merge with develop

.github/workflows/ci.yaml

@@ -1,25 +1,19 @@
 name: ci
-
 on:
   # Trigger the workflow on push to master or develop, except tag creation
   push:
     branches:
       - 'main'
       - 'develop'
-
   # Trigger the workflow on pull request
   pull_request: ~
-
   # Trigger the workflow manually
   workflow_dispatch: ~
-
   # Trigger after public PR approved for CI
   pull_request_target:
     types: [labeled]
-
   release:
     types: [created]
-
 jobs:
   qa:
     name: qa
@@ -48,7 +42,6 @@ jobs:
 
       - name: Check flake8
         run: flake8 .
-
   setup:
     name: setup
     runs-on: ubuntu-20.04
@@ -95,7 +88,6 @@ jobs:
         run: |
           echo inputs=$(echo "${{ inputs.build_package_inputs || '{}' }}" | yq eval '.' --output-format json --indent 0 -) >> $GITHUB_OUTPUT
           echo inputs-for-ubuntu=$(echo "${{ inputs.build_package_inputs || '{}' }}" | yq eval '. * {"os":"ubuntu-20.04","compiler":"gnu-10","compiler_cc":"gcc-10","compiler_cxx":"g++-10","compiler_fc":"gfortran-10"}' --output-format json --indent 0 -) >> $GITHUB_OUTPUT
-
   test:
     name: test
     needs:
@@ -150,16 +142,11 @@ jobs:
         uses: codecov/codecov-action@v3
         with:
           files: coverage.xml
-
   deploy:
     needs: test
-
     if: ${{ github.event_name == 'release' }}
-
     name: Upload to Pypi
-
     runs-on: ubuntu-latest
-
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python
@@ -176,4 +163,4 @@ jobs:
           TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
         run: |
           python setup.py sdist
-          twine upload dist/*
+          twine upload dist/*

polytope/datacube/backends/FDB_datacube.py

@@ -1,12 +1,8 @@
-import os
 from copy import deepcopy
 
-from .datacube import Datacube, IndexTree
+import pyfdb
 
-# TODO: probably need to do this more general...
-os.environ["DYLD_LIBRARY_PATH"] = "/Users/male/build/fdb-bundle/lib"
-os.environ["FDB_HOME"] = "/Users/male/git/fdb-home"
-import pyfdb  # noqa: E402
+from .datacube import Datacube, IndexTree
 
 
 def glue(path, unmap_path):
@@ -23,12 +19,12 @@ def __init__(self, config={}, axis_options={}):
         self.axis_options = axis_options
         self.grid_mapper = None
         self.axis_counter = 0
-        self._axes = {}
+        self._axes = None
         treated_axes = []
         self.non_complete_axes = []
         self.complete_axes = []
         self.blocked_axes = []
-        self.transformation = {}
+        self.transformation = None
         self.fake_axes = []
 
         partial_request = config

polytope/datacube/backends/datacube.py

@@ -43,7 +43,9 @@ def _create_axes(self, name, values, transformation_type_key, transformation_opt
 
             # first need to change the values so that we have right type
             values = transformation.change_val_type(axis_name, values)
-            if axis_name not in self._axes.keys():
+            if self._axes is None:
+                DatacubeAxis.create_standard(axis_name, values, self)
+            elif axis_name not in self._axes.keys():
                 DatacubeAxis.create_standard(axis_name, values, self)
             # add transformation tag to axis, as well as transformation options for later
             setattr(self._axes[axis_name], has_transform[transformation_type_key], True)  # where has_transform is a
@@ -66,7 +68,9 @@ def _check_and_add_axes(self, options, name, values):
             self._add_all_transformation_axes(options, name, values)
         else:
             if name not in self.blocked_axes:
-                if name not in self._axes.keys():
+                if self._axes is None:
+                    DatacubeAxis.create_standard(name, values, self)
+                elif name not in self._axes.keys():
                     DatacubeAxis.create_standard(name, values, self)
 
     def has_index(self, path: DatacubePath, axis, index):

polytope/datacube/backends/xarray.py

@@ -12,13 +12,13 @@ def __init__(self, dataarray: xr.DataArray, axis_options={}):
         self.axis_options = axis_options
         self.grid_mapper = None
         self.axis_counter = 0
-        self._axes = {}
+        self._axes = None
         self.dataarray = dataarray
         treated_axes = []
         self.non_complete_axes = []
         self.complete_axes = []
         self.blocked_axes = []
-        self.transformation = {}
+        self.transformation = None
         self.fake_axes = []
         for name, values in dataarray.coords.variables.items():
             if name in dataarray.dims:

polytope/datacube/datacube_axis.py

@@ -1,4 +1,4 @@
-from abc import ABC, abstractmethod, abstractproperty
+from abc import ABC, abstractmethod
 from copy import deepcopy
 from typing import Any, List
 
