Merge branch 'dev' into stable

OSOceanAcoustics · Mar 14, 2023 · a806a77 · a806a77
2 parents ca24ad1 + 739beb0
commit a806a77
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Showing 92 changed files with 8,527 additions and 2,406 deletions.
diff --git a/.ci_helpers/docker/http.dockerfile b/.ci_helpers/docker/http.dockerfile
@@ -1,3 +1,4 @@
 FROM httpd:2.4
+ARG TARGETPLATFORM
 
 COPY echopype/test_data /usr/local/apache2/htdocs/data
diff --git a/.ci_helpers/docker/minioci.dockerfile b/.ci_helpers/docker/minioci.dockerfile
@@ -1,4 +1,5 @@
 FROM minio/minio
+ARG TARGETPLATFORM
 
 # Install git
 RUN microdnf install git

diff --git a/.ci_helpers/py3.10.yaml b/.ci_helpers/py3.10.yaml
@@ -14,4 +14,3 @@ dependencies:
   - s3fs==2022.5.0
   - matplotlib-base
   - cmocean
-  - mamba=0.20.0
diff --git a/.ci_helpers/py3.8.yaml b/.ci_helpers/py3.8.yaml
@@ -14,4 +14,3 @@ dependencies:
   - s3fs==2022.5.0
   - matplotlib-base
   - cmocean
-  - mamba=0.20.0
diff --git a/.ci_helpers/py3.9.yaml b/.ci_helpers/py3.9.yaml
@@ -14,4 +14,3 @@ dependencies:
   - s3fs==2022.5.0
   - matplotlib-base
   - cmocean
-  - mamba=0.20.0
diff --git a/.ci_helpers/run-test.py b/.ci_helpers/run-test.py
@@ -32,6 +32,8 @@
     "utils": {},
     "visualize": {},
     "metrics": {},
+    "mask": {},
+    "consolidate": {},
 }
 
 if __name__ == "__main__":
@@ -57,7 +59,7 @@
     )
     args = parser.parse_args()
     if args.local:
-        temp_path = Path("temp_echopype_output")
+        temp_path = Path("~/.echopype/temp_output")
         dump_path = Path("echopype/test_data/dump")
         if temp_path.exists():
             shutil.rmtree(temp_path)

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -47,7 +47,7 @@ jobs:
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
       - name: Setup micromamba
-        uses: mamba-org/provision-with-micromamba@v13
+        uses: mamba-org/provision-with-micromamba@v15
         with:
           environment-file: .ci_helpers/py${{ matrix.python-version }}.yaml
           environment-name: ${{ env.CONDA_ENV }}
@@ -65,7 +65,7 @@ jobs:
       - name: Install dev tools
         shell: bash -l {0}
         run: |
-          mamba install -c conda-forge --yes --file requirements-dev.txt
+          micromamba install -c conda-forge -n ${{ env.CONDA_ENV }} --yes --file requirements-dev.txt
       - name: Install echopype
         shell: bash -l {0}
         run: |
@@ -83,12 +83,12 @@ jobs:
           pytest -vv -rx --numprocesses=${{ 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@v2
+        uses: actions/upload-artifact@v3
         with:
           name: ci_test_log
           path: ci_test_log.log
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
         with:
           file: ./coverage.xml
           flags: unittests

diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
@@ -18,7 +18,7 @@ jobs:
         image_name: ["minioci", "http"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Retrieve test data
         if: matrix.image_name == 'http'
         uses: ./.github/actions/gdrive-rclone
@@ -32,21 +32,22 @@ jobs:
           echo "IMAGE_SPEC=${IMAGE_SPEC}" >> $GITHUB_ENV
           echo "DATE_TAG=${DATE_TAG}" >> $GITHUB_ENV
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v2
       - name: Login to DockerHub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_TOKEN }}
       - name: Build and push
         id: docker_build_push
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v4
         with:
           context: ./
           file: ./.ci_helpers/docker/${{ matrix.image_name }}.dockerfile
           push: true
+          platforms: linux/amd64,linux/arm64
           tags: |
             ${{ env.IMAGE_SPEC }}:${{ env.DATE_TAG }}
             ${{ env.IMAGE_SPEC }}:latest
diff --git a/.github/workflows/ep-install.yaml b/.github/workflows/ep-install.yaml
@@ -18,7 +18,7 @@ jobs:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Setup miniconda
         uses: conda-incubator/setup-miniconda@v2
         with:

