From 0c605a26a17c9177008342ba3b808312d22818c1 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Tue, 3 Oct 2023 09:53:26 -0700 Subject: [PATCH] Fix release workflow and prepare 3.10.0 release (#957) --- .github/PULL_REQUEST_TEMPLATE/release.md | 7 +- CHANGELOG.md | 10 +- docs/CONTRIBUTING.rst | 2 +- environment-ros3.yml | 12 +- requirements-dev.txt | 16 +- requirements-opt.txt | 11 +- requirements.txt | 10 +- test_gallery.py | 9 + .../expanded_example_dynamic_term_set.yaml | 2073 ----------------- tests/unit/test_term_set.py | 3 + .../test_core_GenericDataChunkIterator.py | 8 +- 11 files changed, 55 insertions(+), 2106 deletions(-) delete mode 100644 tests/unit/expanded_example_dynamic_term_set.yaml diff --git a/.github/PULL_REQUEST_TEMPLATE/release.md b/.github/PULL_REQUEST_TEMPLATE/release.md index 795dd3a48..60a725a73 100644 --- a/.github/PULL_REQUEST_TEMPLATE/release.md +++ b/.github/PULL_REQUEST_TEMPLATE/release.md @@ -2,10 +2,11 @@ Prepare for release of HDMF [version] ### Before merging: - [ ] Major and minor releases: Update package versions in `requirements.txt`, `requirements-dev.txt`, - `requirements-doc.txt`, `requirements-min.txt`, `requirements-opt.txt`, `environment-ros3.yml`, and `setup.py` as needed + `requirements-doc.txt`, `requirements-opt.txt`, and `environment-ros3.yml` to the latest versions, + and update dependency ranges in `pyproject.toml` and minimums in `requirements-min.txt` as needed - [ ] Check legal file dates and information in `Legal.txt`, `license.txt`, `README.rst`, `docs/source/conf.py`, and any other locations as needed -- [ ] Update `setup.py` as needed +- [ ] Update `pyproject.toml` as needed - [ ] Update `README.rst` as needed - [ ] Update `src/hdmf/common/hdmf-common-schema` submodule as needed. Check the version number and commit SHA manually - [ ] Update changelog (set release date) in `CHANGELOG.md` and any other docs as needed @@ -13,7 +14,7 @@ Prepare for release of HDMF [version] (`pytest && python test_gallery.py`) - [ ] Run PyNWB tests locally including gallery and validation tests, and inspect all warnings and outputs (`cd pynwb; python test.py -v > out.txt 2>&1`) -- [ ] Test docs locally by going into the `docs` directory and running the following: `make clean && make html` +- [ ] Test docs locally and inspect all warnings and outputs `cd docs; make clean && make html` - [ ] Push changes to this PR and make sure all PRs to be included in this release have been merged - [ ] Check that the readthedocs build for this PR succeeds (build latest to pull the new branch, then activate and build docs for new branch): https://readthedocs.org/projects/hdmf/builds/ diff --git a/CHANGELOG.md b/CHANGELOG.md index e39975b36..dd4d97d0e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,13 @@ # HDMF Changelog +## HDMF 3.10.0 (October 3, 2023) + +Since version 3.9.1 should have been released as 3.10.0 but failed to release on PyPI and conda-forge, this release +will increase the minor version number to 3.10.0. See the 3.9.1 release notes below for new features. + +### Bug fixes +- Fixed issue with testing and deployment of releases. @rly [#957](https://github.com/hdmf-dev/hdmf/pull/957) + ## HDMF 3.9.1 (September 29, 2023) ### Enhancements @@ -20,7 +28,7 @@ - Updated `add_ref_termset` to add all instances of `TermSet` within a given root container. @mavaylon1 [#935](https://github.com/hdmf-dev/hdmf/pull/935) - Added Dynamic Enumerations and Schemasheets support to `TermSet`. @mavaylon1 [#923](https://github.com/hdmf-dev/hdmf/pull/923) - Updated `HERD` to support user defined file name for the `HERD` zip file. @mavaylon1 [#941](https://github.com/hdmf-dev/hdmf/pull/941) -- Added method `Containter.set_data_io`, which wraps an existing data field in a `DataIO`. @bendichter [#938](https://github.com/hdmf-dev/hdmf/pull/938) +- Added method `Container.set_data_io`, which wraps an existing data field in a `DataIO`. @bendichter [#938](https://github.com/hdmf-dev/hdmf/pull/938) ## HDMF 3.8.1 (July 25, 2023) diff --git a/docs/CONTRIBUTING.rst b/docs/CONTRIBUTING.rst index 052fed7b7..777f9a260 100644 --- a/docs/CONTRIBUTING.rst +++ b/docs/CONTRIBUTING.rst @@ -90,7 +90,7 @@ Style Guides Python Code Style Guide ^^^^^^^^^^^^^^^^^^^^^^^ -Before you create a Pull Request, make sure you are following the PEP8_ style guide. . +Before you create a Pull Request, make sure you are following the HDMF style guide. To check whether your code conforms to the HDMF style guide, simply run the ruff_ tool in the project's root directory. ``ruff`` will also sort imports automatically and check against additional code style rules. diff --git a/environment-ros3.yml b/environment-ros3.yml index fff1d0d44..a8f2f0587 100644 --- a/environment-ros3.yml +++ b/environment-ros3.yml @@ -5,11 +5,11 @@ channels: - defaults dependencies: - python==3.11 - - h5py==3.8.0 - - matplotlib==3.7.1 - - numpy==1.24.3 - - pandas==2.0.1 + - h5py==3.9.0 + - matplotlib==3.8.0 + - numpy==1.26.0 + - pandas==2.1.1 - python-dateutil==2.8.2 - - pytest==7.3.1 - - pytest-cov==4.0.0 + - pytest==7.4.2 + - pytest-cov==4.1.0 - setuptools diff --git a/requirements-dev.txt b/requirements-dev.txt index 2b99993e9..760d48262 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -2,12 +2,12 @@ # compute coverage, and create test environments. note that depending on the version of python installed, different # versions of requirements may be installed due to package incompatibilities. # -black==23.3.0 -codespell==2.2.4 -coverage==7.2.5 -pre-commit==3.3.1 -pytest==7.3.1 -pytest-cov==4.0.0 +black==23.9.1 +codespell==2.2.6 +coverage==7.3.2 +pre-commit==3.4.0 +pytest==7.4.2 +pytest-cov==4.1.0 python-dateutil==2.8.2 -ruff==0.0.265 -tox==4.5.1 +ruff==0.0.292 +tox==4.11.3 diff --git a/requirements-opt.txt b/requirements-opt.txt index b52348e3a..644fc80be 100644 --- a/requirements-opt.txt +++ b/requirements-opt.txt @@ -1,7 +1,8 @@ # pinned dependencies that are optional. used to reproduce an entire development environment to use HDMF -tqdm==4.65.0 -zarr==2.14.2 -linkml-runtime==1.5.5; python_version >= "3.9" -schemasheets==0.1.23; python_version >= "3.9" -oaklib==0.5.12; python_version >= "3.9" +tqdm==4.66.1 +zarr==2.16.1 +linkml-runtime==1.6.0; python_version >= "3.9" +schemasheets==0.1.24; python_version >= "3.9" +oaklib==0.5.20; python_version >= "3.9" +pydantic==1.10.13 # linkml-runtime 1.6.0 and related packages require pydantic<2 pyyaml==6.0.1; python_version >= "3.9" diff --git a/requirements.txt b/requirements.txt index 37148add2..df200c4ac 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,8 +1,8 @@ # pinned dependencies to reproduce an entire development environment to use HDMF h5py==3.9.0 importlib-resources==6.0.0; python_version < "3.9" # TODO: remove when minimum python version is 3.9 -jsonschema==4.18.4 -numpy==1.25.1 -pandas==2.0.3 -ruamel.yaml==0.17.32 -scipy==1.11.1 +jsonschema==4.19.1 +numpy==1.26.0 +pandas==2.1.1 +ruamel.yaml==0.17.33 +scipy==1.11.3 diff --git a/test_gallery.py b/test_gallery.py index cb77ac430..970ef93f1 100644 --- a/test_gallery.py +++ b/test_gallery.py @@ -33,6 +33,8 @@ def _import_from_file(script): "and is not guaranteed to maintain backward compatibility" ) +pydantic_warning_re = ("Support for class-based `config` is deprecated, use ConfigDict instead.") + def run_gallery_tests(): global TOTAL, FAILURES, ERRORS @@ -70,6 +72,13 @@ def run_gallery_tests(): message=_numpy_warning_re, category=RuntimeWarning, ) + warnings.filterwarnings( + # this warning is triggered when some linkml dependency like curies uses pydantic in a way that + # will be deprecated in the future + "ignore", + message=pydantic_warning_re, + category=DeprecationWarning, + ) _import_from_file(script) except (ImportError, ValueError) as e: if "linkml" in str(e) and sys.version_info < (3, 9): diff --git a/tests/unit/expanded_example_dynamic_term_set.yaml b/tests/unit/expanded_example_dynamic_term_set.yaml deleted file mode 100644 index a2631696a..000000000 --- a/tests/unit/expanded_example_dynamic_term_set.yaml +++ /dev/null @@ -1,2073 +0,0 @@ -id: https://w3id.org/linkml/examples/nwb_dynamic_enums -title: dynamic enums example -name: nwb_dynamic_enums -description: this schema demonstrates the use of dynamic enums - -prefixes: - linkml: https://w3id.org/linkml/ - CL: http://purl.obolibrary.org/obo/CL_ - -imports: -- linkml:types - -default_range: string - -# ======================== # -# CLASSES # -# ======================== # -classes: - BrainSample: - slots: - - cell_type - -# ======================== # -# SLOTS # -# ======================== # -slots: - cell_type: - required: true - range: NeuronTypeEnum - -# ======================== # -# ENUMS # -# ======================== # -enums: - NeuronTypeEnum: - reachable_from: - source_ontology: obo:cl - source_nodes: - - CL:0000540 ## neuron - include_self: false - relationship_types: - - rdfs:subClassOf - permissible_values: - CL:0000705: - text: CL:0000705 - description: R6 photoreceptor cell - meaning: CL:0000705 - CL:4023108: - text: CL:4023108 - description: oxytocin-secreting magnocellular cell - meaning: CL:4023108 - CL:0004240: - text: CL:0004240 - description: WF1 amacrine cell - meaning: CL:0004240 - CL:0004242: - text: CL:0004242 - description: WF3-1 amacrine cell - meaning: CL:0004242 - CL:1000380: - text: CL:1000380 - description: type 1 vestibular sensory cell of epithelium of macula of saccule - of membranous labyrinth - meaning: CL:1000380 - CL:4023128: - text: CL:4023128 - description: rostral periventricular region of the third ventricle KNDy neuron - meaning: CL:4023128 - CL:0003020: - text: CL:0003020 - description: retinal ganglion cell C outer - meaning: CL:0003020 - CL:4023094: - text: CL:4023094 - description: tufted pyramidal neuron - meaning: CL:4023094 - CL:4023057: - text: CL:4023057 - description: cerebellar inhibitory GABAergic interneuron - meaning: CL:4023057 - CL:2000049: - text: CL:2000049 - description: primary motor cortex pyramidal cell - meaning: CL:2000049 - CL:0000119: - text: CL:0000119 - description: cerebellar Golgi cell - meaning: CL:0000119 - CL:0004227: - text: CL:0004227 - description: flat bistratified amacrine cell - meaning: CL:0004227 - CL:1000606: - text: CL:1000606 - description: kidney nerve cell - meaning: CL:1000606 - CL:1001582: - text: CL:1001582 - description: lateral ventricle neuron - meaning: CL:1001582 - CL:0000165: - text: CL:0000165 - description: neuroendocrine cell - meaning: CL:0000165 - CL:0000555: - text: CL:0000555 - description: neuronal brush cell - meaning: CL:0000555 - CL:0004231: - text: CL:0004231 - description: recurving diffuse amacrine cell - meaning: CL:0004231 - CL:0000687: - text: CL:0000687 - description: R1 photoreceptor cell - meaning: CL:0000687 - CL:0001031: - text: CL:0001031 - description: cerebellar granule cell - meaning: CL:0001031 - CL:0003026: - text: CL:0003026 - description: retinal ganglion cell D1 - meaning: CL:0003026 - CL:4033035: - text: CL:4033035 - description: giant bipolar cell - meaning: CL:4033035 - CL:4023009: - text: CL:4023009 - description: extratelencephalic-projecting glutamatergic cortical neuron - meaning: CL:4023009 - CL:0010022: - text: CL:0010022 - description: cardiac neuron - meaning: CL:0010022 - CL:0000287: - text: CL:0000287 - description: eye photoreceptor cell - meaning: CL:0000287 - CL:0000488: - text: CL:0000488 - description: visible light photoreceptor cell - meaning: CL:0000488 - CL:0003046: - text: CL:0003046 - description: M13 retinal ganglion cell - meaning: CL:0003046 - CL:4023169: - text: CL:4023169 - description: trigeminal neuron - meaning: CL:4023169 - CL:0005007: - text: CL:0005007 - description: Kolmer-Agduhr neuron - meaning: CL:0005007 - CL:0005008: - text: CL:0005008 - description: macular hair cell - meaning: CL:0005008 - CL:4023027: - text: CL:4023027 - description: L5 T-Martinotti sst GABAergic cortical interneuron (Mmus) - meaning: CL:4023027 - CL:4033032: - text: CL:4033032 - description: diffuse bipolar 6 cell - meaning: CL:4033032 - CL:0008021: - text: CL:0008021 - description: anterior lateral line ganglion neuron - meaning: CL:0008021 - CL:4023028: - text: CL:4023028 - description: L5 non-Martinotti sst GABAergic cortical interneuron (Mmus) - meaning: CL:4023028 - CL:4023063: - text: CL:4023063 - description: medial ganglionic eminence derived interneuron - meaning: CL:4023063 - CL:4023032: - text: CL:4023032 - description: ON retinal ganglion cell - meaning: CL:4023032 - CL:0003039: - text: CL:0003039 - description: M8 retinal ganglion cell - meaning: CL:0003039 - CL:0000757: - text: CL:0000757 - description: type 5 cone bipolar cell (sensu Mus) - meaning: CL:0000757 - CL:0000609: - text: CL:0000609 - description: vestibular hair cell - meaning: CL:0000609 - CL:0004219: - text: CL:0004219 - description: A2 amacrine cell - meaning: CL:0004219 - CL:4030028: - text: CL:4030028 - description: glycinergic amacrine cell - meaning: CL:4030028 - CL:0002450: - text: CL:0002450 - description: tether cell - meaning: CL:0002450 - CL:0002374: - text: CL:0002374 - description: ear hair cell - meaning: CL:0002374 - CL:0004124: - text: CL:0004124 - description: retinal ganglion cell C1 - meaning: CL:0004124 - CL:0004115: - text: CL:0004115 - description: retinal ganglion cell B - meaning: CL:0004115 - CL:1000384: - text: CL:1000384 - description: type 2 vestibular sensory cell of epithelium of macula of saccule - of membranous labyrinth - meaning: CL:1000384 - CL:2000037: - text: CL:2000037 - description: posterior lateral line neuromast hair cell - meaning: CL:2000037 - CL:0000673: - text: CL:0000673 - description: Kenyon cell - meaning: CL:0000673 - CL:4023052: - text: CL:4023052 - description: Betz upper motor neuron - meaning: CL:4023052 - CL:0004243: - text: CL:0004243 - description: WF3-2 amacrine cell - meaning: CL:0004243 - CL:1000222: - text: CL:1000222 - description: stomach neuroendocrine cell - meaning: CL:1000222 - CL:0002310: - text: CL:0002310 - description: mammosomatotroph - meaning: CL:0002310 - CL:4023066: - text: CL:4023066 - description: horizontal pyramidal neuron - meaning: CL:4023066 - CL:0000379: - text: CL:0000379 - description: sensory processing neuron - meaning: CL:0000379 - CL:0011006: - text: CL:0011006 - description: Lugaro cell - meaning: CL:0011006 - CL:0004216: - text: CL:0004216 - description: type 5b cone bipolar cell - meaning: CL:0004216 - CL:0004126: - text: CL:0004126 - description: retinal ganglion cell C2 outer - meaning: CL:0004126 - CL:0000108: - text: CL:0000108 - description: cholinergic neuron - meaning: CL:0000108 - CL:0011103: - text: CL:0011103 - description: sympathetic neuron - meaning: CL:0011103 - CL:4023107: - text: CL:4023107 - description: reticulospinal neuron - meaning: CL:4023107 - CL:4023002: - text: CL:4023002 - description: dynamic beta motor neuron - meaning: CL:4023002 - CL:4030048: - text: CL:4030048 - description: striosomal D1 medium spiny neuron - meaning: CL:4030048 - CL:4023163: - text: CL:4023163 - description: spherical bushy cell - meaning: CL:4023163 - CL:4023061: - text: CL:4023061 - description: hippocampal CA4 neuron - meaning: CL:4023061 - CL:0000532: - text: CL:0000532 - description: CAP motoneuron - meaning: CL:0000532 - CL:0000526: - text: CL:0000526 - description: afferent neuron - meaning: CL:0000526 - CL:0003003: - text: CL:0003003 - description: G2 