indexing tests, fix for pytest 8, logging tests

nwb_linkml/pdm.lock

@@ -5,7 +5,7 @@
 groups = ["default", "dev", "plot", "tests"]
 strategy = ["inherit_metadata"]
 lock_version = "4.5.0"
-content_hash = "sha256:20f4f69a117fab515291f53ff39dfd1e13e3c8cbd399f1f7ce308cbea7deeaf0"
+content_hash = "sha256:d9e9b2a7f48f3db3e59cd58907a18aa69f91595d07eca53be0bf53b5fb2ba990"
 
 [[metadata.targets]]
 requires_python = ">=3.10,<3.13"
@@ -70,7 +70,7 @@ name = "black"
 version = "24.8.0"
 requires_python = ">=3.8"
 summary = "The uncompromising code formatter."
-groups = ["default", "dev"]
+groups = ["default"]
 dependencies = [
     "click>=8.0.0",
     "mypy-extensions>=0.4.3",
@@ -219,7 +219,7 @@ name = "click"
 version = "8.1.7"
 requires_python = ">=3.7"
 summary = "Composable command line interface toolkit"
-groups = ["default", "dev", "plot"]
+groups = ["default", "plot"]
 dependencies = [
     "colorama; platform_system == \"Windows\"",
     "importlib-metadata; python_version < \"3.8\"",
@@ -512,7 +512,7 @@ version = "3.0.3"
 requires_python = ">=3.7"
 summary = "Lightweight in-process concurrent programming"
 groups = ["default"]
-marker = "(platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\") and python_version < \"3.13\""
+marker = "platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\""
 files = [
     {file = "greenlet-3.0.3-cp310-cp310-macosx_11_0_universal2.whl", hash = "sha256:9da2bd29ed9e4f15955dd1595ad7bc9320308a3b766ef7f837e23ad4b4aac31a"},
     {file = "greenlet-3.0.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d353cadd6083fdb056bb46ed07e4340b0869c305c8ca54ef9da3421acbdf6881"},
@@ -954,7 +954,7 @@ name = "mypy-extensions"
 version = "1.0.0"
 requires_python = ">=3.5"
 summary = "Type system extensions for programs checked with the mypy type checker."
-groups = ["default", "dev"]
+groups = ["default"]
 files = [
     {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"},
     {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
@@ -1132,7 +1132,7 @@ name = "pathspec"
 version = "0.12.1"
 requires_python = ">=3.8"
 summary = "Utility library for gitignore style pattern matching of file paths."
-groups = ["default", "dev"]
+groups = ["default"]
 files = [
     {file = "pathspec-0.12.1-py3-none-any.whl", hash = "sha256:a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08"},
     {file = "pathspec-0.12.1.tar.gz", hash = "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712"},
@@ -1385,22 +1385,21 @@ files = [
 
 [[package]]
 name = "pytest"
-version = "7.4.4"
+version = "8.3.2"
-requires_python = ">=3.7"
+requires_python = ">=3.8"
 summary = "pytest: simple powerful testing with Python"
 groups = ["default", "dev", "tests"]
 dependencies = [
     "colorama; sys_platform == \"win32\"",
     "exceptiongroup>=1.0.0rc8; python_version < \"3.11\"",
-    "importlib-metadata>=0.12; python_version < \"3.8\"",
     "iniconfig",
     "packaging",
-    "pluggy<2.0,>=0.12",
+    "pluggy<2,>=1.5",
-    "tomli>=1.0.0; python_version < \"3.11\"",
+    "tomli>=1; python_version < \"3.11\"",
 ]
 files = [
-    {file = "pytest-7.4.4-py3-none-any.whl", hash = "sha256:b090cdf5ed60bf4c45261be03239c2c1c22df034fbffe691abe93cd80cea01d8"},
+    {file = "pytest-8.3.2-py3-none-any.whl", hash = "sha256:4ba08f9ae7dcf84ded419494d229b48d0903ea6407b030eaec46df5e6a73bba5"},
-    {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"},
+    {file = "pytest-8.3.2.tar.gz", hash = "sha256:c132345d12ce551242c87269de812483f5bcc87cdbb4722e48487ba194f9fdce"},
 ]
 
 [[package]]
@@ -1759,7 +1758,7 @@ version = "0.2.8"
 requires_python = ">=3.6"
 summary = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml"
 groups = ["default"]
-marker = "platform_python_implementation == \"CPython\" and python_version < \"3.13\""
+marker = "platform_python_implementation == \"CPython\""
 files = [
     {file = "ruamel.yaml.clib-0.2.8-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:b42169467c42b692c19cf539c38d4602069d8c1505e97b86387fcf7afb766e1d"},
     {file = "ruamel.yaml.clib-0.2.8-cp310-cp310-macosx_13_0_arm64.whl", hash = "sha256:07238db9cbdf8fc1e9de2489a4f68474e70dffcb32232db7c08fa61ca0c7c462"},
@@ -1932,13 +1931,13 @@ files = [
 
