From 9b102412af95b1f992b550524686d16eb2640941 Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Tue, 11 Nov 2025 10:37:39 -0800
Subject: [PATCH 01/25] Add extra ENV vars

---
 .../src/packagemanager/pip/runPipCommand.js   | 31 +++++++++++++++++++
 .../packagemanager/pip/runPipCommand.spec.js  | 20 ++++++++++--
 2 files changed, 48 insertions(+), 3 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 793302d..4da7ab4 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -2,6 +2,10 @@ import { ui } from "../../environment/userInteraction.js";
 import { safeSpawn } from "../../utils/safeSpawn.js";
 import { mergeSafeChainProxyEnvironmentVariables } from "../../registryProxy/registryProxy.js";
 import { getCombinedCaBundlePath } from "../../registryProxy/certBundle.js";
+import { knownPipRegistries } from "../../registryProxy/parsePackageFromUrl.js";
+import fs from "node:fs/promises";
+import os from "node:os";
+import path from "node:path";
 
 /**
  * @param {string} command
@@ -20,6 +24,33 @@ export async function runPip(command, args) {
     env.REQUESTS_CA_BUNDLE = combinedCaPath;
     env.SSL_CERT_FILE = combinedCaPath;
 
+    // To counter behavior that is sometimes seen where pip ignores REQUESTS_CA_BUNDLE/SSL_CERT_FILE,
+    // 1. Set additional env vars for pip
+    // 2. Create a pip config file that specifies the cert and trusted hosts
+  
+    env.PIP_CERT = combinedCaPath;
+
+    // Create a temporary pip config file
+    const tmpDir = os.tmpdir();
+    const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
+
+    // Trusted hosts: use knownPipRegistries from parsePackageFromUrl
+    const trustedHosts = Array.from(new Set(knownPipRegistries));
+
+    // Proxy settings
+    const httpProxy = env.HTTP_PROXY || '';
+    const httpsProxy = env.HTTPS_PROXY || '';
+
+    // Build pip config INI
+    let pipConfig = '[global]\n';
+    pipConfig += `cert = ${combinedCaPath}\n`;
+    if (httpProxy) pipConfig += `proxy = ${httpProxy}\n`;
+    if (httpsProxy) pipConfig += `proxy = ${httpsProxy}\n`;
+    if (trustedHosts.length) pipConfig += `trusted-host = ${trustedHosts.join(' ')}\n`;
+
+    await fs.writeFile(pipConfigPath, pipConfig);
+    env.PIP_CONFIG_FILE = pipConfigPath;
+
     const result = await safeSpawn(command, args, {
       stdio: "inherit",
       env,
diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
index d7a0f93..9d330da 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
@@ -43,6 +43,23 @@ describe("runPipCommand environment variable handling", () => {
     mock.reset();
   });
 
+  it("should set PIP_CERT env var and create config file", async () => {
+    const res = await runPip("pip3", ["install", "requests"]);
+    assert.strictEqual(res.status, 0);
+    assert.ok(capturedArgs, "safeSpawn should have been called");
+    // Check PIP_CERT env var
+    assert.strictEqual(
+      capturedArgs.options.env.PIP_CERT,
+      "/tmp/test-combined-ca.pem",
+      "PIP_CERT should be set to combined bundle path"
+    );
+    // Check PIP_CONFIG_FILE env var exists and is a non-empty string
+    const configPath = capturedArgs.options.env.PIP_CONFIG_FILE;
+    assert.ok(configPath, "PIP_CONFIG_FILE should be set");
+    assert.strictEqual(typeof configPath, "string", "PIP_CONFIG_FILE should be a string");
+    assert.ok(configPath.length > 0, "PIP_CONFIG_FILE should be a non-empty path");
+  });
+
   it("should set REQUESTS_CA_BUNDLE and SSL_CERT_FILE for default PyPI (no explicit index)", async () => {
     const res = await runPip("pip3", ["install", "requests"]);
     assert.strictEqual(res.status, 0);
@@ -60,9 +77,6 @@ describe("runPipCommand environment variable handling", () => {
       "/tmp/test-combined-ca.pem",
       "SSL_CERT_FILE should be set to combined bundle path"
     );
-    
-    // Args should be unchanged (no arg injection)
-    assert.deepStrictEqual(capturedArgs.args, ["install", "requests"]);
   });
 
   it("should set CA environment variables even for external/test PyPI mirror (covers non-CLI traffic)", async () => {

From 6a94271a101b523ccc9fa585272a5c65910d85bb Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Tue, 11 Nov 2025 14:28:31 -0800
Subject: [PATCH 02/25] Do not add list of trusted hosts, is security risk

---
 .../safe-chain/src/packagemanager/pip/runPipCommand.js    | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 4da7ab4..30dade4 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -25,18 +25,13 @@ export async function runPip(command, args) {
     env.SSL_CERT_FILE = combinedCaPath;
 
     // To counter behavior that is sometimes seen where pip ignores REQUESTS_CA_BUNDLE/SSL_CERT_FILE,
-    // 1. Set additional env vars for pip
-    // 2. Create a pip config file that specifies the cert and trusted hosts
-  
+    // We will set additional env vars for pip
     env.PIP_CERT = combinedCaPath;
 
     // Create a temporary pip config file
     const tmpDir = os.tmpdir();
     const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
 
-    // Trusted hosts: use knownPipRegistries from parsePackageFromUrl
-    const trustedHosts = Array.from(new Set(knownPipRegistries));
-
     // Proxy settings
     const httpProxy = env.HTTP_PROXY || '';
     const httpsProxy = env.HTTPS_PROXY || '';
@@ -46,7 +41,6 @@ export async function runPip(command, args) {
     pipConfig += `cert = ${combinedCaPath}\n`;
     if (httpProxy) pipConfig += `proxy = ${httpProxy}\n`;
     if (httpsProxy) pipConfig += `proxy = ${httpsProxy}\n`;
-    if (trustedHosts.length) pipConfig += `trusted-host = ${trustedHosts.join(' ')}\n`;
 
     await fs.writeFile(pipConfigPath, pipConfig);
     env.PIP_CONFIG_FILE = pipConfigPath;

From f9d241e4747558de313806a31e76a870338ea7a9 Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Tue, 11 Nov 2025 14:32:12 -0800
Subject: [PATCH 03/25] Fix unused import

---
 packages/safe-chain/src/packagemanager/pip/runPipCommand.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 30dade4..2e8bcbf 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -2,7 +2,6 @@ import { ui } from "../../environment/userInteraction.js";
 import { safeSpawn } from "../../utils/safeSpawn.js";
 import { mergeSafeChainProxyEnvironmentVariables } from "../../registryProxy/registryProxy.js";
 import { getCombinedCaBundlePath } from "../../registryProxy/certBundle.js";
-import { knownPipRegistries } from "../../registryProxy/parsePackageFromUrl.js";
 import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";

From 6bcd3d3b8f08dc051a3edb382e4aca8ed4d48bb3 Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Tue, 11 Nov 2025 15:22:06 -0800
Subject: [PATCH 04/25] Make sure we don't override any environments

---
 .../src/packagemanager/pip/runPipCommand.js   | 42 ++++++++++++-------
 .../packagemanager/pip/runPipCommand.spec.js  | 23 +++++++++-
 2 files changed, 48 insertions(+), 17 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 2e8bcbf..5024655 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -20,29 +20,39 @@ export async function runPip(command, args) {
     // so that any network request made by pip, including those outside explicit CLI args,
     // validates correctly under both MITM'd and tunneled HTTPS.
     const combinedCaPath = getCombinedCaBundlePath();
-    env.REQUESTS_CA_BUNDLE = combinedCaPath;
-    env.SSL_CERT_FILE = combinedCaPath;
 
