[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -2,16 +2,20 @@ default_language_version:
   python: python3.10
   node: 16.14.2
 
+ci:
+  skip: [generate-schemas]
+  autoupdate_schedule: "monthly"
+
 repos:
-  - repo: https://github.com/ambv/black
-    rev: 23.7.0
+  - repo: https://github.com/psf/black
+    rev: 23.10.1
     hooks:
       - id: black
         name: Blacken
         args: ["--config", "pyproject.toml"]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
         exclude: (pydatalab/example_data/)|(.*.snap)
@@ -26,20 +30,20 @@ repos:
       - id: check-symlinks
       - id: mixed-line-ending
 
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.281"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.1.4"
     hooks:
       - id: ruff
         args: [--fix]
 
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.6.2
+    rev: v3.0.3
     hooks:
       - id: prettier
         types_or: [javascript, jsx, vue, html, yaml]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.4.1
+    rev: v1.6.1
     hooks:
       - id: mypy
         additional_dependencies: ["types-all", "pydantic~=1.10"]

webapp/cypress/e2e/batchSampleFeature.cy.js

@@ -65,19 +65,19 @@ function deleteSample(sample_id, delay = 100) {
 
 function getBatchAddCell(row, column, additionalSelectors = "") {
   return cy.get(
-    `[data-testid=batch-add-table] > tbody > tr:nth-of-type(${row}) > td:nth-of-type(${column}) ${additionalSelectors}`
+    `[data-testid=batch-add-table] > tbody > tr:nth-of-type(${row}) > td:nth-of-type(${column}) ${additionalSelectors}`,
   );
 }
 
 function getBatchTemplateCell(column, additionalSelectors = "") {
   return cy.get(
-    `[data-testid=batch-add-table-template] > tbody > td:nth-of-type(${column}) ${additionalSelectors}`
+    `[data-testid=batch-add-table-template] > tbody > td:nth-of-type(${column}) ${additionalSelectors}`,
   );
 }
 
 function getBatchAddError(row, additionalSelectors = "") {
   return cy.get(
-    `[data-testid=batch-add-table] > tbody > tr:nth-of-type(${row}) + td ${additionalSelectors}`
+    `[data-testid=batch-add-table] > tbody > tr:nth-of-type(${row}) + td ${additionalSelectors}`,
   );
 }
 
@@ -279,7 +279,7 @@ describe("Batch sample creation", () => {
     // sample with two components, copied from a sample with no components
     getBatchAddCell(2, 1).type("test102");
     getBatchAddCell(2, 2).type(
-      "sample with two components, copied from a sample with no components"
+      "sample with two components, copied from a sample with no components",
     );
     getBatchAddCell(2, 4, ".vs__search").type("baseA");
     cy.get(".vs__dropdown-menu").within(() => {
@@ -297,7 +297,7 @@ describe("Batch sample creation", () => {
     // sample with one components, copied from a sample with two components
     getBatchAddCell(3, 1).type("test103");
     getBatchAddCell(3, 2).type(
-      "sample with one component, copied from a sample with two components"
+      "sample with one component, copied from a sample with two components",
     );
     getBatchAddCell(3, 4, ".vs__search").type("baseB");
     cy.get(".vs__dropdown-menu").within(() => {
@@ -311,7 +311,7 @@ describe("Batch sample creation", () => {
     // sample with three components, copied from a sample with some of the same components
     getBatchAddCell(4, 1).type("test104");
     getBatchAddCell(4, 2).type(
-      "sample with three components, copied from a sample with some of the same components"
+      "sample with three components, copied from a sample with some of the same components",
     );
     getBatchAddCell(4, 4, ".vs__search").type("baseB");
     cy.get(".vs__dropdown-menu").within(() => {
@@ -352,7 +352,7 @@ describe("Batch sample creation", () => {
     cy.contains("test102").click();
     cy.findByLabelText("Name").should(
       "have.value",
-      "sample with two components, copied from a sample with no components"
+      "sample with two components, copied from a sample with no components",
     );
     cy.contains("this is a description of baseA.");
     cy.get("#synthesis-information table").contains("component1");
@@ -365,7 +365,7 @@ describe("Batch sample creation", () => {
     cy.contains("test103").click();
     cy.findByLabelText("Name").should(
       "have.value",
-      "sample with one component, copied from a sample with two components"
+      "sample with one component, copied from a sample with two components",
     );
     cy.contains("this is a description of baseB.");
     cy.get("#synthesis-information table").contains("component1");
@@ -376,19 +376,19 @@ describe("Batch sample creation", () => {
 
     cy.get("#synthesis-information tbody tr:nth-of-type(1) td:nth-of-type(2) input").should(
       "have.value",
-      "30"
+      "30",
     );
     cy.get("#synthesis-information tbody tr:nth-of-type(1) td:nth-of-type(3) input").should(
       "have.value",
-      "g"
+      "g",
     );
     cy.get("#synthesis-information tbody tr:nth-of-type(2) td:nth-of-type(2) input").should(
       "have.value",
-      "100"
+      "100",
     );
     cy.get("#synthesis-information tbody tr:nth-of-type(2) td:nth-of-type(3) input").should(
       "have.value",
-      "g"
+      "g",
     );
 
