Merge branch 'main' into grid-polygons

Author: dcherian

.github/workflows/ci.yaml

@@ -50,7 +50,7 @@ jobs:
         run: |
           pytest -n auto --cov=./ --cov-report=xml
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v3.1.4
+        uses: codecov/codecov-action@v4.3.0
         with:
           file: ./coverage.xml
           flags: unittests
@@ -114,7 +114,7 @@ jobs:
         run: |
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report cf_xarray/
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v3.1.4
+        uses: codecov/codecov-action@v4.3.0
         with:
           file: mypy_report/cobertura.xml
           flags: mypy

.github/workflows/pypi.yaml

@@ -15,7 +15,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: "3.10"
@@ -41,7 +41,7 @@ jobs:
           else
             echo "✅ Looks good"
           fi
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: releases
           path: dist
@@ -50,11 +50,11 @@ jobs:
     needs: build-artifacts
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: "3.10"
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: releases
           path: dist
@@ -72,7 +72,7 @@ jobs:
 
       - name: Publish package to TestPyPI
         if: github.event_name == 'push'
-        uses: pypa/[email protected].11
+        uses: pypa/[email protected].14
         with:
           password: ${{ secrets.TESTPYPI_TOKEN }}
           repository_url: https://test.pypi.org/legacy/
@@ -91,11 +91,11 @@ jobs:
       id-token: write
 
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: releases
           path: dist
       - name: Publish package to PyPI
-        uses: pypa/[email protected].11
+        uses: pypa/[email protected].14
         with:
           verbose: true

.github/workflows/testpypi-release.yaml

@@ -21,7 +21,7 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: "3.10"
@@ -53,7 +53,7 @@ jobs:
             echo "✅ Looks good"
           fi
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: releases
           path: dist
@@ -62,11 +62,11 @@ jobs:
     needs: build-artifacts
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: "3.10"
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: releases
           path: dist

.github/workflows/upstream-dev-ci.yaml

@@ -22,7 +22,7 @@ jobs:
   upstream-dev:
     name: upstream-dev
     runs-on: ubuntu-latest
-    if: ${{ (contains( github.event.pull_request.labels.*.name, 'test-upstream') && github.event_name == 'pull_request') || github.event_name == 'workflow_dispatch' }}
+    if: ${{ (contains( github.event.pull_request.labels.*.name, 'test-upstream') && github.event_name == 'pull_request') || github.event_name == 'workflow_dispatch' || github.event_name == 'schedule' }}
     defaults:
       run:
         shell: bash -l {0}

.pre-commit-config.yaml

@@ -10,13 +10,13 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.1.1'
+    rev: 'v0.1.9'
     hooks:
       - id: ruff
         args: ["--show-fixes", "--fix"]
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.10.1
+    rev: 23.12.1
     hooks:
       - id: black
 
@@ -36,7 +36,7 @@ repos:
         - mdformat-myst
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+    rev: 1.7.1
     hooks:
         - id: nbqa-black
         - id: nbqa-ruff
@@ -56,7 +56,7 @@ repos:
       - id: debug-statements
 
   - repo: https://github.com/keewis/blackdoc
-    rev: v0.3.8
+    rev: v0.3.9
     hooks:
       - id: blackdoc
         files: .+\.py$

cf_xarray/datasets.py

@@ -503,6 +503,16 @@ def _create_inexact_bounds():
     name="flag_var",
 )
 
+flag_indep_uint16 = xr.DataArray(
+    np.array([1, 10, 100, 1000, 10000, 65535], dtype=np.uint16),
+    dims=("time",),
+    attrs={
+        "flag_masks": [2**i for i in range(16)],
+        "flag_meanings": " ".join([f"flag_{2**i}" for i in range(16)]),
+        "standard_name": "flag_independent",
+    },
+    name="flag_var",
+)
 
 flag_mix = xr.DataArray(
     np.array([4, 8, 13, 5, 10, 14, 7, 3], np.uint8),

cf_xarray/formatting.py

@@ -151,8 +151,47 @@ def _maybe_panel(textgen, title: str, rich: bool):
         return title + ":\n" + text
 