+    if (!env.REQUESTS_CA_BUNDLE) {
+      env.REQUESTS_CA_BUNDLE = combinedCaPath;
+    }
+
+    if (!env.SSL_CERT_FILE) {
+      env.SSL_CERT_FILE = combinedCaPath;
+    }
+    
     // To counter behavior that is sometimes seen where pip ignores REQUESTS_CA_BUNDLE/SSL_CERT_FILE,
     // We will set additional env vars for pip
-    env.PIP_CERT = combinedCaPath;
+    if (!env.PIP_CERT) {
+      env.PIP_CERT = combinedCaPath;
+    }
 
-    // Create a temporary pip config file
-    const tmpDir = os.tmpdir();
-    const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
+    // Only create and set PIP_CONFIG_FILE if not already set
+    if (!env.PIP_CONFIG_FILE) {
+      const tmpDir = os.tmpdir();
+      const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
 
-    // Proxy settings
-    const httpProxy = env.HTTP_PROXY || '';
-    const httpsProxy = env.HTTPS_PROXY || '';
+      // Proxy settings
+      const httpProxy = env.HTTP_PROXY || '';
+      const httpsProxy = env.HTTPS_PROXY || '';
 
-    // Build pip config INI
-    let pipConfig = '[global]\n';
-    pipConfig += `cert = ${combinedCaPath}\n`;
-    if (httpProxy) pipConfig += `proxy = ${httpProxy}\n`;
-    if (httpsProxy) pipConfig += `proxy = ${httpsProxy}\n`;
+      // Build pip config INI
+      let pipConfig = '[global]\n';
+      pipConfig += `cert = ${combinedCaPath}\n`;
+      if (httpProxy) pipConfig += `proxy = ${httpProxy}\n`;
+      if (httpsProxy) pipConfig += `proxy = ${httpsProxy}\n`;
 
-    await fs.writeFile(pipConfigPath, pipConfig);
-    env.PIP_CONFIG_FILE = pipConfigPath;
+      await fs.writeFile(pipConfigPath, pipConfig);
+      env.PIP_CONFIG_FILE = pipConfigPath;
+    }
 
     const result = await safeSpawn(command, args, {
       stdio: "inherit",
diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
index 9d330da..7128bde 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
@@ -4,6 +4,7 @@ import assert from "node:assert";
 describe("runPipCommand environment variable handling", () => {
   let runPip;
   let capturedArgs = null;
+  let customEnv = null;
 
   beforeEach(async () => {
     capturedArgs = null;
@@ -18,11 +19,12 @@ describe("runPipCommand environment variable handling", () => {
       },
     });
 
-    // Mock proxy env merge
+    // Mock proxy env merge, allow custom env override
     mock.module("../../registryProxy/registryProxy.js", {
       namedExports: {
         mergeSafeChainProxyEnvironmentVariables: (env) => ({
           ...env,
+          ...(customEnv || {}),
           HTTPS_PROXY: "http://localhost:8080",
         }),
       },
@@ -43,6 +45,25 @@ describe("runPipCommand environment variable handling", () => {
     mock.reset();
   });
 
+  it("should not overwrite existing env vars for certs and config", async () => {
+    // Set custom env vars before merge
+    customEnv = {
+      REQUESTS_CA_BUNDLE: "/custom/ca-bundle.pem",
+      SSL_CERT_FILE: "/custom/ssl-cert.pem",
+      PIP_CERT: "/custom/pip-cert.pem",
+      PIP_CONFIG_FILE: "/custom/pip.conf"
+    };
+    const res = await runPip("pip3", ["install", "requests"]);
+    assert.strictEqual(res.status, 0);
+    assert.ok(capturedArgs, "safeSpawn should have been called");
+    // Should preserve custom env vars
+    assert.strictEqual(capturedArgs.options.env.REQUESTS_CA_BUNDLE, "/custom/ca-bundle.pem");
+    assert.strictEqual(capturedArgs.options.env.SSL_CERT_FILE, "/custom/ssl-cert.pem");
+    assert.strictEqual(capturedArgs.options.env.PIP_CERT, "/custom/pip-cert.pem");
+    assert.strictEqual(capturedArgs.options.env.PIP_CONFIG_FILE, "/custom/pip.conf");
+    customEnv = null;
+  });
+
   it("should set PIP_CERT env var and create config file", async () => {
     const res = await runPip("pip3", ["install", "requests"]);
     assert.strictEqual(res.status, 0);

From a3d57cbd240e9d6f785cdc42096a90c6709116bb Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Tue, 11 Nov 2025 15:24:59 -0800
Subject: [PATCH 05/25] Cleanup

---
 packages/safe-chain/src/packagemanager/pip/runPipCommand.js | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 5024655..f2eccc5 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -24,18 +24,16 @@ export async function runPip(command, args) {
     if (!env.REQUESTS_CA_BUNDLE) {
       env.REQUESTS_CA_BUNDLE = combinedCaPath;
     }
-
     if (!env.SSL_CERT_FILE) {
       env.SSL_CERT_FILE = combinedCaPath;
     }
-    
+
     // To counter behavior that is sometimes seen where pip ignores REQUESTS_CA_BUNDLE/SSL_CERT_FILE,
     // We will set additional env vars for pip
+
     if (!env.PIP_CERT) {
       env.PIP_CERT = combinedCaPath;
     }
-
-    // Only create and set PIP_CONFIG_FILE if not already set
     if (!env.PIP_CONFIG_FILE) {
       const tmpDir = os.tmpdir();
       const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);

From f2bf5869ba0072243fa35ea4d87d8520253a56ec Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Tue, 11 Nov 2025 15:49:25 -0800
Subject: [PATCH 06/25] Fix linting issue

---
 .../safe-chain/src/packagemanager/pip/runPipCommand.spec.js     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
index 7128bde..627d909 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
@@ -24,7 +24,7 @@ describe("runPipCommand environment variable handling", () => {
       namedExports: {
         mergeSafeChainProxyEnvironmentVariables: (env) => ({
           ...env,
-          ...(customEnv || {}),
+          ...customEnv,
           HTTPS_PROXY: "http://localhost:8080",
         }),
       },

From fdef9e0766aa603c09b5bfeee9acc49357b87fca Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Wed, 12 Nov 2025 13:11:02 -0800
Subject: [PATCH 07/25] Some tweaks

---
 .../safe-chain/src/packagemanager/pip/runPipCommand.js   | 9 +++------
 packages/safe-chain/src/registryProxy/certUtils.js       | 4 ++++
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index f2eccc5..440c02b 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -30,7 +30,6 @@ export async function runPip(command, args) {
 
     // To counter behavior that is sometimes seen where pip ignores REQUESTS_CA_BUNDLE/SSL_CERT_FILE,
     // We will set additional env vars for pip
-
     if (!env.PIP_CERT) {
       env.PIP_CERT = combinedCaPath;
     }
@@ -38,15 +37,13 @@ export async function runPip(command, args) {
       const tmpDir = os.tmpdir();
       const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
 
-      // Proxy settings
-      const httpProxy = env.HTTP_PROXY || '';
-      const httpsProxy = env.HTTPS_PROXY || '';
+      // Proxy settings: prefer GLOBAL_AGENT_HTTP_PROXY, then HTTPS_PROXY, then HTTP_PROXY
+      const proxy = env.GLOBAL_AGENT_HTTP_PROXY || env.HTTPS_PROXY || env.HTTP_PROXY || '';
 
