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Merge pull request #1157 from OSOceanAcoustics/dev
Release/v0.8.1
2 parents 254ee10 + 09e2705 commit 3b69eae

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‎.ci_helpers/py3.8.yaml

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‎.ci_helpers/user_environment.yml

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channels:
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- conda-forge
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dependencies:
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- python=3.8
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- python=3.9
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- ipykernel
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- echopype
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- dask

‎.github/workflows/build.yaml

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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.8", "3.9", "3.10"]
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python-version: ["3.9", "3.10"] # TODO: add back 3.11 once parsed2zarr is fixed
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runs-on: [ubuntu-latest]
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experimental: [false]
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# TODO: Uncomment when netcdf is unpinned
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# include:
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# - runs-on: ubuntu-latest
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# python-version: "3.11"
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# experimental: true
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include:
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- runs-on: ubuntu-latest
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python-version: "3.11"
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experimental: true
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services:
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# TODO: figure out how to update tag when there's a new one
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minio:
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- name: Running All Tests
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shell: bash -l {0}
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run: |
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pytest -vv -rx --numprocesses=${{ env.NUM_WORKERS }} --max-worker-restart=3 --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings |& tee ci_${{ matrix.python-version }}_test_log.log
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- name: Upload ci test log
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if: ${{ success() || failure() }}
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uses: actions/upload-artifact@v3
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with:
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name: ci_test_log
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path: ci_${{ matrix.python-version }}_test_log.log
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pytest -vv -rx --numprocesses=${{ env.NUM_WORKERS }} --max-worker-restart=3 --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings
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- name: Upload code coverage to Codecov
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uses: codecov/codecov-action@v3
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with:

‎.github/workflows/pr.yaml

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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.8", "3.9", "3.10"]
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python-version: ["3.9", "3.10"] # TODO: add back 3.11 once parsed2zarr is fixed
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runs-on: [ubuntu-latest]
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experimental: [false]
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# TODO: Uncomment when netcdf is unpinned
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# include:
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# - runs-on: ubuntu-latest
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# python-version: "3.11"
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# experimental: true
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include:
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- runs-on: ubuntu-latest
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python-version: "3.11"
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experimental: true
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defaults:
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run:
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shell: bash -l {0}
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- name: Running all Tests
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if: contains(github.event.pull_request.title, '[all tests ci]')
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run: |
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pytest -vvv -rx --numprocesses=${{ env.NUM_WORKERS }} --max-worker-restart=3 --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings |& tee ci_${{ matrix.python-version }}_test_log.log
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pytest -vvv -rx --numprocesses=${{ env.NUM_WORKERS }} --max-worker-restart=3 --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings
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- name: Running Tests
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if: ${{ !contains(github.event.pull_request.title, '[all tests ci]') }}
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run: |
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python .ci_helpers/run-test.py --pytest-args="--log-cli-level=WARNING,-vvv,-rx,--numprocesses=${{ env.NUM_WORKERS }},--max-worker-restart=3,--disable-warnings" --include-cov ${{ steps.files.outputs.added_modified_renamed }} |& tee ci_${{ matrix.python-version }}_test_log.log
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- name: Upload ci test log
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if: ${{ success() || failure() }}
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uses: actions/upload-artifact@v3
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with:
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name: ci_test_log
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path: ci_${{ matrix.python-version }}_test_log.log
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python .ci_helpers/run-test.py --pytest-args="--log-cli-level=WARNING,-vvv,-rx,--numprocesses=${{ env.NUM_WORKERS }},--max-worker-restart=3,--disable-warnings" --include-cov ${{ steps.files.outputs.added_modified_renamed }}
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- name: Upload code coverage to Codecov
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uses: codecov/codecov-action@v3
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with:

‎.readthedocs.yml

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build:
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os: ubuntu-22.04
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tools:
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python: "3.8"
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python: "3.9"
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jobs:
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pre_build:
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# Generate the Sphinx configuration for this Jupyter Book so it builds.

‎docs/source/data-format-changes.ipynb

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" - Revise the dimensions of each variable to be consistent across instrument types, with dimensions deemed unnecessary dropped from some variables.\n",
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"- In the `Provenance` group: Add new attributes `combination_*` to the \"combined\" `EchoData` object, mirroring the convention-based attributes `conversion_*`.\n",
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"- In the `Vendor_specific` group: Move filter coefficients and decimation factor from attributes to variables in EK80, to facilitate consistent provenance tracking during `combine_echodata` operations.\n",
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"- Improve the presence and use of variable attributes throughout `EchoData` groups.\n",
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"\n",
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"Version 0.8.0 does not incorporte the capability to read files converted by previous versions of echopype. We recommend using `open_raw` to re-convert the raw data files."
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"- Improve the presence and use of variable attributes throughout `EchoData` groups."
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]
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},
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{
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"cell_type": "markdown",
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"id": "e506a51d",
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"metadata": {},
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"source": [
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":::{Note}\n",
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"Version 0.8.0 does not incorporate the capability to read files converted by previous versions of echopype. We recommend using `open_raw` to re-convert the raw data files.\n",
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":::"
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},
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{
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"More details, including Pull Requests and discussions related to these changes, can be found in the [Release notes](whats-new.html#v0-6-0-2022-may-26)."
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},
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{
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"cell_type": "markdown",
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"id": "touched-concentration",
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"metadata": {},
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"source": [
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"### Convert old files to v0.6.0 format"
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]
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},
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{
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"cell_type": "markdown",
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"id": "fuzzy-sociology",
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"To convert data files from v0.5.x to v0.6.0 format, simply open the old files and re-save them:\n",
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"\n",
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"```python\n",
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"import echopype as ep\n",
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"# open old v0.5.x file and convert it into a v0.6.0-format EchoData object\n",
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"ed = ep.open_converted(\"old_format_file.nc\")\n",
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"ed.to_netcdf(\"new_format_file.nc\")\n",
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"```"
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]
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},
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"id": "stone-trash",
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".xr-section-summary-in + label:before {\n",
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