diff --git a/.github/workflows/packit.yaml b/.github/workflows/packit.yaml
@@ -14,13 +14,13 @@ jobs:
     if: github.repository == 'OSOceanAcoustics/echopype'
     steps:
     - name: Checkout
-      uses: actions/checkout@v2.3.4
+      uses: actions/checkout@v3
       with:
         # fetch all history so that setuptools-scm works
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/setup-python@v2.2.1
+      uses: actions/setup-python@v4.5.0
       with:
         python-version: 3.9
 
@@ -42,7 +42,7 @@ jobs:
         echo ""
         echo "Generated files:"
         ls -lh dist/
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
         name: releases
         path: dist
@@ -52,11 +52,11 @@ jobs:
     needs: build-artifact
     runs-on: ubuntu-20.04
     steps:
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4.5.0
       name: Install Python
       with:
         python-version: 3.9
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v3
       with:
         name: releases
         path: dist

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -43,7 +43,7 @@ jobs:
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
       - name: Setup micromamba
-        uses: mamba-org/provision-with-micromamba@v13
+        uses: mamba-org/provision-with-micromamba@v15
         with:
           environment-file: .ci_helpers/py${{ matrix.python-version }}.yaml
           environment-name: ${{ env.CONDA_ENV }}
@@ -61,7 +61,7 @@ jobs:
       - name: Install dev tools
         shell: bash -l {0}
         run: |
-          mamba install -c conda-forge --yes --file requirements-dev.txt
+          micromamba install -c conda-forge -n ${{ env.CONDA_ENV }} --yes --file requirements-dev.txt
       - name: Install echopype
         shell: bash -l {0}
         run: |
@@ -93,12 +93,12 @@ jobs:
           python .ci_helpers/run-test.py --pytest-args="--log-cli-level=WARNING,-vvv,-rx,--numprocesses=${{ env.NUM_WORKERS }},--max-worker-restart=3,--disable-warnings" --include-cov ${{ steps.files.outputs.added_modified_renamed }} |& tee ci_test_log.log
       - name: Upload ci test log
         if: ${{ success() || failure() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: ci_test_log
           path: ci_test_log.log
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
         with:
           file: ./coverage.xml
           flags: unittests

diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml
@@ -18,13 +18,13 @@ jobs:
     if: github.repository == 'OSOceanAcoustics/echopype'
     steps:
     - name: Checkout
-      uses: actions/checkout@v2.3.4
+      uses: actions/checkout@v3
       with:
         # fetch all history so that setuptools-scm works
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/setup-python@v2.2.1
+      uses: actions/setup-python@v4.5.0
       with:
         python-version: 3.9
 
