release v0.6.0 (#109)

* fix documentation build
* fix deprecation in nafc metqa parser
* Add-convert-input-table (#103)
* add input_table input to configuration
* add another onset timestamp format
* use ruff for linter testing (#106)
* update dependancies
* run all ruff tests and report any failure  right after
* fix nafc ruff check issues
* fix seabird imports
* add input-path-list (#108)
* add input-path-list
* add os path separator compatibility to both cli and configuration
* add test_version module
* fix version to 0.6.0
* fix base and ref in CHANGELOG workflow

.github/workflows/deploy-docs.yaml

@@ -14,6 +14,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'
@@ -32,8 +34,8 @@ jobs:
           git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
       - run: |
           if [[ "${{github.ref_name}}" == "main" ]]; then
-              poetry run mike deploy main --push --force
+              poetry run mike deploy main --push
           else
-              poetry run mike deploy dev --push --force
+              poetry run mike deploy dev --push
           fi
-          poetry run mike set-default dev --push
+          poetry run mike set-default main --push

.github/workflows/test-package.yaml

@@ -26,27 +26,44 @@ jobs:
   testing:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         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
+      - name: ruff check
+        id: ruff_check
         run: poetry run ruff check --output-format=github .
+        continue-on-error: true
+      - name: ruff import sorting check
+        id: ruff_imports
+        run: poetry run ruff check --select I --output-format=github .
+        continue-on-error: true
+      - name: ruff format
+        id: ruff_format
+        run: poetry run ruff format --check .
+        continue-on-error: true
+      - name: Check for ruff issues 
+        if: steps.ruff_check.outcome == 'failure' || steps.ruff_imports.outcome == 'failure' || steps.ruff_format.outcome == 'failure'
+        run: |
+          echo "Some ruff steps failed. Please check the logs for more information.\n"
+          echo "Some of the issues can be fixed by running the following commands:\n"
+          echo " poetry run ruff check --fix . # for fixing all default issues"
+          echo " poetry run ruff check --fix --select I . # for fixing import sorting issues"
+          echo " poetry run ruff format . # for formatting the code"
+          exit 1
+          
       - name: Review if metadata is updated
         uses: dorny/paths-filter@v3
+        continue-on-error: true
         id: changes
         with:
+          base: ${{ github.base_ref }}
+          ref: ${{ github.ref }}
           filters: |
             vocabularies:
               - 'ocean_data_parser/vocabularies/**'
@@ -62,7 +79,9 @@ jobs:
         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
+      - name: CHANGELOG updated check
         if: steps.changes.outputs.changelog == 'false'
-        run: exit 1
+        run: |
+          echo "CHANGELOG.md update is required."
+          exit 1
         

CHANGELOG.md

@@ -5,11 +5,35 @@ 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).
 
+## `0.6.0` - 2024-08-20
+
+### Added
+
+- Add odpy convert `input_table` input through config file, which gives the
+ability to list multiple file glob expression and associated metadata.
+- Add Onset.csv timestamp format: "\d+\/\d+\/\d\d\d\d\s+\d+\:\d+\:\d+" = "%m/%d/%Y %H:%M:%S"
+- Rely on ruff for format and linter testing
+- Add option to pass a list of input_path paths via the configuration file or a 
+os path seperator list via the command line interface or the configuration
+- Add test to test version within package `__init__.py`, `CHANGELOG.md`, and `pyproject.tom`
+
+### Fixed
+
+- seabird parsers module import sorting
+- nafc ruff check issues
+
+## `0.5.2` - 2024-06-22
+
+### Fixed
+
+- Docs build
+
 ## `0.5.1` - 2024-06-20
 
 ### Fixed
 
 - Remove default sentry dsn from convert default configuration file.
+- Fix deprecation issue in nafc.metqa loader
 
 ## `0.5.0` - 2024-06-20
 
@@ -50,4 +74,4 @@ defined via string expression.
 
 ### Removed
 
-- Historical ODF platform vocabulary which wasn't used anywhere.
+- Historical ODF platform vocabulary which wasn't used anywhere.

docs/user_guide/cli.md

@@ -14,3 +14,18 @@ title: odpy CLI
     Example: 
     - `ODPY_LOG_LEVEL=WARNING` will force `odpy` to log only the warning events.
     - `ODPY_CONVERT_OUTPUT_PATH=output` will force `odpy convert` to output to the the local directory `./output/`
+
+
+## Configuration
+
+`odpy convert` can handle a configuration file which also integrates a number of other features. To generate a new configuration, you can use the `--new-config` flag:
+
+```shell
+odpy convert --new-config new_config_file_path.yaml
+```
+
+Or copy the following yaml:
+
+```yaml
+--8<-- "ocean_data_parser/batch/default-batch-config.yaml"
+```

docs/user_guide/index.md

@@ -7,8 +7,8 @@ The ocean-data-parser can be used different ways:
 
 - [ ] Python Import
 
-    - [`from ocean_data_parser import read.file`](read.md)
-    - [`from ocean_data_parser.parsers import ...`](parsers/index.md)
+  - [`from ocean_data_parser import read.file`](read.md)
+  - [`from ocean_data_parser.parsers import ...`](parsers/index.md)
 
 ## Installation
 

docs/user_guide/parsers/index.md

@@ -1,4 +1,4 @@
-# Ocean Data Parsers 
+# Ocean Data Parsers
 
 Each parser can also be imported by itself:
 
@@ -75,4 +75,3 @@ Ocean Data Parser includes the following data format parsers:
 
 - [van_essen_instruments.mon](van-essen-instruments.md#ocean_data_parser.parsers.van_essen_instruments.mon)
 
-

ocean_data_parser/__init__.py

@@ -2,4 +2,4 @@
 from pathlib import Path
 
 PARSERS = re.findall('parser = "(.*)"', (Path(__file__).parent / "read.py").read_text())
-__version__ = "0.5.0"
+__version__ = "0.6.0"