kval 0.3.0__tar.gz

kval-0.3.0/.github/workflows/ci_pytest_kval_macOS.yml

@@ -0,0 +1,35 @@
+name: Run Tests for Kval (MacOS)
+
+on:   
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [macos-latest]
+        python-version: [ "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3  # Use the latest version of actions/checkout
+
+    - name: Set up Python
+      uses: actions/setup-python@v4  # Use the latest version of actions/setup-python
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+        pip install -e '.[dev]'  # This installs the optional dev dependencies, including pytest
+
+    - name: Run tests
+      run: |
+        pytest
+      env:
+        CI: true

kval-0.3.0/.github/workflows/ci_pytest_kval_ubuntu.yml

@@ -0,0 +1,33 @@
+name: Run Tests for Kval (Ubuntu)
+
+on:   
+  workflow_dispatch:
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [ "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3  # Use the latest version of actions/checkout
+
+    - name: Set up Python
+      uses: actions/setup-python@v4  # Use the latest version of actions/setup-python
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+        pip install -e '.[dev]'  # This installs the optional dev dependencies, including pytest
+
+    - name: Run tests
+      run: |
+        pytest
+      env:
+        CI: true

kval-0.3.0/.github/workflows/ci_pytest_kval_ubuntu_py11.yml

@@ -0,0 +1,33 @@
+name: Run Tests for Kval (Ubuntu) (py3.11 only)
+
+on:   
+  workflow_dispatch:
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [ "3.9",]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3  # Use the latest version of actions/checkout
+
+    - name: Set up Python
+      uses: actions/setup-python@v4  # Use the latest version of actions/setup-python
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+        pip install -e '.[dev]'  # This installs the optional dev dependencies, including pytest
+
+    - name: Run tests
+      run: |
+        pytest
+      env:
+        CI: true

kval-0.3.0/.github/workflows/ci_pytest_kval_win.yml

@@ -0,0 +1,35 @@
+name: Run Tests for Kval (Win)
+
+on:   
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ windows-latest]
+        python-version: [ "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3  # Use the latest version of actions/checkout
+
+    - name: Set up Python
+      uses: actions/setup-python@v4  # Use the latest version of actions/setup-python
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+        pip install -e '.[dev]'  # This installs the optional dev dependencies, including pytest
+
+    - name: Run tests
+      run: |
+        pytest
+      env:
+        CI: true

kval-0.3.0/.gitignore

@@ -0,0 +1,75 @@
+#### Øyvind's:
+
+*.pyc
+*.rsk
+development/
+dist/
+kval_local_files
+tests/test_data/rbr_files
+
+#### Defaults:
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+*$py.class
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# mkdocs documentation
+/sitedist/

kval-0.3.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Norwegian Polar Institute Oceanography section
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

