github/TEST_FAIL_TEMPLATE.md
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update_existing: true
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uses: codecov/codecov-action@v3
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deploy:
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name: Deploy
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needs: test
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if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
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runs-on: ubuntu-latest
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environment: release # Needs to be created in the gh repository settings
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permissions:
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# see https://docs.pypi.org/trusted-publishers/
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id-token: write
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contents: write
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with:
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uses: actions/setup-python@v4
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python -m build
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uses: pypa/gh-action-pypi-publish@release/v1
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- uses: softprops/action-gh-release@v1
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with:
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generate_release_notes: true
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# Byte-compiled / optimized / DLL files
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# C extensions
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*.so
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# Distribution / packaging
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build/
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downloads/
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lib/
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parts/
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# Translations
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# enable pre-commit.ci at https://pre-commit.ci/
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# 2. auto updating the pre-commit configuration
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ci:
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autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
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autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
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rev: v0.12.1
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hooks:
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rev: v0.0.257
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rev: 23.1.0
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hooks:
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# # you have to add the things you want to type check against here
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# additional_dependencies:
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# - numpy
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careamics-0.0.1/LICENSE
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BSD 3-Clause License
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Copyright (c) 2023, Jug lab
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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careamics-0.0.1/PKG-INFO
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Metadata-Version: 2.1
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Name: careamics
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Version: 0.0.1
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Summary: CAREamics
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Project-URL: homepage, https://careamics.github.io/
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Project-URL: repository, https://github.com/CAREamics/careamics
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Author-email: Igor Zubarev <igor.zubarev@fht.org>, Joran Deschamps <joran.deschamps@fht.org>
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License: BSD-3-Clause
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License-File: LICENSE
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Classifier: Development Status :: 3 - Alpha
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.8
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Requires-Python: >=3.8
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Provides-Extra: dev
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Requires-Dist: black; extra == 'dev'
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Requires-Dist: ipython; extra == 'dev'
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Requires-Dist: mypy; extra == 'dev'
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Requires-Dist: pdbpp; extra == 'dev'
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Requires-Dist: rich; extra == 'dev'
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Requires-Dist: ruff; extra == 'dev'
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Provides-Extra: test
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Requires-Dist: pytest; extra == 'test'
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Requires-Dist: pytest-cov; extra == 'test'
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Description-Content-Type: text/markdown
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<p align="center">
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<a href="https://careamics.github.io/">
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<img src="https://github.com/CAREamics/.github/blob/main/profile/images/banner_careamics.png">
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</a>
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</p>
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[](https://github.com/CAREamics/careamics/raw/main/LICENSE)
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[](https://pypi.org/project/careamics)
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[](https://python.org)
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[](https://github.com/CAREamics/careamics/actions/workflows/ci.yml)
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[](https://codecov.io/gh/CAREamics/careamics)
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+
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Stay tuned for DL goodies with CAREamics!
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+
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Currently, this version is a place-holder, next version will contain the
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first usable algorithms, as well as examples.
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@@ -0,0 +1,18 @@
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1
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<p align="center">
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2
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<a href="https://careamics.github.io/">
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<img src="https://github.com/CAREamics/.github/blob/main/profile/images/banner_careamics.png">
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</a>
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</p>
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6
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7
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[](https://github.com/CAREamics/careamics/raw/main/LICENSE)
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9
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[](https://pypi.org/project/careamics)
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[](https://python.org)
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[](https://github.com/CAREamics/careamics/actions/workflows/ci.yml)
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[](https://codecov.io/gh/CAREamics/careamics)
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13