@@ -243,7 +243,9 @@ def unmap_total_path_to_datacube(path, unmapped_path):
                         # if we are on the first axis, then need to add the first val to unmapped_path
                         first_val = path.get(cls.name, None)
                         path.pop(cls.name, None)
-                        if cls.name not in unmapped_path:
+                        if unmapped_path is None:
+                            unmapped_path[cls.name] = first_val
+                        elif cls.name not in unmapped_path:
                             # if for some reason, the unmapped_path already has the first axis val, then don't update
                             unmapped_path[cls.name] = first_val
                     if cls.name == transformation._mapped_axes()[1]:
@@ -278,14 +280,11 @@ def find_indices_between(index_ranges, low, up, datacube, method=None):
                                 end = idxs.index(up)
                                 start = max(start - 1, 0)
                                 end = min(end + 1, len(idxs))
-                                # indexes_between = [i for i in indexes if low <= i <= up]
                                 indexes_between = idxs[start:end]
                                 indexes_between_ranges.append(indexes_between)
                             else:
                                 indexes_between = [i for i in idxs if low <= i <= up]
                                 indexes_between_ranges.append(indexes_between)
-                            # indexes_between = [i for i in idxs if low <= i <= up]
-                            # indexes_between_ranges.append(indexes_between)
             return indexes_between_ranges
 
         old_remap = cls.remap
@@ -362,14 +361,11 @@ def find_indices_between(index_ranges, low, up, datacube, method=None):
                                 end = indexes.index(up)
                                 start = max(start - 1, 0)
                                 end = min(end + 1, len(indexes))
-                                # indexes_between = [i for i in indexes if low <= i <= up]
                                 indexes_between = indexes[start:end]
                                 indexes_between_ranges.append(indexes_between)
                             else:
                                 indexes_between = [i for i in indexes if low <= i <= up]
                                 indexes_between_ranges.append(indexes_between)
-                            # indexes_between = [i for i in indexes if low <= i <= up]
-                            # indexes_between_ranges.append(indexes_between)
             return indexes_between_ranges
 
         def remap(range):
@@ -437,25 +433,11 @@ def find_indices_between(index_ranges, low, up, datacube, method=None):
                                     end = indexes.index(up)
                                     start = max(start - 1, 0)
                                     end = min(end + 1, len(indexes))
-                                    # indexes_between = [i for i in indexes if low <= i <= up]
                                     indexes_between = indexes[start:end]
                                     indexes_between_ranges.append(indexes_between)
                                 else:
                                     indexes_between = [i for i in indexes if low <= i <= up]
                                     indexes_between_ranges.append(indexes_between)
-                            # if method == "surrounding":
-                            #     start = indexes.index(low)
-                            #     end = indexes.index(up)
-                            #     start = max(start-1, 0)
-                            #     end = min(end+1, len(indexes))
-                            #     # indexes_between = [i for i in indexes if low <= i <= up]
-                            #     indexes_between = indexes[start:end]
-                            #     indexes_between_ranges.append(indexes_between)
-                            # else:
-                            #     indexes_between = [i for i in indexes if low <= i <= up]
-                            #     indexes_between_ranges.append(indexes_between)
-                            # indexes_between = [i for i in indexes if low <= i <= up]
-                            # indexes_between_ranges.append(indexes_between)
             return indexes_between_ranges
 
         def remap(range):
@@ -527,14 +509,11 @@ def find_indices_between(index_ranges, low, up, datacube, method=None):
                                 end = indexes.index(up)
                                 start = max(start - 1, 0)
                                 end = min(end + 1, len(indexes))
-                                # indexes_between = [i for i in indexes if low <= i <= up]
                                 indexes_between = indexes[start:end]
                                 indexes_between_ranges.append(indexes_between)
                             else:
                                 indexes_between = [i for i in indexes if low <= i <= up]
                                 indexes_between_ranges.append(indexes_between)
-                            # indexes_between = [i for i in indexes if low <= i <= up]
-                            # indexes_between_ranges.append(indexes_between)
             return indexes_between_ranges
 
         def remap(range):
@@ -562,18 +541,6 @@ def update_axis(self):
             self = cyclic(self)
         return self
 
