Merge pull request OSOceanAcoustics#560 from OSOceanAcoustics/dev

Release/v0.5.6

.ci_helpers/py3.10.yaml

@@ -0,0 +1,19 @@
+name: echopype
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - dask
+  - matplotlib
+  - netCDF4
+  - numpy
+  - pynmea2
+  - pytz
+  - scipy
+  - xarray
+  - zarr
+  - fsspec
+  - requests
+  - aiohttp
+  - s3fs
+  - mamba=0.20.0

.ci_helpers/py3.7.yaml

@@ -16,4 +16,4 @@ dependencies:
   - requests
   - aiohttp
   - s3fs
-  - mamba
+  - mamba=0.20.0

.ci_helpers/py3.8.yaml

@@ -16,4 +16,4 @@ dependencies:
   - requests
   - aiohttp
   - s3fs
-  - mamba
+  - mamba=0.20.0

.ci_helpers/py3.9.yaml

@@ -16,4 +16,4 @@ dependencies:
   - requests
   - aiohttp
   - s3fs
-  - mamba
+  - mamba=0.20.0

.github/workflows/ci.yaml

@@ -20,11 +20,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8]
-        experimental: [false]
         include:
+        - python-version: 3.7
+          experimental: false
+        - python-version: 3.8
+          experimental: false
         - python-version: 3.9
           experimental: true
+        - python-version: "3.10"
+          experimental: true
     services:
       # TODO: figure out how to update tag when there's a new one
       minio:
@@ -71,15 +75,15 @@ jobs:
           use-mamba: true
           auto-activate-base: false
           use-only-tar-bz2: true
-      - name: Update mamba
-        shell: bash -l {0}
-        run: |
-          conda update -c conda-forge --yes mamba
       - name: Print conda env
         shell: bash -l {0}
         run: |
           conda info
           conda list
+      - name: Remove docker-compose python
+        if: ${{ matrix.python-version == '3.10' }}
+        shell: bash -l {0}
+        run: sed -i "/docker-compose/d" requirements-dev.txt
       - name: Install dev tools
         shell: bash -l {0}
         run: |
@@ -91,7 +95,7 @@ jobs:
       - name: Running All Tests
         shell: bash -l {0}
         run: |
-          pytest -vv -rx --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings |& tee ci_${{ matrix.python-version }}_test_log.log
+          pytest -vv -rx --numprocesses=4 --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

.github/workflows/packit.yaml

@@ -0,0 +1,88 @@
+name: Packaging
+
+# Only run for tagged releases
+on:
+  push:
+    branches:
+      - dev
+  workflow_dispatch:
+
+jobs:
+  build-artifact:
+    name: Build echopype package
+    runs-on: ubuntu-20.04
+    if: github.repository == 'OSOceanAcoustics/echopype'
+    steps:
+    - name: Checkout
+      uses: actions/[email protected]
+      with:
+        # fetch all history so that setuptools-scm works
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/[email protected]
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: python -m pip install setuptools wheel
+
+    # This step is only necessary for testing purposes and for TestPyPI
+    - name: Fix up version string for TestPyPI
+      if: ${{ !startsWith(github.ref, 'refs/tags') }}
+      run: |
+        # Change setuptools-scm local_scheme to "no-local-version" so the
+        # local part of the version isn't included, making the version string
+        # compatible with PyPI.
+        sed --in-place "s/node-and-date/no-local-version/g" setup.py
+
+    - name: Build source and wheel distributions
+      run: |
+        python setup.py sdist bdist_wheel
+        echo ""
+        echo "Generated files:"
+        ls -lh dist/
+    - uses: actions/upload-artifact@v2
+      with:
+        name: releases
+        path: dist
+
+  test-built-dist:
+    name: Test echopype package
+    needs: build-artifact
+    runs-on: ubuntu-20.04
+    steps:
+    - uses: actions/setup-python@v2
+      name: Install Python
+      with:
+        python-version: 3.9
+    - uses: actions/download-artifact@v2
+      with:
+        name: releases
+        path: dist
+    - name: List contents of built dist
+      run: |
+        ls -ltrh
+        ls -ltrh dist
+    - name: Upgrade pip
+      run: |
+        sleep 3
+        python -m pip install --upgrade pip
+    - name: Check wheel file
+      run: |
+        python -m pip uninstall --yes echopype
+        echo "=== Testing wheel file ==="
+        # Install wheel to get dependencies and check import
+        wheel_file=$(ls ./dist | grep ".whl")
+        python -m pip install ./dist/$wheel_file
+        python -c "import echopype; print(echopype.__version__)"
+        echo "=== Done testing wheel file ==="
+    - name: Check source tar
+      run: |
+        python -m pip uninstall --yes echopype
+        echo "=== Testing source tar file ==="
+        # Install tar gz and check import
+        source_file=$(ls ./dist | grep ".tar.gz")
+        python -m pip install ./dist/$source_file
+        python -c "import echopype; print(echopype.__version__)"
+        echo "=== Done testing source tar file ==="