kval-0.3.0/PKG-INFO

@@ -0,0 +1,185 @@
+Metadata-Version: 2.4
+Name: kval
+Version: 0.3.0
+Summary: Tools for oceanographic data processing and analysis in Python
+Project-URL: Homepage, https://github.com/NPIOcean/kval/
+Author-email: Øyvind Foss <oyvind.foss@npolar.no>
+Maintainer: Norwegian Polar Institute, Oceanography section
+Maintainer-email: "Øyvind Foss, NPI" <oyvind.foss@npolar.no>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3 :: Only
+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: Topic :: Scientific/Engineering :: Oceanography
+Requires-Python: >=3.9
+Requires-Dist: cartopy>=0.21.1
+Requires-Dist: cftime>=1.6.2
+Requires-Dist: cmocean>=3.0.3
+Requires-Dist: glob2>=0.7
+Requires-Dist: ipykernel>=6.26.0
+Requires-Dist: ipympl>=0.9.3
+Requires-Dist: jupyter>=1.0.0
+Requires-Dist: matplotlib>=3.7.2
+Requires-Dist: mplcursors>=0.5.3
+Requires-Dist: numpy>=1.23
+Requires-Dist: pandas>=2.1.0
+Requires-Dist: pygeomag>=1.1.0
+Requires-Dist: pyrsktools>=1.1.1
+Requires-Dist: scipy>=1.11.3
+Requires-Dist: seawater>=3.3.4
+Requires-Dist: tqdm>=4.66.1
+Requires-Dist: xarray>=2023.10.1
+Requires-Dist: xlrd>=2.0.1
+Provides-Extra: compliance
+Requires-Dist: compliance-checker>=5.1.0; extra == 'compliance'
+Provides-Extra: dev
+Requires-Dist: pytest>=8.1.1; extra == 'dev'
+Description-Content-Type: text/markdown
+
+![image](graphics/kval_banner.png)
+
+Collection of Python functions for working with oceanography data processing and analysis.
+
+Maintained by the Oceanography section at the [Norwegian Polar Institute](https://www.npolar.no/en/).
+
+Supported by the project [HiAOOS](https://hiaoos.eu/).
+___
+
+Last release,`0.3.0`:
+
+
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15229098.svg)](https://doi.org/10.5281/zenodo.15229098)
+
+
+
+- This version is used to work out pypi and conda distribution.
+- An updated version with improved documentation and a code overhaul is planned for Spring 2025.
+
+__
+
+*In active development.*
+
+____
+<details>
+<summary><strong>CORE FUNCTIONALITY</strong></summary>
+
+##### Submodules
+
+
+- `file`: Converting to and from various file format (e.g. read CTD .cnv data to xarray/netCDF)
+- `data`: Data post-processing and QC (e.g. CTD post-processing)
+- `metadata`: Handling and standardizing metadata according to CF conventions
+- `plots*`: Various tools to help make nice (matplotlib) figures
+- `maps`: Tools for making maps
+- `geo`: Geographical calculations (coordinate transformations, point-to-point distances etc)
+- `ocean`: Oceanography-specific tools (e.g. (`*`) vertical modes, turner angles, wkb scaling, geostrophical calculations)
+- `calc`: Various useful functions for numerical calculations.
+- `util`: Various backend support functions and wrappers for xarray functionality.
+- `signal`: Filtering, spectral analysis, etc.
+
+`*` Not implemented
+
+</details>
+
+____
+
+<details>
+<summary><strong>GENERAL PRINCIPLES</strong></summary>
+
+*Note: These are aspirational guidelines and not always adhered to in the current code structure. We will try to get there!*
+
+###### Code
+
+- Written in Python (>=3.8).
+- Tailored for use in a [Jupyter] notebook environment.
+- Data and metadata should be stored in [xarray(https://docs.xarray.dev/en/stable/)] `Datasets`.
+    - Intermediate operations using, e.g., `numpy` or `pandas` objects are fine, but the end user should only interact with `Datasets`.