     cy.findByText("a comment is added here.");
@@ -398,7 +398,7 @@ describe("Batch sample creation", () => {
     cy.contains("test104").click();
     cy.findByLabelText("Name").should(
       "have.value",
-      "sample with three components, copied from a sample with some of the same components"
+      "sample with three components, copied from a sample with some of the same components",
     );
     cy.contains("this is a description of baseB.");
     cy.get("#synthesis-information table").contains("component2");
@@ -408,27 +408,27 @@ describe("Batch sample creation", () => {
 
     cy.get("#synthesis-information tbody tr:nth-of-type(1) td:nth-of-type(2) input").should(
       "have.value",
-      "30"
+      "30",
     );
     cy.get("#synthesis-information tbody tr:nth-of-type(1) td:nth-of-type(3) input").should(
       "have.value",
-      "g"
+      "g",
     );
     cy.get("#synthesis-information tbody tr:nth-of-type(2) td:nth-of-type(2) input").should(
       "have.value",
-      "100"
+      "100",
     );
     cy.get("#synthesis-information tbody tr:nth-of-type(2) td:nth-of-type(3) input").should(
       "have.value",
-      "g"
+      "g",
     );
     cy.get("#synthesis-information tbody tr:nth-of-type(3) td:nth-of-type(2) input").should(
       "have.value",
-      ""
+      "",
     );
     cy.get("#synthesis-information tbody tr:nth-of-type(3) td:nth-of-type(3) input").should(
       "have.value",
-      "g"
+      "g",
     );
 
     cy.findByText("a description of the synthesis here");

webapp/cypress/e2e/editPage.cy.js

@@ -119,19 +119,19 @@ describe("Edit Page", () => {
 
     cy.get("#synthesis-information tbody tr:nth-of-type(1) td:nth-of-type(2) input").should(
       "have.value",
-      10
+      10,
     );
     cy.get("#synthesis-information tbody tr:nth-of-type(1) td:nth-of-type(3) input").should(
       "have.value",
-      "mL"
+      "mL",
     );
     cy.get("#synthesis-information tbody tr:nth-of-type(2) td:nth-of-type(2) input").should(
       "have.value",
-      0.001
+      0.001,
     );
     cy.get("#synthesis-information tbody tr:nth-of-type(2) td:nth-of-type(3) input").should(
       "have.value",
-      "pints"
+      "pints",
     );
   });
 
@@ -141,11 +141,11 @@ describe("Edit Page", () => {
     cy.get("#synthesis-information tbody > tr").should("have.length", 2);
     cy.get("#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input").should(
       "have.value",
-      0.001
+      0.001,
     );
     cy.get("#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(3) input").should(
       "have.value",
-      "pints"
+      "pints",
     );
 
     cy.get("#synthesis-information tbody > tr:nth-of-type(1) .close").click();
@@ -158,7 +158,7 @@ describe("Edit Page", () => {
     cy.get("#synthesis-information").contains("component2");
     cy.get("#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input").should(
       "have.value",
-      ""
+      "",
     ); // should be reset, not a previous value
 
     cy.get("svg.add-row-button").click();
@@ -169,36 +169,36 @@ describe("Edit Page", () => {
     cy.get("#synthesis-information").contains("Na2O");
     cy.get("#synthesis-information tbody > tr:nth-of-type(2) td:nth-of-type(2) input").should(
       "have.value",
-      ""
+      "",
     ); // should be reset, not a previous value
   });
 
   it("tries to add a non-numeric value into quantity", () => {
     cy.findByText("editable_sample").click();
     cy.get("#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input").type(
-      "100.001"
+      "100.001",
     );
     cy.get(
-      "#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input.red-border"
+      "#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input.red-border",
     ).should("not.exist");
     cy.get("#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input")
       .clear()
       .type("1");
     cy.get(
-      "#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input.red-border"
+      "#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input.red-border",
     ).should("not.exist");
     cy.get("#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input")
       .clear()
       .type("word");
     cy.get(
-      "#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input.red-border"
+      "#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input.red-border",
     ).should("exist");
 
     cy.get("#synthesis-information tbody > tr:nth-of-type(2) td:nth-of-type(2) input")
       .clear()
       .type("$");
     cy.get(
-      "#synthesis-information tbody > tr:nth-of-type(2) td:nth-of-type(2) input.red-border"
+      "#synthesis-information tbody > tr:nth-of-type(2) td:nth-of-type(2) input.red-border",
     ).should("exist");
 
     cy.get("#synthesis-information tbody > tr:nth-of-type(1) td:nth-of-type(2) input")

webapp/cypress/e2e/sampleTablePage.cy.js

@@ -135,7 +135,7 @@ describe("Sample table page", () => {
     cy.request({ url: `${API_URL}/get-item-data/12345678910`, failOnStatusCode: false }).then(
       (resp) => {
         expect(resp.status).to.be.gte(400).lt(500);
-      }
+      },
     );
   });
 
