careamics 0.0.1__tar.gz → 0.1.0rc2__tar.gz

careamics-0.1.0rc2/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,33 @@
+---
+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]
+
+**Environment:**
+Please add here the content of your conda environment with versions.
+
+**Additional context**
+Add any other context about the problem here.

careamics-0.1.0rc2/.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-0.1.0rc2}/.github/TEST_FAIL_TEMPLATE.md

@@ -2,11 +2,11 @@
 title: "{{ env.TITLE }}"
 labels: [bug]
 ---
-The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC.
 
-The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
-with commit: {{ sha }}
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }} {{ env.BACKEND }}
+with commit: {{ sha }}.
 
-Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
+Full run: https://github.com/CAREamics/careamics-portfolio/actions/runs/{{ env.RUN_ID }}
 
 (This post will be updated if another test fails, as long as this issue remains open.)

careamics-0.1.0rc2/.github/dependabot.yml

@@ -0,0 +1,11 @@
+---
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+    - package-ecosystem: github-actions
+      directory: /
+      schedule:
+          interval: weekly
+      commit-message:
+          prefix: 'ci(dependabot):'

careamics-0.1.0rc2/.github/pull_request_template.md

@@ -0,0 +1,22 @@
+* **Please check if the PR fulfills these requirements**
+- [ ] The commit message is clear
+- [ ] Pre-commit hooks have been run 
+- [ ] Tests for the changes have been added (for bug fixes/features)
+- [ ] Docs have been added / updated (for bug fixes / features)
+
+
+* **What kind of change does this PR introduce?** (Bug fix, feature, docs update, ...)
+
+
+* **What is the current behavior?** (You can also link to an open issue here)
+<!-- Mention related issues if applicable -->
+
+
+* **What is the new behavior (if this is a feature change)?**
+
+
+* **Does this PR introduce a breaking change?** (What changes might users need to make in their application due to this PR?)
+
+
+* **Other information**:
+

careamics-0.1.0rc2/.github/workflows/ci.yml

@@ -0,0 +1,109 @@
+---
+name: CI
+
+on:
+    push:
+        branches:
+            - main
+        tags:
+            - v*.*.*
+    pull_request:
+    workflow_dispatch:
+    schedule:
+    # run every week (for --pre release tests)
+        - cron: 0 0 * * 0
+
+jobs:
+    check-manifest:
+    # check-manifest is a tool that checks that all files in version control are
+    # included in the sdist (unless explicitly excluded)
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - run: pipx run check-manifest
+
+    test:
+        name: ${{ matrix.platform }} (${{ matrix.python-version }})
+        runs-on: ${{ matrix.platform }}
+        strategy:
+            fail-fast: false
+            matrix:
+                python-version: ['3.8', '3.9', '3.10', '3.11']
+                platform: [ubuntu-latest, macos-latest, windows-latest]
+
+        steps:
+            - name: 🛑 Cancel Previous Runs
+              uses: styfle/cancel-workflow-action@0.12.0
+              with:
+                  access_token: ${{ github.token }}
+
+            - uses: actions/checkout@v4
+
+            - name: 🐍 Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v5
+              with:
+                  python-version: ${{ matrix.python-version }}
+                  cache-dependency-path: pyproject.toml
+                  cache: pip
+
+            - name: Install Dependencies
+              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' || ''  }}
+
+            - name: 🧪 Run Tests
+              run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing -m "not gpu"
+
+            # If something goes wrong with --pre tests, we can open an issue in the repo
+            - name: 📝 Report --pre Failures
+              if: failure() && github.event_name == 'schedule'
+              uses: JasonEtco/create-an-issue@v2
+              env:
+                  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+                  PLATFORM: ${{ matrix.platform }}
+                  PYTHON: ${{ matrix.python-version }}
+                  RUN_ID: ${{ github.run_id }}
+                  TITLE: '[test-bot] pip install --pre is failing'
+              with:
+                  filename: .github/TEST_FAIL_TEMPLATE.md
+                  update_existing: true
+
+            - name: Coverage
+              uses: codecov/codecov-action@v3
+
+    deploy:
+        name: Deploy
+        needs: test
+        if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+        runs-on: ubuntu-latest
+
+        permissions:
+            # IMPORTANT: this permission is mandatory for trusted publishing on PyPi
+            # see https://docs.pypi.org/trusted-publishers/
+            id-token: write
+            # This permission allows writing releases
+            contents: write
+
+        steps:
+            - uses: actions/checkout@v4
+              with:
+                  fetch-depth: 0
+
+            - name: 🐍 Set up Python
+              uses: actions/setup-python@v5
+              with:
+                  python-version: 3.x
+
+            - name: 👷 Build
+              run: |
+                  python -m pip install build
+                  python -m build
+
+            - name: 🚢 Publish to PyPI
+              uses: pypa/gh-action-pypi-publish@release/v1
+
+            - uses: softprops/action-gh-release@v1
+              with:
+                  generate_release_notes: true
+                  files: ./dist/*

