PyOPIA 2.8.1__tar.gz → 2.9.0__tar.gz

pyopia-2.9.0/.gitignore

@@ -0,0 +1,277 @@
+
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+.python-version
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+.mr.developer.cfg
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+.pydevproject
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+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
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+# Pyre type checker
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+### Vim ###
+# Swap
+[._]*.s[a-v][a-z]
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+Session.vim
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+.vscode
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+!.vscode/settings.json
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+.history
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+### ipynb checkpoints
+**/*.ipynb_checkpoints/
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+*.zip
+notebooks/header.tfl.txt
+notebooks/keras_model.h5
+notebooks/github-test-holo.ipynb
+
+test-report/*
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+.DS_Store
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+
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+model/*
+notebooks/model/*
+*.keras
+*.png
+*-summary.txt
+/dev/*

{pyopia-2.8.1 → pyopia-2.9.0}/PKG-INFO

@@ -1,59 +1,62 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: PyOPIA
-Version: 2.8.1
+Version: 2.9.0
 Summary: A Python Ocean Particle Image Analysis toolbox.
-Home-page: https://github.com/sintef/pyopia
-Keywords: Ocean,Particles,Imaging,Measurement,Size distribution
-Author: Emlyn Davies
-Author-email: emlyn.davies@sintef.no
-Requires-Python: >=3.12,<4.0
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.12
-Provides-Extra: classification
-Provides-Extra: classification-arm64
-Requires-Dist: cmocean (>=3.0.3,<4.0.0)
-Requires-Dist: dask (>=2024.8.1)
-Requires-Dist: flake8 (>=6.1.0,<7.0.0)
-Requires-Dist: gdown (>=4.7.1,<5.0.0)
-Requires-Dist: h5netcdf (>=1.3.0)
-Requires-Dist: h5py (>=3.9.0,<4.0.0)
-Requires-Dist: imageio (>=2.31.3,<3.0.0)
-Requires-Dist: ipykernel (>=6.19.4)
-Requires-Dist: jupyter-book (>=0.15.1,<0.16.0)
-Requires-Dist: keras (==3.5.0) ; extra == "classification-arm64" or extra == "classification"
-Requires-Dist: matplotlib (>=3.7)
-Requires-Dist: myst-nb (>=0.17.2,<0.18.0)
-Requires-Dist: nbclient (==0.7)
-Requires-Dist: nbconvert (>=7.16.4,<8.0.0)
-Requires-Dist: numpy (>=1.24.0,<2.0.0)
-Requires-Dist: pandas[computation] (>=2.1.1,<3.0.0)
-Requires-Dist: poetry-version-plugin (>=0.2.0,<0.3.0)
-Requires-Dist: pytest (>=7.2.0)
-Requires-Dist: pytest-error-for-skips (>=2.0.2,<3.0.0)
-Requires-Dist: readthedocs-sphinx-search (>=0.3.2,<0.4.0)
-Requires-Dist: scikit-image (>=0.24.0,<0.25.0)
-Requires-Dist: scipy (>=1.11.2,<2.0.0)
-Requires-Dist: sphinx (==5.0)
-Requires-Dist: sphinx-copybutton (>=0.5.2,<0.6.0)
-Requires-Dist: sphinx-rtd-theme (>=0.5.0)
-Requires-Dist: sphinx-togglebutton (>=0.3.2,<0.4.0)
-Requires-Dist: sphinxcontrib-napoleon (>=0.7)
-Requires-Dist: tensorflow-cpu (>=2.16.2,<3.0.0) ; extra == "classification"
-Requires-Dist: tensorflow-macos (>=2.16.2,<3.0.0) ; (sys_platform == "darwin" and platform_machine == "arm64") and (extra == "classification-arm64")
-Requires-Dist: toml (>=0.10.2,<0.11.0)
-Requires-Dist: tqdm (>=4.66.1,<5.0.0)
-Requires-Dist: typer[all] (>=0.9.0,<0.10.0)
-Requires-Dist: urllib3 (<2.0)
-Requires-Dist: xarray (>=2023.12.0,<2024.0.0)
-Project-URL: Documentation, https://pyopia.readthedocs.io
 Project-URL: Repository, https://github.com/sintef/pyopia
+Project-URL: Documentation, https://pyopia.readthedocs.io
+Author-email: Emlyn Davies <emlyn.davies@sintef.no>, "Alex Nimmo Smith@plymouth.ac.uk" <alex.nimmo.smith@plymouth.ac.uk>
+License-File: LICENSE
+Keywords: Imaging,Measurement,Ocean,Particles,Size distribution
+Requires-Python: ~=3.12
+Requires-Dist: cmocean<4,>=3.0.3
+Requires-Dist: dask>=2024.8.1
+Requires-Dist: flake8<7,>=6.1.0
+Requires-Dist: gdown<5,>=4.7.1
+Requires-Dist: h5netcdf>=1.3.0
+Requires-Dist: h5py<4,>=3.9.0
+Requires-Dist: imageio<3,>=2.31.3
+Requires-Dist: ipykernel>=6.19.4
+Requires-Dist: jupyter-book<0.16,>=0.15.1
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: myst-nb<0.18,>=0.17.2
+Requires-Dist: nbclient==0.7
+Requires-Dist: nbconvert<8,>=7.16.4
+Requires-Dist: numpy<2,>=1.24.0
+Requires-Dist: pandas[computation]<3,>=2.1.1
+Requires-Dist: poetry-version-plugin<0.3,>=0.2.0
+Requires-Dist: pytest-error-for-skips<3,>=2.0.2
+Requires-Dist: pytest>=7.2.0
+Requires-Dist: readthedocs-sphinx-search<0.4,>=0.3.2
+Requires-Dist: scikit-image<0.25,>=0.24.0
+Requires-Dist: scipy<2,>=1.11.2
+Requires-Dist: sphinx-copybutton<0.6,>=0.5.2
+Requires-Dist: sphinx-rtd-theme>=0.5.0
+Requires-Dist: sphinx-togglebutton<0.4,>=0.3.2
+Requires-Dist: sphinx==5.0
+Requires-Dist: sphinxcontrib-napoleon>=0.7
+Requires-Dist: toml<0.11,>=0.10.2
+Requires-Dist: tqdm<5,>=4.66.1
+Requires-Dist: typer[all]<0.10,>=0.9.0
+Requires-Dist: urllib3<2.0
+Requires-Dist: xarray<2024,>=2023.12.0
+Provides-Extra: classification
+Requires-Dist: keras==3.5.0; extra == 'classification'
+Requires-Dist: tensorflow<3,>=2.16.2; extra == 'classification'
 Description-Content-Type: text/markdown
 
