merge

.github/workflows/r-ci.yml

@@ -52,11 +52,6 @@ jobs:
       - name: Bootstrap
         run: cd apis/r && tools/r-ci.sh bootstrap
 
-      - name: Set pkgType to binary (macOS)
-        if: ${{ matrix.os == 'macOS-latest' }}
-        run: cat("\noptions(pkgType = 'binary')\n", file = "~/.Rprofile", append = TRUE)
-        shell: Rscript {0}
-
       - name: Install BioConductor package SingleCellExperiment
         run: cd apis/r && tools/r-ci.sh install_bioc SingleCellExperiment
 
@@ -89,12 +84,12 @@ jobs:
       - name: Dependencies
         run: cd apis/r && tools/r-ci.sh install_all
 
-      - name: Install dataset packages from source (macOS)
-        if: ${{ matrix.os == 'macOS-latest' }}
-        run: cd apis/r && _CI_PKG_TYPE_=both _CI_USE_BIOC_=true Rscript tools/install_missing_deps.R
+      # - name: Install dataset packages from source (macOS)
+      #   if: ${{ matrix.os == 'macOS-latest' }}
+      #   run: cd apis/r && _CI_PKG_TYPE_=both _CI_USE_BIOC_=true Rscript tools/install_missing_deps.R
 
-      - name: CMake
-        uses: lukka/get-cmake@latest
+      # - name: CMake
+      #   uses: lukka/get-cmake@latest
 
       #- name: MkVars
       #  run: mkdir ~/.R && echo "CXX17FLAGS=-Wno-deprecated-declarations -Wno-deprecated" > ~/.R/Makevars
@@ -106,8 +101,8 @@ jobs:
       #  if: ${{ matrix.os == 'ubuntu-latest' }}
       #  run: sudo ldconfig
       #
-      - name: Update Packages
-        run: Rscript -e 'update.packages(ask=FALSE)'
+      # - name: Update Packages
+      #   run: Rscript -e 'update.packages(ask=FALSE)'
 
       # - name: Build Package
       #   run: cd apis/r && R CMD build --no-build-vignettes --no-manual .
@@ -126,7 +121,7 @@ jobs:
         run: cd apis/r && tools/r-ci.sh run_tests
 
       - name: Coverage
-        if: ${{ matrix.os == 'ubuntu-latest' && matrix.covr == 'yes' }}
+        if: ${{ matrix.os == 'ubuntu-latest' && matrix.covr == 'yes' && github.event_name == 'workflow_dispatch' }}
         run: apis/r/tools/r-ci.sh coverage
 
       - name: View Logs

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     - id: mypy
       additional_dependencies:
         - "pandas-stubs==1.5.3.230214"
-        - "somacore==1.0.10"
+        - "somacore==1.0.11"
         - "types-setuptools==67.4.0.3"
       args: ["--config-file=apis/python/pyproject.toml", "apis/python/src", "apis/python/devtools"]
       pass_filenames: false

Makefile

@@ -8,12 +8,15 @@ help:
 # install 
 # -------------------------------------------------------------------
 
-# set default variable values, if non-null
+# Set default variable values, if non-null
+# * build=Debug creates binary artifacts with symbols, e.g. for gdb
+# * cmake_verbose=true creates Makefiles that produce full compile lines when executed
 build ?= Release
+cmake_verbose ?= false
 
 .PHONY: install
 install: clean
-	@./scripts/bld --prefix=${prefix} --tiledb=${tiledb} --build=${build}
+	@./scripts/bld --prefix=${prefix} --tiledb=${tiledb} --build=${build} --cmake-verbose=${cmake_verbose}
 	@TILEDB_PATH=${tiledb} pip install -v -e apis/python
 
