careamics 0.0.2__tar.gz → 0.0.4__tar.gz

{careamics-0.0.2 → careamics-0.0.4}/.github/workflows/ci.yml

@@ -53,7 +53,7 @@ jobs:
           python -m pip install .[dev] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
 
       - name: 🧪 Run Tests
-        run: pytest --color=yes --cov --cov-config=pyproject.toml --cov-report=xml --cov-report=term-missing 
+        run: pytest --color=yes -m "not lvae"
 
       # If something goes wrong with --pre tests, we can open an issue in the repo
       - name: 📝 Report --pre Failures
@@ -69,11 +69,6 @@ jobs:
           filename: .github/TEST_FAIL_TEMPLATE.md
           update_existing: true
 
-      - name: Coverage
-        uses: codecov/codecov-action@v3
-        with:
-          version: v0.7.3
-
   deploy:
     name: Release
     needs: test

careamics-0.0.4/.github/workflows/codecov.yml

@@ -0,0 +1,49 @@
+name: codecov
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9"]
+        platform: [ubuntu-latest]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        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 .[dev] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+
+      - name: 🧪 Run Tests
+        run: pytest --color=yes --cov --cov-config=pyproject.toml --cov-report=xml --cov-report=term-missing 
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+        with:
+          version: v0.7.3

careamics-0.0.4/.github/workflows/lvae.yml

@@ -0,0 +1,62 @@
+name: lvae
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9"]
+        platform: [ubuntu-latest, windows-latest]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        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 .[dev] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+
+      - name: 🧪 Run Tests
+        run: pytest --color=yes -m lvae
+
+      # 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
+

{careamics-0.0.2 → careamics-0.0.4}/.pre-commit-config.yaml

@@ -9,12 +9,12 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.18
+    rev: v0.19
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.6
+    rev: v0.6.3
     hooks:
       - id: ruff
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*"
@@ -26,11 +26,12 @@ repos:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.1
+    rev: v1.11.2
     hooks:
       - id: mypy
         files: "^src/"
-        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*"
+        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
@@ -38,10 +39,10 @@ repos:
 
   # check docstrings
   - repo: https://github.com/numpy/numpydoc
-    rev: v1.8.0rc2
+    rev: v1.8.0
     hooks:
       - id: numpydoc-validation
-        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*"      
+        exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/losses/lvae/.*"      
 
   # # jupyter linting and formatting
   # - repo: https://github.com/nbQA-dev/nbQA

{careamics-0.0.2 → careamics-0.0.4}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.3
 Name: careamics
-Version: 0.0.2
+Version: 0.0.4
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
-Author-email: Melisande Croft <melisande.croft@fht.org>, Joran Deschamps <joran.deschamps@fht.org>, Igor Zubarev <igor.zubarev@fht.org>
+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
@@ -16,16 +16,17 @@ 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: bioimageio-core>=0.6.9
 Requires-Dist: numpy<2.0.0
 Requires-Dist: psutil
-Requires-Dist: pydantic>=2.5
+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: zarr<3.0.0
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'

careamics-0.0.4/codecov.yml

@@ -0,0 +1,5 @@
+coverage:
+  status:
+    project:
+      default:
+        threshold: 2%

careamics-0.0.4/mypy.ini

@@ -0,0 +1,17 @@
+[mypy]
+ignore_missing_imports = True
+
+[mypy-careamics.lvae_training.*]
+follow_imports = skip
+
+[mypy-careamics.models.lvae.*]
+follow_imports = skip
+
+[mypy-careamics.losses.loss_factory]
+follow_imports = skip
+
+[mypy-careamics.losses.lvae.losses]
+follow_imports = skip
+
+[mypy-careamics.config.likelihood_model]
+follow_imports = skip

