careamics 0.0.4.1__tar.gz → 0.0.5__tar.gz

careamics-0.0.5/.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-0.0.5/.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-0.0.5/.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-0.0.5/.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-0.0.5/.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-0.0.5/.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-0.0.5/.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    # Files stored in repository root
+    directory: "/"
+    schedule:
+      interval: "daily"
+      time: "08:00"
+    groups:
+      python-packages:
+        patterns:
+          - "*"

{careamics-0.0.4.1 → careamics-0.0.5}/.pre-commit-config.yaml

@@ -9,29 +9,29 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.19
+    rev: v0.22
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.3
+    rev: v0.7.2
     hooks:
       - id: ruff
-        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*"
+        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^scripts/.*"
         args: [--fix, --target-version, py38]
 
   - 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: v1.13.0
     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
           - types-PyYAML
@@ -42,7 +42,7 @@ 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 +55,6 @@ repos:
 
   # strip out jupyter notebooks
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.0
     hooks:
       - id: nbstripout

{careamics-0.0.4.1 → careamics-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.4.1
+Version: 0.0.5
 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: pillow<=10.3.0
+Requires-Dist: psutil<=6.1
 Requires-Dist: pydantic<2.9,>=2.5
-Requires-Dist: pytorch-lightning>=2.2.0
-Requires-Dist: pyyaml
+Requires-Dist: pytorch-lightning<=2.4,>=2.2
+Requires-Dist: pyyaml!=6.0.0,<=6.0.2
 Requires-Dist: scikit-image<=0.23.2
-Requires-Dist: tifffile
-Requires-Dist: torch>=2.0.0
-Requires-Dist: torchvision
+Requires-Dist: tifffile<=2024.8.30
+Requires-Dist: torch<=2.5,>=2.0
+Requires-Dist: torchvision<=0.20
 Requires-Dist: typer==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'
@@ -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-0.0.4.1 → careamics-0.0.5}/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-0.0.4.1 → careamics-0.0.5}/pyproject.toml

@@ -43,17 +43,18 @@ classifiers = [
 ]
 dependencies = [
     'numpy<2.0.0',
-    'torch>=2.0.0',
-    'torchvision',
-    'bioimageio.core>=0.6.9',
-    'tifffile',
-    'psutil',
+    'torch>=2.0,<=2.5',
+    'torchvision<=0.20',
+    'bioimageio.core==0.7',
+    'tifffile<=2024.8.30',
+    'psutil<=6.1',
     'pydantic>=2.5,<2.9',
-    'pytorch_lightning>=2.2.0',
-    'pyyaml',
+    'pytorch_lightning>=2.2,<=2.4',
+    'pyyaml<=6.0.2,!=6.0.0',
     'typer==0.12.3',
     'scikit-image<=0.23.2',
     'zarr<3.0.0',
+    'pillow<=10.3.0',
 ]
 
 [project.optional-dependencies]
@@ -62,6 +63,7 @@ dev = [
     "pre-commit",
     "pytest",
     "pytest-cov",
+    "onnx",
     "sybil",      # doctesting
 ]
 
@@ -193,4 +195,3 @@ exclude = [ # don't report on objects that match any of these regex
     "test_*",
     "src/careamics/lvae_training/*",
 ]
-

careamics-0.0.5/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()