       // Build pip config INI
       let pipConfig = '[global]\n';
       pipConfig += `cert = ${combinedCaPath}\n`;
-      if (httpProxy) pipConfig += `proxy = ${httpProxy}\n`;
-      if (httpsProxy) pipConfig += `proxy = ${httpsProxy}\n`;
+      if (proxy) pipConfig += `proxy = ${proxy}\n`;
 
       await fs.writeFile(pipConfigPath, pipConfig);
       env.PIP_CONFIG_FILE = pipConfigPath;
diff --git a/packages/safe-chain/src/registryProxy/certUtils.js b/packages/safe-chain/src/registryProxy/certUtils.js
index a2fb7bb..aa23d79 100644
--- a/packages/safe-chain/src/registryProxy/certUtils.js
+++ b/packages/safe-chain/src/registryProxy/certUtils.js
@@ -48,6 +48,10 @@ export function generateCertForHost(hostname) {
       digitalSignature: true,
       keyEncipherment: true,
     },
+    {
+      name: "extKeyUsage",
+      serverAuth: true,
+    },
   ]);
   cert.sign(ca.privateKey, forge.md.sha256.create());
 

From f215368c4a97531e2875044347174145c04fb84b Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Wed, 12 Nov 2025 13:30:22 -0800
Subject: [PATCH 08/25] Some small fixes

---
 packages/safe-chain/src/packagemanager/pip/runPipCommand.js | 3 +++
 packages/safe-chain/src/registryProxy/certUtils.js          | 6 ++++++
 2 files changed, 9 insertions(+)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 440c02b..12a3748 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -24,6 +24,7 @@ export async function runPip(command, args) {
     if (!env.REQUESTS_CA_BUNDLE) {
       env.REQUESTS_CA_BUNDLE = combinedCaPath;
     }
+    
     if (!env.SSL_CERT_FILE) {
       env.SSL_CERT_FILE = combinedCaPath;
     }
@@ -33,6 +34,8 @@ export async function runPip(command, args) {
     if (!env.PIP_CERT) {
       env.PIP_CERT = combinedCaPath;
     }
+
+    // PIP_CONFIG file is created to ensure proxy and cert settings are applied even if env vars are ignored for certificates (e.g. Python 3.11 and up).
     if (!env.PIP_CONFIG_FILE) {
       const tmpDir = os.tmpdir();
       const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
diff --git a/packages/safe-chain/src/registryProxy/certUtils.js b/packages/safe-chain/src/registryProxy/certUtils.js
index aa23d79..6b326c8 100644
--- a/packages/safe-chain/src/registryProxy/certUtils.js
+++ b/packages/safe-chain/src/registryProxy/certUtils.js
@@ -49,6 +49,12 @@ export function generateCertForHost(hostname) {
       keyEncipherment: true,
     },
     {
+      /*
+        extKeyUsage serverAuth is required for TLS server authentication.
+        This is especially important for Python venv environments, which use their own
+        certificate validation logic and will reject certificates lacking the serverAuth EKU.
+        Adding serverAuth does not impact other usages
+      */
       name: "extKeyUsage",
       serverAuth: true,
     },

From 285906ea9d610d9960928d1e41a10a109f531f27 Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Wed, 12 Nov 2025 13:39:58 -0800
Subject: [PATCH 09/25] Update doc

---
 packages/safe-chain/src/packagemanager/pip/runPipCommand.js | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 12a3748..0f5e697 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -29,13 +29,12 @@ export async function runPip(command, args) {
       env.SSL_CERT_FILE = combinedCaPath;
     }
 
-    // To counter behavior that is sometimes seen where pip ignores REQUESTS_CA_BUNDLE/SSL_CERT_FILE,
-    // We will set additional env vars for pip
+    // https://pip.pypa.io/en/stable/topics/https-certificates/ explains that the --cert option (which we're providing via both INI and PIP_CERT)
+    // is necessary for pip to use custom certs for later versions.
     if (!env.PIP_CERT) {
       env.PIP_CERT = combinedCaPath;
     }
 
-    // PIP_CONFIG file is created to ensure proxy and cert settings are applied even if env vars are ignored for certificates (e.g. Python 3.11 and up).
     if (!env.PIP_CONFIG_FILE) {
       const tmpDir = os.tmpdir();
       const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);

From fbd11c6d443ea93ab90cd011a34f8078e3cffd31 Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Wed, 12 Nov 2025 14:01:06 -0800
Subject: [PATCH 10/25] Update

---
 packages/safe-chain/src/packagemanager/pip/runPipCommand.js | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 0f5e697..f3e7aa9 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -24,13 +24,14 @@ export async function runPip(command, args) {
     if (!env.REQUESTS_CA_BUNDLE) {
       env.REQUESTS_CA_BUNDLE = combinedCaPath;
     }
+
+    // https://pip.pypa.io/en/stable/topics/https-certificates/ explains that the --cert option (which we're providing via both INI and PIP_CERT)
+    // Testing has shown that REQUESTS_CA_BUNDLE alone is not sufficient; PIP_CERT, SSL_CERT_FILE, or pip config cert is also needed in some cases.
     
     if (!env.SSL_CERT_FILE) {
       env.SSL_CERT_FILE = combinedCaPath;
     }
 
-    // https://pip.pypa.io/en/stable/topics/https-certificates/ explains that the --cert option (which we're providing via both INI and PIP_CERT)
-    // is necessary for pip to use custom certs for later versions.
     if (!env.PIP_CERT) {
       env.PIP_CERT = combinedCaPath;
     }

From 61c9f1a1efe6a173f2872a5aa70770918082b572 Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Thu, 13 Nov 2025 11:14:45 -0800
Subject: [PATCH 11/25] Merge config file if it exists

---
 package-lock.json                             |  10 ++
 packages/safe-chain-bun/package.json          |   2 +-
 packages/safe-chain/package.json              |   1 +
 .../src/packagemanager/pip/runPipCommand.js   |  59 ++++++--
 .../packagemanager/pip/runPipCommand.spec.js  | 130 ++++++++++++++++++
 test/e2e/DockerTestContainer.js               |   2 +-
 6 files changed, 193 insertions(+), 11 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index a9c32df..068e544 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1090,6 +1090,15 @@
         "node": ">=0.8.19"
       }
     },
+    "node_modules/ini": {
+      "version": "6.0.0",
+      "resolved": "https://registry.npmjs.org/ini/-/ini-6.0.0.tgz",
+      "integrity": "sha512-IBTdIkzZNOpqm7q3dRqJvMaldXjDHWkEDfrwGEQTs5eaQMWV+djAhR+wahyNNMAa+qpbDUhBMVt4ZKNwpPm7xQ==",
+      "license": "ISC",
+      "engines": {
+        "node": "^20.17.0 || >=22.9.0"
+      }
+    },
     "node_modules/ip-address": {
       "version": "9.0.5",
       "resolved": "https://registry.npmjs.org/ip-address/-/ip-address-9.0.5.tgz",
@@ -2083,6 +2092,7 @@
         "certifi": "^14.5.15",
         "chalk": "5.4.1",
         "https-proxy-agent": "7.0.6",
+        "ini": "^6.0.0",
         "make-fetch-happen": "14.0.3",
         "node-forge": "1.3.1",
         "npm-registry-fetch": "18.0.2",
diff --git a/packages/safe-chain-bun/package.json b/packages/safe-chain-bun/package.json
index b5a9e3e..ca154b8 100644
--- a/packages/safe-chain-bun/package.json
+++ b/packages/safe-chain-bun/package.json
@@ -27,4 +27,4 @@
   "peerDependencies": {
     "bun": ">=1.2.21"
   }
-}
\ No newline at end of file
+}
diff --git a/packages/safe-chain/package.json b/packages/safe-chain/package.json
index f21a372..5f8da60 100644
--- a/packages/safe-chain/package.json
+++ b/packages/safe-chain/package.json
@@ -38,6 +38,7 @@
     "certifi": "^14.5.15",
     "chalk": "5.4.1",
     "https-proxy-agent": "7.0.6",
+    "ini": "^6.0.0",
     "make-fetch-happen": "14.0.3",
     "node-forge": "1.3.1",
     "npm-registry-fetch": "18.0.2",
diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index f3e7aa9..96cdcf8 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -3,8 +3,10 @@ import { safeSpawn } from "../../utils/safeSpawn.js";
 import { mergeSafeChainProxyEnvironmentVariables } from "../../registryProxy/registryProxy.js";
 import { getCombinedCaBundlePath } from "../../registryProxy/certBundle.js";
 import fs from "node:fs/promises";
+import fsSync from "node:fs";
 import os from "node:os";
 import path from "node:path";
+import ini from "ini";
 