{careamics-0.0.2 → careamics-0.0.4}/pyproject.toml

@@ -23,8 +23,12 @@ readme = "README.md"
 requires-python = ">=3.9"
 license = { text = "BSD-3-Clause" }
 authors = [
+    { name = 'CAREamics team', email = 'rse@fht.org' },
+    { name = 'Ashesh', email = 'ashesh.ashesh@fht.org' },
+    { name = 'Federico Carrara', email = 'federico.carrara@fht.org' },
     { name = 'Melisande Croft', email = 'melisande.croft@fht.org' },
     { name = 'Joran Deschamps', email = 'joran.deschamps@fht.org' },
+    { name = 'Vera Galinova', email = 'vera.galinova@fht.org' },
     { name = 'Igor Zubarev', email = 'igor.zubarev@fht.org' },
 ]
 classifiers = [
@@ -41,12 +45,13 @@ dependencies = [
     'numpy<2.0.0',
     'torch>=2.0.0',
     'torchvision',
-    'bioimageio.core>=0.6.0',
+    'bioimageio.core>=0.6.9',
     'tifffile',
     'psutil',
-    'pydantic>=2.5',
+    'pydantic>=2.5,<2.9',
     'pytorch_lightning>=2.2.0',
     'pyyaml',
+    'typer==0.12.3',
     'scikit-image<=0.23.2',
     'zarr<3.0.0',
 ]
@@ -71,6 +76,10 @@ tensorboard = ["tensorboard", "protobuf==3.20.3"]
 homepage = "https://careamics.github.io/"
 repository = "https://github.com/CAREamics/careamics"
 
+# cli
+[project.scripts]
+careamics = "careamics.cli.main:run"
+
 # https://beta.ruff.rs/docs
 [tool.ruff]
 line-length = 88
@@ -137,7 +146,10 @@ filterwarnings = [
 ]
 addopts = "-p no:doctest"
 
-#markers = ["gpu: marks tests as requiring gpu"]
+markers = [
+    # "gpu: marks tests as requiring gpu",
+    "lvae: marks tests as testing lvae",
+]
 
 # https://coverage.readthedocs.io/en/6.4/config.html
 [tool.coverage.report]
@@ -181,3 +193,4 @@ exclude = [ # don't report on objects that match any of these regex
     "test_*",
     "src/careamics/lvae_training/*",
 ]
+

{careamics-0.0.2 → careamics-0.0.4}/src/careamics/careamist.py

@@ -13,10 +13,7 @@ from pytorch_lightning.callbacks import (
 )
 from pytorch_lightning.loggers import TensorBoardLogger, WandbLogger
 
-from careamics.config import (
-    Configuration,
-    load_configuration,
-)
+from careamics.config import Configuration, FCNAlgorithmConfig, load_configuration
 from careamics.config.support import (
     SupportedAlgorithm,
     SupportedArchitecture,
@@ -25,7 +22,7 @@ from careamics.config.support import (
 )
 from careamics.dataset.dataset_utils import reshape_array
 from careamics.lightning import (
-    CAREamicsModule,
+    FCNModule,
     HyperParametersCallback,
     PredictDataModule,
     ProgressBarCallback,
@@ -51,8 +48,6 @@ class CAREamist:
     work_dir : str, optional
         Path to working directory in which to save checkpoints and logs,
         by default None.
-    experiment_name : str, by default "CAREamics"
-        Experiment name used for checkpoints.
     callbacks : list of Callback, optional
         List of callbacks to use during training and prediction, by default None.
 
@@ -78,8 +73,7 @@ class CAREamist:
     def __init__(  # numpydoc ignore=GL08
         self,
         source: Union[Path, str],
-        work_dir: Optional[str] = None,
-        experiment_name: str = "CAREamics",
+        work_dir: Optional[Union[Path, str]] = None,
         callbacks: Optional[list[Callback]] = None,
     ) -> None: ...
 
@@ -87,8 +81,7 @@ class CAREamist:
     def __init__(  # numpydoc ignore=GL08
         self,
         source: Configuration,
-        work_dir: Optional[str] = None,
-        experiment_name: str = "CAREamics",
+        work_dir: Optional[Union[Path, str]] = None,
         callbacks: Optional[list[Callback]] = None,
     ) -> None: ...
 
@@ -96,7 +89,6 @@ class CAREamist:
         self,
         source: Union[Path, str, Configuration],
         work_dir: Optional[Union[Path, str]] = None,
-        experiment_name: str = "CAREamics",
         callbacks: Optional[list[Callback]] = None,
     ) -> None:
         """
@@ -109,18 +101,13 @@ class CAREamist:
 
         If no working directory is provided, the current working directory is used.
 
-        If `source` is a checkpoint, then `experiment_name` is used to name the
-        checkpoint, and is recorded in the configuration.
-
         Parameters
         ----------
         source : pathlib.Path or str or CAREamics Configuration
             Path to a configuration file or a trained model.
-        work_dir : str, optional
+        work_dir : str or pathlib.Path, optional
             Path to working directory in which to save checkpoints and logs,
             by default None.
-        experiment_name : str, optional
-            Experiment name used for checkpoints, by default "CAREamics".
         callbacks : list of Callback, optional
             List of callbacks to use during training and prediction, by default None.
 