-PyOpia
+PyOPIA
 ===============================
 
 A Python Ocean Particle Image Analysis toolbox
 
+# Quick tryout of PyOPIA
+
+1) Install [uv](https://docs.astral.sh/uv/getting-started/installation)
+2) Run PyOPIA classification tests on database particles
+```bash
+uv run --python 3.12 --with git+https://github.com/SINTEF/pyopia --with tensorflow==2.16.2 --with keras==3.5.0 python -m pyopia.tests.test_classify
+```
+
 # Documentation:
 
 [![Jupyter Book Badge](https://jupyterbook.org/badge.svg)](https://pyopia.readthedocs.io) [![Documentation](https://readthedocs.org/projects/pyopia/badge/?version=latest)](https://pyopia.readthedocs.io/en/latest/?badge=latest)
@@ -104,9 +107,8 @@ Users are expected to be familiar with Python. Please refer to the recommended i
 
 ## For developers from source
 
-Install [Python](https://github.com/conda-forge/miniforge/#download) version 3.10.
 
-A prompt such as is provided by the [miniforge installation](https://github.com/conda-forge/miniforge/#download) may be used for the following:
+Install (uv)[https://docs.astral.sh/uv/getting-started/installation/]
 
 1. Navigate to the folder where you want to install pyopia using the 'cd' command.
 
@@ -118,44 +120,18 @@ git clone https://github.com/SINTEF/pyopia.git
 cd pyopia
 ```
 
-For the next steps, you need to be located in the directory that contains the file 'environment.yml'.
-
-1. (optional, but recommended) Create a virtual environment using the environment.yml. This will create an environment called pyopia, but with no dependencies installed. Dependencies are managed by poetry (in step 2):
-
-```bash
-conda env create -f environment.yml
-```
-and activate the environment:
-
-```bash
-conda activate pyopia
-```
+For the next steps, you need to be located in the PyOPIA root directory that contains the file 'pyproject.toml'.
 
-2. Install dependencies using poetry:
+2. Install all requirements with
 