 /**
  * @param {string} command
@@ -36,20 +38,59 @@ export async function runPip(command, args) {
       env.PIP_CERT = combinedCaPath;
     }
 
-    if (!env.PIP_CONFIG_FILE) {
-      const tmpDir = os.tmpdir();
-      const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
+    // Proxy settings: prefer GLOBAL_AGENT_HTTP_PROXY, then HTTPS_PROXY, then HTTP_PROXY
+    const proxy = env.GLOBAL_AGENT_HTTP_PROXY || env.HTTPS_PROXY || env.HTTP_PROXY || '';
 
-      // Proxy settings: prefer GLOBAL_AGENT_HTTP_PROXY, then HTTPS_PROXY, then HTTP_PROXY
-      const proxy = env.GLOBAL_AGENT_HTTP_PROXY || env.HTTPS_PROXY || env.HTTP_PROXY || '';
+    const tmpDir = os.tmpdir();
+    const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
+
+    if (!env.PIP_CONFIG_FILE) {
 
       // Build pip config INI
-      let pipConfig = '[global]\n';
-      pipConfig += `cert = ${combinedCaPath}\n`;
-      if (proxy) pipConfig += `proxy = ${proxy}\n`;
-
+      /** @type {{ global: { cert: string, proxy?: string } }} */
+      const configObj = { global: { cert: combinedCaPath } };
+      if (proxy) {
+        configObj.global.proxy = proxy;
+      }
+      const pipConfig = ini.stringify(configObj);
       await fs.writeFile(pipConfigPath, pipConfig);
       env.PIP_CONFIG_FILE = pipConfigPath;
+    } else if (fsSync.existsSync(env.PIP_CONFIG_FILE)) {
+      // Existing pip config file present and exists on disk.
+      // Lets merge in our cert and proxy settings if not already present
+      const userConfig = env.PIP_CONFIG_FILE;
+      
+      ui.writeVerbose("Safe-chain: Merging user provided PIP_CONFIG_FILE with safe-chain certificate and proxy settings.");
+
+      // Read the existing config without modifying it
+      let content = await fs.readFile(userConfig, "utf-8");
+      const parsed = ini.parse(content);
+
+      // Ensure [global] section exists
+      parsed.global = parsed.global || {};
+
+      // Adding CERT and PROXY
+      // If either is already set, there's no neeed to throw an error; mitm might fail and throw later if the proxy config is invalid
+
+      // Cert
+      if (typeof parsed.global.cert === "undefined") {
+        ui.writeVerbose("Safe-chain: Adding cert to existing PIP_CONFIG_FILE.");
+        parsed.global.cert = combinedCaPath;
+      }
+
+      // Proxy
+      if (typeof parsed.global.proxy === "undefined") {
+        if (proxy) {
+          ui.writeVerbose("Safe-chain: Adding proxy to existing PIP_CONFIG_FILE.");
+          parsed.global.proxy = proxy;
+        }
+      }
+
+      const updated = ini.stringify(parsed);
+
+      // Save to a new temp file to avoid overwriting user's original config
+      await fs.writeFile(pipConfigPath, updated, "utf-8");
+      env.PIP_CONFIG_FILE = pipConfigPath;
     }
 
     const result = await safeSpawn(command, args, {
diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
index 627d909..b3d7b2e 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
@@ -1,5 +1,9 @@
 import { describe, it, beforeEach, afterEach, mock } from "node:test";
 import assert from "node:assert";
+import fs from "node:fs/promises";
+import os from "node:os";
+import path from "node:path";
+import ini from "ini";
 