+- Code should adhere to [PEP8](https://peps.python.org/pep-0008/) style guide, and all functions should have docstrings.
+- All functionality should have associated [pytest](https://docs.pytest.org/en/7.4.x/) tests.
+    - Unit tests of individual functions are found in `tests/unit_tests/`. Its directory structure and contents should mirror that of `src/kval`.
+    - Tests of more complex functionality (e.g. processing pipelines using multiple modules) should be put in  `tests/functional_tests/`.
+    - A collection of sample data to be used in testing is found in `tests/test_data/`. Should aim to cover a wide range of input data, but we also don't want this to become *too* bulky - try to keep file size to a minimum.
+
+###### Metadata
+
+- All operations that modify data should be recorded in the file metadata.
+- Wherever possibly, and at as early a stage as possible, all available useful metadata should be added to Datasets.
+- Metadata formatting should adhere to [CF](http://cfconventions.org/) and [ACDD](https://wiki.esipfed.org/Attribute_Convention_for_Data_Discovery_1-3) conventions, supplemented by:
+    - [OceanSITES](http://www.oceansites.org/docs/oceansites_data_format_reference_manual_20140917.pdf)
+    - [2021 NPI NetCDF guidelines](https://gitlab.com/npolar/netcdf-creator/-/blob/main/docs/netcdf_standard_npi.pdf?ref_type=heads)
+
+###### Project
+
+- The project is maintained by the Oceanography section at the [Norwegian Polar Institute](www.npolar.no/en).
+    - External contributions (pull requests, issues, whatever) are very welcome!
+- We will attempt to follow the guidelines from the
+  [Scientific Python Library Development Guide](https://learn.scientific-python.org/development/).
+- *Releases* will be published relatively often, whenever a new functionality has been added.
+   Releases will be archived on [zenodo](www.zenodo.org) and given a DOI.
+
+###### Contributing
+
+Pull requests, issues, etc are very welcome!
+
+*[Something about branches here]*
+
+*[Something about python style, test suite]*
+
+
+</details>
+
+____
+
+
+<details>
+<summary><strong>RELEASE NOTES</strong></summary>
+
+
+
+
+
+- **0.3.0** *(CURRENT, released 16 April 2025)*:
+    - Refactoring of large parts of the code for structure, clarity and efficiency.
+    - ~~Complete reproducability and self-documentation in the CTD processing functionality.~~
+    - Adding mooring processing functionality
+        - ~~Functionality for parsing moored CTD sensors (RBR and SBE)~~
+        - Functionality for basic processing source file -> CF-NetCDF
+    - ~~Test suite (comprehensive but not entirely complete)~~
+    - ~~Decluttering the repo bringing it down from its currently bloated state.~~
+    - Started useful documentation with somenotebook examples (need a lot of work).
+    - Released to PyPi and conda-forge.
+    - Many other improvements and additions.
+
+
+- **0.4.0** *(PLANNED for spring 2025)*
+
+- Complete (useful) documentation with good notebook examples of core functionality.
+- Expanded test suite for good coverage of basic functionality plus
+- *Possibly*:
+    - Parsing data from inductive loggers.
+    - Breaking out NPI-specific stuff (if there really is that much of it) to a sepåarate libraru, ´naust´.
+
+
+- *0.0.2*:
+    - Name change from `oceanograpy` to `kval`.
+    - Introduction of test suite.
+    - Other minor changes.
+
+- *0.0.1:*
+    - Initial release.
+    - Functionality tailored for CTD processing.
+
+
+
+
+</details>
+
+
+
+