 
-def find_set_bits(mask, value, repeated_masks):
-    bitpos = np.arange(8)[::-1]
+def _get_bit_length(dtype):
+    # Check if dtype is a numpy dtype, if not, convert it
+    if not isinstance(dtype, np.dtype):
+        dtype = np.dtype(dtype)
+
+    # Calculate the bit length
+    bit_length = 8 * dtype.itemsize
+
+    return bit_length
+
+
+def _unpackbits(mask, bit_length):
+    # Ensure the array is a numpy array
+    arr = np.asarray(mask)
+
+    # Create an output array of the appropriate shape
+    output_shape = arr.shape + (bit_length,)
+    output = np.zeros(output_shape, dtype=np.uint8)
+
+    # Unpack bits
+    for i in range(bit_length):
+        output[..., i] = (arr >> i) & 1
+
+    return output[..., ::-1]
+
+
+def _max_chars_for_bit_length(bit_length):
+    """
+    Find the maximum characters needed for a fixed-width display
+    for integer values of a certain bit_length. Use calculation
+    for signed integers, since it conservatively will always have
+    enough characters for signed or unsigned.
+    """
+    # Maximum value for signed integers of this bit length
+    max_val = 2 ** (bit_length - 1) - 1
+    # Add 1 for the negative sign
+    return len(str(max_val)) + 1
+
+
+def find_set_bits(mask, value, repeated_masks, bit_length):
+    bitpos = np.arange(bit_length)[::-1]
     if mask not in repeated_masks:
         if value == 0:
             return [-1]
@@ -161,8 +200,8 @@ def find_set_bits(mask, value, repeated_masks):
         else:
             return [int(np.log2(mask))]
     else:
-        allset = bitpos[np.unpackbits(np.uint8(mask)) == 1]
-        setbits = bitpos[np.unpackbits(np.uint8(mask & value)) == 1]
+        allset = bitpos[_unpackbits(mask, bit_length) == 1]
+        setbits = bitpos[_unpackbits(mask & value, bit_length) == 1]
         return [b if abs(b) in setbits else -b for b in allset]
 
 
@@ -184,25 +223,30 @@ def _format_flags(accessor, rich):
     #     for f, (m, _) in flag_dict.items()
     #     if m is not None and m not in repeated_masks
     # ]
+
+    bit_length = _get_bit_length(accessor._obj.dtype)
+    mask_width = _max_chars_for_bit_length(bit_length)
+    key_width = max(len(key) for key in flag_dict)
+
     bit_text = []
     value_text = []
     for key, (mask, value) in flag_dict.items():
         if mask is None:
             bit_text.append("✗" if rich else "")
             value_text.append(str(value))
             continue
-        bits = find_set_bits(mask, value, repeated_masks)
-        bitstring = ["."] * 8
+        bits = find_set_bits(mask, value, repeated_masks, bit_length)
+        bitstring = ["."] * bit_length
         if bits == [-1]:
             continue
         else:
             for b in bits:
                 bitstring[abs(b)] = _format_cf_name("1" if b >= 0 else "0", rich)
         text = "".join(bitstring[::-1])
         value_text.append(
-            f"{mask} & {value}"
+            f"{mask:{mask_width}} & {value}"
             if key in excl_flags and value is not None
-            else str(mask)
+            else f"{mask:{mask_width}}"
         )
         bit_text.append(text if rich else f" / Bit: {text}")
 
@@ -230,7 +274,9 @@ def _format_flags(accessor, rich):
     else:
         rows = []
         for val, bit, key in zip(value_text, bit_text, flag_dict):
-            rows.append(f"{TAB}{_format_cf_name(key, rich)}: {TAB} {val} {bit}")
+            rows.append(
+                f"{TAB}{_format_cf_name(key, rich):>{key_width}}: {TAB} {val} {bit}"
+            )
         return _print_rows("Flag Meanings", rows, rich)