Merge pull request #1157 from OSOceanAcoustics/dev

Release/v0.8.1
OSOceanAcoustics · Sep 2, 2023 · 3b69eae · 3b69eae
2 parents 254ee10 + 09e2705
commit 3b69eae
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diff --git a/.ci_helpers/py3.8.yaml b/.ci_helpers/py3.8.yaml
diff --git a/.ci_helpers/user_environment.yml b/.ci_helpers/user_environment.yml
@@ -2,7 +2,7 @@ name: echopype
 channels:
   - conda-forge
 dependencies:
-  - python=3.8
+  - python=3.9
   - ipykernel
   - echopype
   - dask

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -21,14 +21,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]  # TODO: add back 3.11 once parsed2zarr is fixed
         runs-on: [ubuntu-latest]
         experimental: [false]
-        # TODO: Uncomment when netcdf is unpinned
-        # include:
-        # - runs-on: ubuntu-latest
-        #   python-version: "3.11"
-        #   experimental: true
+        include:
+        - runs-on: ubuntu-latest
+          python-version: "3.11"
+          experimental: true
     services:
       # TODO: figure out how to update tag when there's a new one
       minio:
@@ -81,13 +80,7 @@ jobs:
       - name: Running All Tests
         shell: bash -l {0}
         run: |
-          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
-      - name: Upload ci test log
-        if: ${{ success() || failure() }}
-        uses: actions/upload-artifact@v3
-        with:
-          name: ci_test_log
-          path: ci_${{ matrix.python-version }}_test_log.log
+          pytest -vv -rx --numprocesses=${{ env.NUM_WORKERS }} --max-worker-restart=3 --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings
       - name: Upload code coverage to Codecov
         uses: codecov/codecov-action@v3
         with:

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -17,14 +17,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]  # TODO: add back 3.11 once parsed2zarr is fixed
         runs-on: [ubuntu-latest]
         experimental: [false]
-        # TODO: Uncomment when netcdf is unpinned
-        # include:
-        # - runs-on: ubuntu-latest
-        #   python-version: "3.11"
-        #   experimental: true
+        include:
+        - runs-on: ubuntu-latest
+          python-version: "3.11"
+          experimental: true
     defaults:
       run:
         shell: bash -l {0}
@@ -88,17 +87,11 @@ jobs:
       - name: Running all Tests
         if: contains(github.event.pull_request.title, '[all tests ci]')
         run: |
-          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
+          pytest -vvv -rx --numprocesses=${{ env.NUM_WORKERS }} --max-worker-restart=3 --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings
       - name: Running Tests
         if: ${{ !contains(github.event.pull_request.title, '[all tests ci]') }}
         run: |
-          python .ci_helpers/run-test.py --pytest-args="--log-cli-level=WARNING,-vvv,-rx,--numprocesses=${{ 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
-      - name: Upload ci test log
-        if: ${{ success() || failure() }}
-        uses: actions/upload-artifact@v3
-        with:
-          name: ci_test_log
-          path: ci_${{ matrix.python-version }}_test_log.log
+          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 }}
       - name: Upload code coverage to Codecov
         uses: codecov/codecov-action@v3
         with:

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.9"
   jobs:
     pre_build:
       # Generate the Sphinx configuration for this Jupyter Book so it builds.