 .PHONY: r-build

apis/python/setup.py

@@ -329,7 +329,8 @@ def run(self):
         "pyarrow>=9.0.0; platform_system!='Darwin'",
         "scanpy>=1.9.2",
         "scipy",
-        "somacore==1.0.10",
+        # Note: the somacore version is in .pre-commit-config.yaml too
+        "somacore==1.0.11",
         "tiledb~=0.28.0",
         "typing-extensions",  # Note "-" even though `import typing_extensions`
     ],

apis/python/src/tiledbsoma/__init__.py

@@ -147,7 +147,12 @@
 from ._constants import SOMA_JOINID
 from ._dataframe import DataFrame
 from ._dense_nd_array import DenseNDArray
-from ._exception import AlreadyExistsError, DoesNotExistError, SOMAError
+from ._exception import (
+    AlreadyExistsError,
+    DoesNotExistError,
+    NotCreateableError,
+    SOMAError,
+)
 from ._experiment import Experiment
 from ._factory import open
 from ._general_utilities import (
@@ -192,6 +197,7 @@
     "get_storage_engine",
     "IntIndexer",
     "Measurement",
+    "NotCreateableError",
     "open",
     "ResultOrder",
     "show_package_versions",

apis/python/src/tiledbsoma/_collection.py

@@ -39,9 +39,11 @@
 from ._dense_nd_array import DenseNDArray
 from ._exception import (
     AlreadyExistsError,
+    NotCreateableError,
     SOMAError,
     is_already_exists_error,
     is_does_not_exist_error,
+    is_not_createable_error,
 )
 from ._funcs import typeguard_ignore
 from ._sparse_nd_array import SparseNDArray
@@ -119,6 +121,8 @@ def create(
         Raises:
             tiledbsoma.AlreadyExistsError:
                 If the underlying object already exists at the given URI.
+            tiledbsoma.NotCreateableError:
+                If the URI is malformed for a particular storage backend.
             TileDBError:
                 If unable to create the underlying object.
 
@@ -137,6 +141,8 @@ def create(
         except tiledb.TileDBError as tdbe:
             if is_already_exists_error(tdbe):
                 raise AlreadyExistsError(f"{uri!r} already exists")
+            if is_not_createable_error(tdbe):
+                raise NotCreateableError(f"{uri!r} cannot be created")
             raise
 
     @classmethod
@@ -469,14 +475,10 @@ def __getitem__(self, key: str) -> CollectionElementType:
             context = self.context
             timestamp = self.tiledb_timestamp_ms
 
-            try:
-                clib_type = entry.entry.wrapper_type.clib_type
-                wrapper = _tdb_handles.open(uri, mode, context, timestamp, clib_type)
-                entry.soma = _factory.reify_handle(wrapper)
-            except SOMAError:
-                entry.soma = _factory._open_internal(
-                    entry.entry.wrapper_type.open, uri, mode, context, timestamp
-                )
+            clib_type = entry.entry.wrapper_type.clib_type
+            wrapper = _tdb_handles.open(uri, mode, context, timestamp, clib_type)
+            entry.soma = _factory.reify_handle(wrapper)
+
             # Since we just opened this object, we own it and should close it.
             self._close_stack.enter_context(entry.soma)
         return cast(CollectionElementType, entry.soma)

apis/python/src/tiledbsoma/_common_nd_array.py

@@ -16,7 +16,12 @@
 import tiledb
 
 from . import _arrow_types, _util
-from ._exception import AlreadyExistsError, is_already_exists_error
+from ._exception import (
+    AlreadyExistsError,
+    NotCreateableError,
+    is_already_exists_error,
+    is_not_createable_error,
+)
 from ._tiledb_array import TileDBArray
 from ._types import OpenTimestamp
 from .options._soma_tiledb_context import (
@@ -80,6 +85,8 @@ def create(
                 If the ``shape`` is unsupported.
             tiledbsoma.AlreadyExistsError:
                 If the underlying object already exists at the given URI.
+            tiledbsoma.NotCreateableError:
+                If the URI is malformed for a particular storage backend.
             TileDBError:
                 If unable to create the underlying object.
 
@@ -103,6 +110,8 @@ def create(
         except tiledb.TileDBError as tdbe:
             if is_already_exists_error(tdbe):
                 raise AlreadyExistsError(f"{uri!r} already exists")
+            if is_not_createable_error(tdbe):
+                raise NotCreateableError(f"{uri!r} cannot be created")
             raise
 
     @property