Merge pull request #7 from danielfromearth/develop

Update main

.flake8

@@ -0,0 +1,12 @@
+[flake8]
+ignore = E501, E302
+exclude =
+    # No need to traverse our git directory
+    .git,
+    # There's no value in checking cache directories
+    __pycache__,
+    # The conf file is mostly autogenerated, ignore it
+    docs/source/conf.py,
+    # This contains our built documentation
+    build,
+max-complexity = 12

.github/workflows/lint_and_test_and_bump.yml

@@ -0,0 +1,113 @@
+name: Lint and Test
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push events
+  push:
+    branches: [ develop, release/**, main, feature/**, issue/**, issues/** ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build-linux:
+    name: Lint and Test
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install Poetry
+      uses: abatilo/[email protected]
+      with:
+        poetry-version: 1.3.2
+
+    - name: Get version
+      id: get-version
+      run: |
+        echo "current_version=$(poetry version | awk '{print $2}')" >> $GITHUB_OUTPUT
+        echo "pyproject_name=$(poetry version | awk '{print $1}')" >> $GITHUB_ENV
+
+    - name: Bump pre-alpha version
+      # If triggered by push to a feature branch
+      if: |
+        ${{ startsWith(github.ref, 'refs/heads/issue') }}      ||
+        ${{ startsWith(github.ref, 'refs/heads/dependabot/') }} ||
+        ${{ startsWith(github.ref, 'refs/heads/feature/') }}
+      run: |
+        new_ver="${{ steps.get-version.outputs.current_version }}+$(git rev-parse --short ${GITHUB_SHA})"
+        poetry version $new_ver
+        echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
+
+    - name: Bump alpha version
+      # If triggered by push to the develop branch
+      if: ${{ github.ref == 'refs/heads/develop' }}
+      run: |
+        poetry version prerelease
+        echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
+        echo "venue=sit" >> $GITHUB_ENV
+
+    - name: Bump rc version
+      # If triggered by push to a release branch
+      if: ${{ startsWith(github.ref, 'refs/heads/release/') }}
+      env:
+        # True if the version already has a 'rc' pre-release identifier
+        BUMP_RC: ${{ contains(steps.get-version.outputs.current_version, 'rc') }}
+      run: |
+        if [ "$BUMP_RC" = true ]; then
+          poetry version prerelease
+        else
+          poetry version ${GITHUB_REF#refs/heads/release/}rc1
+        fi
+        echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
+        echo "venue=uat" >> $GITHUB_ENV
+
+    - name: Release version
+      # If triggered by push to the main branch
+      if: ${{ startsWith(github.ref, 'refs/heads/main') }}
+      env:
+        CURRENT_VERSION: ${{ steps.get-version.outputs.current_version }}
+      # Remove rc* from end of version string
+      # The ${string%%substring} syntax below deletes the longest match of $substring from back of $string.
+      run: |
+        poetry version ${CURRENT_VERSION%%rc*}
+        echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
+        echo "venue=ops" >> $GITHUB_ENV
+
+    - name: Install bumblebee
+      run: poetry install
+
+    - name: Lint
+      run: |
+        poetry run pylint concatenator
+        poetry run flake8 concatenator
+
+    - name: Test with pytest
+      run: |
+        poetry run pytest
+
+#    - name: Commit Version Bump
+#      # If building develop, a release branch, or main then we commit the version bump back to the repo
+#      if: |
+#        github.ref == 'refs/heads/develop' ||
+#        github.ref == 'refs/heads/main'    ||
+#        startsWith(github.ref, 'refs/heads/release')
+#      run: |
+#        git config --global user.name 'bumblebee bot'
+#        git config --global user.email '[email protected]'
+#        git commit -am "/version ${{ env.software_version }}"
+#        git push
+#
+#    - name: Push Tag
+#      if: |
+#        github.ref == 'refs/heads/develop' ||
+#        github.ref == 'refs/heads/main'    ||
+#        startsWith(github.ref, 'refs/heads/release')
+#      run: |
+#        git config user.name "${GITHUB_ACTOR}"
+#        git config user.email "${GITHUB_ACTOR}@users.noreply.github.com"
+#        git tag -a "${{ env.software_version }}" -m "Version ${{ env.software_version }}"
+#        git push origin "${{ env.software_version }}"

