From ef18825f9ee581b70959726822c6a90788cf62ae Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Wed, 20 Nov 2024 14:16:21 -0800
Subject: [PATCH 1/3] Prohibit non-null assertions
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From rule doc page¹:

    It's generally better to structure program logic so that TypeScript
    understands when values may be nullable.

Also added a comment to eventually move to use
plugin:@typescript-eslint/strict which includes this rule.

¹ <https://typescript-eslint.io/rules/no-non-null-assertion/>
---
 .eslintrc.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.eslintrc.yaml b/.eslintrc.yaml
index 51926d896..66510929b 100644
--- a/.eslintrc.yaml
+++ b/.eslintrc.yaml
@@ -24,6 +24,9 @@ rules:
   eqeqeq: error
   "@typescript-eslint/no-empty-function": ["error", { "allow": ["arrowFunctions"] }]
   "@typescript-eslint/no-explicit-any": off # Allow explicit any to make incremental TypeScript adoption easier.
+  # TODO: use strict ruleset which includes no-non-null-assertion.
+  # Not possible while strictNullChecks is disabled in tsconfig.
+  "@typescript-eslint/no-non-null-assertion": "error"
   no-unused-vars: off
   "@typescript-eslint/no-unused-vars": ["error", { "argsIgnorePattern": "^_", "destructuredArrayIgnorePattern": "^_" }]
   no-use-before-define: off

From 4592e2a983ef039fba742c4c5b8c807d9446df71 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Wed, 20 Nov 2024 14:46:46 -0800
Subject: [PATCH 2/3] Prohibit type assertions

This should not be used unless there is no other way for the TypeScript
compiler to infer the type properly. In such cases, a comment with
per-line exception should be used.

I will address existing violations in subsequent commits.
---
 .eslintrc.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.eslintrc.yaml b/.eslintrc.yaml
index 66510929b..93a1c56b3 100644
--- a/.eslintrc.yaml
+++ b/.eslintrc.yaml
@@ -22,6 +22,7 @@ globals:
 rules:
   # Code quality rules
   eqeqeq: error
+  "@typescript-eslint/consistent-type-assertions": ["error", { assertionStyle: 'never' }]
   "@typescript-eslint/no-empty-function": ["error", { "allow": ["arrowFunctions"] }]
   "@typescript-eslint/no-explicit-any": off # Allow explicit any to make incremental TypeScript adoption easier.
   # TODO: use strict ruleset which includes no-non-null-assertion.

From 6215591c49fc0c7b63065276bdc530b8bba5dd6a Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Wed, 20 Nov 2024 14:47:30 -0800
Subject: [PATCH 3/3] Remove unnecessary type assertions

The types can already be inferred with existing usage.
---
 src/util/entropyCreateStateFromJsons.ts | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/util/entropyCreateStateFromJsons.ts b/src/util/entropyCreateStateFromJsons.ts
index bd042373e..0745c532a 100644
--- a/src/util/entropyCreateStateFromJsons.ts
+++ b/src/util/entropyCreateStateFromJsons.ts
@@ -103,7 +103,7 @@ export const genomeMap = (annotations: JsonAnnotations): GenomeAnnotation => {
     .map(([annotationKey, annotation]) => {
       const geneName = annotation.gene || annotationKey;
       if (!(geneName in annotationsPerGene)) annotationsPerGene[geneName] = {};
-      const gene = annotationsPerGene[geneName] as JsonAnnotations;  // TODO - why do I need to cast?
+      const gene = annotationsPerGene[geneName];
       gene[annotationKey] = annotation;
     })
 
@@ -167,7 +167,7 @@ function validColor(color:(string|undefined)) {
 function* nextColorGenerator() {
   let i=0;
   while (true) {
-    yield genotypeColors[i++] as string;
+    yield genotypeColors[i++];
     if (i===genotypeColors.length) i=0;
   }
 }