 describe("runPipCommand environment variable handling", () => {
   let runPip;
@@ -145,4 +149,130 @@ describe("runPipCommand environment variable handling", () => {
       "HTTPS_PROXY should be set by proxy merge"
     );
   });
+
+  it("should create a new temp config when existing config exists (original file untouched)", async () => {
+    const tmpDir = os.tmpdir();
+    const userCfgPath = path.join(tmpDir, `safe-chain-test-pip-${Date.now()}.ini`);
+    const initial = "[global]\nindex-url = https://example.com/simple\n";
+    await fs.writeFile(userCfgPath, initial, "utf-8");
+
+    customEnv = { PIP_CONFIG_FILE: userCfgPath };
+    const res = await runPip("pip3", ["install", "requests"]);
+    assert.strictEqual(res.status, 0);
+    const newCfgPath = capturedArgs.options.env.PIP_CONFIG_FILE;
+    assert.notStrictEqual(newCfgPath, userCfgPath, "should point to a new temp config file");
+
+    // Original file unchanged
+    const originalContent = await fs.readFile(userCfgPath, "utf-8");
+    const originalParsed = ini.parse(originalContent);
+    assert.strictEqual(originalParsed.global.cert, undefined, "original file should not gain cert");
+
+    // New file has merged settings
+    const newContent = await fs.readFile(newCfgPath, "utf-8");
+    const newParsed = ini.parse(newContent);
+    assert.strictEqual(newParsed.global.cert, "/tmp/test-combined-ca.pem", "new config should include cert");
+    assert.strictEqual(newParsed.global.proxy, "http://localhost:8080", "new config should include proxy from env");
+    assert.strictEqual(newParsed.global["index-url"], "https://example.com/simple", "index-url should be preserved");
+    customEnv = null;
+  });
+
+  it("should create new config with proxy set from env (ini-validated)", async () => {
+    // No PIP_CONFIG_FILE in env => creation path
+    const res = await runPip("pip3", ["install", "requests"]);
+    assert.strictEqual(res.status, 0);
+
+    const configPath = capturedArgs.options.env.PIP_CONFIG_FILE;
+    const content = await fs.readFile(configPath, "utf-8");
+    const parsed = ini.parse(content);
+    assert.ok(parsed.global, "[global] should exist after creation");
+    assert.strictEqual(
+      parsed.global.proxy,
+      "http://localhost:8080",
+      "proxy should be set from merged env"
+    );
+    assert.strictEqual(
+      parsed.global.cert,
+      "/tmp/test-combined-ca.pem",
+      "cert should be set during creation"
+    );
+  });
+
+  it("should create new temp config adding cert but preserving existing proxy (original file unchanged)", async () => {
+    const tmpDir = os.tmpdir();
+    const userCfgPath = path.join(tmpDir, `safe-chain-test-pip-${Date.now()}.ini`);
+    const initial = "[global]\nproxy = http://original:9999\n";
+    await fs.writeFile(userCfgPath, initial, "utf-8");
+
+    customEnv = { PIP_CONFIG_FILE: userCfgPath };
+    const res = await runPip("pip3", ["install", "requests"]);
+    assert.strictEqual(res.status, 0);
+    const newCfgPath = capturedArgs.options.env.PIP_CONFIG_FILE;
+    assert.notStrictEqual(newCfgPath, userCfgPath, "should use a new temp config file");
+
+    // Original file unchanged
+    const originalParsed = ini.parse(await fs.readFile(userCfgPath, "utf-8"));
+    assert.strictEqual(originalParsed.global.cert, undefined, "original file should not gain cert");
+    assert.strictEqual(originalParsed.global.proxy, "http://original:9999", "original proxy remains");
+
+    // New file merged: cert added (was missing), proxy preserved (was present)
+    const newParsed = ini.parse(await fs.readFile(newCfgPath, "utf-8"));
+    assert.strictEqual(newParsed.global.cert, "/tmp/test-combined-ca.pem", "new cert injected");
+    assert.strictEqual(newParsed.global.proxy, "http://original:9999", "existing proxy should be preserved in new file");
+    customEnv = null;
+  });
+
+  it("should create new temp config preserving existing cert and proxy while leaving original file unchanged", async () => {
+    const tmpDir = os.tmpdir();
+    const cfgPath = path.join(tmpDir, `safe-chain-test-pip-${Date.now()}.ini`);
+    const initialIni = [
+      "[global]",
+      "cert = /path/to/existing.pem",
+      "proxy = http://original:9999",
+      ""
+    ].join("\n");
+    await fs.writeFile(cfgPath, initialIni, "utf-8");
+
+    customEnv = { PIP_CONFIG_FILE: cfgPath };
+    const res = await runPip("pip3", ["install", "requests"]);
+    assert.strictEqual(res.status, 0, "execution should succeed");
+    const newCfgPath = capturedArgs.options.env.PIP_CONFIG_FILE;
+    assert.notStrictEqual(newCfgPath, cfgPath, "should use a newly generated temp config file");
+
+    // Original file stays untouched
+    const originalContent = await fs.readFile(cfgPath, "utf-8");
+    const originalParsed = ini.parse(originalContent);
+    assert.strictEqual(originalParsed.global.cert, "/path/to/existing.pem", "original cert preserved");
+    assert.strictEqual(originalParsed.global.proxy, "http://original:9999", "original proxy preserved");
+
+    // New temp config preserves existing values (no override when already set)
+    const newContent = await fs.readFile(newCfgPath, "utf-8");
+    const newParsed = ini.parse(newContent);
+    assert.strictEqual(newParsed.global.cert, "/path/to/existing.pem", "existing cert preserved in new temp config");
+    assert.strictEqual(newParsed.global.proxy, "http://original:9999", "existing proxy preserved in new temp config");
+    customEnv = null;
+  });
+
+  it("should create new temp config preserving existing cert and adding missing proxy", async () => {
+    const tmpDir = os.tmpdir();
+    const userCfgPath = path.join(tmpDir, `safe-chain-test-pip-${Date.now()}.ini`);
+    const initial = "[global]\ncert = /path/to/existing.pem\n";
+    await fs.writeFile(userCfgPath, initial, "utf-8");
+
+    customEnv = { PIP_CONFIG_FILE: userCfgPath };
+    const res = await runPip("pip3", ["install", "requests"]);
+    assert.strictEqual(res.status, 0);
+    const newCfgPath = capturedArgs.options.env.PIP_CONFIG_FILE;
+    assert.notStrictEqual(newCfgPath, userCfgPath, "should produce a new temp config file");
+
+    // Original remains unchanged
+    const originalParsed = ini.parse(await fs.readFile(userCfgPath, "utf-8"));
+    assert.strictEqual(originalParsed.global.cert, "/path/to/existing.pem", "original cert unchanged");
+    assert.strictEqual(originalParsed.global.proxy, undefined, "original proxy still missing");
+
+    // New file preserves existing cert and adds proxy (since it was missing)
+    const newParsed = ini.parse(await fs.readFile(newCfgPath, "utf-8"));
+    assert.strictEqual(newParsed.global.cert, "/path/to/existing.pem", "existing cert preserved (not overridden)");
+    assert.strictEqual(newParsed.global.proxy, "http://localhost:8080", "proxy added from env");
+    customEnv = null;
+  });
 });
diff --git a/test/e2e/DockerTestContainer.js b/test/e2e/DockerTestContainer.js
index ec1af3c..289b451 100644
--- a/test/e2e/DockerTestContainer.js
+++ b/test/e2e/DockerTestContainer.js
@@ -33,7 +33,7 @@ export class DockerTestContainer {
       ].join(" ");
 
       execSync(
-        `docker build -t ${imageName} -f ${dockerFile} ${contextPath} ${buildArgs}`,
+        `docker build --no-cache -t ${imageName} -f ${dockerFile} ${contextPath} ${buildArgs}`,
         {
           stdio: "ignore",
         }

From a0e24b172275ef450e14dd1625977645ee070465 Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Thu, 13 Nov 2025 11:21:53 -0800
Subject: [PATCH 12/25] Update comments

---
 packages/safe-chain/src/packagemanager/pip/runPipCommand.js | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 96cdcf8..4198686 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -70,7 +70,9 @@ export async function runPip(command, args) {
       parsed.global = parsed.global || {};
 
       // Adding CERT and PROXY
-      // If either is already set, there's no neeed to throw an error; mitm might fail and throw later if the proxy config is invalid
+      // If either is already set, there's no neeed to throw an error
+      // MITM might fail and throw later if the proxy config is invalid
+      // This ensures that no malware will be installed by safe-chain
 
       // Cert
       if (typeof parsed.global.cert === "undefined") {

From 4ee18973dee7dc53ae8f764f3fc21056af002caa Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Thu, 13 Nov 2025 12:48:04 -0800
Subject: [PATCH 13/25] Fix unit test

---
 .../safe-chain/src/packagemanager/pip/runPipCommand.spec.js    | 3 +++
 test/e2e/DockerTestContainer.js                                | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
index b3d7b2e..ecd8e0f 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
@@ -29,7 +29,10 @@ describe("runPipCommand environment variable handling", () => {
         mergeSafeChainProxyEnvironmentVariables: (env) => ({
           ...env,
           ...customEnv,
+          // Force deterministic proxy for tests regardless of ambient env
+          GLOBAL_AGENT_HTTP_PROXY: "http://localhost:8080",
           HTTPS_PROXY: "http://localhost:8080",
+          HTTP_PROXY: "",
         }),
       },
     });
diff --git a/test/e2e/DockerTestContainer.js b/test/e2e/DockerTestContainer.js
index 289b451..ec1af3c 100644
--- a/test/e2e/DockerTestContainer.js
+++ b/test/e2e/DockerTestContainer.js
@@ -33,7 +33,7 @@ export class DockerTestContainer {
       ].join(" ");
 
       execSync(
-        `docker build --no-cache -t ${imageName} -f ${dockerFile} ${contextPath} ${buildArgs}`,
+        `docker build -t ${imageName} -f ${dockerFile} ${contextPath} ${buildArgs}`,
         {
           stdio: "ignore",
         }

From f4ff18304aa50a1c201c41fe76b387400388670d Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Thu, 13 Nov 2025 13:20:11 -0800
Subject: [PATCH 14/25] Fix imports

---
 package-lock.json                | 8 ++++++++
 packages/safe-chain/package.json | 1 +
 2 files changed, 9 insertions(+)

diff --git a/package-lock.json b/package-lock.json
index 068e544..94b6921 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -411,6 +411,13 @@
         "node": ">=14"
       }
     },
+    "node_modules/@types/ini": {
+      "version": "4.1.1",
+      "resolved": "https://registry.npmjs.org/@types/ini/-/ini-4.1.1.tgz",
+      "integrity": "sha512-MIyNUZipBTbyUNnhvuXJTY7B6qNI78meck9Jbv3wk0OgNwRyOOVEKDutAkOs1snB/tx0FafyR6/SN4Ps0hZPeg==",
+      "dev": true,
+      "license": "MIT"
+    },
     "node_modules/@types/make-fetch-happen": {
       "version": "10.0.4",
       "resolved": "https://registry.npmjs.org/@types/make-fetch-happen/-/make-fetch-happen-10.0.4.tgz",
@@ -2114,6 +2121,7 @@
         "safe-chain": "bin/safe-chain.js"
       },
       "devDependencies": {
+        "@types/ini": "^4.1.1",
         "@types/make-fetch-happen": "^10.0.4",
         "@types/node": "^18.19.130",
         "@types/node-forge": "^1.3.14",
diff --git a/packages/safe-chain/package.json b/packages/safe-chain/package.json
index 5f8da60..6394bc6 100644
--- a/packages/safe-chain/package.json
+++ b/packages/safe-chain/package.json
@@ -46,6 +46,7 @@
     "semver": "7.7.2"
   },
   "devDependencies": {
+  "@types/ini": "^4.1.1",
     "@types/make-fetch-happen": "^10.0.4",
     "@types/node": "^18.19.130",
     "@types/npm-registry-fetch": "^8.0.9",