.github/workflows/lint_and_test_on_pull_request.yml

@@ -0,0 +1,38 @@
+name: Receive PR
+
+# read-only repo token
+# no access to secrets
+on:
+  pull_request:
+    # Sequence of patterns matched against refs/heads
+    branches:
+      - feature/**
+      - issue/**
+      - issues/**
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install Poetry
+      uses: abatilo/[email protected]
+      with:
+        poetry-version: 1.3.2
+
+    - name: Install bumblebee
+      run: poetry install
+
+    - name: Lint
+      run: |
+        poetry run pylint concatenator
+        poetry run flake8 concatenator
+
+    - name: Test with pytest
+      run: |
+        poetry run pytest

.pre-commit-config.yaml

@@ -20,7 +20,7 @@ repos:
         exclude: doc/data/messages/(r/reimported|w/wrong-import-order|u/ungrouped-imports|m/misplaced-future|m/multiple-imports)/bad.py
 
   - repo: https://github.com/pylint-dev/pylint
-    rev: v2.17.4
+    rev: v3.0.0a7
     hooks:
       - id: pylint
         name: pylint
@@ -34,14 +34,19 @@ repos:
             "--rcfile=.pylintrc", # Link to your config file
           ]
 
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.1.1
+    rev: v1.5.1
     hooks:
       - id: mypy
 
   # Other Linters
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.29.0
+    rev: v1.32.0
     hooks:
       - id: yamllint
         args: ["-d {extends: relaxed, rules: {line-length: {max: 120}}}"]

concatenator/__init__.py

@@ -0,0 +1,4 @@
+"""Convenience variables used across the package."""
+
+GROUP_DELIM = '__'
+COORD_DELIM = "  "

concatenator/attribute_handling.py

@@ -0,0 +1,87 @@
+"""
+attribute_handling.py
+
+Functions for converting "coordinates" in netCDF variable attributes
+ between paths that reference a group hierarchy and flattened paths.
+"""
+import re
+
+import netCDF4
+
+from concatenator import COORD_DELIM, GROUP_DELIM
+
+
+def regroup_coordinate_attribute(attribute_string: str) -> str:
+    """
+    Examples
+    --------
+    >>> coord_att = "__Time_and_Position__time  __Time_and_Position__instrument_fov_latitude  __Time_and_Position__instrument_fov_longitude"
+    >>> _flatten_coordinate_attribute(coord_att)
+        Time_and_Position/time  Time_and_Position/instrument_fov_latitude  Time_and_Position/instrument_fov_longitude
+
+    Parameters
+    ----------
+    attribute_string : str
+
+    Returns
+    -------
+    str
+    """
+    # Use the separator that's in the attribute string only if all separators in the string are the same.
+    # Otherwise, we will use our own default separator.
+    whitespaces = re.findall(r'\s+', attribute_string)
+    if len(set(whitespaces)) <= 1:
+        new_sep = whitespaces[0]
+    else:
+        new_sep = COORD_DELIM
+
+    return new_sep.join(
+        '/'.join(c.split(GROUP_DELIM))[1:]
+        for c
+        in attribute_string.split()  # split on any whitespace
+    )
+
+
+def flatten_coordinate_attribute_paths(dataset: netCDF4.Dataset,
+                                       var: netCDF4.Variable,
+                                       variable_name: str) -> None:
+    """Flatten the paths of variables referenced in the coordinates attribute."""
+    if 'coordinates' in var.ncattrs():
+        coord_att = var.getncattr('coordinates')
+
+        new_coord_att = _flatten_coordinate_attribute(coord_att)
+
+        dataset.variables[variable_name].setncattr('coordinates', new_coord_att)
+
+
+def _flatten_coordinate_attribute(attribute_string: str) -> str:
+    """Converts attributes that specify group membership via "/" to use new group delimiter, even for the root level.
+
+    Examples
+    --------
+    >>> coord_att = "Time_and_Position/time  Time_and_Position/instrument_fov_latitude  Time_and_Position/instrument_fov_longitude"
+    >>> _flatten_coordinate_attribute(coord_att)
+        __Time_and_Position__time  __Time_and_Position__instrument_fov_latitude  __Time_and_Position__instrument_fov_longitude
+
+    Parameters
+    ----------
+    attribute_string : str
+
+    Returns
+    -------
+    str
+    """
+    # Use the separator that's in the attribute string only if all separators in the string are the same.
+    # Otherwise, we will use our own default separator.
+    whitespaces = re.findall(r'\s+', attribute_string)
+    if len(set(whitespaces)) <= 1:
+        new_sep = whitespaces[0]
+    else:
+        new_sep = COORD_DELIM
+
+    # A new string is constructed.
+    return new_sep.join(
+        f'{GROUP_DELIM}{c.replace("/", GROUP_DELIM)}'
+        for c
+        in attribute_string.split()  # split on any whitespace
+    )