diff --git a/docs/source/data-format-changes.ipynb b/docs/source/data-format-changes.ipynb
@@ -41,9 +41,17 @@
         "    - Revise the dimensions of each variable to be consistent across instrument types, with dimensions deemed unnecessary dropped from some variables.\n",
         "- In the `Provenance` group: Add new attributes `combination_*` to the \"combined\" `EchoData` object, mirroring the convention-based attributes `conversion_*`.\n",
         "- 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",
-        "- Improve the presence and use of variable attributes throughout `EchoData` groups.\n",
-        "\n",
-        "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."
+        "- Improve the presence and use of variable attributes throughout `EchoData` groups."
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "id": "e506a51d",
+      "metadata": {},
+      "source": [
+        ":::{Note}\n",
+        "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",
+        ":::"
       ]
     },
     {
@@ -93,29 +101,6 @@
         "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)."
       ]
     },
-    {
-      "cell_type": "markdown",
-      "id": "touched-concentration",
-      "metadata": {},
-      "source": [
-        "### Convert old files to v0.6.0 format"
-      ]
-    },
-    {
-      "cell_type": "markdown",
-      "id": "fuzzy-sociology",
-      "metadata": {},
-      "source": [
-        "To convert data files from v0.5.x to v0.6.0 format, simply open the old files and re-save them:\n",
-        "\n",
-        "```python\n",
-        "import echopype as ep\n",
-        "# open old v0.5.x file and convert it into a v0.6.0-format EchoData object\n",
-        "ed = ep.open_converted(\"old_format_file.nc\")\n",
-        "ed.to_netcdf(\"new_format_file.nc\")\n",
-        "```"
-      ]
-    },
     {
       "cell_type": "markdown",
       "id": "stone-trash",
@@ -288,7 +273,7 @@
               "\n",
               ".xr-section-summary-in + label:before {\n",
               "  display: inline-block;\n",
-              "  content: '►';\n",
+              "  content: '\u25ba';\n",
               "  font-size: 11px;\n",
               "  width: 15px;\n",
               "  text-align: center;\n",
@@ -299,7 +284,7 @@
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label:before {\n",
-              "  content: '▼';\n",
+              "  content: '\u25bc';\n",
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label > span {\n",
@@ -663,7 +648,7 @@
               "\n",
               ".xr-section-summary-in + label:before {\n",
               "  display: inline-block;\n",
-              "  content: '►';\n",
+              "  content: '\u25ba';\n",
               "  font-size: 11px;\n",
               "  width: 15px;\n",
               "  text-align: center;\n",
@@ -674,7 +659,7 @@
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label:before {\n",
-              "  content: '▼';\n",
+              "  content: '\u25bc';\n",
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label > span {\n",
@@ -1045,7 +1030,7 @@
               "\n",
               ".xr-section-summary-in + label:before {\n",
               "  display: inline-block;\n",
-              "  content: '►';\n",
+              "  content: '\u25ba';\n",
               "  font-size: 11px;\n",
               "  width: 15px;\n",
               "  text-align: center;\n",
@@ -1056,7 +1041,7 @@
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label:before {\n",
-              "  content: '▼';\n",
+              "  content: '\u25bc';\n",
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label > span {\n",
@@ -1829,7 +1814,7 @@
               "\n",
               ".xr-section-summary-in + label:before {\n",
               "  display: inline-block;\n",
-              "  content: '►';\n",
+              "  content: '\u25ba';\n",
               "  font-size: 11px;\n",
               "  width: 15px;\n",
               "  text-align: center;\n",
@@ -1840,7 +1825,7 @@
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label:before {\n",
-              "  content: '▼';\n",
+              "  content: '\u25bc';\n",
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label > span {\n",
@@ -2203,7 +2188,7 @@
               "\n",
               ".xr-section-summary-in + label:before {\n",
               "  display: inline-block;\n",
-              "  content: '►';\n",
+              "  content: '\u25ba';\n",
               "  font-size: 11px;\n",
               "  width: 15px;\n",
               "  text-align: center;\n",
@@ -2214,7 +2199,7 @@
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label:before {\n",
-              "  content: '▼';\n",
+              "  content: '\u25bc';\n",
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label > span {\n",
@@ -2574,7 +2559,7 @@
               "\n",
               ".xr-section-summary-in + label:before {\n",
               "  display: inline-block;\n",
-              "  content: '►';\n",
+              "  content: '\u25ba';\n",
               "  font-size: 11px;\n",
               "  width: 15px;\n",
               "  text-align: center;\n",
@@ -2585,7 +2570,7 @@
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label:before {\n",
-              "  content: '▼';\n",
+              "  content: '\u25bc';\n",
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label > span {\n",
@@ -2946,7 +2931,7 @@
               "\n",
               ".xr-section-summary-in + label:before {\n",
               "  display: inline-block;\n",
-              "  content: '►';\n",
+              "  content: '\u25ba';\n",
               "  font-size: 11px;\n",
               "  width: 15px;\n",
               "  text-align: center;\n",
@@ -2957,7 +2942,7 @@
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label:before {\n",
-              "  content: '▼';\n",
+              "  content: '\u25bc';\n",
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label > span {\n",
@@ -3439,7 +3424,7 @@
               "\n",
               ".xr-section-summary-in + label:before {\n",
               "  display: inline-block;\n",
-              "  content: '►';\n",
+              "  content: '\u25ba';\n",
               "  font-size: 11px;\n",
               "  width: 15px;\n",
               "  text-align: center;\n",
@@ -3450,7 +3435,7 @@
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label:before {\n",
-              "  content: '▼';\n",
+              "  content: '\u25bc';\n",
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label > span {\n",
@@ -3800,7 +3785,7 @@
               "\n",
               ".xr-section-summary-in + label:before {\n",
               "  display: inline-block;\n",
-              "  content: '►';\n",
+              "  content: '\u25ba';\n",
               "  font-size: 11px;\n",
               "  width: 15px;\n",
               "  text-align: center;\n",
@@ -3811,7 +3796,7 @@
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label:before {\n",
-              "  content: '▼';\n",
+              "  content: '\u25bc';\n",
               "}\n",
               "\n",
               ".xr-section-summary-in:checked + label > span {\n",