 [[package]]
 name = "sybil"
-version = "5.0.3"
+version = "6.1.1"
 requires_python = ">=3.7"
 summary = "Automated testing for the examples in your code and documentation."
 groups = ["dev", "tests"]
 files = [
-    {file = "sybil-5.0.3-py3-none-any.whl", hash = "sha256:6f3c30822169895c4fb34c8366bdb132cf62bb68fb1d03d2ebb05282eab08c95"},
+    {file = "sybil-6.1.1-py3-none-any.whl", hash = "sha256:04ae5e17997bc5166ba3da0d6244767c397e129f399a1aa23c89b30a704fec2c"},
-    {file = "sybil-5.0.3.tar.gz", hash = "sha256:20dfe3a35a8d1ffcb4311434d1abf38c030c91064d75ff6b56ddd1060e08e758"},
+    {file = "sybil-6.1.1.tar.gz", hash = "sha256:8fb4f2c3582d1fe6705d1ae3a31f93fec7619f634940a8fcbf5d1b7d18183917"},
 ]
 
 [[package]]

nwb_linkml/pyproject.toml

@@ -37,16 +37,15 @@ plot = [
 ]
 tests = [
     "nwb-linkml",
-    "pytest<8.0.0,>=7.4.0",
+    "pytest>=8.0.0",
     "pytest-depends<2.0.0,>=1.0.1",
     "pytest-cov<5.0.0,>=4.1.0",
-    "sybil<6.0.0,>=5.0.3",
+    "sybil>=6.0.3",
     "requests-cache>=1.2.1",
 ]
 dev = [
     "nwb-linkml[tests]",
     "ruff>=0.5.0",
-    "black>=24.4.2",
 ]
 
 [tool.pdm]

nwb_linkml/src/nwb_linkml/maps/hdmf.py

@@ -1,24 +0,0 @@
-"""
-Mapping functions for handling HDMF classes like DynamicTables
-"""
-
-from typing import Any, List, Optional
-
-import h5py
-
-
-def dereference_reference_vector(dset: h5py.Dataset, data: Optional[List[Any]]) -> List:
-    """
-    Given a compound dataset with indices, counts, and object references, dereference to values
-
-    Data is of the form
-    (idx_start, count, target)
-    """
-    # assume all these references are to the same target
-    # and the index is in the 3rd position
-    if data is None:
-        data = dset[:]
-
-    target = dset.parent.get(data[0][-1])
-    res = [target[d[0] : d[0] + d[1]] for d in data]
-    return res

nwb_linkml/tests/test_includes/test_hdmf.py

@@ -213,10 +213,47 @@ def test_aligned_dynamictable(intracellular_recordings_table):
 
 def test_dynamictable_mixin_indexing():
     """
-    This is just a placeholder test to say that indexing is tested above
+    Can index values from a dynamictable
-    with actual model objects in case i ever ctrl+f for this
     """
-    pass
+
+    class MyData(DynamicTableMixin):
+        col_1: hdmf.VectorData[NDArray[Shape["*"], int]]
+        col_2: hdmf.VectorData[NDArray[Shape["*"], int]]
+        col_3: hdmf.VectorData[NDArray[Shape["*"], int]]
+
+    cols = {
+        "col_1": np.arange(10),
+        "col_2": np.arange(10),
+        "col_3": np.arange(10),
+        "col_4": np.arange(10),
+        "col_5": np.arange(10),
+    }
+    colnames = [c for c in cols]
+    inst = MyData(**cols)
+
+    row = inst[0]
+    # successfully get a single row :)
+    assert row.shape == (1, 5)
+    assert row.columns.tolist() == colnames
+
+    # slice a range of rows
+    rows = inst[0:3]
+    assert rows.shape == (3, 5)
+
+    # get a single column
+    col = inst["col_1"]
+    assert all(col.value == np.arange(10))
+
+    # get a single cell
+    val = inst[5, "col_2"]
+    assert val == 5
+    val = inst[5, 1]
+    assert val == 5
+
+    # get a slice of rows and columns
+    subsection = inst[0:3, 0:3]
+    assert subsection.shape == (3, 3)
+    assert subsection.columns.tolist() == colnames[0:3]
 
 
 def test_dynamictable_mixin_colnames():

nwb_linkml/tests/test_logging.py

@@ -0,0 +1,35 @@
+from pathlib import Path
+
+from nwb_linkml.logging import init_logger
+
+
+def test_init_logger(capsys, tmp_path):
+    """
+    We should be able to
+    - log to file and stdout
+    - with separable levels
+    """
+
+    log_dir = Path(tmp_path) / "logs"
+    log_dir.mkdir()
+    log_file = log_dir / "nwb_linkml.test_logger.log"
+    logger = init_logger(name="test_logger", log_dir=log_dir, level="INFO", file_level="WARNING")
+    warn_msg = "Both loggers should show"
+    logger.warning(warn_msg)
+
+    # can't test for presence of string because logger can split lines depending on size of console
+    # but there should be one WARNING in stdout
+    captured = capsys.readouterr()
+    assert "WARNING" in captured.out
+
+    with open(log_file, "r") as lfile:
+        log_str = lfile.read()
+    assert "WARNING" in log_str
+
+    info_msg = "Now only stdout should show"
+    logger.info(info_msg)
+    captured = capsys.readouterr()
+    assert "INFO" in captured.out
+    with open(log_file, "r") as lfile:
+        log_str = lfile.read()
+    assert "INFO" not in log_str