Merge branch 'master' into mpiarray-jrs-bak

.github/workflows/main.yml

@@ -15,19 +15,21 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Set up Python 3.9
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v2
         with:
           python-version: 3.9
 
       - name: Install apt dependencies
         run: |
-          sudo apt-get update && sudo apt-get install -y libopenmpi-dev openmpi-bin
+          sudo apt-get update
+          sudo apt-get install -y libopenmpi-dev openmpi-bin libhdf5-serial-dev
 
       - name: Install pip dependencies
         run: |
-          pip install pylint==2.7.0 pylint-ignore flake8 pytest black mpi4py pyinstrument psutil
+          pip install pylint==2.7.0 pylint-ignore flake8 pytest black mpi4py pyinstrument psutil pytest-lazy-fixture
           pip install -r requirements.txt
           python setup.py develop
+          pip install .[compression]
 
       - name: Run flake8
         run: flake8 --show-source --ignore=E501,E741,E203,W503,E266 caput
@@ -47,17 +49,21 @@ jobs:
 
     - name: Install apt dependencies
       run: |
-        sudo apt-get update && sudo apt-get install -y libopenmpi-dev openmpi-bin
+        sudo apt-get update
+        sudo apt-get install -y libopenmpi-dev openmpi-bin libhdf5-serial-dev
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install pip dependencies
       run: |
+        pip install h5py
         pip install -r requirements.txt
-        pip install mpi4py pytest psutil
+        pip install zarr==2.8.1
+        pip install mpi4py numcodecs==0.7.3 bitshuffle
+        pip install pytest pytest-lazy-fixture
         python setup.py develop
 
     - name: Run serial tests
@@ -78,10 +84,15 @@ jobs:
     - uses: actions/checkout@v2
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
         python-version: 3.9
 
+    - name: Install apt dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libhdf5-serial-dev
+
     - name: Install pip dependencies
       run: |
         pip install -r requirements.txt

caput/config.py

@@ -482,6 +482,62 @@ def _prop(config):
     return prop
 
 
+def file_format(default=None):
+    """A property type that accepts only "zarr", or "hdf5".
+
+    Returns the selected `caput.fileformat.FileFormat` subclass or `caput.fileformats.HDF5` if `value == default`.
+
+    Parameters
+    ----------
+    default : optional
+        The optional default value.
+
+    Returns
+    -------
+    prop : Property
+        A property instance setup to validate a file format.
+
+    Raises
+    ------
+    ValueError
+        If the default value is not `"hdf5"` or `"zarr"`.
+
+    Examples
+    --------
+    Should be used like::
+
+        class Project:
+
+            mode = file_format(default='zarr')
+    """
+    options = ("hdf5", "zarr")
+
+    def _prop(val):
+        from . import fileformats
+
+        if val is None:
+            return None
+
+        if not isinstance(val, str):
+            CaputConfigError(
+                f"Input {repr(val)} is of type {type(val).__name__} (expected str or None)."
+            )
+
+        val = val.lower()
+        if val == "hdf5":
+            return fileformats.HDF5
+        if val == "zarr":
+            return fileformats.Zarr
+        raise CaputConfigError(f"Input {repr(val)} needs to be one of {options})")
+
+    if default is not None and (
+        (not isinstance(default, str)) or (default.lower() not in options)
+    ):
+        raise CaputConfigError(f"Default value {repr(default)} must be in {options}")
+
+    return Property(proptype=_prop, default=default)
+
+
 class _line_dict(dict):
     """A private dict subclass that also stores line numbers for debugging."""