-    @abstractproperty
-    def name(self) -> str:
-        pass
-
-    @abstractproperty
-    def tol(self) -> Any:
-        pass
-
-    @abstractproperty
-    def range(self) -> List[Any]:
-        pass
-
     # Convert from user-provided value to CONTINUOUS type (e.g. float, pd.timestamp)
     @abstractmethod
     def parse(self, value: Any) -> Any:
@@ -645,7 +612,6 @@ def find_indices_between(self, index_ranges, low, up, datacube, method=None):
                     end = indexes.index(up)
                     start = max(start - 1, 0)
                     end = min(end + 1, len(indexes))
-                    # indexes_between = [i for i in indexes if low <= i <= up]
                     indexes_between = indexes[start:end]
                     indexes_between_ranges.append(indexes_between)
                 else:
@@ -657,7 +623,10 @@ def find_indices_between(self, index_ranges, low, up, datacube, method=None):
     def create_standard(name, values, datacube):
         values = np.array(values)
         DatacubeAxis.check_axis_type(name, values)
-        datacube._axes[name] = deepcopy(_type_to_axis_lookup[values.dtype.type])
+        if datacube._axes is None:
+            datacube._axes = {name: deepcopy(_type_to_axis_lookup[values.dtype.type])}
+        else:
+            datacube._axes[name] = deepcopy(_type_to_axis_lookup[values.dtype.type])
         datacube._axes[name].name = name
         datacube.axis_counter += 1
 
@@ -673,11 +642,12 @@ def check_axis_type(name, values):
 @mapper
 @type_change
 class IntDatacubeAxis(DatacubeAxis):
-    name = None
-    tol = 1e-12
-    range = None
-    transformations = []
-    type = 0
+    def __init__(self):
+        self.name = None
+        self.tol = 1e-12
+        self.range = None
+        self.transformations = []
+        self.type = 0
 
     def parse(self, value: Any) -> Any:
         return float(value)
@@ -697,11 +667,12 @@ def serialize(self, value):
 @mapper
 @type_change
 class FloatDatacubeAxis(DatacubeAxis):
-    name = None
-    tol = 1e-12
-    range = None
-    transformations = []
-    type = 0.0
+    def __init__(self):
+        self.name = None
+        self.tol = 1e-12
+        self.range = None
+        self.transformations = []
+        self.type = 0.0
 
     def parse(self, value: Any) -> Any:
         return float(value)
@@ -718,11 +689,12 @@ def serialize(self, value):
 
 @merge
 class PandasTimestampDatacubeAxis(DatacubeAxis):
-    name = None
-    tol = 1e-12
-    range = None
-    transformations = []
-    type = pd.Timestamp("2000-01-01T00:00:00")
+    def __init__(self):
+        self.name = None
+        self.tol = 1e-12
+        self.range = None
+        self.transformations = []
+        self.type = pd.Timestamp("2000-01-01T00:00:00")
 
     def parse(self, value: Any) -> Any:
         if isinstance(value, np.str_):
@@ -747,11 +719,12 @@ def offset(self, value):
 
 @merge
 class PandasTimedeltaDatacubeAxis(DatacubeAxis):
-    name = None
-    tol = 1e-12
-    range = None
-    transformations = []
-    type = np.timedelta64(0, "s")
+    def __init__(self):
+        self.name = None
+        self.tol = 1e-12
+        self.range = None
+        self.transformations = []
+        self.type = np.timedelta64(0, "s")
 
     def parse(self, value: Any) -> Any:
         if isinstance(value, np.str_):
@@ -776,10 +749,11 @@ def offset(self, value):
 
 @type_change
 class UnsliceableDatacubeAxis(DatacubeAxis):
-    name = None
-    tol = float("NaN")
-    range = None
-    transformations = []
+    def __init__(self):
+        self.name = None
+        self.tol = float("NaN")
+        self.range = None
+        self.transformations = []
 
     def parse(self, value: Any) -> Any:
         return value

polytope/datacube/transformations/datacube_mappers.py

@@ -2762,14 +2762,14 @@ def axes_idx_to_octahedral_idx(self, first_idx, second_idx):
         else:
             for i in range(first_idx - 1):
                 if i <= self._resolution - 1:
-                    octa_idx += 16 + 4 * i
+                    octa_idx += 20 + 4 * i
                 else:
                     i = i - self._resolution + 1
                     if i == 1:
                         octa_idx += 16 + 4 * self._resolution
                     else:
                         i = i - 1
-                        octa_idx += 16 + 4 * (self._resolution - i + 1)
+                        octa_idx += 16 + 4 * (self._resolution - i)
             octa_idx += second_idx
         return octa_idx