@@ -46,7 +46,7 @@ jobs:
         echo ""
         echo "Generated files:"
         ls -lh dist/
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
         name: releases
         path: dist
@@ -56,11 +56,11 @@ jobs:
     needs: build-artifact
     runs-on: ubuntu-20.04
     steps:
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4.5.0
       name: Install Python
       with:
         python-version: 3.9
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v3
       with:
         name: releases
         path: dist
@@ -69,7 +69,7 @@ jobs:
         ls -ltrh
         ls -ltrh dist
     - name: Publish to Test PyPI
-      uses: pypa/gh-action-pypi-publish@v1.4.2
+      uses: pypa/gh-action-pypi-publish@v1.6.4
       with:
         password: ${{ secrets.TEST_PYPI_API_TOKEN }}
         repository_url: https://test.pypi.org/legacy/
@@ -99,11 +99,11 @@ jobs:
     if: startsWith(github.ref, 'refs/tags')
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v3
       with:
         name: releases
         path: dist
     - name: Publish to PyPI
-      uses: pypa/gh-action-pypi-publish@v1.4.2
+      uses: pypa/gh-action-pypi-publish@v1.6.4
       with:
         password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.github/workflows/windows-utils.yaml b/.github/workflows/windows-utils.yaml
@@ -0,0 +1,69 @@
+name: windows-utils-test
+
+on:
+  push:
+    paths-ignore: [".ci_helpers/docker/**", "**/docker.yaml"]
+  pull_request:
+    paths-ignore: [".ci_helpers/docker/**", "**/docker.yaml"]
+  pull_request_target:
+    paths-ignore: [".ci_helpers/docker/**", "**/docker.yaml"]
+  workflow_dispatch:
+
+env:
+  CONDA_ENV: echopype
+
+jobs:
+  windows-test:
+      name: windows-${{ matrix.python-version }}-build
+      runs-on: "windows-latest"
+      continue-on-error: ${{ matrix.experimental }}
+      strategy:
+        fail-fast: false
+        matrix:
+          include:
+          - python-version: 3.9
+            experimental: false
+      defaults:
+        run:
+          shell: powershell
+      steps:
+        - name: Checkout repo
+          uses: actions/checkout@v3
+          with:
+            fetch-depth: 0 # Fetch all history for all branches and tags.
+        - name: Set environment variables
+          run: |
+            echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
+        - name: Setup miniconda w/mamba
+          uses: conda-incubator/setup-miniconda@v2
+          with:
+            python-version: ${{ matrix.python-version }}
+            mamba-version: "*"
+            channels: conda-forge,defaults
+            channel-priority: true
+            activate-environment: ${{ env.CONDA_ENV }}
+            environment-file: .ci_helpers/py${{ matrix.python-version }}.yaml
+        # Currently problematic! See https://github.com/mamba-org/mamba/issues/2157
+        # - name: Setup micromamba
+        #   uses: mamba-org/provision-with-micromamba@v15
+        #   with:
+        #     environment-file: .ci_helpers/py${{ matrix.python-version }}.yaml
+        #     environment-name: ${{ env.CONDA_ENV }}
+        #     cache-env: true
+        #     cache-env-key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles(format('.ci_helpers/py{0}.yaml', matrix.python-version)) }}
+        - name: Print conda info
+          run: |
+            conda info
+            conda list
+            conda config --show-sources
+            conda config --show
+            printenv | sort
+        - name: Install dev tools
+          run: |
+            mamba install -c conda-forge -n ${{ env.CONDA_ENV }} --yes --file requirements-dev.txt
+        - name: Install echopype
+          run: |
+            python -m pip install -e .
+        - name: Running all Tests
+          run: |
+            pytest -vvv -rx --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings echopype/tests/utils |& tee ci_${{ matrix.python-version }}_test_log.log
diff --git a/.github/workflows/windows.yaml b/.github/workflows/windows.yaml
@@ -37,7 +37,7 @@ jobs:
             - 8080:80
       steps:
         - name: Checkout repo
-          uses: actions/checkout@v2
+          uses: actions/checkout@v3
         - name: Copying test data to http server
           run: |
             rm .\echopype\test_data -r -fo
@@ -46,12 +46,12 @@ jobs:
             # Check data endpoint
             curl http://localhost:8080/data/
         - name: Setup Python
-          uses: actions/setup-python@v1
+          uses: actions/setup-python@v4.5.0
           with:
             python-version: ${{ matrix.python-version }}
             architecture: x64
         - name: Cache conda
-          uses: actions/cache@v2
+          uses: actions/cache@v3.2.5
           env:
             # Increase this value to reset cache if '.ci_helpers/py{0}.yaml' has not changed
             CACHE_NUMBER: 0

diff --git a/.gitignore b/.gitignore
@@ -29,7 +29,6 @@ toolbox
 *.mat
 ek60/
 azfp/
-temp_echopype_output/
 notebooks/*_dev/
 _echopype_version.py
 !echopype/test_data