From 474d91d29ae1bb87741875274edfaa63d3501066 Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Thu, 13 Nov 2025 13:32:49 -0800
Subject: [PATCH 15/25] Indentation

---
 packages/safe-chain/package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packages/safe-chain/package.json b/packages/safe-chain/package.json
index 6394bc6..186d810 100644
--- a/packages/safe-chain/package.json
+++ b/packages/safe-chain/package.json
@@ -46,7 +46,7 @@
     "semver": "7.7.2"
   },
   "devDependencies": {
-  "@types/ini": "^4.1.1",
+    "@types/ini": "^4.1.1",
     "@types/make-fetch-happen": "^10.0.4",
     "@types/node": "^18.19.130",
     "@types/npm-registry-fetch": "^8.0.9",

From 0b3cc1c17543ebb864df0f0d72a8751dfd4756ff Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Thu, 13 Nov 2025 15:50:14 -0800
Subject: [PATCH 16/25] Some more cleanup

---
 .../src/packagemanager/pip/runPipCommand.js   | 38 ++++++++++---------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 4198686..9d68c81 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -23,20 +23,8 @@ export async function runPip(command, args) {
     // validates correctly under both MITM'd and tunneled HTTPS.
     const combinedCaPath = getCombinedCaBundlePath();
 
-    if (!env.REQUESTS_CA_BUNDLE) {
-      env.REQUESTS_CA_BUNDLE = combinedCaPath;
-    }
-
-    // https://pip.pypa.io/en/stable/topics/https-certificates/ explains that the --cert option (which we're providing via both INI and PIP_CERT)
-    // Testing has shown that REQUESTS_CA_BUNDLE alone is not sufficient; PIP_CERT, SSL_CERT_FILE, or pip config cert is also needed in some cases.
-    
-    if (!env.SSL_CERT_FILE) {
-      env.SSL_CERT_FILE = combinedCaPath;
-    }
-
-    if (!env.PIP_CERT) {
-      env.PIP_CERT = combinedCaPath;
-    }
+    // https://pip.pypa.io/en/stable/topics/https-certificates/ explains that the --cert option (which we're providing via INI file)
+    // will tell pip to use the provided CA bundle for HTTPS verification.
 
     // Proxy settings: prefer GLOBAL_AGENT_HTTP_PROXY, then HTTPS_PROXY, then HTTP_PROXY
     const proxy = env.GLOBAL_AGENT_HTTP_PROXY || env.HTTPS_PROXY || env.HTTP_PROXY || '';
@@ -45,7 +33,6 @@ export async function runPip(command, args) {
     const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
 
     if (!env.PIP_CONFIG_FILE) {
-
       // Build pip config INI
       /** @type {{ global: { cert: string, proxy?: string } }} */
       const configObj = { global: { cert: combinedCaPath } };
@@ -55,6 +42,7 @@ export async function runPip(command, args) {
       const pipConfig = ini.stringify(configObj);
       await fs.writeFile(pipConfigPath, pipConfig);
       env.PIP_CONFIG_FILE = pipConfigPath;
+
     } else if (fsSync.existsSync(env.PIP_CONFIG_FILE)) {
       // Existing pip config file present and exists on disk.
       // Lets merge in our cert and proxy settings if not already present
@@ -72,18 +60,17 @@ export async function runPip(command, args) {
       // Adding CERT and PROXY
       // If either is already set, there's no neeed to throw an error
       // MITM might fail and throw later if the proxy config is invalid
-      // This ensures that no malware will be installed by safe-chain
 
       // Cert
       if (typeof parsed.global.cert === "undefined") {
-        ui.writeVerbose("Safe-chain: Adding cert to existing PIP_CONFIG_FILE.");
+        ui.writeVerbose("Safe-chain: Adding cert to temporary PIP_CONFIG_FILE.");
         parsed.global.cert = combinedCaPath;
       }
 
       // Proxy
       if (typeof parsed.global.proxy === "undefined") {
         if (proxy) {
-          ui.writeVerbose("Safe-chain: Adding proxy to existing PIP_CONFIG_FILE.");
+          ui.writeVerbose("Safe-chain: Adding proxy to temporary PIP_CONFIG_FILE.");
           parsed.global.proxy = proxy;
         }
       }
@@ -93,6 +80,21 @@ export async function runPip(command, args) {
       // Save to a new temp file to avoid overwriting user's original config
       await fs.writeFile(pipConfigPath, updated, "utf-8");
       env.PIP_CONFIG_FILE = pipConfigPath;
+
+    } else {
+      // The user provided PIP_CONFIG_FILE does not exist on disk
+      // PIP will handle this as an error and inform the user
+    }
+
+    // REQUESTS_CA_BUNDLE, SSL_CERT_FILE and PIP_CERT as extra safety nets.
+    if (!env.REQUESTS_CA_BUNDLE) {
+      env.REQUESTS_CA_BUNDLE = combinedCaPath;
+    }
+    if (!env.SSL_CERT_FILE) {
+      env.SSL_CERT_FILE = combinedCaPath;
+    }
+    if (!env.PIP_CERT) {
+      env.PIP_CERT = combinedCaPath;
     }
 
     const result = await safeSpawn(command, args, {

From 7039961d4ccd50054c55876cd8f7812838e485db Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Thu, 13 Nov 2025 15:50:37 -0800
Subject: [PATCH 17/25] Bugfix

---
 packages/safe-chain/src/packagemanager/pip/runPipCommand.js | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 9d68c81..309ee47 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -23,7 +23,7 @@ export async function runPip(command, args) {
     // validates correctly under both MITM'd and tunneled HTTPS.
     const combinedCaPath = getCombinedCaBundlePath();
 
-    // https://pip.pypa.io/en/stable/topics/https-certificates/ explains that the --cert option (which we're providing via INI file)
+    // https://pip.pypa.io/en/stable/topics/https-certificates/ explains that the 'cert' param (which we're providing via INI file)
     // will tell pip to use the provided CA bundle for HTTPS verification.
 
     // Proxy settings: prefer GLOBAL_AGENT_HTTP_PROXY, then HTTPS_PROXY, then HTTP_PROXY
@@ -46,9 +46,8 @@ export async function runPip(command, args) {
     } else if (fsSync.existsSync(env.PIP_CONFIG_FILE)) {
       // Existing pip config file present and exists on disk.
       // Lets merge in our cert and proxy settings if not already present
-      const userConfig = env.PIP_CONFIG_FILE;
-      
       ui.writeVerbose("Safe-chain: Merging user provided PIP_CONFIG_FILE with safe-chain certificate and proxy settings.");
+      const userConfig = env.PIP_CONFIG_FILE;
 
       // Read the existing config without modifying it
       let content = await fs.readFile(userConfig, "utf-8");

From c6bcd6f646e331cdb7282f8b73dc4ebea3518c93 Mon Sep 17 00:00:00 2001
From: Sander Declerck <sander@sdsoftware.be>
Date: Fri, 14 Nov 2025 14:12:44 +0100
Subject: [PATCH 18/25] Add feature flag in setup for python support.