 ```bash
-poetry install
+uv sync --all-extras
 ```
 
-Optional dependecies (for classification), can be installed like this:
-
-```bash
-poetry install --extras "classification"
-```
-
-or for arm/silicon systems:
-
-```bash
-poetry install --extras "classification-arm64"
-```
-
-Note: If poetry spends ages resolving dependencies, you can install a development environment with pip, like this: `pip install -e ".[classification]"` or for arm/silicon: `pip install -e ".[classification-arm64]"`
-
-
 3. (optional) Run local tests:
 
 ```bash
-poetry run pytest
+uv run pytest
 ```
 
 #### Version numbering
@@ -178,4 +154,3 @@ sphinx-build -b html ./docs/ ./docs/build
 # License
 
 PyOpia is licensed under the BSD3 license. See LICENSE. All contributors should be recognised & aknowledged.
-

{pyopia-2.8.1 → pyopia-2.9.0}/README.md

@@ -1,8 +1,16 @@
-PyOpia
+PyOPIA
 ===============================
 
 A Python Ocean Particle Image Analysis toolbox
 
+# Quick tryout of PyOPIA
+
+1) Install [uv](https://docs.astral.sh/uv/getting-started/installation)
+2) Run PyOPIA classification tests on database particles
+```bash
+uv run --python 3.12 --with git+https://github.com/SINTEF/pyopia --with tensorflow==2.16.2 --with keras==3.5.0 python -m pyopia.tests.test_classify
+```
+
 # Documentation:
 
 [![Jupyter Book Badge](https://jupyterbook.org/badge.svg)](https://pyopia.readthedocs.io) [![Documentation](https://readthedocs.org/projects/pyopia/badge/?version=latest)](https://pyopia.readthedocs.io/en/latest/?badge=latest)
@@ -53,9 +61,8 @@ Users are expected to be familiar with Python. Please refer to the recommended i
 
 ## For developers from source
 
-Install [Python](https://github.com/conda-forge/miniforge/#download) version 3.10.
 
-A prompt such as is provided by the [miniforge installation](https://github.com/conda-forge/miniforge/#download) may be used for the following:
+Install (uv)[https://docs.astral.sh/uv/getting-started/installation/]
 
 1. Navigate to the folder where you want to install pyopia using the 'cd' command.
 
@@ -67,44 +74,18 @@ git clone https://github.com/SINTEF/pyopia.git
 cd pyopia
 ```
 
-For the next steps, you need to be located in the directory that contains the file 'environment.yml'.
-
-1. (optional, but recommended) Create a virtual environment using the environment.yml. This will create an environment called pyopia, but with no dependencies installed. Dependencies are managed by poetry (in step 2):
-
-```bash
-conda env create -f environment.yml
-```
-and activate the environment:
-
-```bash
-conda activate pyopia
-```
+For the next steps, you need to be located in the PyOPIA root directory that contains the file 'pyproject.toml'.
 
-2. Install dependencies using poetry:
+2. Install all requirements with
 
 ```bash
-poetry install
+uv sync --all-extras
 ```
 
-Optional dependecies (for classification), can be installed like this:
-
-```bash
-poetry install --extras "classification"
-```
-
-or for arm/silicon systems:
-
-```bash
-poetry install --extras "classification-arm64"
-```
-
-Note: If poetry spends ages resolving dependencies, you can install a development environment with pip, like this: `pip install -e ".[classification]"` or for arm/silicon: `pip install -e ".[classification-arm64]"`
-
-
 3. (optional) Run local tests:
 
 ```bash
-poetry run pytest
+uv run pytest
 ```
 
 #### Version numbering

pyopia-2.9.0/pyopia/__init__.py

@@ -0,0 +1 @@
+__version__ = "2.9.1"

{pyopia-2.8.1 → pyopia-2.9.0}/pyopia/cli.py

@@ -172,28 +172,13 @@ def process(config_filename: str, num_chunks: int = 1, strategy: str = 'block'):
 
         progress.console.print("[blue]INITIALISE PIPELINE")
 