@@ -203,7 +203,7 @@ describe("Sample table page", () => {
     cy.request({ url: `${API_URL}/get-item-data/_122rwre`, failOnStatusCode: false }).then(
       (resp) => {
         expect(resp.status).to.be.gte(400).lt(500);
-      }
+      },
     );
   });
 });

webapp/public/index.html

@@ -1,4 +1,4 @@
-<!DOCTYPE html>
+<!doctype html>
 <html lang="">
   <head>
     <meta charset="utf-8" />

webapp/src/components/CollectionTable.vue

@@ -80,7 +80,7 @@ export default {
     deleteCollection(collection) {
       if (
         confirm(
-          `Are you sure you want to delete collection "${collection.collection_id}"?\nThis will not delete any items.`
+          `Are you sure you want to delete collection "${collection.collection_id}"?\nThis will not delete any items.`,
         )
       ) {
         deleteCollection(collection.collection_id, collection);

webapp/src/components/CreateSampleModal.vue

@@ -164,7 +164,7 @@ export default {
         this.name,
         startingCollection,
         extraData,
-        this.selectedItemToCopy && this.selectedItemToCopy.item_id
+        this.selectedItemToCopy && this.selectedItemToCopy.item_id,
       )
         .then(() => {
           this.$emit("update:modelValue", false); // close this modal

webapp/src/components/FancyCollectionSampleTable.vue

@@ -126,7 +126,7 @@ export default {
       const idsSelected = this.itemsSelected.map((x) => x.item_id);
       if (
         confirm(
-          `Are you sure you want to remove ${this.itemsSelected.length} selected items (${idsSelected}) from this collection?`
+          `Are you sure you want to remove ${this.itemsSelected.length} selected items (${idsSelected}) from this collection?`,
         )
       ) {
         console.log("deleting...");

webapp/src/components/FancySampleTable.vue

@@ -119,7 +119,7 @@ export default {
       const idsSelected = this.itemsSelected.map((x) => x.item_id);
       if (
         confirm(
-          `Are you sure you want to delete ${this.itemsSelected.length} selected items (${idsSelected})?`
+          `Are you sure you want to delete ${this.itemsSelected.length} selected items (${idsSelected})?`,
         )
       ) {
         console.log("deleting...");

webapp/src/components/FileSelectDropdown.vue

@@ -62,7 +62,7 @@ export default {
         updateBlockFromServer(
           this.item_id,
           this.block_id,
-          this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id]
+          this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id],
         );
       }
     },

webapp/src/components/FileSelectModal.vue

@@ -98,7 +98,7 @@ export default {
           oldest_cache_update = new Date(response_json.meta.oldest_cache_update + "Z");
           seconds_since_oldest_update = (new Date() - oldest_cache_update) / 1000;
           console.log(
-            `loadCachedTree received, oldest dir update was ${seconds_since_oldest_update} s ago`
+            `loadCachedTree received, oldest dir update was ${seconds_since_oldest_update} s ago`,
           );
         }
       }

webapp/src/components/ItemGraph.vue

@@ -130,7 +130,7 @@ export default {
           "background-color",
           element.data("special") == 1
             ? itemTypes[element.data("type")].lightColor
-            : itemTypes[element.data("type")].navbarColor
+            : itemTypes[element.data("type")].navbarColor,
         );
         element.style("border-width", element.data("special") == 1 ? 2 : 0);
         element.style("border-color", "grey");

webapp/src/components/MessageBubble.vue

@@ -72,7 +72,7 @@ export default {
           const { svg } = await mermaid.render(
             "mermaid_" + Math.floor(Math.random() * 1000000),
             el.textContent,
-            el
+            el,
           );
           el.innerHTML = svg;
         });

webapp/src/components/datablocks/ChatBlock.vue

@@ -133,7 +133,7 @@ export default {
       await updateBlockFromServer(
         this.item_id,
         this.block_id,
-        this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id]
+        this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id],
       );
       this.isLoading = false;
     },
@@ -144,7 +144,7 @@ export default {
       await updateBlockFromServer(
         this.item_id,
         this.block_id,
-        this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id]
+        this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id],
       ).catch(() => {
         this.messages.push(last_message);
       });

webapp/src/components/datablocks/CycleBlock.vue

@@ -239,7 +239,7 @@ export default {
       updateBlockFromServer(
         this.item_id,
         this.block_id,
-        this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id]
+        this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id],
       ).then(() => {
         this.bokehPlotLimitedWidth = this.derivative_mode != "dQ/dV";
         this.isReplotButtonDisplayed = false;