---
 packages/safe-chain/bin/safe-chain.js         |  19 +++-
 .../safe-chain/src/config/cliArguments.js     |  32 +++++-
 .../src/shell-integration/helpers.js          |  24 ++--
 .../src/shell-integration/setup-ci.js         |  26 +++--
 .../safe-chain/src/shell-integration/setup.js |   7 +-
 .../include-python/init-fish.fish             |  88 ++++++++++++++
 .../include-python/init-posix.sh              |  80 +++++++++++++
 .../include-python/init-pwsh.ps1              | 107 ++++++++++++++++++
 .../startup-scripts/init-fish.fish            |  18 ---
 .../startup-scripts/init-posix.sh             |  18 ---
 .../startup-scripts/init-pwsh.ps1             |  19 ----
 test/e2e/pip-ci.e2e.spec.js                   |  64 ++++++++---
 test/e2e/pip.e2e.spec.js                      |  11 +-
 13 files changed, 413 insertions(+), 100 deletions(-)
 create mode 100644 packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-fish.fish
 create mode 100644 packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-posix.sh
 create mode 100644 packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-pwsh.ps1

diff --git a/packages/safe-chain/bin/safe-chain.js b/packages/safe-chain/bin/safe-chain.js
index 30f4086..94e4e1f 100755
--- a/packages/safe-chain/bin/safe-chain.js
+++ b/packages/safe-chain/bin/safe-chain.js
@@ -6,6 +6,7 @@ import { ui } from "../src/environment/userInteraction.js";
 import { setup } from "../src/shell-integration/setup.js";
 import { teardown } from "../src/shell-integration/teardown.js";
 import { setupCi } from "../src/shell-integration/setup-ci.js";
+import { initializeCliArguments } from "../src/config/cliArguments.js";
 
 if (process.argv.length < 3) {
   ui.writeError("No command provided. Please provide a command to execute.");
@@ -14,6 +15,8 @@ if (process.argv.length < 3) {
   process.exit(1);
 }
 
+initializeCliArguments(process.argv);
+
 const command = process.argv[2];
 
 if (command === "help" || command === "--help" || command === "-h") {
@@ -56,6 +59,11 @@ function writeHelp() {
       "safe-chain setup"
     )}: This will setup your shell to wrap safe-chain around npm, npx, yarn, pnpm, pnpx, bun, bunx, pip and pip3.`
   );
+  ui.writeInformation(
+    `    ${chalk.yellow(
+      "--include-python"
+    )}: Experimental: include Python package managers (pip, pip3) in the setup.`
+  );
   ui.writeInformation(
     `- ${chalk.cyan(
       "safe-chain teardown"
@@ -67,9 +75,14 @@ function writeHelp() {
     )}: This will setup safe-chain for CI environments by creating shims and modifying the PATH.`
   );
   ui.writeInformation(
-    `- ${chalk.cyan(
-      "safe-chain --version"
-    )} (or ${chalk.cyan("-v")}): Display the current version of safe-chain.`
+    `    ${chalk.yellow(
+      "--include-python"
+    )}: Experimental: include Python package managers (pip, pip3) in the setup.`
+  );
+  ui.writeInformation(
+    `- ${chalk.cyan("safe-chain --version")} (or ${chalk.cyan(
+      "-v"
+    )}): Display the current version of safe-chain.`
   );
   ui.emptyLine();
 }
diff --git a/packages/safe-chain/src/config/cliArguments.js b/packages/safe-chain/src/config/cliArguments.js
index 04645d8..ba16042 100644
--- a/packages/safe-chain/src/config/cliArguments.js
+++ b/packages/safe-chain/src/config/cliArguments.js
@@ -1,8 +1,9 @@
 /**
- * @type {{loggingLevel: string | undefined}}
+ * @type {{loggingLevel: string | undefined, includePython: boolean}}
  */
 const state = {
   loggingLevel: undefined,
+  includePython: false,
 };
 
 const SAFE_CHAIN_ARG_PREFIX = "--safe-chain-";
@@ -27,6 +28,7 @@ export function initializeCliArguments(args) {
   }
 
   setLoggingLevel(safeChainArgs);
+  setIncludePython(args);
 
   return remainingArgs;
 }
@@ -64,3 +66,31 @@ function setLoggingLevel(args) {
 export function getLoggingLevel() {
   return state.loggingLevel;
 }
+
+/**
+ * @param {string[]} args
+ */
+function setIncludePython(args) {
+  // This flag doesn't have the --safe-chain- prefix because
+  // it is only used for the safe-chain command itself and
+  // not when wrapped around package manager commands.
+  state.includePython = hasFlagArg(args, "--include-python");
+}
+
+export function includePython() {
+  return state.includePython;
+}
+
+/**
+ * @param {string[]} args
+ * @param {string} flagName
+ * @returns {boolean}
+ */
+function hasFlagArg(args, flagName) {
+  for (const arg of args) {
+    if (arg.toLowerCase() === flagName.toLowerCase()) {
+      return true;
+    }
+  }
+  return false;
+}
diff --git a/packages/safe-chain/src/shell-integration/helpers.js b/packages/safe-chain/src/shell-integration/helpers.js
index c405c54..da8e98b 100644
--- a/packages/safe-chain/src/shell-integration/helpers.js
+++ b/packages/safe-chain/src/shell-integration/helpers.js
@@ -2,28 +2,30 @@ import { spawnSync } from "child_process";
 import * as os from "os";
 import fs from "fs";
 import path from "path";
+import { ECOSYSTEM_JS, ECOSYSTEM_PY } from "../config/settings.js";
 
 /**
  * @typedef {Object} AikidoTool
  * @property {string} tool
  * @property {string} aikidoCommand
+ * @property {string} ecoSystem
  */
 
 /**
  * @type {AikidoTool[]}
  */
 export const knownAikidoTools = [
-  { tool: "npm", aikidoCommand: "aikido-npm" },
-  { tool: "npx", aikidoCommand: "aikido-npx" },
-  { tool: "yarn", aikidoCommand: "aikido-yarn" },
-  { tool: "pnpm", aikidoCommand: "aikido-pnpm" },
-  { tool: "pnpx", aikidoCommand: "aikido-pnpx" },
-  { tool: "bun", aikidoCommand: "aikido-bun" },
-  { tool: "bunx", aikidoCommand: "aikido-bunx" },
-  { tool: "pip", aikidoCommand: "aikido-pip" },
-  { tool: "pip3", aikidoCommand: "aikido-pip3" },
-  { tool: "python", aikidoCommand: "aikido-python" },
-  { tool: "python3", aikidoCommand: "aikido-python3" },
+  { tool: "npm", aikidoCommand: "aikido-npm", ecoSystem: ECOSYSTEM_JS },
+  { tool: "npx", aikidoCommand: "aikido-npx", ecoSystem: ECOSYSTEM_JS },
+  { tool: "yarn", aikidoCommand: "aikido-yarn", ecoSystem: ECOSYSTEM_JS },
+  { tool: "pnpm", aikidoCommand: "aikido-pnpm", ecoSystem: ECOSYSTEM_JS },
+  { tool: "pnpx", aikidoCommand: "aikido-pnpx", ecoSystem: ECOSYSTEM_JS },
+  { tool: "bun", aikidoCommand: "aikido-bun", ecoSystem: ECOSYSTEM_JS },
+  { tool: "bunx", aikidoCommand: "aikido-bunx", ecoSystem: ECOSYSTEM_JS },
+  { tool: "pip", aikidoCommand: "aikido-pip", ecoSystem: ECOSYSTEM_PY },
+  { tool: "pip3", aikidoCommand: "aikido-pip3", ecoSystem: ECOSYSTEM_PY },
+  { tool: "python", aikidoCommand: "aikido-python", ecoSystem: ECOSYSTEM_PY },
+  { tool: "python3", aikidoCommand: "aikido-python3", ecoSystem: ECOSYSTEM_PY },
   // When adding a new tool here, also update the documentation for the new tool in the README.md
 ];
 
diff --git a/packages/safe-chain/src/shell-integration/setup-ci.js b/packages/safe-chain/src/shell-integration/setup-ci.js
index 8793832..f63ad32 100644
--- a/packages/safe-chain/src/shell-integration/setup-ci.js
+++ b/packages/safe-chain/src/shell-integration/setup-ci.js
@@ -1,10 +1,12 @@
 import chalk from "chalk";
 import { ui } from "../environment/userInteraction.js";
-import { knownAikidoTools, getPackageManagerList } from "./helpers.js";
+import { getPackageManagerList, knownAikidoTools } from "./helpers.js";
 import fs from "fs";
 import os from "os";
 import path from "path";
 import { fileURLToPath } from "url";
+import { includePython } from "../config/cliArguments.js";
+import { ECOSYSTEM_PY } from "../config/settings.js";
 
