careamics 0.0.1__tar.gz → 0.0.3__tar.gz

careamics-0.0.3/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,34 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Code snippet allowing reproducing the behaviour:
+```python
+# code here
+```
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Version [e.g. 22]
+- microscopy-portfolio version [e.g. 0.0.5]
+
+**Environment:**
+Please add here the content of your conda environment with versions.
+
+**Additional context**
+Add any other context about the problem here.

careamics-0.0.3/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

{careamics-0.0.1 → careamics-0.0.3}/.github/TEST_FAIL_TEMPLATE.md

@@ -9,4 +9,4 @@ with commit: {{ sha }}
 
 Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
 
-(This post will be updated if another test fails, as long as this issue remains open.)
+(This post will be updated if another test fails, as long as this issue remains open.)

careamics-0.0.3/.github/pull_request_template.md

@@ -0,0 +1,39 @@
+### Description
+
+Please provide a brief description of the changes in this PR. Include any relevant context or background information.
+
+- **What**: Clearly and concisely describe what changes you have made.
+- **Why**: Explain the reasoning behind these changes. What problem are you solving? Why is this change necessary?
+- **How**: Describe how you implemented these changes. Provide an overview of the approach and any important implementation details.
+
+### Changes Made
+
+- **Added**: List new features or files added.
+- **Modified**: Describe existing features or files modified.
+- **Removed**: Detail features or files that were removed.
+
+### Related Issues
+
+Link to any related issues or discussions. Use keywords like "Fixes", "Resolves", or "Closes" to link to issues automatically.
+
+- Fixes #
+- Resolves #
+- Closes #
+
+### Breaking changes
+
+Describe any breaking change.
+
+
+### Additional Notes and Examples
+
+Include any additional notes or context that reviewers should be aware of, including snippets of code illustrating your new feature.
+
+---
+
+**Please ensure your PR meets the following requirements:**
+
+- [ ] Code builds and passes tests locally, including doctests
+- [ ] New tests have been added (for bug fixes/features)
+- [ ] Pre-commit passes
+- [ ] PR to the documentation exists (for bug fixes / features)

{careamics-0.0.1 → careamics-0.0.3}/.github/workflows/ci.yml

@@ -27,8 +27,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-        platform: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
+        platform: [ubuntu-latest, macos-13, windows-latest]
 
     steps:
       - name: 🛑 Cancel Previous Runs
@@ -49,10 +50,10 @@ jobs:
         run: |
           python -m pip install -U pip
           # if running a cron job, we add the --pre flag to test against pre-releases
-          python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+          python -m pip install .[dev] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
 
       - name: 🧪 Run Tests
-        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+        run: pytest --color=yes --cov --cov-config=pyproject.toml --cov-report=xml --cov-report=term-missing 
 
       # If something goes wrong with --pre tests, we can open an issue in the repo
       - name: 📝 Report --pre Failures
@@ -70,39 +71,40 @@ jobs:
 
       - name: Coverage
         uses: codecov/codecov-action@v3
+        with:
+          version: v0.7.3
 
   deploy:
-    name: Deploy
+    name: Release
     needs: test
     if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
     runs-on: ubuntu-latest
-    environment: release # Needs to be created in the gh repository settings
+
     permissions:
-      # IMPORTANT: this permission is mandatory for trusted publishing on PyPi
-      # see https://docs.pypi.org/trusted-publishers/
+      # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write
 
       # This permission allows writing releases
       contents: write
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      - name: 🐍 Set up Python
-        uses: actions/setup-python@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.x"
+          python-version: "3.9"
 
-      - name: 👷 Build
+      - name: Build
         run: |
           python -m pip install build
           python -m build
 
-      - name: 🚢 Publish to PyPI
+      - name: Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
 
-      - uses: softprops/action-gh-release@v1
+      - uses: softprops/action-gh-release@v2
         with:
-          generate_release_notes: true
+          generate_release_notes: true

careamics-0.0.3/.gitignore

@@ -0,0 +1,170 @@
+.vscode
+*.DS_Store
+**/.DS_Store
+**/.ipynb_checkpoints
+
+# torch related
+**/lightning_logs
+**/*.ckpt
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+**/__pycache__
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+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/
+.pytest*
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+**/.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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
+
+# ruff
+.ruff_cache
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

careamics-0.0.3/.pre-commit-config.yaml

@@ -0,0 +1,60 @@
+# enable pre-commit.ci at https://pre-commit.ci/
+# it adds:
+# 1. auto fixing pull requests
+# 2. auto updating the pre-commit configuration
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.18
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.6
+    hooks:
+      - id: ruff
+        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*"
+        args: [--fix, --target-version, py38]
+
+  - repo: https://github.com/psf/black
+    rev: 24.8.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.1
+    hooks:
+      - id: mypy
+        files: "^src/"
+        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/config/likelihood_model.py|^src/careamics/losses/loss_factory.py|^src/careamics/losses/lvae/losses.py"
+        args: ['--config-file', 'mypy.ini']
+        additional_dependencies:
+          - numpy
+          - types-PyYAML
+          - types-setuptools
+
+  # check docstrings
+  - repo: https://github.com/numpy/numpydoc
+    rev: v1.8.0rc2
+    hooks:
+      - id: numpydoc-validation
+        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/losses/lvae/.*"      
+
+  # # jupyter linting and formatting
+  # - repo: https://github.com/nbQA-dev/nbQA
+  #   rev: 1.8.5
+  #   hooks:
+  #     - id: nbqa-ruff
+  #       args: [--fix]
+  #     - id: nbqa-black
+  #     #- id: nbqa-mypy
+
+  # strip out jupyter notebooks
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout

{careamics-0.0.1 → careamics-0.0.3}/LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2023, Jug lab
+Copyright (c) 2023, CAREamics contributors
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

careamics-0.0.3/PKG-INFO

@@ -0,0 +1,78 @@
+Metadata-Version: 2.3
+Name: careamics
+Version: 0.0.3
+Summary: Toolbox for running N2V and friends.
+Project-URL: homepage, https://careamics.github.io/
+Project-URL: repository, https://github.com/CAREamics/careamics
+Author-email: CAREamics team <rse@fht.org>, Ashesh <ashesh.ashesh@fht.org>, Federico Carrara <federico.carrara@fht.org>, Melisande Croft <melisande.croft@fht.org>, Joran Deschamps <joran.deschamps@fht.org>, Vera Galinova <vera.galinova@fht.org>, Igor Zubarev <igor.zubarev@fht.org>
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+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: Typing :: Typed
+Requires-Python: >=3.9
+Requires-Dist: bioimageio-core>=0.6.0
+Requires-Dist: numpy<2.0.0
+Requires-Dist: psutil
+Requires-Dist: pydantic>=2.5
+Requires-Dist: pytorch-lightning>=2.2.0
+Requires-Dist: pyyaml
+Requires-Dist: scikit-image<=0.23.2
+Requires-Dist: tifffile
+Requires-Dist: torch>=2.0.0
+Requires-Dist: torchvision
+Requires-Dist: zarr<3.0.0
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: sybil; extra == 'dev'
+Provides-Extra: examples
+Requires-Dist: careamics-portfolio; extra == 'examples'
+Requires-Dist: jupyter; extra == 'examples'
+Requires-Dist: matplotlib; extra == 'examples'
+Provides-Extra: tensorboard
+Requires-Dist: protobuf==3.20.3; extra == 'tensorboard'
+Requires-Dist: tensorboard; extra == 'tensorboard'
+Provides-Extra: wandb
+Requires-Dist: wandb; extra == 'wandb'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <a href="https://careamics.github.io/">
+    <img src="https://raw.githubusercontent.com/CAREamics/.github/main/profile/images/banner_careamics.png">
+  </a>
+</p>
+
+# CAREamics
+
+[![License](https://img.shields.io/pypi/l/careamics.svg?color=green)](https://github.com/CAREamics/careamics/blob/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/careamics.svg?color=green)](https://pypi.org/project/careamics)
+[![Python Version](https://img.shields.io/pypi/pyversions/careamics.svg?color=green)](https://python.org)
+[![CI](https://github.com/CAREamics/careamics/actions/workflows/ci.yml/badge.svg)](https://github.com/CAREamics/careamics/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/CAREamics/careamics/branch/main/graph/badge.svg)](https://codecov.io/gh/CAREamics/careamics)
+
+
+CAREamics is a PyTorch library aimed at simplifying the use of Noise2Void and its many
+variants and cousins (CARE, Noise2Noise, N2V2, P(P)N2V, HDN, muSplit etc.).
+
+## Why CAREamics?
+
+Noise2Void is a widely used denoising algorithm, and is readily available from the `n2v`
+python package. However, `n2v` is based on TensorFlow, while more recent methods 
+denoising methods (PPN2V, DivNoising, HDN) are all implemented in PyTorch, but are 
+lacking the extra features that would make them usable by the community.
+
+The aim of CAREamics is to provide a PyTorch library reuniting all the latest methods
+in one package, while providing a simple and consistent API. The library relies on 
+PyTorch Lightning as a back-end. In addition, we will provide extensive documentation and 
+tutorials on how to best apply these methods in a scientific context.
+
+## Installation and use
+
+Check out the [documentation](https://careamics.github.io/) for installation instructions and guides!

careamics-0.0.3/README.md

@@ -0,0 +1,33 @@
+<p align="center">
+  <a href="https://careamics.github.io/">
+    <img src="https://raw.githubusercontent.com/CAREamics/.github/main/profile/images/banner_careamics.png">
+  </a>
+</p>
+
+# CAREamics
+
+[![License](https://img.shields.io/pypi/l/careamics.svg?color=green)](https://github.com/CAREamics/careamics/blob/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/careamics.svg?color=green)](https://pypi.org/project/careamics)
+[![Python Version](https://img.shields.io/pypi/pyversions/careamics.svg?color=green)](https://python.org)
+[![CI](https://github.com/CAREamics/careamics/actions/workflows/ci.yml/badge.svg)](https://github.com/CAREamics/careamics/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/CAREamics/careamics/branch/main/graph/badge.svg)](https://codecov.io/gh/CAREamics/careamics)
+
+
+CAREamics is a PyTorch library aimed at simplifying the use of Noise2Void and its many
+variants and cousins (CARE, Noise2Noise, N2V2, P(P)N2V, HDN, muSplit etc.).
+
+## Why CAREamics?
+
+Noise2Void is a widely used denoising algorithm, and is readily available from the `n2v`
+python package. However, `n2v` is based on TensorFlow, while more recent methods 
+denoising methods (PPN2V, DivNoising, HDN) are all implemented in PyTorch, but are 
+lacking the extra features that would make them usable by the community.
+
+The aim of CAREamics is to provide a PyTorch library reuniting all the latest methods
+in one package, while providing a simple and consistent API. The library relies on 
+PyTorch Lightning as a back-end. In addition, we will provide extensive documentation and 
+tutorials on how to best apply these methods in a scientific context.
+
+## Installation and use
+
+Check out the [documentation](https://careamics.github.io/) for installation instructions and guides!