.github/workflows/pr.yaml

@@ -2,7 +2,7 @@ name: Test PR
 
 on:
   pull_request:
-    paths-ignore: [".ci_helpers/docker/**", "**/docker.yaml"]
+    paths-ignore: [".ci_helpers/docker/**", "**/docker.yaml", "docs"]
 
 env:
   CONDA_ENV: echopype
@@ -16,11 +16,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8]
-        experimental: [false]
         include:
+        - python-version: 3.7
+          experimental: false
+        - python-version: 3.8
+          experimental: false
         - python-version: 3.9
           experimental: true
+        - python-version: "3.10"
+          experimental: true
     services:
       # TODO: figure out how to update tag when there's a new one
       minio:
@@ -67,15 +71,15 @@ jobs:
           use-mamba: true
           auto-activate-base: false
           use-only-tar-bz2: true
-      - name: Update mamba
-        shell: bash -l {0}
-        run: |
-          conda update -c conda-forge --yes mamba
       - name: Print conda env
         shell: bash -l {0}
         run: |
           conda info
           conda list
+      - name: Remove docker-compose python
+        if: ${{ matrix.python-version == '3.10' }}
+        shell: bash -l {0}
+        run: sed -i "/docker-compose/d" requirements-dev.txt
       - name: Install dev tools
         shell: bash -l {0}
         run: |
@@ -96,12 +100,12 @@ jobs:
         if: contains(github.event.pull_request.labels.*.name, 'Needs Complete Testing')
         shell: bash -l {0}
         run: |
-          pytest -vv -rx --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings |& tee ci_${{ matrix.python-version }}_test_log.log
+          pytest -vvv -rx --numprocesses=4 --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings |& tee ci_${{ matrix.python-version }}_test_log.log
       - name: Running Tests
         if: "!contains(github.event.pull_request.labels.*.name, 'Needs Complete Testing')"
         shell: bash -l {0}
         run: |
-          python .ci_helpers/run-test.py --pytest-args="--log-cli-level=WARNING,-vv,-rx,--disable-warnings" --include-cov ${{ steps.files.outputs.added_modified_renamed }} |& tee ci_test_log.log
+          python .ci_helpers/run-test.py --pytest-args="--log-cli-level=WARNING,-vvv,-rx,--numprocesses=4,--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

.github/workflows/pypi.yaml

@@ -74,6 +74,7 @@ jobs:
         password: ${{ secrets.TEST_PYPI_API_TOKEN }}
         repository_url: https://test.pypi.org/legacy/
         verbose: true
+        skip_existing: true
     - name: Check pypi packages
       run: |
         sleep 3

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 exclude: |
   (?x)^(
-    docs/|
     echopype/tests/|
     echopype/test_data/|
     echopype/process/|
     echopype/visualize/|
     echopype/convert/add_ancillary.py|
-    echopype/convert/convert_combine.py
+    echopype/convert/convert_combine.py|
+    docs/source/conf.py
   )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -35,3 +35,15 @@ repos:
     rev: 4.0.1
     hooks:
       - id: flake8
+
+  - repo: https://github.com/executablebooks/jupyter-book
+    rev: v0.12.1
+    hooks:
+    - id: jb-to-sphinx
+      args: ["docs/source"]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.1.0
+    hooks:
+      - id: codespell
+        args: ["-w", "docs/source", "echopype"]

.readthedocs.yml

@@ -22,6 +22,10 @@ python:
    install:
       - requirements: requirements.txt
       - requirements: docs/requirements.txt
+      - method: pip
+        path: .
+        extra_requirements:
+           - plot
       - method: setuptools
         path: .
 #   system_packages: true

README.md

@@ -92,4 +92,4 @@ Echopype is licensed under the open source [Apache 2.0 license](https://opensour
 
 ---------------
 
-Copyright (c) 2018-2021, echopype Developers.
+Copyright (c) 2018-2022, echopype Developers.

docs/Makefile

@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/requirements.txt

@@ -1,5 +1,6 @@
 sphinx_rtd_theme
 sphinx-automodapi
 sphinxcontrib-mermaid
+jupyter-book
 numpydoc
-docutils<0.18
+docutils<0.18

docs/source/_config.yml

@@ -0,0 +1,47 @@
+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: ""
+author: Echopype Developers
+copyright: "2022"
+logo: _static/echopype_logo_square.png
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: 'off'
+  timeout: -1
+
+# Define the name of the latex output file for PDF builds
+# latex:
+#   latex_documents:
+#     targetname: book.tex
+
+# Add a bibtex file so that we can create citations
+# bibtex_bibfiles:
+#   - references.bib
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/OSOceanAcoustics/echopype  # Online location of your book
+  path_to_book: docs  # Optional path to your book, relative to the repository root
+  branch: main  # Which branch of the repository should be used when creating links (optional)
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  home_page_in_navbar: false
+  use_issues_button: true
+  use_repository_button: true
+
+sphinx:
+  extra_extensions: [
+    'sphinx_automodapi.automodapi',
+    'numpydoc',
+    # 'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.githubpages',
+    'sphinxcontrib.mermaid'
+  ]