careamics 0.0.4.2__tar.gz → 0.0.6__tar.gz

careamics-0.0.6/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,50 @@
+---
+name: Bug report
+about: Create a report to help us improve CAREamics
+title: "[BUG]"
+labels: bug
+assignees: ''
+---
+
+## Describe the bug
+<!-- A clear and concise description of what the bug is. -->
+
+[description here]
+
+## To Reproduce
+
+Code snippet allowing reproducing the behaviour:
+```python
+# [code here]
+
+```
+
+Error message:
+``` python
+# [copy your error message here]
+```
+
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+## System
+<!-- Please fill in the following information, you can check the package versions using `conda list` -->
+> [!IMPORTANT]
+> - OS: [e.g. iOS]
+> - Python version [e.g. 3.9]
+> - PyTorch version [e.g. 2.3]
+> - PyTorch lightning version [e.g. 2.4]
+> - CAREamics version [e.g. 0.0.4]
+
+### Environment
+<!-- Please copy here the content of your environment, you can use `conda env export > environment.yml` in unix-style command. -->
+
+```yaml
+# [your environment here]
+```
+
+
+## Additional context
+
+<!-- Add any other context about the problem here. -->
+
+[additional context here (if applicable)]

careamics-0.0.6/.github/ISSUE_TEMPLATE/example_report.md

@@ -0,0 +1,24 @@
+---
+name: Example report
+about: Tell us about how you use CAREamics
+title: "[Example]"
+labels: example
+assignees: ''
+---
+
+## Task
+<!-- A description of what you are trying to achieve. -->
+
+[description here]
+
+## Results
+<!-- Description of the results obtained with CAREamics. -->
+
+[description here]
+
+
+## References
+
+<!-- Potential references, such as your preprint or article. -->
+
+[additional context here]

careamics-0.0.6/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for CAREamics
+title: '[Feature]'
+labels: feature
+assignees: ''
+
+---
+
+## Problem
+<!-- A clear and concise description of what the problem is. -->
+
+[your problem description here]
+
+
+## Potential solution
+<!-- A clear and concise description of what you want to happen. -->
+
+[potential solution here, if applicable]
+

careamics-0.0.6/.github/ISSUE_TEMPLATE/interoperability_request.md

@@ -0,0 +1,24 @@
+---
+name: Interoperability request
+about: Tell us about potential synergies for CAREamics
+title: "[Interoperability]"
+labels: interoperability
+assignees: ''
+---
+
+## Description
+<!-- A clear and concise description of what other software or tool CAREamics could be compatible with. -->
+
+[description here]
+
+## Limitations to interfacing
+<!-- Description of the current limitations and challenges to interfacing CAREamics with this other tool. -->
+
+[description here]
+
+
+## References
+
+<!-- Add any other context, links, publications, guidelines that are relevant to interfacing the tool with other libraries. -->
+
+[additional context here]

careamics-0.0.6/.github/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,13 @@
+---
+name: Question
+about: Ask us anything about CAREamics
+title: "[Question]"
+labels: question
+assignees: ''
+---
+
+## Question
+<!-- A clear question about CAREamics and how to use it. -->
+
+[question here]
+

careamics-0.0.6/.github/ISSUE_TEMPLATE/refactoring_suggestion.md

@@ -0,0 +1,40 @@
+---
+name: Refactoring suggestion
+about: Suggest a way to improve CAREamics' codebase
+title: "[Refactoring]"
+labels: refactoring
+assignees: ''
+---
+
+## Description
+<!-- A description of the current pain points. -->
+
+[description here]
+
+### Which part of the code?
+
+- [links to code]
+
+### Examples
+
+``` python
+# [example of the pain points and their consequences]
+```
+
+## Potential solutions
+
+<!-- Describe potential solutions in different sections. -->
+
+### [Name of Solution 1]
+
+<!-- A description of a potential solution. -->
+
+``` python
+# [suggested change to code for Solution 1]
+```
+
+## References
+
+<!-- Add any other context, links to other codebase, PEP, best practices, etc. that could help understand or validate the solution -->
+
+[additional context here]

careamics-0.0.6/.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    # Files stored in repository root
+    directory: "/"
+    schedule:
+      interval: "daily"
+      time: "08:00"
+    ignore:
+      - dependency-name: "numpy"

{careamics-0.0.4.2 → careamics-0.0.6}/.pre-commit-config.yaml

@@ -9,31 +9,32 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.19
+    rev: v0.23
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.3
+    rev: v0.8.6
     hooks:
       - id: ruff
-        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*"
-        args: [--fix, --target-version, py38]
+        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^scripts/.*"
+        args: [--fix, --target-version, py39]
 
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.14.1
     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']
+        args: ["--config-file", "mypy.ini"]
         additional_dependencies:
-          - numpy
+          - numpy<2.0.0
+          - pydantic
           - types-PyYAML
           - types-setuptools
 
@@ -42,7 +43,7 @@ repos:
     rev: v1.8.0
     hooks:
       - id: numpydoc-validation
-        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/losses/lvae/.*"      
+        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/losses/lvae/.*|^scripts/.*"
 
   # # jupyter linting and formatting
   # - repo: https://github.com/nbQA-dev/nbQA
@@ -55,6 +56,6 @@ repos:
 
   # strip out jupyter notebooks
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout

careamics-0.0.6/CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+rse@fht.org.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