kval-0.3.0/README.md

@@ -0,0 +1,142 @@
+![image](graphics/kval_banner.png)
+
+Collection of Python functions for working with oceanography data processing and analysis.
+
+Maintained by the Oceanography section at the [Norwegian Polar Institute](https://www.npolar.no/en/).
+
+Supported by the project [HiAOOS](https://hiaoos.eu/).
+___
+
+Last release,`0.3.0`:
+
+
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15229098.svg)](https://doi.org/10.5281/zenodo.15229098)
+
+
+
+- This version is used to work out pypi and conda distribution.
+- An updated version with improved documentation and a code overhaul is planned for Spring 2025.
+
+__
+
+*In active development.*
+
+____
+<details>
+<summary><strong>CORE FUNCTIONALITY</strong></summary>
+
+##### Submodules
+
+
+- `file`: Converting to and from various file format (e.g. read CTD .cnv data to xarray/netCDF)
+- `data`: Data post-processing and QC (e.g. CTD post-processing)
+- `metadata`: Handling and standardizing metadata according to CF conventions
+- `plots*`: Various tools to help make nice (matplotlib) figures
+- `maps`: Tools for making maps
+- `geo`: Geographical calculations (coordinate transformations, point-to-point distances etc)
+- `ocean`: Oceanography-specific tools (e.g. (`*`) vertical modes, turner angles, wkb scaling, geostrophical calculations)
+- `calc`: Various useful functions for numerical calculations.
+- `util`: Various backend support functions and wrappers for xarray functionality.
+- `signal`: Filtering, spectral analysis, etc.
+
+`*` Not implemented
+
+</details>
+
+____
+
+<details>
+<summary><strong>GENERAL PRINCIPLES</strong></summary>
+
+*Note: These are aspirational guidelines and not always adhered to in the current code structure. We will try to get there!*
+
+###### Code
+
+- Written in Python (>=3.8).
+- Tailored for use in a [Jupyter] notebook environment.
+- Data and metadata should be stored in [xarray(https://docs.xarray.dev/en/stable/)] `Datasets`.
+    - Intermediate operations using, e.g., `numpy` or `pandas` objects are fine, but the end user should only interact with `Datasets`.
+- Code should adhere to [PEP8](https://peps.python.org/pep-0008/) style guide, and all functions should have docstrings.
+- All functionality should have associated [pytest](https://docs.pytest.org/en/7.4.x/) tests.
+    - Unit tests of individual functions are found in `tests/unit_tests/`. Its directory structure and contents should mirror that of `src/kval`.
+    - Tests of more complex functionality (e.g. processing pipelines using multiple modules) should be put in  `tests/functional_tests/`.
+    - A collection of sample data to be used in testing is found in `tests/test_data/`. Should aim to cover a wide range of input data, but we also don't want this to become *too* bulky - try to keep file size to a minimum.
+
+###### Metadata
+
+- All operations that modify data should be recorded in the file metadata.
+- Wherever possibly, and at as early a stage as possible, all available useful metadata should be added to Datasets.
+- Metadata formatting should adhere to [CF](http://cfconventions.org/) and [ACDD](https://wiki.esipfed.org/Attribute_Convention_for_Data_Discovery_1-3) conventions, supplemented by:
+    - [OceanSITES](http://www.oceansites.org/docs/oceansites_data_format_reference_manual_20140917.pdf)
+    - [2021 NPI NetCDF guidelines](https://gitlab.com/npolar/netcdf-creator/-/blob/main/docs/netcdf_standard_npi.pdf?ref_type=heads)
+
+###### Project
+
+- The project is maintained by the Oceanography section at the [Norwegian Polar Institute](www.npolar.no/en).
+    - External contributions (pull requests, issues, whatever) are very welcome!
+- We will attempt to follow the guidelines from the
+  [Scientific Python Library Development Guide](https://learn.scientific-python.org/development/).
+- *Releases* will be published relatively often, whenever a new functionality has been added.
+   Releases will be archived on [zenodo](www.zenodo.org) and given a DOI.
+
+###### Contributing
+
+Pull requests, issues, etc are very welcome!
+
+*[Something about branches here]*
+
+*[Something about python style, test suite]*
+
+
+</details>
+
+____
+
+
+<details>
+<summary><strong>RELEASE NOTES</strong></summary>
+
+
+
+
+
+- **0.3.0** *(CURRENT, released 16 April 2025)*:
+    - Refactoring of large parts of the code for structure, clarity and efficiency.
+    - ~~Complete reproducability and self-documentation in the CTD processing functionality.~~
+    - Adding mooring processing functionality
+        - ~~Functionality for parsing moored CTD sensors (RBR and SBE)~~
+        - Functionality for basic processing source file -> CF-NetCDF
+    - ~~Test suite (comprehensive but not entirely complete)~~
+    - ~~Decluttering the repo bringing it down from its currently bloated state.~~
+    - Started useful documentation with somenotebook examples (need a lot of work).
+    - Released to PyPi and conda-forge.
+    - Many other improvements and additions.
+
+
+- **0.4.0** *(PLANNED for spring 2025)*
+
+- Complete (useful) documentation with good notebook examples of core functionality.
+- Expanded test suite for good coverage of basic functionality plus
+- *Possibly*:
+    - Parsing data from inductive loggers.
+    - Breaking out NPI-specific stuff (if there really is that much of it) to a sepåarate libraru, ´naust´.
+
+
+- *0.0.2*:
+    - Name change from `oceanograpy` to `kval`.
+    - Introduction of test suite.
+    - Other minor changes.
+
+- *0.0.1:*
+    - Initial release.
+    - Functionality tailored for CTD processing.
+
+
+
+
+</details>
+
+
+
+