Add the latest changes to main branch

.github/workflows/deploy-docs.yaml

@@ -25,16 +25,15 @@ jobs:
           restore-keys: |
             mkdocs-material-
       - run: |
-          python -m pip install --upgrade pip
-          pip install ".[dev]"
-          pip install -r docs-requirements.txt
+          pip install poetry
+          poetry install --with docs,geo
       - run: |
           git config --global user.name "${GITHUB_ACTOR}"
           git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
       - run: |
           if [[ "${{github.ref_name}}" == "main" ]]; then
-              mike deploy main --push --force
+              poetry run mike deploy main --push --force
           else
-              mike deploy dev --push --force
+              poetry run mike deploy dev --push --force
           fi
-          mike set-default dev --push
+          poetry run mike set-default dev --push

.github/workflows/test-docs.yaml

@@ -22,11 +22,10 @@ jobs:
           restore-keys: |
             mkdocs-material-
       - run: |
-        python -m pip install --upgrade pip
-          pip install -r docs-requirements.txt
-          pip install ".[dev]"
+          pip install poetry
+          poetry install --with docs,geo
       - run: |
           git config --global user.name "${GITHUB_ACTOR}"
           git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
       - run: |
-          mike deploy test
+          poetry run mkdocs build -s -d test

.github/workflows/test-package.yaml

@@ -0,0 +1,68 @@
+name: Test package for linter issues and run tests
+
+on:
+  pull_request:
+    branches:
+      - main
+      - development
+    paths:
+      - .github/workflows/test-package.yaml
+      - setup.py
+      - MANIFEST.in
+      - ocean_data_parser/**
+      - tests/**
+
+  push:
+    branches:
+      - main
+      - development
+    paths:
+      - setup.py
+      - MANIFEST.in
+      - ocean_data_parser/**
+      - tests/**
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install poetry
+          poetry install --with dev,geo
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Run ruff
+        run: poetry run ruff check --output-format=github .
+      - name: Review if metadata is updated
+        uses: dorny/paths-filter@v3
+        id: changes
+        with:
+          filters: |
+            vocabularies:
+              - 'ocean_data_parser/vocabularies/**'
+              - 'ocean_data_parser/metatadata/**'
+              - 'tests/test_metadata.py'
+            changelog:
+              - 'CHANGELOG.md'
+      - name: Run tests with metadata tests
+        if: steps.changes.outputs.vocabularies == 'true'
+        run: poetry run pytest -W error::UserWarning --nerc-vocab -n auto
+      - name: Run tests without metadata tests
+        if: steps.changes.outputs.vocabularies == 'false'
+        run: poetry run pytest -W error::UserWarning -k "not test_metadata" -n auto
+      - name: Run benchmark
+        run: poetry run pytest tests/run_benchmark.py  --benchmark-json output.json
+      - name: Update CHANGELOG
+        if: steps.changes.outputs.changelog == 'false'
+        run: exit 1
+

.gitignore

@@ -11,9 +11,6 @@ dist/
 /pycurrents
 .DS_Store
 
-.vscode/launch.json
-
-.vscode/settings.json
 /**/local_tests/*
 /tests/**/*_test.nc
 pdc-amundsen-conversion.log
@@ -45,3 +42,6 @@ docs/user_guide/vocabularies/*.md
 docs/user_guide/parsers/parser-list.md
 
 site/**
+.python-version
+
+.vscode/launch.json

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.pytestEnabled": true,
+    "python.testing.unittestEnabled": false,
+}

CHANGELOG.md

@@ -0,0 +1,47 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## `0.5.0` - 2024-06-20
+
+### Added
+
+- Test get_path_generation_input on all test files and parsers
+- Run all tests in parallel with pytest-xdist
+- Add --parser-kwargs option to odpy convert command line interface to pass
+inputs to parser
+
+### Fixed
+
+- Fix star_oddi parser time variable to output a datetime dataarray.
+- Fix onset parser date time handling.
+- Avoid reimporting parser if already imported in read.file with parser
+defined via string expression.
+- Fix Amundsen int timestamp format
+- Drop trip_tag attribute from dfo.nafc.pcnv parser
+- Make dfo.nafc.pcnv parser attempt to retrieve metqa file info by default.
+
+## `v0.4.0` - 2024-05-04
+
+### Added
+
+- Test platforms vocabulary items and match them to NERC C17 vocabulary.
+
+### Changed
+
+- Refactor Seabird Parser
+  - Handle better processing related attributes
+    - On-platform processing
+    - SBE Data Processing modules
+    - Post processing (NAFC pcnv Format `* QA Applied:`)
+  - Retrieve more of the information available stored within Seabird header as attributes
+  - Structure history
+- Upgrade odf.bio reference NetCDF to reflect the changes.
+- Upgrate dfo platforms for the odf and nafc parsers.
+
+### Removed
+
+- Historical ODF platform vocabulary which wasn't used anywhere.

