Updates for new OnClass.

YosefLab · Dec 10, 2023 · cbe3c51 · cbe3c51
1 parent 6b95ddf
commit cbe3c51
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Showing 10 changed files with 3,330 additions and 2,507 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,55 +6,42 @@ default_stages:
     - push
 minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/psf/black
-      rev: 22.10.0
-      hooks:
-          - id: black
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0-alpha.4
-      hooks:
-          - id: prettier
     - repo: https://github.com/asottile/blacken-docs
-      rev: v1.12.1
+      rev: 1.16.0
       hooks:
           - id: blacken-docs
-    - repo: https://github.com/PyCQA/isort
-      rev: 5.12.0
-      hooks:
-          - id: isort
-    - repo: https://github.com/asottile/yesqa
-      rev: v1.4.0
+    - repo: https://github.com/pre-commit/mirrors-prettier
+      rev: v3.1.0
       hooks:
-          - id: yesqa
-            additional_dependencies:
-                - flake8-tidy-imports
-                - flake8-docstrings
-                - flake8-rst-docstrings
-                - flake8-comprehensions
-                - flake8-bugbear
-                - flake8-blind-except
+          - id: prettier
+            # Newer versions of node don't work on systems that have an older version of GLIBC
+            # (in particular Ubuntu 18.04 and Centos 7)
+            # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+            # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+            # https://github.com/jupyterlab/jupyterlab/issues/12675
+            language_version: "17.9.1"
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.1.6
+      hooks:
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix]
+          - id: ruff-format
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.3.0
+      rev: v4.5.0
       hooks:
           - id: detect-private-key
           - id: check-ast
           - id: end-of-file-fixer
-            exclude_types: [svg]
           - id: mixed-line-ending
             args: [--fix=lf]
           - id: trailing-whitespace
           - id: check-case-conflict
-    - repo: https://github.com/PyCQA/autoflake
-      rev: v1.7.7
-      hooks:
-          - id: autoflake
-            args:
-                - --in-place
-                - --remove-all-unused-imports
-                - --remove-unused-variable
-                - --ignore-init-module-imports
-    - repo: https://github.com/asottile/pyupgrade
-      rev: v3.2.0
-      hooks:
-          - id: pyupgrade
-            args: [--py3-plus, --py38-plus, --keep-runtime-typing]
+    - repo: local
+      hooks:
+          - id: forbid-to-commit
+            name: Don't commit rej files
+            entry: |
+                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+                Fix the merge conflicts manually and remove the .rej files.
+            language: fail
+            files: '.*\.rej$'
diff --git a/ontology/cl.obo b/ontology/cl.obo
@@ -186463,7 +186463,7 @@ relationship: innervated_by UBERON:0001884 ! phrenic nerve
 relationship: never_in_taxon NCBITaxon:8782 {source="Wikipedia:Thoracic_diaphragm#Comparative_anatomy_and_evolution"} ! Aves
 relationship: only_in_taxon NCBITaxon:40674 {source="PMID:23586979"} ! Mammalia
 property_value: UBPROP:0000001 "The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]." xsd:string {source="GO:0060539"}
-property_value: UBPROP:0000003 "The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000713", ontology="VHOG", source="ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278", source="http://bgee.unil.ch/"}
+property_value: UBPROP:0000003 "The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new devices that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000713", ontology="VHOG", source="ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278", source="http://bgee.unil.ch/"}
 property_value: UBPROP:0000007 "phrenic" xsd:string
 property_value: UBPROP:0000008 "The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3]" xsd:string
 property_value: UBPROP:0000008 "The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution)" xsd:string
@@ -276045,13 +276045,13 @@ is_a: RO:0002104 ! has plasma membrane part
 
 [Typedef]
 id: RO:0017001
-name: device utilizes material
-def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." []
+name: devices utilizes material
+def: "X devices utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." []
 synonym: "utilizes" BROAD []
-property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string
+property_value: IAO:0000112 "A diagnostic testing devices utilizes a specimen." xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 xsd:string
 property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 xsd:string
-property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string
+property_value: IAO:0000232 "A diagnostic testing devices utilizes a specimen means that the diagnostic testing devices is capable of an assay, and this assay a specimen as its input." xsd:string
 property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string
 holds_over_chain: capable_of has_input
 creation_date: 2021-11-08T12:00:00Z