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+
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14
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+
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15
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+
Stay tuned for DL goodies with CAREamics!
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16
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+
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|
17
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+
Currently, this version is a place-holder, next version will contain the
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18
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+
first usable algorithms, as well as examples.
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@@ -0,0 +1,144 @@
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1
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# https://peps.python.org/pep-0517/
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[build-system]
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requires = ["hatchling", "hatch-vcs"]
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build-backend = "hatchling.build"
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# read more about configuring hatch at:
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# https://hatch.pypa.io/latest/config/build/
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# https://hatch.pypa.io/latest/config/metadata/
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[tool.hatch.version]
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source = "vcs"
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# https://peps.python.org/pep-0621/
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|
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[project]
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name = "careamics"
|
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15
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dynamic = ["version"]
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description = "CAREamics"
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readme = "README.md"
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|
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requires-python = ">=3.8"
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license = { text = "BSD-3-Clause" }
|
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authors = [
|
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|
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{ name = "Igor Zubarev", email = "igor.zubarev@fht.org" },
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{ name = "Joran Deschamps", email = "joran.deschamps@fht.org" },
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|
+
]
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|
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classifiers = [
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+
"Development Status :: 3 - Alpha",
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|
+
"Programming Language :: Python :: 3",
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|
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"Programming Language :: Python :: 3.8",
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|
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"Programming Language :: Python :: 3.9",
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+
"Programming Language :: Python :: 3.10",
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|
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"Programming Language :: Python :: 3.11",
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|
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|
+
# "License :: OSI Approved :: BSD License",
|
|
32
|
+
# "Typing :: Typed",
|
|
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|
+
]
|
|
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|
+
# add your package dependencies here
|
|
35
|
+
dependencies = []
|
|
36
|
+
|
|
37
|
+
# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
|
|
38
|
+
# "extras" (e.g. for `pip install .[test]`)
|
|
39
|
+
[project.optional-dependencies]
|
|
40
|
+
# add dependencies used for testing here
|
|
41
|
+
test = ["pytest", "pytest-cov"]
|
|
42
|
+
# add anything else you like to have in your dev environment here
|
|
43
|
+
dev = [
|
|
44
|
+
"black",
|
|
45
|
+
"ipython",
|
|
46
|
+
"mypy",
|
|
47
|
+
"pdbpp", # https://github.com/pdbpp/pdbpp
|
|
48
|
+
"rich", # https://github.com/Textualize/rich
|
|
49
|
+
"ruff",
|
|
50
|
+
]
|
|
51
|
+
|
|
52
|
+
[project.urls]
|
|
53
|
+
homepage = "https://careamics.github.io/"
|
|
54
|
+
repository = "https://github.com/CAREamics/careamics"
|
|
55
|
+
|
|
56
|
+
# Entry points
|
|
57
|
+
# https://peps.python.org/pep-0621/#entry-points
|
|
58
|
+
# same as console_scripts entry point
|
|
59
|
+
# [project.scripts]
|
|
60
|
+
# careamics-cli = "careamics:main_cli"
|
|
61
|
+
|
|
62
|
+
# [project.entry-points."some.group"]
|
|
63
|
+
# tomatoes = "careamics:main_tomatoes"
|
|
64
|
+
# https://github.com/charliermarsh/ruff
|
|
65
|
+
[tool.ruff]
|
|
66
|
+
line-length = 88
|
|
67
|
+
target-version = "py38"
|
|
68
|
+
# https://beta.ruff.rs/docs/rules/
|
|
69
|
+
extend-select = [
|
|
70
|
+
"E", # style errors
|
|
71
|
+
"W", # style warnings
|
|
72
|
+
"F", # flakes
|
|
73
|
+
"D", # pydocstyle
|
|
74
|
+
"I", # isort
|
|
75
|
+
"U", # pyupgrade
|
|
76
|
+
# "S", # bandit
|
|
77
|
+
"C", # flake8-comprehensions
|
|
78
|
+
"B", # flake8-bugbear
|
|
79
|
+
"A001", # flake8-builtins
|
|
80
|
+
"RUF", # ruff-specific rules
|
|
81
|
+
]
|
|
82
|
+
# I do this to get numpy-style docstrings AND retain
|
|
83
|
+
# D417 (Missing argument descriptions in the docstring)
|
|
84
|
+
# otherwise, see:
|
|
85
|
+
# https://beta.ruff.rs/docs/faq/#does-ruff-support-numpy-or-google-style-docstrings
|
|
86
|
+
# https://github.com/charliermarsh/ruff/issues/2606
|
|
87
|
+
extend-ignore = [
|
|
88
|
+
"D100", # Missing docstring in public module
|
|
89
|
+
"D107", # Missing docstring in __init__
|
|
90
|
+
"D203", # 1 blank line required before class docstring
|
|
91
|
+
"D212", # Multi-line docstring summary should start at the first line
|
|
92
|
+
"D213", # Multi-line docstring summary should start at the second line
|
|
93
|
+
"D401", # First line should be in imperative mood
|
|
94
|
+
"D413", # Missing blank line after last section
|
|
95
|
+
"D416", # Section name should end with a colon
|
|
96
|
+
]
|
|
97
|
+
|
|
98
|
+
[tool.ruff.per-file-ignores]
|
|
99
|
+
"tests/*.py" = ["D", "S"]
|
|
100
|
+
"setup.py" = ["D"]
|
|
101
|
+
|
|
102
|
+
# https://mypy.readthedocs.io/en/stable/config_file.html
|
|
103
|
+
[tool.mypy]
|
|
104
|
+
files = "src/**/"
|
|
105
|
+
strict = true
|
|
106
|
+
disallow_any_generics = false
|
|
107
|
+
disallow_subclassing_any = false
|
|
108
|
+
show_error_codes = true
|
|
109
|
+
pretty = true
|
|
110
|
+
|
|
111
|
+
# # module specific overrides
|
|
112
|
+
# [[tool.mypy.overrides]]
|
|
113
|
+
# module = ["numpy.*",]
|
|
114
|
+
# ignore_errors = true
|
|
115
|
+
# https://docs.pytest.org/en/6.2.x/customize.html
|
|
116
|
+
[tool.pytest.ini_options]
|
|
117
|
+
minversion = "6.0"
|
|
118
|
+
testpaths = ["tests"]
|
|
119
|
+
filterwarnings = ["error"]
|
|
120
|
+
|
|
121
|
+
# https://coverage.readthedocs.io/en/6.4/config.html
|
|
122
|
+
[tool.coverage.report]
|
|
123
|
+
exclude_lines = [
|
|
124
|
+
"pragma: no cover",
|
|
125
|
+
"if TYPE_CHECKING:",
|
|
126
|
+
"@overload",
|
|
127
|
+
"except ImportError",
|
|
128
|
+
"\\.\\.\\.",
|
|
129
|
+
"raise NotImplementedError()",
|
|
130
|
+
]
|
|
131
|
+
[tool.coverage.run]
|
|
132
|
+
source = ["src"]
|
|
133
|
+
|
|
134
|
+
# https://github.com/mgedmin/check-manifest#configuration
|
|
135
|
+
# add files that you want check-manifest to explicitly ignore here
|
|
136
|
+
# (files that are in the repo but shouldn't go in the package)
|
|
137
|
+
[tool.check-manifest]
|
|
138
|
+
ignore = [
|
|
139
|
+
".github_changelog_generator",
|
|
140
|
+
".pre-commit-config.yaml",
|
|
141
|
+
".ruff_cache/**/*",
|
|
142
|
+
"setup.py",
|
|
143
|
+
"tests/**/*",
|
|
144
|
+
]
|