seagliderOG1 0.0.1a3__tar.gz

seagliderog1-0.0.1a3/.github/workflows/docs.yml

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+name: Test documentation build
+
+on:
+  pull_request:
+    paths:
+      - '**.py'
+      - '**.ipynb'
+      - '**.rst'
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+    - name: checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Setup Micromamba ${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v2.0.1
+      with:
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 pip
+          --file requirements-dev.txt
+          --channel conda-forge
+
+    - name: Install seagliderOG1
+      shell: bash -l {0}
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
+
+    - name: Build documentation
+      shell: bash -l {0}
+      run: |
+        set -e
+        jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb --ExecutePreprocessor.allow_errors=True
+        mv notebooks/*output.ipynb docs/source/
+        pushd docs
+        make clean html 
+        popd

seagliderog1-0.0.1a3/.github/workflows/pypi.yml

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+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+# See also https://docs.github.com/en/actions/use-cases-and-examples/building-and-testing/building-and-testing-python
+name: Publish to PyPI
+
+on:
+  release:
+    types:
+      - published
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+
+    - name: Get tags
+      run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+      shell: bash
+
+    - name: Install build tools
+      run: |
+        python -m pip install --upgrade pip wheel setuptools setuptools_scm build twine
+
+      shell: bash
+
+    - name: Build binary wheel
+      run: python -m build --sdist --wheel . --outdir dist
+
+    - name: CheckFiles
+      run: |
+        ls dist
+      shell: bash
+
+    - name: Test wheels
+      run: |
+        cd dist && python -m pip install *.whl
+        python -m twine check *
+      shell: bash
+
+    - name: Publish a Python distribution to PyPI
+      if: success() && github.event_name == 'release'
+      uses: pypa/gh-action-pypi-publish@release/v1

seagliderog1-0.0.1a3/.github/workflows/tests.yml

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+name: Run tests
+
+on: 
+  push:
+    branches:
+      - main
+      - eleanor-patch-22
+    paths:
+      - '**.py'
+      - '**.ipynb'
+  pull_request:
+    branches:
+      - main
+      - eleanor-patch-22
+    paths:
+      - '**.py'
+      - '**.ipynb'
+
+jobs:
+  job_mytests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.8", "3.12"]
+      fail-fast: true
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - name: Run a one-line script
+      run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
+    - uses: actions/checkout@v4
+
+    - name: Setup Micromamba Python ${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=${{ matrix.python-version }} --file requirements-dev.txt --channel conda-forge
+
+    - name: Install seagliderOG1
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
+
+    - name: Full Tests
+      run: |
+        python -m pytest --cov=seagliderOG1 --cov-report term-missing  tests/

seagliderog1-0.0.1a3/.gitignore

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+# Test data
+data/*test*.nc
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+*_version.py
+
+# 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
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Mac/OSX
+.DS_Store
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+.idea
+de421.bsp

seagliderog1-0.0.1a3/LICENSE

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+MIT License
+
+Copyright (c) 2024 Eleanor Frajka-Williams
+
+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.

seagliderog1-0.0.1a3/PKG-INFO

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+Metadata-Version: 2.1
+Name: seagliderOG1
+Version: 0.0.1a3
+Summary: Convert from Seaglider basestation to OG1 format
+Maintainer-email: Eleanor Frajka-Williams <eleanorfrajka@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2024 Eleanor Frajka-Williams
+        
+        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.
+        
+Project-URL: documentation, https://github.com/eleanorfrajka/seagliderOG1
+Project-URL: homepage, https://github.com/eleanorfrajka/seagliderOG1
+Project-URL: repository, https://github.com/eleanorfrajka/seagliderOG1
+Classifier: Programming Language :: Python :: 3 :: Only
+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
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: netcdf4
+Requires-Dist: pooch
+Requires-Dist: xarray
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: pandas
+Requires-Dist: seaborn
+Requires-Dist: scipy
+Requires-Dist: cmocean
+Requires-Dist: skyfield
+Requires-Dist: tqdm
+Requires-Dist: gsw
+Requires-Dist: sgp4>=2.14
+Requires-Dist: cartopy
+Requires-Dist: importlib_resources
+
+# seagliderOG1
+
+This repository is intended to convert Seaglider basestation files (`pSSSDDDD*.nc`) into [OG1 format](https://oceangliderscommunity.github.io/OG-format-user-manual/OG_Format.html).
+
+Code is based on code from [votoutils](https://github.com/voto-ocean-knowledge/votoutils/blob/main/votoutils/glider/convert_to_og1.py).
+
+### Organisation
+
+Scripts within the `seagliderOG1` package are divided by functionality:
+
+- **readers.py** reads basestation files (`*.nc`) from a server or local directory
+- **writers.py** writes OG1 `*.nc` files, default directory `data/`
+- **plotters.py** contains some basic plotting and viewing functions
+- **convertOG1.py** converts the basestation files to OG1 format
+- **vocabularies.py** contains some of the vocabulary translation (might be better as a YAML file)
+- *seaglider_registr.txt* has checksums for data files
+- **tools.py** functions the user may want to use
+- **utilities.py** functions the user probably will never need to call (only used in other functions)
+
+### Directory 
+File directory structure is as follows.
+
+seagliderOG1/
+- .github/
+- config/
+    - OG1_author.yaml
+    - OG1_global_attrs.yaml
+    - OG1_global_attrs.yaml
+    -  OG1_sensor_attrs.yaml
+    - OG1_var_names.yaml
+    - OG1_vocab_attrs.yaml
+    - mission_yaml.yaml
+- data/
+    - test.nc
+- notebooks/
+    - dev_notebooks/
+        - dev-troubleshoot.ipynb
+        - download_and_register.ipynb
+    - demo.ipynb
+- seagliderOG1/
+    - convertOG1.py
+    - plotters.py
+    - readers.py
+    - seaglider_registry.txt
+    - tools.py
+    - utilities.py
+    - vocabularies.py
+    - writers.py
+- tests/
+    - test_readers.py
+- .gitignore
+- LICENSE
+- README.md
+- requirements-dev.txt
+- requirements.txt
+
+
+### Status
+
+Active development by one.  Many things may break - not yet ready for collaboration.