-    def process_file_list(file_list, c):
-        processing_pipeline = pyopia.pipeline.Pipeline(pipeline_config)
-
-        with get_custom_progress_bar(f'[blue]Processing progress (chunk {c})', disable=c != 0) as pbar:
-            for filename in pbar.track(file_list, description=f'[blue]Processing progress (chunk {c})'):
-                try:
-                    logger.debug(f'Chunk {c} starting to process {filename}')
-                    processing_pipeline.run(filename)
-                except Exception as e:
-                    logger.warning('[red]An error occured in processing, ' +
-                                   'skipping rest of pipeline and moving to next image.' +
-                                   f'(chunk {c})')
-                    logger.error(e)
-                    logger.debug(''.join(traceback.format_tb(e.__traceback__)))
-
     # With one chunk we keep the non-multiprocess functionality to ensure backwards compatibility
     job_list = []
     if num_chunks == 1:
-        process_file_list(raw_files, 0)
+        process_file_list(raw_files, pipeline_config, 0)
     else:
         for c, chunk in enumerate(raw_files.chunked_files):
-            job = multiprocessing.Process(target=process_file_list, args=(chunk, c))
+            job = multiprocessing.Process(target=process_file_list, args=(chunk, pipeline_config, c))
             job_list.append(job)
 
     # Start all the jobs
@@ -239,6 +224,38 @@ def merge_mfdata(path_to_data: str, prefix='*', overwrite_existing_partials: boo
                                        chunk_size=chunk_size)
 
 
+def process_file_list(file_list, pipeline_config, c):
+    '''Run a PyOPIA processing pipeline for a chuncked list of files based on a given config.toml
+
+    Parameters
+    ----------
+    file_list : str
+        List of file paths to process, where each file will be passed individually through the processing pipeline
+
+    pipeline_config : str
+        Loaded config.toml file to initialize the processing pipeline and setup logging
+
+    c : int
+        Chunk index for tracking progress and logging. If set to 0, enables the
+        progress bar; for other values, the progress bar is disabled.
+    '''
+    processing_pipeline = pyopia.pipeline.Pipeline(pipeline_config)
+    setup_logging(pipeline_config)
+    logger = logging.getLogger('rich')
+
+    with get_custom_progress_bar(f'[blue]Processing progress (chunk {c})', disable=c != 0) as pbar:
+        for filename in pbar.track(file_list, description=f'[blue]Processing progress (chunk {c})'):
+            try:
+                logger.debug(f'Chunk {c} starting to process {filename}')
+                processing_pipeline.run(filename)
+            except Exception as e:
+                logger.warning('[red]An error occured in processing, ' +
+                               'skipping rest of pipeline and moving to next image.' +
+                               f'(chunk {c})')
+                logger.error(e)
+                logger.debug(''.join(traceback.format_tb(e.__traceback__)))
+
+
 def setup_logging(pipeline_config):
     '''Configure logging
 