retinal ganglion cell - meaning: CL:0003003 - CL:0000530: - text: CL:0000530 - description: primary neuron (sensu Teleostei) - meaning: CL:0000530 - CL:4023045: - text: CL:4023045 - description: medulla-projecting glutamatergic neuron of the primary motor - cortex - meaning: CL:4023045 - CL:3000004: - text: CL:3000004 - description: peripheral sensory neuron - meaning: CL:3000004 - CL:0000544: - text: CL:0000544 - description: slowly adapting mechanoreceptor cell - meaning: CL:0000544 - CL:4030047: - text: CL:4030047 - description: matrix D2 medium spiny neuron - meaning: CL:4030047 - CL:0004220: - text: CL:0004220 - description: flag amacrine cell - meaning: CL:0004220 - CL:4023125: - text: CL:4023125 - description: KNDy neuron - meaning: CL:4023125 - CL:0004228: - text: CL:0004228 - description: broad diffuse amacrine cell - meaning: CL:0004228 - CL:4023122: - text: CL:4023122 - description: oxytocin receptor sst GABAergic cortical interneuron - meaning: CL:4023122 - CL:1000379: - text: CL:1000379 - description: type 1 vestibular sensory cell of epithelium of macula of utricle - of membranous labyrinth - meaning: CL:1000379 - CL:0011111: - text: CL:0011111 - description: gonadotropin-releasing hormone neuron - meaning: CL:0011111 - CL:0003042: - text: CL:0003042 - description: M9-OFF retinal ganglion cell - meaning: CL:0003042 - CL:0003030: - text: CL:0003030 - description: M3 retinal ganglion cell - meaning: CL:0003030 - CL:0003011: - text: CL:0003011 - description: G8 retinal ganglion cell - meaning: CL:0003011 - CL:0000202: - text: CL:0000202 - description: auditory hair cell - meaning: CL:0000202 - CL:0002271: - text: CL:0002271 - description: type EC1 enteroendocrine cell - meaning: CL:0002271 - CL:4023013: - text: CL:4023013 - description: corticothalamic-projecting glutamatergic cortical neuron - meaning: CL:4023013 - CL:4023114: - text: CL:4023114 - description: calyx vestibular afferent neuron - meaning: CL:4023114 - CL:0003045: - text: CL:0003045 - description: M12 retinal ganglion cell - meaning: CL:0003045 - CL:0002487: - text: CL:0002487 - description: cutaneous/subcutaneous mechanoreceptor cell - meaning: CL:0002487 - CL:4030053: - text: CL:4030053 - description: Island of Calleja granule cell - meaning: CL:4030053 - CL:0000490: - text: CL:0000490 - description: photopic photoreceptor cell - meaning: CL:0000490 - CL:2000023: - text: CL:2000023 - description: spinal cord ventral column interneuron - meaning: CL:2000023 - CL:1000381: - text: CL:1000381 - description: type 1 vestibular sensory cell of epithelium of crista of ampulla - of semicircular duct of membranous labyrinth - meaning: CL:1000381 - CL:0003013: - text: CL:0003013 - description: G10 retinal ganglion cell - meaning: CL:0003013 - CL:0000602: - text: CL:0000602 - description: pressoreceptor cell - meaning: CL:0000602 - CL:4023039: - text: CL:4023039 - description: amygdala excitatory neuron - meaning: CL:4023039 - CL:4030043: - text: CL:4030043 - description: matrix D1 medium spiny neuron - meaning: CL:4030043 - CL:0000105: - text: CL:0000105 - description: pseudounipolar neuron - meaning: CL:0000105 - CL:0004137: - text: CL:0004137 - description: retinal ganglion cell A2 inner - meaning: CL:0004137 - CL:1001436: - text: CL:1001436 - description: hair-tylotrich neuron - meaning: CL:1001436 - CL:1001503: - text: CL:1001503 - description: olfactory bulb tufted cell - meaning: CL:1001503 - CL:0000406: - text: CL:0000406 - description: CNS short range interneuron - meaning: CL:0000406 - CL:2000087: - text: CL:2000087 - description: dentate gyrus of hippocampal formation basket cell - meaning: CL:2000087 - CL:0000534: - text: CL:0000534 - description: primary interneuron (sensu Teleostei) - meaning: CL:0000534 - CL:0000246: - text: CL:0000246 - description: Mauthner neuron - meaning: CL:0000246 - CL:0003027: - text: CL:0003027 - description: retinal ganglion cell D2 - meaning: CL:0003027 - CL:0000752: - text: CL:0000752 - description: cone retinal bipolar cell - meaning: CL:0000752 - CL:0000410: - text: CL:0000410 - description: CNS long range interneuron - meaning: CL:0000410 - CL:0009000: - text: CL:0009000 - description: sensory neuron of spinal nerve - meaning: CL:0009000 - CL:0000754: - text: CL:0000754 - description: type 2 cone bipolar cell (sensu Mus) - meaning: CL:0000754 - CL:0002309: - text: CL:0002309 - description: corticotroph - meaning: CL:0002309 - CL:0010009: - text: CL:0010009 - description: camera-type eye photoreceptor cell - meaning: CL:0010009 - CL:4023069: - text: CL:4023069 - description: medial ganglionic eminence derived GABAergic cortical interneuron - meaning: CL:4023069 - CL:0000102: - text: CL:0000102 - description: polymodal neuron - meaning: CL:0000102 - CL:0000694: - text: CL:0000694 - description: R3 photoreceptor cell - meaning: CL:0000694 - CL:0004183: - text: CL:0004183 - description: retinal ganglion cell B3 - meaning: CL:0004183 - CL:0000693: - text: CL:0000693 - description: neurogliaform cell - meaning: CL:0000693 - CL:0000760: - text: CL:0000760 - description: type 8 cone bipolar cell (sensu Mus) - meaning: CL:0000760 - CL:4023001: - text: CL:4023001 - description: static beta motor neuron - meaning: CL:4023001 - CL:1000424: - text: CL:1000424 - description: chromaffin cell of paraaortic body - meaning: CL:1000424 - CL:0000120: - text: CL:0000120 - description: granule cell - meaning: CL:0000120 - CL:0002312: - text: CL:0002312 - description: somatotroph - meaning: CL:0002312 - CL:0000107: - text: CL:0000107 - description: autonomic neuron - meaning: CL:0000107 - CL:2000047: - text: CL:2000047 - description: brainstem motor neuron - meaning: CL:2000047 - CL:4023080: - text: CL:4023080 - description: stellate L6 intratelencephalic projecting glutamatergic neuron - of the primary motor cortex (Mmus) - meaning: CL:4023080 - CL:0000848: - text: CL:0000848 - description: microvillous olfactory receptor neuron - meaning: CL:0000848 - CL:0004213: - text: CL:0004213 - description: type 3a cone bipolar cell - meaning: CL:0004213 - CL:0000116: - text: CL:0000116 - description: pioneer neuron - meaning: CL:0000116 - CL:4023187: - text: CL:4023187 - description: koniocellular cell - meaning: CL:4023187 - CL:4023116: - text: CL:4023116 - description: type 2 spiral ganglion neuron - meaning: CL:4023116 - CL:0008015: - text: CL:0008015 - description: inhibitory motor neuron - meaning: CL:0008015 - CL:0003048: - text: CL:0003048 - description: L cone cell - meaning: CL:0003048 - CL:1000082: - text: CL:1000082 - description: stretch receptor cell - meaning: CL:1000082 - CL:0003031: - text: CL:0003031 - description: M3-ON retinal ganglion cell - meaning: CL:0003031 - CL:1001474: - text: CL:1001474 - description: medium spiny neuron - meaning: CL:1001474 - CL:0000745: - text: CL:0000745 - description: retina horizontal cell - meaning: CL:0000745 - CL:0002515: - text: CL:0002515 - description: interrenal norepinephrine type cell - meaning: CL:0002515 - CL:2000027: - text: CL:2000027 - description: cerebellum basket cell - meaning: CL:2000027 - CL:0004225: - text: CL:0004225 - description: spider amacrine cell - meaning: CL:0004225 - CL:4023031: - text: CL:4023031 - description: L4 sst GABAergic cortical interneuron (Mmus) - meaning: CL:4023031 - CL:0008038: - text: CL:0008038 - description: alpha motor neuron - meaning: CL:0008038 - CL:4033030: - text: CL:4033030 - description: diffuse bipolar 3b cell - meaning: CL:4033030 - CL:0000336: - text: CL:0000336 - description: adrenal medulla chromaffin cell - meaning: CL:0000336 - CL:0000751: - text: CL:0000751 - description: rod bipolar cell - meaning: CL:0000751 - CL:0008037: - text: CL:0008037 - description: gamma motor neuron - meaning: CL:0008037 - CL:0003028: - text: CL:0003028 - description: M1 retinal ganglion cell - meaning: CL:0003028 - CL:0003016: - text: CL:0003016 - description: G11-OFF retinal ganglion cell - meaning: CL:0003016 - CL:0004239: - text: CL:0004239 - description: wavy bistratified amacrine cell - meaning: CL:0004239 - CL:4023168: - text: CL:4023168 - description: somatosensory neuron - meaning: CL:4023168 - CL:4023018: - text: CL:4023018 - description: pvalb GABAergic cortical interneuron - meaning: CL:4023018 - CL:0004138: - text: CL:0004138 - description: retinal ganglion cell A2 - meaning: CL:0004138 - CL:0000750: - text: CL:0000750 - description: OFF-bipolar cell - meaning: CL:0000750 - CL:0000709: - text: CL:0000709 - description: R8 photoreceptor cell - meaning: CL:0000709 - CL:0004214: - text: CL:0004214 - description: type 3b cone bipolar cell - meaning: CL:0004214 - CL:0003047: - text: CL:0003047 - description: M14 retinal ganglion cell - meaning: CL:0003047 - CL:0015000: - text: CL:0015000 - description: cranial motor neuron - meaning: CL:0015000 - CL:0003036: - text: CL:0003036 - description: M7 retinal ganglion cell - meaning: CL:0003036 - CL:0000397: - text: CL:0000397 - description: ganglion interneuron - meaning: CL:0000397 - CL:1001509: - text: CL:1001509 - description: glycinergic neuron - meaning: CL:1001509 - CL:4023038: - text: CL:4023038 - description: L6b glutamatergic cortical neuron - meaning: CL:4023038 - CL:0000112: - text: CL:0000112 - description: columnar neuron - meaning: CL:0000112 - CL:0002517: - text: CL:0002517 - description: interrenal epinephrin secreting cell - meaning: CL:0002517 - CL:1000383: - text: CL:1000383 - description: type 2 vestibular sensory cell of epithelium of macula of utricle - of membranous labyrinth - meaning: CL:1000383 - CL:0004116: - text: CL:0004116 - description: retinal ganglion cell C - meaning: CL:0004116 - CL:4023113: - text: CL:4023113 - description: bouton vestibular afferent neuron - meaning: CL:4023113 - CL:0003034: - text: CL:0003034 - description: M5 retinal ganglion cell - meaning: CL:0003034 - CL:0011005: - text: CL:0011005 - description: GABAergic interneuron - meaning: CL:0011005 - CL:0011105: - text: CL:0011105 - description: dopamanergic interplexiform cell - meaning: CL:0011105 - CL:0000749: - text: CL:0000749 - description: ON-bipolar cell - meaning: CL:0000749 - CL:0000498: - text: CL:0000498 - description: inhibitory interneuron - meaning: CL:0000498 - CL:4023071: - text: CL:4023071 - description: L5/6 cck cortical GABAergic interneuron (Mmus) - meaning: CL:4023071 - CL:1000245: - text: CL:1000245 - description: posterior lateral line ganglion neuron - meaning: CL:1000245 - CL:0004139: - text: CL:0004139 - description: retinal ganglion cell A2 outer - meaning: CL:0004139 - CL:0000531: - text: CL:0000531 - description: primary sensory neuron (sensu Teleostei) - meaning: CL:0000531 - CL:0004125: - text: CL:0004125 - description: retinal ganglion cell C2 inner - meaning: CL:0004125 - CL:4023064: - text: CL:4023064 - description: caudal ganglionic eminence derived interneuron - meaning: CL:4023064 - CL:4030049: - text: CL:4030049 - description: striosomal D2 medium spiny neuron - meaning: CL:4030049 - CL:0017002: - text: CL:0017002 - description: prostate neuroendocrine cell - meaning: CL:0017002 - CL:0000756: - text: CL:0000756 - description: type 4 cone bipolar cell (sensu Mus) - meaning: CL:0000756 - CL:0000707: - text: CL:0000707 - description: R7 photoreceptor cell - meaning: CL:0000707 - CL:0000700: - text: CL:0000700 - description: dopaminergic neuron - meaning: CL:0000700 - CL:0003002: - text: CL:0003002 - description: G1 retinal ganglion cell - meaning: CL:0003002 - CL:1000001: - text: CL:1000001 - description: retrotrapezoid nucleus neuron - meaning: CL:1000001 - CL:4023007: - text: CL:4023007 - description: L2/3 bipolar vip GABAergic cortical interneuron (Mmus) - meaning: CL:4023007 - CL:0000528: - text: CL:0000528 - description: nitrergic neuron - meaning: CL:0000528 - CL:0000639: - text: CL:0000639 - description: basophil cell of pars distalis of adenohypophysis - meaning: CL:0000639 - CL:0000849: - text: CL:0000849 - description: crypt olfactory receptor neuron - meaning: CL:0000849 - CL:0011110: - text: CL:0011110 - description: histaminergic neuron - meaning: CL:0011110 - CL:0005025: - text: CL:0005025 - description: visceromotor neuron - meaning: CL:0005025 - CL:0003001: - text: CL:0003001 - description: bistratified retinal ganglion cell - meaning: CL:0003001 - CL:0004241: - text: CL:0004241 - description: WF2 amacrine cell - meaning: CL:0004241 - CL:4023019: - text: CL:4023019 - description: L5/6 cck, vip cortical GABAergic interneuron (Mmus) - meaning: CL:4023019 - CL:4023040: - text: CL:4023040 - description: L2/3-6 intratelencephalic projecting glutamatergic cortical neuron - meaning: CL:4023040 - CL:1001435: - text: CL:1001435 - description: periglomerular cell - meaning: CL:1001435 - CL:4023127: - text: CL:4023127 - description: arcuate nucleus of hypothalamus KNDy neuron - meaning: CL:4023127 - CL:0003007: - text: CL:0003007 - description: G4-OFF retinal ganglion cell - meaning: CL:0003007 - CL:0000101: - text: CL:0000101 - description: sensory neuron - meaning: CL:0000101 - CL:2000097: - text: CL:2000097 - description: midbrain dopaminergic neuron - meaning: CL:2000097 - CL:4023095: - text: CL:4023095 - description: untufted pyramidal neuron - meaning: CL:4023095 - CL:0003004: - text: CL:0003004 - description: G3 retinal ganglion cell - meaning: CL:0003004 - CL:0000527: - text: CL:0000527 - description: efferent neuron - meaning: CL:0000527 - CL:1000382: - text: CL:1000382 - description: type 2 vestibular sensory cell of stato-acoustic epithelium - meaning: CL:1000382 - CL:4033019: - text: CL:4033019 - description: ON-blue cone bipolar cell - meaning: CL:4033019 - CL:0000589: - text: CL:0000589 - description: cochlear inner hair cell - meaning: CL:0000589 - CL:4023160: - text: CL:4023160 - description: cartwheel cell - meaning: CL:4023160 - CL:1001437: - text: CL:1001437 - description: hair-down neuron - meaning: CL:1001437 - CL:0011102: - text: CL:0011102 - description: parasympathetic neuron - meaning: CL:0011102 - CL:2000029: - text: CL:2000029 - description: central nervous system neuron - meaning: CL:2000029 - CL:4023115: - text: CL:4023115 - description: type 1 spiral ganglion neuron - meaning: CL:4023115 - CL:0002311: - text: CL:0002311 - description: mammotroph - meaning: CL:0002311 - CL:0003025: - text: CL:0003025 - description: retinal ganglion cell C3 - meaning: CL:0003025 - CL:4030050: - text: CL:4030050 - description: D1/D2-hybrid medium spiny neuron - meaning: CL:4030050 - CL:4023118: - text: CL:4023118 - description: L5/6 non-Martinotti sst GABAergic cortical interneuron (Mmus) - meaning: CL:4023118 - CL:4023110: - text: CL:4023110 - description: amygdala pyramidal neuron - meaning: CL:4023110 - CL:0002273: - text: CL:0002273 - description: type ECL enteroendocrine cell - meaning: CL:0002273 - CL:0003050: - text: CL:0003050 - description: S cone cell - meaning: CL:0003050 - CL:4023121: - text: CL:4023121 - description: sst chodl GABAergic cortical interneuron - meaning: CL:4023121 - CL:4023020: - text: CL:4023020 - description: dynamic gamma motor neuron - meaning: CL:4023020 - CL:0004246: - text: CL:0004246 - description: monostratified cell - meaning: CL:0004246 - CL:0000495: - text: CL:0000495 - description: blue sensitive photoreceptor cell - meaning: CL:0000495 - CL:0000029: - text: CL:0000029 - description: neural crest derived neuron - meaning: CL:0000029 - CL:0004001: - text: CL:0004001 - description: local interneuron - meaning: CL:0004001 - CL:0000551: - text: CL:0000551 - description: unimodal nocireceptor - meaning: CL:0000551 - CL:0003006: - text: CL:0003006 - description: G4-ON retinal ganglion cell - meaning: CL:0003006 - CL:4023011: - text: CL:4023011 - description: lamp5 GABAergic cortical interneuron - meaning: CL:4023011 - CL:4023109: - text: CL:4023109 - description: vasopressin-secreting magnocellular cell - meaning: CL:4023109 - CL:0000121: - text: CL:0000121 - description: Purkinje cell - meaning: CL:0000121 - CL:0000678: - text: CL:0000678 - description: commissural neuron - meaning: CL:0000678 - CL:0004252: - text: CL:0004252 - description: medium field retinal amacrine cell - meaning: CL:0004252 - CL:0000103: - text: CL:0000103 - description: bipolar neuron - meaning: CL:0000103 - CL:4033036: - text: CL:4033036 - description: OFFx cell - meaning: CL:4033036 - CL:4023014: - text: CL:4023014 - description: L5 vip cortical GABAergic interneuron (Mmus) - meaning: CL:4023014 - CL:0008031: - text: CL:0008031 - description: cortical interneuron - meaning: CL:0008031 - CL:0008010: - text: CL:0008010 - description: cranial somatomotor neuron - meaning: CL:0008010 - CL:0000637: - text: CL:0000637 - description: chromophil cell of anterior pituitary gland - meaning: CL:0000637 - CL:0003014: - text: CL:0003014 - description: G11 retinal ganglion cell - meaning: CL:0003014 - CL:4033029: - text: CL:4033029 - description: diffuse bipolar 3a cell - meaning: CL:4033029 - CL:0002611: - text: CL:0002611 - description: neuron of the dorsal spinal cord - meaning: CL:0002611 - CL:0010010: - text: CL:0010010 - description: cerebellar stellate cell - meaning: CL:0010010 - CL:1000465: - text: CL:1000465 - description: chromaffin cell of ovary - meaning: CL:1000465 - CL:0000761: - text: CL:0000761 - description: type 9 cone bipolar cell (sensu Mus) - meaning: CL:0000761 - CL:0004226: - text: CL:0004226 - description: monostratified amacrine cell - meaning: CL:0004226 - CL:0004253: - text: CL:0004253 - description: wide field retinal amacrine cell - meaning: CL:0004253 - CL:4023075: - text: CL:4023075 - description: L6 tyrosine hydroxylase sst GABAergic cortical interneuron (Mmus) - meaning: CL:4023075 - CL:4023068: - text: CL:4023068 - description: thalamic excitatory neuron - meaning: CL:4023068 - CL:1000377: - text: CL:1000377 - description: dense-core granulated cell of epithelium of trachea - meaning: CL:1000377 - CL:4023089: - text: CL:4023089 - description: nest basket cell - meaning: CL:4023089 - CL:4023189: - text: CL:4023189 - description: parasol ganglion cell of retina - meaning: CL:4023189 - CL:0000856: - text: CL:0000856 - description: neuromast hair cell - meaning: CL:0000856 - CL:4023025: - text: CL:4023025 - description: long-range projecting sst GABAergic cortical interneuron (Mmus) - meaning: CL:4023025 - CL:0003043: - text: CL:0003043 - description: M10 retinal ganglion cell - meaning: CL:0003043 - CL:4023000: - text: CL:4023000 - description: beta motor neuron - meaning: CL:4023000 - CL:4023048: - text: CL:4023048 - description: L4/5 intratelencephalic projecting glutamatergic neuron of the - primary motor cortex - meaning: CL:4023048 - CL:0000855: - text: CL:0000855 - description: sensory hair cell - meaning: CL:0000855 - CL:4023070: - text: CL:4023070 - description: caudal ganglionic eminence derived GABAergic cortical interneuron - meaning: CL:4023070 - CL:0002070: - text: CL:0002070 - description: type I vestibular sensory cell - meaning: CL:0002070 - CL:2000028: - text: CL:2000028 - description: cerebellum glutamatergic neuron - meaning: CL:2000028 - CL:0000533: - text: CL:0000533 - description: primary motor neuron (sensu Teleostei) - meaning: CL:0000533 - CL:4023083: - text: CL:4023083 - description: chandelier cell - meaning: CL:4023083 - CL:2000034: - text: CL:2000034 - description: anterior lateral line neuromast hair cell - meaning: CL:2000034 - CL:0003015: - text: CL:0003015 - description: G11-ON retinal ganglion cell - meaning: CL:0003015 - CL:0000204: - text: CL:0000204 - description: acceleration receptive cell - meaning: CL:0000204 - CL:4033031: - text: CL:4033031 - description: diffuse bipolar 4 cell - meaning: CL:4033031 - CL:0003024: - text: CL:0003024 - description: retinal ganglion cell C inner - meaning: CL:0003024 - CL:4023074: - text: CL:4023074 - description: mammillary body neuron - meaning: CL:4023074 - CL:2000089: - text: CL:2000089 - description: dentate gyrus granule cell - meaning: CL:2000089 - CL:4033028: - text: CL:4033028 - description: diffuse bipolar 2 cell - meaning: CL:4033028 - CL:0000110: - text: CL:0000110 - description: peptidergic neuron - meaning: CL:0000110 - CL:4033002: - text: CL:4033002 - description: neuroendocrine cell of epithelium of crypt of Lieberkuhn - meaning: CL:4033002 - CL:4033027: - text: CL:4033027 - description: diffuse bipolar 1 cell - meaning: CL:4033027 - CL:3000003: - text: CL:3000003 - description: sympathetic cholinergic neuron - meaning: CL:3000003 - CL:4023158: - text: CL:4023158 - description: octopus cell of the mammalian cochlear nucleus - meaning: CL:4023158 - CL:0000118: - text: CL:0000118 - description: basket cell - meaning: CL:0000118 - CL:0004223: - text: CL:0004223 - description: AB diffuse-1 amacrine cell - meaning: CL:0004223 - CL:4030054: - text: CL:4030054 - description: RXFP1-positive interface island D1-medium spiny neuron - meaning: CL:4030054 - CL:0002610: - text: CL:0002610 - description: raphe nuclei neuron - meaning: CL:0002610 - CL:4023026: - text: CL:4023026 - description: direct pathway medium spiny neuron - meaning: CL:4023026 - CL:4023016: - text: CL:4023016 - description: vip GABAergic cortical interneuron - meaning: CL:4023016 - CL:0004237: - text: CL:0004237 - description: fountain amacrine cell - meaning: CL:0004237 - CL:0003035: - text: CL:0003035 - description: M6 retinal ganglion cell - meaning: CL:0003035 - CL:1001611: - text: CL:1001611 - description: cerebellar neuron - meaning: CL:1001611 - CL:0000591: - text: CL:0000591 - description: warmth sensing thermoreceptor cell - meaning: CL:0000591 - CL:0002613: - text: CL:0002613 - description: striatum neuron - meaning: CL:0002613 - CL:0000496: - text: CL:0000496 - description: green sensitive photoreceptor cell - meaning: CL:0000496 - CL:0007011: - text: CL:0007011 - description: enteric neuron - meaning: CL:0007011 - CL:2000056: - text: CL:2000056 - description: Meynert cell - meaning: CL:2000056 - CL:0003040: - text: CL:0003040 - description: M9 retinal ganglion cell - meaning: CL:0003040 - CL:0004250: - text: CL:0004250 - description: bistratified retinal amacrine cell - meaning: CL:0004250 - CL:0003029: - text: CL:0003029 - description: M2 retinal ganglion cell - meaning: CL:0003029 - CL:4023017: - text: CL:4023017 - description: sst GABAergic cortical interneuron - meaning: CL:4023017 - CL:0008028: - text: CL:0008028 - description: visual system neuron - meaning: CL:0008028 - CL:0008039: - text: CL:0008039 - description: lower motor neuron - meaning: CL:0008039 - CL:2000086: - text: CL:2000086 - description: neocortex basket cell - meaning: CL:2000086 - CL:4023023: - text: CL:4023023 - description: L5,6 neurogliaform lamp5 GABAergic cortical interneuron (Mmus) - meaning: CL:4023023 - CL:0000697: - text: CL:0000697 - description: R4 photoreceptor cell - meaning: CL:0000697 - CL:2000088: - text: CL:2000088 - description: Ammon's horn basket cell - meaning: CL:2000088 - CL:0004232: - text: CL:0004232 - description: starburst amacrine cell - meaning: CL:0004232 - CL:4023041: - text: CL:4023041 - description: L5 extratelencephalic projecting glutamatergic cortical neuron - meaning: CL:4023041 - CL:0004121: - text: CL:0004121 - description: retinal ganglion cell B2 - meaning: CL:0004121 - CL:0000748: - text: CL:0000748 - description: retinal bipolar neuron - meaning: CL:0000748 - CL:4023164: - text: CL:4023164 - description: globular bushy cell - meaning: CL:4023164 - CL:0000536: - text: CL:0000536 - description: secondary motor neuron (sensu Teleostei) - meaning: CL:0000536 - CL:1000466: - text: CL:1000466 - description: chromaffin cell of right ovary - meaning: CL:1000466 - CL:0011001: - text: CL:0011001 - description: spinal cord motor neuron - meaning: CL:0011001 - CL:0000755: - text: CL:0000755 - description: type 3 cone bipolar cell (sensu Mus) - meaning: CL:0000755 - CL:0004238: - text: CL:0004238 - description: asymmetric bistratified amacrine cell - meaning: CL:0004238 - CL:0004161: - text: CL:0004161 - description: 510 nm-cone - meaning: CL:0004161 - CL:0000198: - text: CL:0000198 - description: pain receptor cell - meaning: CL:0000198 - CL:0003038: - text: CL:0003038 - description: M7-OFF retinal ganglion cell - meaning: CL:0003038 - CL:0003033: - text: CL:0003033 - description: M4 retinal ganglion cell - meaning: CL:0003033 - CL:0012001: - text: CL:0012001 - description: neuron of the forebrain - meaning: CL:0012001 - CL:0011104: - text: CL:0011104 - description: interplexiform cell - meaning: CL:0011104 - CL:0003049: - text: CL:0003049 - description: M cone cell - meaning: CL:0003049 - CL:2000032: - text: CL:2000032 - description: peripheral nervous system neuron - meaning: CL:2000032 - CL:0011100: - text: CL:0011100 - description: galanergic neuron - meaning: CL:0011100 - CL:0008025: - text: CL:0008025 - description: noradrenergic neuron - meaning: CL:0008025 - CL:0000122: - text: CL:0000122 - description: stellate neuron - meaning: CL:0000122 - CL:0003005: - text: CL:0003005 - description: G4 retinal ganglion cell - meaning: CL:0003005 - CL:0000699: - text: CL:0000699 - description: paraganglial type 1 cell - meaning: CL:0000699 - CL:4033050: - text: CL:4033050 - description: catecholaminergic neuron - meaning: CL:4033050 - CL:1001502: - text: CL:1001502 - description: mitral cell - meaning: CL:1001502 - CL:0002069: - text: CL:0002069 - description: type II vestibular sensory cell - meaning: CL:0002069 - CL:4023065: - text: CL:4023065 - description: meis2 expressing cortical GABAergic cell - meaning: CL:4023065 - CL:4023077: - text: CL:4023077 - description: bitufted neuron - meaning: CL:4023077 - CL:0000847: - text: CL:0000847 - description: ciliated olfactory receptor neuron - meaning: CL:0000847 - CL:4023188: - text: CL:4023188 - description: midget ganglion cell of retina - meaning: CL:4023188 - CL:2000090: - text: CL:2000090 - description: dentate gyrus of hippocampal formation stellate cell - meaning: CL:2000090 - CL:0000568: - text: CL:0000568 - description: amine precursor uptake and decarboxylation cell - meaning: CL:0000568 - CL:1000426: - text: CL:1000426 - description: chromaffin cell of adrenal gland - meaning: CL:1000426 - CL:0000100: - text: CL:0000100 - description: motor neuron - meaning: CL:0000100 - CL:0011109: - text: CL:0011109 - description: hypocretin-secreting neuron - meaning: CL:0011109 - CL:4023171: - text: CL:4023171 - description: trigeminal motor neuron - meaning: CL:4023171 - CL:1001434: - text: CL:1001434 - description: olfactory bulb interneuron - meaning: CL:1001434 - CL:0000494: - text: CL:0000494 - description: UV sensitive photoreceptor cell - meaning: CL:0000494 - CL:0004117: - text: CL:0004117 - description: retinal ganglion cell A - meaning: CL:0004117 - CL:0000205: - text: CL:0000205 - description: thermoreceptor cell - meaning: CL:0000205 - CL:0004217: - text: CL:0004217 - description: H1 horizontal cell - meaning: CL:0004217 - CL:0000200: - text: CL:0000200 - description: touch receptor cell - meaning: CL:0000200 - CL:4023111: - text: CL:4023111 - description: cerebral cortex pyramidal neuron - meaning: CL:4023111 - CL:4032001: - text: CL:4032001 - description: reelin GABAergic cortical interneuron - meaning: CL:4032001 - CL:4023076: - text: CL:4023076 - description: Martinotti neuron - meaning: CL:4023076 - CL:0000753: - text: CL:0000753 - description: type 1 cone bipolar cell (sensu Mus) - meaning: CL:0000753 - CL:1001451: - text: CL:1001451 - description: sensory neuron of dorsal root ganglion - meaning: CL:1001451 - CL:4023021: - text: CL:4023021 - description: static gamma motor neuron - meaning: CL:4023021 - CL:0002066: - text: CL:0002066 - description: Feyrter cell - meaning: CL:0002066 - CL:0000598: - text: CL:0000598 - description: pyramidal neuron - meaning: CL:0000598 - CL:0000702: - text: CL:0000702 - description: R5 photoreceptor cell - meaning: CL:0000702 - CL:0008049: - text: CL:0008049 - description: Betz cell - meaning: CL:0008049 - CL:0001033: - text: CL:0001033 - description: hippocampal granule cell - meaning: CL:0001033 - CL:0000587: - text: CL:0000587 - description: cold sensing thermoreceptor cell - meaning: CL:0000587 - CL:4023161: - text: CL:4023161 - description: unipolar brush cell - meaning: CL:4023161 - CL:2000031: - text: CL:2000031 - description: lateral line ganglion neuron - meaning: CL:2000031 - CL:4023119: - text: CL:4023119 - description: displaced amacrine cell - meaning: CL:4023119 - CL:1001569: - text: CL:1001569 - description: hippocampal interneuron - meaning: CL:1001569 - CL:4023130: - text: CL:4023130 - description: kisspeptin neuron - meaning: CL:4023130 - CL:4023090: - text: CL:4023090 - description: small basket cell - meaning: CL:4023090 - CL:4023033: - text: CL:4023033 - description: OFF retinal ganglion cell - meaning: CL:4023033 - CL:4023112: - text: CL:4023112 - description: vestibular afferent neuron - meaning: CL:4023112 - CL:0004234: - text: CL:0004234 - description: diffuse multistratified amacrine cell - meaning: CL:0004234 - CL:0002082: - text: CL:0002082 - description: type II cell of adrenal medulla - meaning: CL:0002082 - CL:0010011: - text: CL:0010011 - description: cerebral cortex GABAergic interneuron - meaning: CL:0010011 - CL:4030052: - text: CL:4030052 - description: nucleus accumbens shell and olfactory tubercle D2 medium spiny - neuron - meaning: CL:4030052 - CL:0000604: - text: CL:0000604 - description: retinal rod cell - meaning: CL:0000604 - CL:4030027: - text: CL:4030027 - description: GABAergic amacrine cell - meaning: CL:4030027 - CL:1001561: - text: CL:1001561 - description: vomeronasal sensory neuron - meaning: CL:1001561 - CL:0000210: - text: CL:0000210 - description: photoreceptor cell - meaning: CL:0000210 - CL:4023012: - text: CL:4023012 - description: near-projecting glutamatergic cortical neuron - meaning: CL:4023012 - CL:4023087: - text: CL:4023087 - description: fan Martinotti neuron - meaning: CL:4023087 - CL:0000028: - text: CL:0000028 - description: CNS neuron (sensu Nematoda and Protostomia) - meaning: CL:0000028 - CL:0000006: - text: CL:0000006 - description: neuronal receptor cell - meaning: CL:0000006 - CL:0004247: - text: CL:0004247 - description: bistratified cell - meaning: CL:0004247 - CL:0010012: - text: CL:0010012 - description: cerebral cortex neuron - meaning: CL:0010012 - CL:0004245: - text: CL:0004245 - description: indoleamine-accumulating amacrine cell - meaning: CL:0004245 - CL:0004224: - text: CL:0004224 - description: AB diffuse-2 amacrine cell - meaning: CL:0004224 - CL:0003009: - text: CL:0003009 - description: G6 retinal ganglion cell - meaning: CL:0003009 - CL:0000679: - text: CL:0000679 - description: glutamatergic neuron - meaning: CL:0000679 - CL:0000166: - text: CL:0000166 - description: chromaffin cell - meaning: CL:0000166 - CL:4023088: - text: CL:4023088 - description: large basket cell - meaning: CL:4023088 - CL:4030057: - text: CL:4030057 - description: eccentric medium spiny neuron - meaning: CL:4030057 - CL:4023024: - text: CL:4023024 - description: neurogliaform lamp5 GABAergic cortical interneuron (Mmus) - meaning: CL:4023024 - CL:0005024: - text: CL:0005024 - description: somatomotor neuron - meaning: CL:0005024 - CL:4023049: - text: CL:4023049 - description: L5 intratelencephalic projecting glutamatergic neuron of the - primary motor cortex - meaning: CL:4023049 - CL:0000573: - text: CL:0000573 - description: retinal cone cell - meaning: CL:0000573 - CL:4023123: - text: CL:4023123 - description: hypothalamus kisspeptin neuron - meaning: CL:4023123 - CL:0000376: - text: CL:0000376 - description: humidity receptor cell - meaning: CL:0000376 - CL:0004235: - text: CL:0004235 - description: AB broad diffuse-1 amacrine cell - meaning: CL:0004235 - CL:0000106: - text: CL:0000106 - description: unipolar neuron - meaning: CL:0000106 - CL:0001032: - text: CL:0001032 - description: cortical granule cell - meaning: CL:0001032 - CL:0000561: - text: CL:0000561 - description: amacrine cell - meaning: CL:0000561 - CL:4023093: - text: CL:4023093 - description: stellate pyramidal neuron - meaning: CL:4023093 - CL:0000247: - text: CL:0000247 - description: Rohon-Beard neuron - meaning: CL:0000247 - CL:0003008: - text: CL:0003008 - description: G5 retinal ganglion cell - meaning: CL:0003008 - CL:0000203: - text: CL:0000203 - description: gravity sensitive cell - meaning: CL:0000203 - CL:0003037: - text: CL:0003037 - description: M7-ON retinal ganglion cell - meaning: CL:0003037 - CL:0004221: - text: CL:0004221 - description: flag A amacrine cell - meaning: CL:0004221 - CL:0000638: - text: CL:0000638 - description: acidophil cell of pars distalis of adenohypophysis - meaning: CL:0000638 - CL:0004229: - text: CL:0004229 - description: A2-like amacrine cell - meaning: CL:0004229 - CL:4023120: - text: CL:4023120 - description: cochlea auditory hair cell - meaning: CL:4023120 - CL:0008032: - text: CL:0008032 - description: rosehip neuron - meaning: CL:0008032 - CL:0008027: - text: CL:0008027 - description: rod bipolar cell (sensu Mus) - meaning: CL:0008027 - CL:0000497: - text: CL:0000497 - description: red sensitive photoreceptor cell - meaning: CL:0000497 - CL:4023062: - text: CL:4023062 - description: dentate gyrus neuron - meaning: CL:4023062 - CL:0002516: - text: CL:0002516 - description: interrenal chromaffin cell - meaning: CL:0002516 - CL:0004119: - text: CL:0004119 - description: retinal ganglion cell B1 - meaning: CL:0004119 - CL:4030039: - text: CL:4030039 - description: von Economo neuron - meaning: CL:4030039 - CL:4023036: - text: CL:4023036 - description: chandelier pvalb GABAergic cortical interneuron - meaning: CL:4023036 - CL:0000117: - text: CL:0000117 - description: CNS neuron (sensu Vertebrata) - meaning: CL:0000117 - CL:4023015: - text: CL:4023015 - description: sncg GABAergic cortical interneuron - meaning: CL:4023015 - CL:4033033: - text: CL:4033033 - description: flat midget bipolar cell - meaning: CL:4033033 - CL:0000626: - text: CL:0000626 - description: olfactory granule cell - meaning: CL:0000626 - CL:0004218: - text: CL:0004218 - description: H2 horizontal cell - meaning: CL:0004218 - CL:0004233: - text: CL:0004233 - description: DAPI-3 amacrine cell - meaning: CL:0004233 - CL:0003021: - text: CL:0003021 - description: retinal ganglion cell C4 - meaning: CL:0003021 - CL:0000489: - text: CL:0000489 - description: scotopic photoreceptor cell - meaning: CL:0000489 - CL:4023159: - text: CL:4023159 - description: double bouquet cell - meaning: CL:4023159 - CL:0002612: - text: CL:0002612 - description: neuron of the ventral spinal cord - meaning: CL:0002612 - CL:0000476: - text: CL:0000476 - description: thyrotroph - meaning: CL:0000476 - CL:4033034: - text: CL:4033034 - description: invaginating midget bipolar cell - meaning: CL:4033034 - CL:4023029: - text: CL:4023029 - description: indirect pathway medium spiny neuron - meaning: CL:4023029 - CL:0004236: - text: CL:0004236 - description: AB broad diffuse-2 amacrine cell - meaning: CL:0004236 - CL:0003017: - text: CL:0003017 - description: retinal ganglion cell B3 outer - meaning: CL:0003017 - CL:0000759: - text: CL:0000759 - description: type 7 cone bipolar cell (sensu Mus) - meaning: CL:0000759 - CL:0000740: - text: CL:0000740 - description: retinal ganglion cell - meaning: CL:0000740 - CL:0004120: - text: CL:0004120 - description: retinal ganglion cell A1 - meaning: CL:0004120 - CL:3000002: - text: CL:3000002 - description: sympathetic noradrenergic neuron - meaning: CL:3000002 - CL:0003023: - text: CL:0003023 - description: retinal ganglion cell C6 - meaning: CL:0003023 - CL:0000690: - text: CL:0000690 - description: R2 photoreceptor cell - meaning: CL:0000690 - CL:4023047: - text: CL:4023047 - description: L2/3 intratelencephalic projecting glutamatergic neuron of the - primary motor cortex - meaning: CL:4023047 - CL:4023022: - text: CL:4023022 - description: canopy lamp5 GABAergic cortical interneuron (Mmus) - meaning: CL:4023022 - CL:4023060: - text: CL:4023060 - description: hippocampal CA1-3 neuron - meaning: CL:4023060 - CL:0000758: - text: CL:0000758 - description: type 6 cone bipolar cell (sensu Mus) - meaning: CL:0000758 - CL:0000535: - text: CL:0000535 - description: secondary neuron (sensu Teleostei) - meaning: CL:0000535 - CL:4023055: - text: CL:4023055 - description: corticothalamic VAL/VM projecting glutamatergic neuron of the - primary motor cortex - meaning: CL:4023055 - CL:1000467: - text: CL:1000467 - description: chromaffin cell of left ovary - meaning: CL:1000467 - CL:0011002: - text: CL:0011002 - description: lateral motor column neuron - meaning: CL:0011002 - CL:0004244: - text: CL:0004244 - description: WF4 amacrine cell - meaning: CL:0004244 - CL:1000223: - text: CL:1000223 - description: lung neuroendocrine cell - meaning: CL:1000223 - CL:1000385: - text: CL:1000385 - description: type 2 vestibular sensory cell of epithelium of crista of ampulla - of semicircular duct of membranous labyrinth - meaning: CL:1000385 - CL:0000691: - text: CL:0000691 - description: stellate interneuron - meaning: CL:0000691 - CL:4023008: - text: CL:4023008 - description: intratelencephalic-projecting glutamatergic cortical neuron - meaning: CL:4023008 - CL:4023044: - text: CL:4023044 - description: non-medulla, extratelencephalic-projecting glutamatergic neuron - of the primary motor cortex - meaning: CL:4023044 - CL:0000850: - text: CL:0000850 - description: serotonergic neuron - meaning: CL:0000850 - CL:0000695: - text: CL:0000695 - description: Cajal-Retzius cell - meaning: CL:0000695 - CL:0003051: - text: CL:0003051 - description: UV cone cell - meaning: CL:0003051 - CL:0000402: - text: CL:0000402 - description: CNS interneuron - meaning: CL:0000402 - CL:0005023: - text: CL:0005023 - description: branchiomotor neuron - meaning: CL:0005023 - CL:4023043: - text: CL:4023043 - description: L5/6 near-projecting glutamatergic neuron of the primary motor - cortex - meaning: CL:4023043 - CL:0004162: - text: CL:0004162 - description: 360 nm-cone - meaning: CL:0004162 - CL:0011003: - text: CL:0011003 - description: magnocellular neurosecretory cell - meaning: CL:0011003 - CL:0004230: - text: CL:0004230 - description: diffuse bistratified amacrine cell - meaning: CL:0004230 - CL:1001505: - text: CL:1001505 - description: parvocellular neurosecretory cell - meaning: CL:1001505 - CL:0011106: - text: CL:0011106 - description: GABAnergic interplexiform cell - meaning: CL:0011106 - CL:0000437: - text: CL:0000437 - description: gonadtroph - meaning: CL:0000437 - CL:4023010: - text: CL:4023010 - description: alpha7 GABAergic cortical interneuron (Mmus) - meaning: CL:4023010 - CL:4023046: - text: CL:4023046 - description: L6b subplate glutamatergic neuron of the primary motor cortex - meaning: CL:4023046 - CL:0000109: - text: CL:0000109 - description: adrenergic neuron - meaning: CL:0000109 - CL:0011000: - text: CL:0011000 - description: dorsal horn interneuron - meaning: CL:0011000 - CL:0000251: - text: CL:0000251 - description: extramedullary cell - meaning: CL:0000251 - CL:0003044: - text: CL:0003044 - description: M11 retinal ganglion cell - meaning: CL:0003044 - CL:4023053: - text: CL:4023053 - description: spinal interneuron synapsing Betz cell - meaning: CL:4023053 - CL:1000378: - text: CL:1000378 - description: type 1 vestibular sensory cell of stato-acoustic epithelium - meaning: CL:1000378 - CL:4023124: - text: CL:4023124 - description: dentate gyrus kisspeptin neuron - meaning: CL:4023124 - CL:1000427: - text: CL:1000427 - description: adrenal cortex chromaffin cell - meaning: CL:1000427 - CL:0000207: - text: CL:0000207 - description: olfactory receptor cell - meaning: CL:0000207 - CL:4023162: - text: CL:4023162 - description: bushy cell - meaning: CL:4023162 - CL:2000019: - text: CL:2000019 - description: compound eye photoreceptor cell - meaning: CL:2000019 - CL:4023086: - text: CL:4023086 - description: T Martinotti neuron - meaning: CL:4023086 - CL:0003012: - text: CL:0003012 - description: G9 retinal ganglion cell - meaning: CL:0003012 - CL:0002270: - text: CL:0002270 - description: type EC2 enteroendocrine cell - meaning: CL:0002270 - CL:2000024: - text: CL:2000024 - description: spinal cord medial motor column neuron - meaning: CL:2000024 - CL:0003022: - text: CL:0003022 - description: retinal ganglion cell C5 - meaning: CL:0003022 - CL:0000104: - text: CL:0000104 - description: multipolar neuron - meaning: CL:0000104 - CL:4023050: - text: CL:4023050 - description: L6 intratelencephalic projecting glutamatergic neuron of the - primary motor cortex - meaning: CL:4023050 - CL:4023030: - text: CL:4023030 - description: L2/3/5 fan Martinotti sst GABAergic cortical interneuron (Mmus) - meaning: CL:4023030 - CL:0000741: - text: CL:0000741 - description: spinal accessory motor neuron - meaning: CL:0000741 - CL:4033010: - text: CL:4033010 - description: neuroendocrine cell of epithelium of lobar bronchus - meaning: CL:4033010 - CL:1000425: - text: CL:1000425 - description: chromaffin cell of paraganglion - meaning: CL:1000425 - CL:4030051: - text: CL:4030051 - description: nucleus accumbens shell and olfactory tubercle D1 medium spiny - neuron - meaning: CL:4030051 - CL:0000567: - text: CL:0000567 - description: polymodal nocireceptor - meaning: CL:0000567 - CL:0004215: - text: CL:0004215 - description: type 5a cone bipolar cell - meaning: CL:0004215 - CL:0003032: - text: CL:0003032 - description: M3-OFF retinal ganglion cell - meaning: CL:0003032 - CL:4023079: - text: CL:4023079 - description: midbrain-derived inhibitory neuron - meaning: CL:4023079 - CL:0000099: - text: CL:0000099 - description: interneuron - meaning: CL:0000099 - CL:0000253: - text: CL:0000253 - description: eurydendroid cell - meaning: CL:0000253 - CL:0008013: - text: CL:0008013 - description: cranial visceromotor neuron - meaning: CL:0008013 - CL:0005000: - text: CL:0005000 - description: spinal cord interneuron - meaning: CL:0005000 - CL:0004222: - text: CL:0004222 - description: flag B amacrine cell - meaning: CL:0004222 - CL:0000617: - text: CL:0000617 - description: GABAergic neuron - meaning: CL:0000617 - CL:0003010: - text: CL:0003010 - description: G7 retinal ganglion cell - meaning: CL:0003010 - CL:0000577: - text: CL:0000577 - description: type EC enteroendocrine cell - meaning: CL:0000577 - CL:0003018: - text: CL:0003018 - description: retinal ganglion cell B3 inner - meaning: CL:0003018 - CL:0002083: - text: CL:0002083 - description: type I cell of adrenal medulla - meaning: CL:0002083 - CL:4023081: - text: CL:4023081 - description: inverted L6 intratelencephalic projecting glutamatergic neuron - of the primary motor cortex (Mmus) - meaning: CL:4023081 - CL:0004251: - text: CL:0004251 - description: narrow field retinal amacrine cell - meaning: CL:0004251 - CL:4023092: - text: CL:4023092 - description: inverted pyramidal neuron - meaning: CL:4023092 - CL:0002608: - text: CL:0002608 - description: hippocampal neuron - meaning: CL:0002608 - CL:0008048: - text: CL:0008048 - description: upper motor neuron - meaning: CL:0008048 - CL:0011113: - text: CL:0011113 - description: spiral ganglion neuron - meaning: CL:0011113 - CL:0000601: - text: CL:0000601 - description: cochlear outer hair cell - meaning: CL:0000601 - CL:0003041: - text: CL:0003041 - description: M9-ON retinal ganglion cell - meaning: CL:0003041 - CL:4023042: - text: CL:4023042 - description: L6 corticothalamic-projecting glutamatergic cortical neuron - meaning: CL:4023042 - CL:0000199: - text: CL:0000199 - description: mechanoreceptor cell - meaning: CL:0000199 - CL:1001571: - text: CL:1001571 - description: hippocampal pyramidal neuron - meaning: CL:1001571 - CL:2000048: - text: CL:2000048 - description: anterior horn motor neuron - meaning: CL:2000048 - CL:4023170: - text: CL:4023170 - description: trigeminal sensory neuron - meaning: CL:4023170 - CL:0002614: - text: CL:0002614 - description: neuron of the substantia nigra - meaning: CL:0002614 diff --git a/tests/unit/test_term_set.py b/tests/unit/test_term_set.py index 465fee074..43a3f92b9 100644 --- a/tests/unit/test_term_set.py +++ b/tests/unit/test_term_set.py @@ -97,6 +97,9 @@ def test_enum_expander_output(self): self.assertEqual(convert_path, expected_path) + filename = os.path.splitext(os.path.basename(schema_path))[0] + remove_test_file(f"tests/unit/expanded_{filename}.yaml") + def test_folder_output(self): folder = os.path.join(CUR_DIR, "test_term_set_input", "schemasheets") termset = TermSet(schemasheets_folder=folder) diff --git a/tests/unit/utils_test/test_core_GenericDataChunkIterator.py b/tests/unit/utils_test/test_core_GenericDataChunkIterator.py index f05a295f8..debac9cab 100644 --- a/tests/unit/utils_test/test_core_GenericDataChunkIterator.py +++ b/tests/unit/utils_test/test_core_GenericDataChunkIterator.py @@ -20,7 +20,7 @@ TQDM_INSTALLED = False -class TestPickleableNumpyArrayDataChunkIterator(GenericDataChunkIterator): +class PickleableNumpyArrayDataChunkIterator(GenericDataChunkIterator): def __init__(self, array: np.ndarray, **kwargs): self.array = array self._kwargs = kwargs @@ -41,7 +41,7 @@ def _to_dict(self) -> dict: @staticmethod def _from_dict(dictionary: dict) -> Callable: array = pickle.loads(dictionary["array"]) - return TestPickleableNumpyArrayDataChunkIterator(array=array, **dictionary["kwargs"]) + return PickleableNumpyArrayDataChunkIterator(array=array, **dictionary["kwargs"]) class GenericDataChunkIteratorTests(TestCase): @@ -428,10 +428,10 @@ def test_tqdm_not_installed(self): self.assertFalse(dci.display_progress) def test_pickle(self): - pre_dump_iterator = TestPickleableNumpyArrayDataChunkIterator(array=self.test_array) + pre_dump_iterator = PickleableNumpyArrayDataChunkIterator(array=self.test_array) post_dump_iterator = pickle.loads(pickle.dumps(pre_dump_iterator)) - assert isinstance(post_dump_iterator, TestPickleableNumpyArrayDataChunkIterator) + assert isinstance(post_dump_iterator, PickleableNumpyArrayDataChunkIterator) assert post_dump_iterator.chunk_shape == pre_dump_iterator.chunk_shape assert post_dump_iterator.buffer_shape == pre_dump_iterator.buffer_shape assert_array_equal(post_dump_iterator.array, pre_dump_iterator.array)