careamics 0.1.0rc5__tar.gz → 0.1.0rc7__tar.gz

careamics-0.1.0rc7/.github/TEST_FAIL_TEMPLATE.md

@@ -0,0 +1,12 @@
+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+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 }}
+
+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.)

{careamics-0.1.0rc5 → careamics-0.1.0rc7}/.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        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]
 

{careamics-0.1.0rc5 → careamics-0.1.0rc7}/.gitignore

@@ -6,3 +6,4 @@
 .coverage
 coverage.xml
 lightning_logs
+.mypy_cache

{careamics-0.1.0rc5 → careamics-0.1.0rc7}/.pre-commit-config.yaml

@@ -9,14 +9,15 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.16
+    rev: v0.18
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.4.7
     hooks:
       - id: ruff
+        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*"
         args: [--fix, --target-version, py38]
 
   - repo: https://github.com/psf/black
@@ -29,6 +30,7 @@ repos:
     hooks:
       - id: mypy
         files: "^src/"
+        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*"
         additional_dependencies:
           - numpy
           - types-PyYAML
@@ -39,15 +41,16 @@ repos:
     rev: v1.7.0
     hooks:
       - id: numpydoc-validation
+        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/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
+  # # 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

{careamics-0.1.0rc5 → careamics-0.1.0rc7}/PKG-INFO

@@ -1,30 +1,32 @@
 Metadata-Version: 2.3
 Name: careamics
-Version: 0.1.0rc5
+Version: 0.1.0rc7
 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>
+Author-email: Melisande Croft <melisande.croft@fht.org>, Joran Deschamps <joran.deschamps@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 :: 3.8
 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-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
+Requires-Dist: scikit-image<=0.23.2
 Requires-Dist: tifffile
 Requires-Dist: torch>=2.0.0
-Requires-Dist: zarr
+Requires-Dist: torchvision
+Requires-Dist: zarr<3.0.0
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'
 Requires-Dist: pytest; extra == 'dev'

{careamics-0.1.0rc5 → careamics-0.1.0rc7}/examples/2D/n2v/example_BSD68_lightning.ipynb

@@ -18,11 +18,7 @@
     "    CAREamicsPredictDataModule,\n",
     "    CAREamicsTrainDataModule,\n",
     ")\n",
-<<<<<<< Updated upstream
     "from careamics.lightning_prediction import CAREamicsPredictionLoop\n",
-=======
-    "from careamics.lightning_prediction import CAREamicsFiring\n",
->>>>>>> Stashed changes
     "from careamics.utils.metrics import psnr"
    ]
   },
@@ -172,11 +168,7 @@
     "train_data_module = CAREamicsTrainDataModule(\n",
     "    train_data=train_path,\n",
     "    val_data=val_path,\n",
-<<<<<<< Updated upstream
     "    data_type=\"tiff\",  # to use np.ndarray, set data_type to \"array\"\n",
-=======
-    "    data_type=\"tiff\",\n",
->>>>>>> Stashed changes
     "    patch_size=(64, 64),\n",
     "    axes=\"SYX\",\n",
     "    batch_size=128,\n",