pyopia-2.9.0/pyproject.toml

@@ -0,0 +1,79 @@
+[project]
+name = "PyOPIA"
+version = "2.9.0"
+description = "A Python Ocean Particle Image Analysis toolbox."
+authors = [
+    { name = "Emlyn Davies", email = "emlyn.davies@sintef.no" },
+    { name = "Alex Nimmo Smith@plymouth.ac.uk", email = "alex.nimmo.smith@plymouth.ac.uk" },
+]
+requires-python = "~=3.12"
+readme = "README.md"
+keywords = [
+    "Ocean",
+    "Particles",
+    "Imaging",
+    "Measurement",
+    "Size distribution",
+]
+dependencies = [
+    "flake8>=6.1.0,<7",
+    "numpy>=1.24.0,<2",
+    "scipy>=1.11.2,<2",
+    "pytest>=7.2.0",
+    "imageio>=2.31.3,<3",
+    "matplotlib>=3.7",
+    "tqdm>=4.66.1,<5",
+    "pytest-error-for-skips>=2.0.2,<3",
+    "nbclient==0.7",
+    "sphinx==5.0",
+    "sphinx-rtd-theme>=0.5.0",
+    "sphinxcontrib-napoleon>=0.7",
+    "sphinx-togglebutton>=0.3.2,<0.4",
+    "sphinx-copybutton>=0.5.2,<0.6",
+    "readthedocs-sphinx-search>=0.3.2,<0.4",
+    "myst-nb>=0.17.2,<0.18",
+    "jupyter-book>=0.15.1,<0.16",
+    "ipykernel>=6.19.4",
+    "urllib3<2.0",
+    "gdown>=4.7.1,<5",
+    "cmocean>=3.0.3,<4",
+    "toml>=0.10.2,<0.11",
+    "xarray>=2023.12.0,<2024",
+    "typer[all]>=0.9.0,<0.10",
+    "pandas[computation]>=2.1.1,<3",
+    "h5py>=3.9.0,<4",
+    "poetry-version-plugin>=0.2.0,<0.3",
+    "dask>=2024.8.1",
+    "nbconvert>=7.16.4,<8",
+    "h5netcdf>= 1.3.0",
+    "scikit-image>=0.24.0,<0.25",
+]
+
+[project.optional-dependencies]
+
+classification = [
+    "tensorflow>=2.16.2,<3",
+    "keras==3.5.0",
+]
+
+[project.urls]
+Repository = "https://github.com/sintef/pyopia"
+Documentation = "https://pyopia.readthedocs.io"
+
+[project.scripts]
+pyopia = "pyopia.cli:app"
+
+[tool.hatch.build.targets.sdist]
+include = ["pyopia"]
+
+[tool.hatch.build.targets.wheel]
+include = ["pyopia"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.poetry-version-plugin]
+source = "init"
+
+[tool.setuptools_scm]

pyopia-2.8.1/pyopia/__init__.py

@@ -1 +0,0 @@
-__version__ = '2.8.1'

pyopia-2.8.1/pyproject.toml

@@ -1,66 +0,0 @@
-[tool.poetry]
-name = "PyOPIA"
-version = "0"
-description = "A Python Ocean Particle Image Analysis toolbox."
-authors = [
-    "Emlyn Davies <emlyn.davies@sintef.no>",
-    "Alex Nimmo Smith@plymouth.ac.uk <alex.nimmo.smith@plymouth.ac.uk>"
-]
-readme = "README.md"
-repository = "https://github.com/sintef/pyopia"
-documentation = "https://pyopia.readthedocs.io"
-keywords = ["Ocean", "Particles", "Imaging", "Measurement", "Size distribution"]
-packages = [{include = "pyopia"}]
-
-[tool.poetry.dependencies]
-python = "^3.12"
-flake8 = "^6.1.0"
-numpy = "^1.24.0"
-scipy = "^1.11.2"
-pytest = ">=7.2.0"
-imageio = "^2.31.3"
-matplotlib = ">=3.7"
-tqdm = "^4.66.1"
-pytest-error-for-skips = "^2.0.2"
-nbclient = "0.7"
-sphinx = "5.0"
-sphinx-rtd-theme = ">=0.5.0"
-sphinxcontrib-napoleon = ">=0.7"
-sphinx-togglebutton = "^0.3.2"
-sphinx-copybutton = "^0.5.2"
-readthedocs-sphinx-search = "^0.3.2"
-myst-nb = "^0.17.2"
-jupyter-book = "^0.15.1"
-ipykernel = ">=6.19.4"
-urllib3 = "<2.0"
-gdown = "^4.7.1"
-cmocean = "^3.0.3"
-toml = "^0.10.2"
-xarray = "^2023.12.0"
-typer = {extras = ["all"], version = "^0.9.0"}
-pandas = {version = "^2.1.1", extras = ["computation"]}
-h5py = "^3.9.0"
-poetry-version-plugin = "^0.2.0"
-tensorflow-macos = {version = "^2.16.2", optional = true, markers = "sys_platform == 'darwin' and platform_machine == 'arm64'"}
-tensorflow-cpu = {version = "^2.16.2", optional = true}
-keras = {version = "3.5.0", optional = true}
-dask = ">=2024.8.1"
-nbconvert = "^7.16.4"
-h5netcdf = ">= 1.3.0"
-scikit-image = "^0.24.0"
-
-[tool.poetry.extras]
-classification-arm64 = ["tensorflow-macos", "keras"]
-classification = ["tensorflow-cpu", "keras"]
-
-[tool.poetry-version-plugin]
-source = "init"
-
-[tool.poetry.scripts]
-pyopia = "pyopia.cli:app"
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
-
-[tool.setuptools_scm]