seagliderog1-0.0.1a3/README.md

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+# seagliderOG1
+
+This repository is intended to convert Seaglider basestation files (`pSSSDDDD*.nc`) into [OG1 format](https://oceangliderscommunity.github.io/OG-format-user-manual/OG_Format.html).
+
+Code is based on code from [votoutils](https://github.com/voto-ocean-knowledge/votoutils/blob/main/votoutils/glider/convert_to_og1.py).
+
+### Organisation
+
+Scripts within the `seagliderOG1` package are divided by functionality:
+
+- **readers.py** reads basestation files (`*.nc`) from a server or local directory
+- **writers.py** writes OG1 `*.nc` files, default directory `data/`
+- **plotters.py** contains some basic plotting and viewing functions
+- **convertOG1.py** converts the basestation files to OG1 format
+- **vocabularies.py** contains some of the vocabulary translation (might be better as a YAML file)
+- *seaglider_registr.txt* has checksums for data files
+- **tools.py** functions the user may want to use
+- **utilities.py** functions the user probably will never need to call (only used in other functions)
+
+### Directory 
+File directory structure is as follows.
+
+seagliderOG1/
+- .github/
+- config/
+    - OG1_author.yaml
+    - OG1_global_attrs.yaml
+    - OG1_global_attrs.yaml
+    -  OG1_sensor_attrs.yaml
+    - OG1_var_names.yaml
+    - OG1_vocab_attrs.yaml
+    - mission_yaml.yaml
+- data/
+    - test.nc
+- notebooks/
+    - dev_notebooks/
+        - dev-troubleshoot.ipynb
+        - download_and_register.ipynb
+    - demo.ipynb
+- seagliderOG1/
+    - convertOG1.py
+    - plotters.py
+    - readers.py
+    - seaglider_registry.txt
+    - tools.py
+    - utilities.py
+    - vocabularies.py
+    - writers.py
+- tests/
+    - test_readers.py
+- .gitignore
+- LICENSE
+- README.md
+- requirements-dev.txt
+- requirements.txt
+
+
+### Status
+
+Active development by one.  Many things may break - not yet ready for collaboration.

seagliderog1-0.0.1a3/config/OG1_author.yaml

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+contributor_name: Eleanor Frajka-Williams
+contributor_email: eleanorfrajka@gmail.com
+contributor_role: Data scientist
+contributor_role_vocabulary: http://vocab.nerc.ac.uk/search_nvs/W08
+contributing_institutions: University of Hamburg - Institute of Oceanography
+contributing_institutions_vocabulary: https://edmo.seadatanet.org/report/1156
+contributing_institutions_role: Data scientist
+contributing_institutions_role_vocabulary: http://vocab.nerc.ac.uk/search_nvs/W08

seagliderog1-0.0.1a3/config/OG1_global_attrs.yaml

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+attr_to_add:
+  title: OceanGliders trajectory file
+  platform: sub-surface gliders
+  platform_vocabulary: https://vocab.nerc.ac.uk/collection/L06/current/27
+  featureType: trajectoryProfile
+  Conventions: CF-1.10,OG-1.0
+  rtqc_method: No QC applied
+  rtqc_method_doi: n/a
+#  doi: ''
+#  data_url: ''
+attr_as_is: !!set
+  geospatial_lon_min: null
+  institution: null
+  disclaimer: null
+  file_version: null
+  geospatial_vertical_max: null
+  geospatial_vertical_min: null
+  project: null
+  keywords: null
+  acknowledgment: null
+  id: null
+  geospatial_lat_min: null
+  naming_authority: null
+  keywords_vocabulary: null
+  geospatial_lon_max: null
+  geospatial_lat_max: null
+  date_created: null
+  license: null
+attr_to_rename:
+  site: summary
+  uri: uuid
+  uri_comment: UUID
+  comment: history
+  id: PLATFORM_SERIAL_NUMBER
+attr_to_var:
+  landstation_version: base_station_version
+  glider_firmware_version: seaglider_software_version