careamics-0.1.0rc2/.gitignore

@@ -0,0 +1,5 @@
+.vscode
+*__pycache__
+.pytest*
+*.DS_Store*
+**/.ipynb_checkpoints

careamics-0.1.0rc2/.pre-commit-config.yaml

@@ -0,0 +1,62 @@
+---
+# 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: v0.15
+      hooks:
+          - id: validate-pyproject
+
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.1.6
+      hooks:
+          - id: ruff
+            args: [--fix, --target-version, py38]
+
+    - repo: https://github.com/psf/black
+      rev: 23.11.0
+      hooks:
+          - id: black
+
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v1.7.1
+      hooks:
+          - id: mypy
+            files: ^src/
+            additional_dependencies:
+                - numpy
+                - types-PyYAML
+
+  # check docstrings
+    - repo: https://github.com/numpy/numpydoc
+      rev: v1.6.0
+      hooks:
+          - id: numpydoc-validation
+
+  # jupyter linting and formatting
+    - repo: https://github.com/nbQA-dev/nbQA
+      rev: 1.7.1
+      hooks:
+          - id: nbqa-ruff
+            args: [--fix]
+          - id: nbqa-black
+  #- id: nbqa-mypy
+
+  # strip out jupyter notebooks
+    - repo: https://github.com/kynan/nbstripout
+      rev: 0.6.1
+      hooks:
+          - id: nbstripout
+
+  # yaml formatter
+    - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+      rev: 0.2.3
+      hooks:
+          - id: yamlfmt

{careamics-0.0.1 → careamics-0.1.0rc2}/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-0.1.0rc2/PKG-INFO

@@ -0,0 +1,81 @@
+Metadata-Version: 2.1
+Name: careamics
+Version: 0.1.0rc2
+Summary: Toolbox for running N2V and friends.
+Project-URL: homepage, https://careamics.github.io/
+Project-URL: repository, https://github.com/CAREamics/careamics
+Author-email: Igor Zubarev <igor.zubarev@fht.org>, Joran Deschamps <joran.deschamps@fht.org>, Vera Galinova <vera.galinova@fht.org>, Mehdi Seifi <mehdi.seifi@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 :: 3.8
+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: >=3.8
+Requires-Dist: bioimageio-core
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pyyaml
+Requires-Dist: scikit-image
+Requires-Dist: tifffile
+Requires-Dist: torch
+Requires-Dist: torchvision
+Requires-Dist: zarr
+Provides-Extra: all
+Requires-Dist: careamics-portfolio; extra == 'all'
+Requires-Dist: ipython; extra == 'all'
+Requires-Dist: itkwidgets; extra == 'all'
+Requires-Dist: jupyter; extra == 'all'
+Requires-Dist: pre-commit; extra == 'all'
+Requires-Dist: pytest; extra == 'all'
+Requires-Dist: pytest-cov; extra == 'all'
+Requires-Dist: torchsummary; extra == 'all'
+Requires-Dist: wandb; extra == 'all'
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Provides-Extra: notebooks
+Requires-Dist: careamics-portfolio; extra == 'notebooks'
+Requires-Dist: ipython; extra == 'notebooks'
+Requires-Dist: itkwidgets; extra == 'notebooks'
+Requires-Dist: jupyter; extra == 'notebooks'
+Requires-Dist: torchsummary; extra == 'notebooks'
+Requires-Dist: wandb; extra == 'notebooks'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: wandb; extra == 'test'
+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)
+
+## Installation
+
+``` bash
+pip install careamics
+```
+For more details on the options please follow the installation [guide](https://careamics.github.io/installation/).
+
+<!-- 
+## Contributing
+
+## Citing us 
+
+-->

{careamics-0.0.1 → careamics-0.1.0rc2}/README.md

@@ -1,18 +1,27 @@
 <p align="center">
   <a href="https://careamics.github.io/">
-    <img src="https://github.com/CAREamics/.github/blob/main/profile/images/banner_careamics.png">
+    <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/raw/main/LICENSE)
+[![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)
 
+## Installation
 
-Stay tuned for DL goodies with CAREamics!
+``` bash
+pip install careamics
+```
+For more details on the options please follow the installation [guide](https://careamics.github.io/installation/).
 
-Currently, this version is a place-holder, next version will contain the 
-first usable algorithms, as well as examples.
+<!-- 
+## Contributing
+
+## Citing us 
+
+-->