From 08e9c002a6b80354025a80dca3bf42d49e01a82b Mon Sep 17 00:00:00 2001
From: Laura Demkowicz-Duffy <dev@demkowiczduffy.co.uk>
Date: Fri, 15 Nov 2024 14:08:10 +0000
Subject: [PATCH 1/4] refactor(julia): disable julia startup file for julia
 package update

---
 src/steps/generic.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/steps/generic.rs b/src/steps/generic.rs
index ba3e1a2c..f44b499f 100644
--- a/src/steps/generic.rs
+++ b/src/steps/generic.rs
@@ -910,7 +910,7 @@ pub fn update_julia_packages(ctx: &ExecutionContext) -> Result<()> {
 
     ctx.run_type()
         .execute(julia)
-        .args(["-e", "using Pkg; Pkg.update()"])
+        .args(["--startup-file=no", "-e", "using Pkg; Pkg.update()"])
         .status_checked()
 }
 

From 75cce2201582456ab60b6985768c2b036b080cce Mon Sep 17 00:00:00 2001
From: Laura Demkowicz-Duffy <dev@demkowiczduffy.co.uk>
Date: Sat, 16 Nov 2024 13:46:56 +0000
Subject: [PATCH 2/4] feat(julia): add configuration option for julia startup
 file

---
 config.example.toml  |  8 ++++++++
 src/config.rs        | 16 ++++++++++++++++
 src/steps/generic.rs | 13 +++++++++----
 3 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/config.example.toml b/config.example.toml
index 30354f18..4c3dc991 100644
--- a/config.example.toml
+++ b/config.example.toml
@@ -270,3 +270,11 @@
 # and the update will be installed system-wide, i.e., available to all users.
 # (default: false)
 # use_sudo = false
+
+[julia]
+# If enabled, Topgrade invokes julia with the --startup-file=yes CLI option.
+#
+# This may be desirable to avoid loading outdated packages with "using" directives
+# in the startup file which would cause the update run to fail.
+# (default: true)
+# startup_file = true
diff --git a/src/config.rs b/src/config.rs
index e09c4a0b..04026e9f 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -452,6 +452,11 @@ pub struct Lensfun {
     use_sudo: Option<bool>,
 }
 
+#[derive(Deserialize, Default, Debug, Merge)]
+pub struct JuliaConfig {
+    startup_file: Option<bool>,
+}
+
 #[derive(Deserialize, Default, Debug, Merge)]
 #[serde(deny_unknown_fields)]
 /// Configuration file
@@ -518,6 +523,9 @@ pub struct ConfigFile {
 
     #[merge(strategy = crate::utils::merge_strategies::inner_merge_opt)]
     lensfun: Option<Lensfun>,
+
+    #[merge(strategy = crate::utils::merge_strategies::inner_merge_opt)]
+    julia: Option<JuliaConfig>,
 }
 
 fn config_directory() -> PathBuf {
@@ -1632,6 +1640,14 @@ impl Config {
             .and_then(|lensfun| lensfun.use_sudo)
             .unwrap_or(false)
     }
+
+    pub fn julia_use_startup_file(&self) -> bool {
+        self.config_file
+            .julia
+            .as_ref()
+            .and_then(|julia| julia.startup_file)
+            .unwrap_or(true)
+    }
 }
 
 #[cfg(test)]
diff --git a/src/steps/generic.rs b/src/steps/generic.rs
index f44b499f..c4e323dd 100644
--- a/src/steps/generic.rs
+++ b/src/steps/generic.rs
@@ -908,10 +908,15 @@ pub fn update_julia_packages(ctx: &ExecutionContext) -> Result<()> {
 
     print_separator(t!("Julia Packages"));
 
-    ctx.run_type()
-        .execute(julia)
-        .args(["--startup-file=no", "-e", "using Pkg; Pkg.update()"])
-        .status_checked()
+    let mut executor = ctx.run_type().execute(julia);
+
+    executor.arg(if ctx.config().julia_use_startup_file() {
+        "--startup-file=yes"
+    } else {
+        "--startup-file=no"
+    });
+
+    executor.args(["-e", "using Pkg; Pkg.update()"]).status_checked()
 }
 
 pub fn run_helm_repo_update(ctx: &ExecutionContext) -> Result<()> {

From 42fd87a96f7a626856c12ce266f2216976f358f0 Mon Sep 17 00:00:00 2001
From: Laura Demkowicz-Duffy <dev@demkowiczduffy.co.uk>
Date: Mon, 18 Nov 2024 12:09:12 +0000
Subject: [PATCH 3/4] fix: deny unknown fields on JuliaConfig deserialisation

Co-authored-by: SteveLauC <stevelauc@outlook.com>
---
 src/config.rs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/config.rs b/src/config.rs
index 04026e9f..eab7b336 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -453,6 +453,7 @@ pub struct Lensfun {
 }
 
 #[derive(Deserialize, Default, Debug, Merge)]
+#[serde(deny_unknown_fields)]
 pub struct JuliaConfig {
     startup_file: Option<bool>,
 }

From 25957a89781ae5e11809ee4f073d55832fe111a8 Mon Sep 17 00:00:00 2001
From: Laura Demkowicz-Duffy <dev@demkowiczduffy.co.uk>
Date: Mon, 18 Nov 2024 12:11:28 +0000
Subject: [PATCH 4/4] doc(julia): clarify startup_file option purpose

---
 config.example.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/config.example.toml b/config.example.toml
index 4c3dc991..080f53ac 100644
--- a/config.example.toml
+++ b/config.example.toml
@@ -272,9 +272,9 @@
 # use_sudo = false
 
 [julia]
-# If enabled, Topgrade invokes julia with the --startup-file=yes CLI option.
+# If disabled, Topgrade invokes julia with the --startup-file=no CLI option.
 #
 # This may be desirable to avoid loading outdated packages with "using" directives
-# in the startup file which would cause the update run to fail.
+# in the startup file, which might cause the update run to fail.
 # (default: true)
 # startup_file = true