{careamics-0.0.4.2 → careamics-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.4.2
+Version: 0.0.6
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -16,19 +16,21 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Typing :: Typed
 Requires-Python: >=3.9
-Requires-Dist: bioimageio-core>=0.6.9
+Requires-Dist: bioimageio-core==0.7
 Requires-Dist: numpy<2.0.0
-Requires-Dist: psutil
-Requires-Dist: pydantic<2.9,>=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: typer==0.12.3
+Requires-Dist: pillow<=11.1.0
+Requires-Dist: psutil<=6.1.1
+Requires-Dist: pydantic<2.11,>=2.5
+Requires-Dist: pytorch-lightning<=2.5.0.post0,>=2.2
+Requires-Dist: pyyaml!=6.0.0,<=6.0.2
+Requires-Dist: scikit-image<=0.25.0
+Requires-Dist: tifffile<=2025.1.10
+Requires-Dist: torch<=2.5.1,>=2.0
+Requires-Dist: torchvision<=0.20.1
+Requires-Dist: typer<=0.15.1,>=0.12.3
 Requires-Dist: zarr<3.0.0
 Provides-Extra: dev
+Requires-Dist: onnx; extra == 'dev'
 Requires-Dist: pre-commit; extra == 'dev'
 Requires-Dist: pytest; extra == 'dev'
 Requires-Dist: pytest-cov; extra == 'dev'
@@ -38,7 +40,7 @@ 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: protobuf==5.29.1; extra == 'tensorboard'
 Requires-Dist: tensorboard; extra == 'tensorboard'
 Provides-Extra: wandb
 Requires-Dist: wandb; extra == 'wandb'
@@ -57,6 +59,7 @@ Description-Content-Type: text/markdown
 [![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)
+[![Image.sc](https://img.shields.io/badge/Got%20a%20question%3F-Image.sc-blue)](https://forum.image.sc/)
 
 
 CAREamics is a PyTorch library aimed at simplifying the use of Noise2Void and its many

{careamics-0.0.4.2 → careamics-0.0.6}/README.md

@@ -11,6 +11,7 @@
 [![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)
+[![Image.sc](https://img.shields.io/badge/Got%20a%20question%3F-Image.sc-blue)](https://forum.image.sc/)
 
 
 CAREamics is a PyTorch library aimed at simplifying the use of Noise2Void and its many

{careamics-0.0.4.2 → careamics-0.0.6}/mypy.ini

@@ -1,5 +1,6 @@
 [mypy]
 ignore_missing_imports = True
+plugins = pydantic.mypy
 
 [mypy-careamics.lvae_training.*]
 follow_imports = skip

{careamics-0.0.4.2 → careamics-0.0.6}/pyproject.toml

@@ -43,17 +43,18 @@ classifiers = [
 ]
 dependencies = [
     'numpy<2.0.0',
-    'torch>=2.0.0',
-    'torchvision',
-    'bioimageio.core>=0.6.9',
-    'tifffile',
-    'psutil',
-    'pydantic>=2.5,<2.9',
-    'pytorch_lightning>=2.2.0',
-    'pyyaml',
-    'typer==0.12.3',
-    'scikit-image<=0.23.2',
+    'torch>=2.0,<=2.5.1',
+    'torchvision<=0.20.1',
+    'bioimageio.core==0.7',
+    'tifffile<=2025.1.10',
+    'psutil<=6.1.1',
+    'pydantic>=2.5,<2.11',
+    'pytorch_lightning>=2.2,<=2.5.0.post0',
+    'pyyaml<=6.0.2,!=6.0.0',
+    'typer>=0.12.3,<=0.15.1',
+    'scikit-image<=0.25.0',
     'zarr<3.0.0',
+    'pillow<=11.1.0',
 ]
 
 [project.optional-dependencies]
@@ -62,6 +63,7 @@ dev = [
     "pre-commit",
     "pytest",
     "pytest-cov",
+    "onnx",
     "sybil",      # doctesting
 ]
 
@@ -70,7 +72,7 @@ examples = ["jupyter", "careamics-portfolio", "matplotlib"]
 
 # loggers
 wandb = ["wandb"]
-tensorboard = ["tensorboard", "protobuf==3.20.3"]
+tensorboard = ["tensorboard", "protobuf==5.29.1"]
 
 [project.urls]
 homepage = "https://careamics.github.io/"
@@ -188,9 +190,9 @@ checks = [
     "GL02", # Closing quotes should be placed in the line after the last text 
     # in the docstring
     "GL03", # Double line break found
+    "RT04", # Return value description should start with a capital letter
 ]
 exclude = [ # don't report on objects that match any of these regex
     "test_*",
     "src/careamics/lvae_training/*",
 ]
-

careamics-0.0.6/scripts/export_bmz_readme.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+"""Export a README file for the bioimage model zoo."""
+from pathlib import Path
+
+from careamics.config import create_n2v_configuration
+from careamics.model_io.bioimage._readme_factory import readme_factory
+
+
+def main():
+    # create configuration
+    config = create_n2v_configuration(
+        experiment_name="export_bmz_readme",
+        data_type="array",
+        axes="YX",
+        patch_size=(64, 64),
+        batch_size=2,
+        num_epochs=10,
+    )
+    # export README
+    readme_path = readme_factory(
+        config=config, careamics_version="0.1.0", data_description="Mydata"
+    )
+
+    # copy file to __file__
+    readme_path.rename(Path(__file__).parent / "README.md")
+
+
+if __name__ == "__main__":
+    main()

careamics-0.0.6/src/careamics/__init__.py

@@ -0,0 +1,28 @@
+"""Main CAREamics module."""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("careamics")
+except PackageNotFoundError:
+    __version__ = "uninstalled"
+
+__all__ = [
+    "CAREamist",
+    "Configuration",
+    "algorithm_factory",
+    "configuration_factory",
+    "data_factory",
+    "load_configuration",
+    "save_configuration",
+]
+
+from .careamist import CAREamist
+from .config import (
+    Configuration,
+    algorithm_factory,
+    configuration_factory,
+    data_factory,
+    load_configuration,
+    save_configuration,
+)