@@ -148,9 +135,12 @@ class CAREamist:
             self.cfg = source
 
             # instantiate model
-            self.model = CAREamicsModule(
-                algorithm_config=self.cfg.algorithm_config,
-            )
+            if isinstance(self.cfg.algorithm_config, FCNAlgorithmConfig):
+                self.model = FCNModule(
+                    algorithm_config=self.cfg.algorithm_config,
+                )
+            else:
+                raise NotImplementedError("Architecture not supported.")
 
         # path to configuration file or model
         else:
@@ -164,9 +154,12 @@ class CAREamist:
                 self.cfg = load_configuration(source)
 
                 # instantiate model
-                self.model = CAREamicsModule(
-                    algorithm_config=self.cfg.algorithm_config,
-                )
+                if isinstance(self.cfg.algorithm_config, FCNAlgorithmConfig):
+                    self.model = FCNModule(
+                        algorithm_config=self.cfg.algorithm_config,
+                    )  # type: ignore
+                else:
+                    raise NotImplementedError("Architecture not supported.")
 
             # attempt loading a pre-trained model
             else:
@@ -192,6 +185,13 @@ class CAREamist:
         # instantiate trainer
         self.trainer = Trainer(
             max_epochs=self.cfg.training_config.num_epochs,
+            precision=self.cfg.training_config.precision,
+            max_steps=self.cfg.training_config.max_steps,
+            check_val_every_n_epoch=self.cfg.training_config.check_val_every_n_epoch,
+            enable_progress_bar=self.cfg.training_config.enable_progress_bar,
+            accumulate_grad_batches=self.cfg.training_config.accumulate_grad_batches,
+            gradient_clip_val=self.cfg.training_config.gradient_clip_val,
+            gradient_clip_algorithm=self.cfg.training_config.gradient_clip_algorithm,
             callbacks=self.callbacks,
             default_root_dir=self.work_dir,
             logger=self.experiment_logger,
@@ -247,6 +247,12 @@ class CAREamist:
                 EarlyStopping(self.cfg.training_config.early_stopping_callback)
             )
 
+    def stop_training(self) -> None:
+        """Stop the training loop."""
+        # raise stop training flag
+        self.trainer.should_stop = True
+        self.trainer.limit_val_batches = 0  # skip  validation
+
     # TODO: is there are more elegant way than calling train again after _train_on_paths
     def train(
         self,
@@ -393,9 +399,14 @@ class CAREamist:
         datamodule : TrainDataModule
             Datamodule to train on.
         """
-        # record datamodule
+        # register datamodule
         self.train_datamodule = datamodule
 
+        # set defaults (in case `stop_training` was called before)
+        self.trainer.should_stop = False
+        self.trainer.limit_val_batches = 1.0  # 100%
+
+        # train
         self.trainer.fit(self.model, datamodule=datamodule)
 
     def _train_on_array(
@@ -511,7 +522,7 @@ class CAREamist:
         tile_overlap: tuple[int, ...] = (48, 48),
         axes: Optional[str] = None,
         data_type: Optional[Literal["tiff", "custom"]] = None,
-        tta_transforms: bool = True,
+        tta_transforms: bool = False,
         dataloader_params: Optional[dict] = None,
         read_source_func: Optional[Callable] = None,
         extension_filter: str = "",
@@ -527,7 +538,7 @@ class CAREamist:
         tile_overlap: tuple[int, ...] = (48, 48),
         axes: Optional[str] = None,
         data_type: Optional[Literal["array"]] = None,
-        tta_transforms: bool = True,
+        tta_transforms: bool = False,
         dataloader_params: Optional[dict] = None,
     ) -> Union[list[NDArray], NDArray]: ...
 
@@ -540,7 +551,7 @@ class CAREamist:
         tile_overlap: Optional[tuple[int, ...]] = (48, 48),
         axes: Optional[str] = None,
         data_type: Optional[Literal["array", "tiff", "custom"]] = None,
-        tta_transforms: bool = True,
+        tta_transforms: bool = False,
         dataloader_params: Optional[dict] = None,
         read_source_func: Optional[Callable] = None,
         extension_filter: str = "",

careamics-0.0.4/src/careamics/cli/__init__.py

@@ -0,0 +1,5 @@
+"""
+Package containing functions called by the careamics cli.
+
+Built using third party package Typer.
+"""