LICENSE.md

@@ -658,7 +658,7 @@ notice like this when it starts in an interactive mode:
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.
 
-The hypothetical commands `show w' and `show c' should show the appropriate
+The hypothetical commands `show w' and`show c' should show the appropriate
 parts of the General Public License.  Of course, your program's commands
 might be different; for a GUI interface, you would use an "about box".
 

README.md

@@ -1,57 +1,58 @@
-<!-- NOTE: All sections are placeholders. Use the relevant ones-->
 
 ![Logo](docs/images/logo_EN_FR-1024x208.png#gh-light-mode-only)
 ![Logo](docs/images/cioos-national_EN_FR_W-01.png#gh-dark-mode-only)
 
-<!-- Make a favicon/logo using something like:
-
-* https://favicon.io/
-* https://www.shopify.com/tools/logo-maker/open-source-software
-* https://primitive.lol/ -->
-
 # ocean-data-parser
 
 <!-- You can get project-relevant badges from: [shields.io](https://shields.io/) -->
 
 [![Build documentation](https://github.com/cioos-siooc/ocean-data-parser/actions/workflows/deploy-docs.yaml/badge.svg)](https://github.com/cioos-siooc/ocean-data-parser/actions/workflows/deploy-docs.yaml)
 
-
 `ocean-data-parser` - a Python package for parsing oceanographic proprietary data formats to [xarray Dataset](https://docs.xarray.dev/en/stable/). Documentation [here](https://cioos-siooc.github.io/ocean-data-parser/).
 
 ## Installation
+
 Install the package with the following command, ideally within a virtual environment:
 
 ```console
 pip install git+https://github.com/cioos-siooc/ocean-data-parser.git
 ```
 
 ### How to
+
 #### odpy cli
+
 Once installed, the package is usable via the command line interface:
+
 ```console
 odpy --help
 ```
 
 To batch convert a series of files to NetCDF:
+
 ```
 odpy convert -i '**/*.cnv' -p 'seabird.cnv'
 ```
+
 #### Format auto-detection
+
 Load a compatible file with the automated parser detection method:
 
 ```python
-import ocean_data_parser.parsers
+import ocean_data_parser.read
 
 # Load a file to an xarray object
-ds = ocean_data_parser.parsers.file('Path to file')
+ds = ocean_data_parser.read.file('Path to file')
 
 # Save to netcdf
 ds.to_netcdf('save-path.nc')
 ```
+
 !!!warning
     The parser detection method relies on the file extension and the first few lines present within the given file.
 
 Or specify the specific parser to use for this file format:
+
 ``` python
 from ocean_data_parser.parsers import seabird
 
@@ -61,10 +62,11 @@ ds = seabird.cnv('Path to seabird cnv file')
 # Save to netcdf
 ds.to_netcdf('save-path.nc')
 ```
+
 The `ocean-data-parser` can then be used within either a Python package, script or jupyter notebook. See the [documentation Notebook section](https://cioos-siooc.github.io/ocean-data-parser) for examples of how to use the package within a jupyter notebook.
 
 ## Contributions
 
-All contributions are welcome! 
+All contributions are welcome!
 
-Please create a new [discussion](https://github.com/cioos-siooc/ocean-data-parser/discussions) or [issue](https://github.com/cioos-siooc/ocean-data-parser/issues) within the GitHub repository for any questions, ideas and suggestions. 
+Please create a new [discussion](https://github.com/cioos-siooc/ocean-data-parser/discussions) or [issue](https://github.com/cioos-siooc/ocean-data-parser/issues) within the GitHub repository for any questions, ideas and suggestions.