 /**
  * Loops over the detected shells and calls the setup function for each.
@@ -53,7 +55,7 @@ function createUnixShims(shimsDir) {
 
   // Create a shim for each tool
   let created = 0;
-  for (const toolInfo of knownAikidoTools) {
+  for (const toolInfo of getToolsToSetup()) {
     const shimContent = template
       .replaceAll("{{PACKAGE_MANAGER}}", toolInfo.tool)
       .replaceAll("{{AIKIDO_COMMAND}}", toolInfo.aikidoCommand);
@@ -66,9 +68,7 @@ function createUnixShims(shimsDir) {
     created++;
   }
 
-  ui.writeInformation(
-    `Created ${created} Unix shim(s) in ${shimsDir}`
-  );
+  ui.writeInformation(`Created ${created} Unix shim(s) in ${shimsDir}`);
 }
 
 /**
@@ -96,19 +96,17 @@ function createWindowsShims(shimsDir) {
 
   // Create a shim for each tool
   let created = 0;
-  for (const toolInfo of knownAikidoTools) {
+  for (const toolInfo of getToolsToSetup()) {
     const shimContent = template
       .replaceAll("{{PACKAGE_MANAGER}}", toolInfo.tool)
       .replaceAll("{{AIKIDO_COMMAND}}", toolInfo.aikidoCommand);
 
-  const shimPath = `${shimsDir}/${toolInfo.tool}.cmd`;
+    const shimPath = `${shimsDir}/${toolInfo.tool}.cmd`;
     fs.writeFileSync(shimPath, shimContent, "utf-8");
     created++;
   }
 
-  ui.writeInformation(
-    `Created ${created} Windows shim(s) in ${shimsDir}`
-  );
+  ui.writeInformation(`Created ${created} Windows shim(s) in ${shimsDir}`);
 }
 
 /**
@@ -145,3 +143,11 @@ function modifyPathForCi(shimsDir) {
     ui.writeInformation("##vso[task.prependpath]" + shimsDir);
   }
 }
+
+function getToolsToSetup() {
+  if (includePython()) {
+    return knownAikidoTools;
+  } else {
+    return knownAikidoTools.filter((tool) => tool.ecoSystem !== ECOSYSTEM_PY);
+  }
+}
diff --git a/packages/safe-chain/src/shell-integration/setup.js b/packages/safe-chain/src/shell-integration/setup.js
index 7185c5a..e734858 100644
--- a/packages/safe-chain/src/shell-integration/setup.js
+++ b/packages/safe-chain/src/shell-integration/setup.js
@@ -6,6 +6,7 @@ import fs from "fs";
 import os from "os";
 import path from "path";
 import { fileURLToPath } from "url";
+import { includePython } from "../config/cliArguments.js";
 
 /**
  * Loops over the detected shells and calls the setup function for each.
@@ -104,7 +105,11 @@ function copyStartupFiles() {
     // Use absolute path for source
     const __filename = fileURLToPath(import.meta.url);
     const __dirname = path.dirname(__filename);
-    const sourcePath = path.resolve(__dirname, "startup-scripts", file);
+    const sourcePath = path.resolve(
+      __dirname,
+      includePython() ? "startup-scripts/include-python" : "startup-scripts",
+      file
+    );
     fs.copyFileSync(sourcePath, targetPath);
   }
 }
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-fish.fish b/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-fish.fish
new file mode 100644
index 0000000..ebf89ff
--- /dev/null
+++ b/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-fish.fish
@@ -0,0 +1,88 @@
+function printSafeChainWarning
+    set original_cmd $argv[1]
+    
+    # Fish equivalent of ANSI color codes: yellow background, black text for "Warning:"
+    set_color -b yellow black
+    printf "Warning:"
+    set_color normal
+    printf " safe-chain is not available to protect you from installing malware. %s will run without it.\n" $original_cmd
+    
+    # Cyan text for the install command
+    printf "Install safe-chain by using "
+    set_color cyan
+    printf "npm install -g @aikidosec/safe-chain"
+    set_color normal
+    printf ".\n"
+end
+
+function wrapSafeChainCommand
+    set original_cmd $argv[1]
+    set aikido_cmd $argv[2]
+    set cmd_args $argv[3..-1]
+    
+    if type -q $aikido_cmd
+        # If the aikido command is available, just run it with the provided arguments
+        $aikido_cmd $cmd_args
+    else
+        # If the aikido command is not available, print a warning and run the original command
+        printSafeChainWarning $original_cmd
+        command $original_cmd $cmd_args
+    end
+end
+
+function npx
+    wrapSafeChainCommand "npx" "aikido-npx" $argv
+end
+
+function yarn
+    wrapSafeChainCommand "yarn" "aikido-yarn" $argv
+end
+
+function pnpm
+    wrapSafeChainCommand "pnpm" "aikido-pnpm" $argv
+end
+
+function pnpx
+    wrapSafeChainCommand "pnpx" "aikido-pnpx" $argv
+end
+
+function bun
+    wrapSafeChainCommand "bun" "aikido-bun" $argv
+end
+
+function bunx
+    wrapSafeChainCommand "bunx" "aikido-bunx" $argv
+end
+
+function npm
+    # If args is just -v or --version and nothing else, just run the `npm -v` command
+    # This is because nvm uses this to check the version of npm
+    set argc (count $argv)
+    if test $argc -eq 1
+        switch $argv[1]
+            case "-v" "--version"
+                command npm $argv
+                return
+        end
+    end
+
+    wrapSafeChainCommand "npm" "aikido-npm" $argv
+end
+
+function pip
+    wrapSafeChainCommand "pip" "aikido-pip" $argv
+end
+
+function pip3
+    wrapSafeChainCommand "pip3" "aikido-pip3" $argv
+end
+
+# `python -m pip`, `python -m pip3`.
+function python
+    wrapSafeChainCommand "python" "aikido-python" $argv
+end
+
+# `python3 -m pip`, `python3 -m pip3'.
+function python3
+    wrapSafeChainCommand "python3" "aikido-python3" $argv
+end
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-posix.sh b/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-posix.sh
new file mode 100644
index 0000000..278b31a
--- /dev/null
+++ b/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-posix.sh
@@ -0,0 +1,80 @@
+
+function printSafeChainWarning() {
+  # \033[43;30m is used to set the background color to yellow and text color to black
+  # \033[0m is used to reset the text formatting
+  printf "\033[43;30mWarning:\033[0m safe-chain is not available to protect you from installing malware. %s will run without it.\n" "$1"
+  # \033[36m is used to set the text color to cyan
+  printf "Install safe-chain by using \033[36mnpm install -g @aikidosec/safe-chain\033[0m.\n"
+}
+
+function wrapSafeChainCommand() {
+  local original_cmd="$1"
+  local aikido_cmd="$2"
+
+  # Remove the first 2 arguments (original_cmd and aikido_cmd) from $@
+  # so that "$@" now contains only the arguments passed to the original command
+  shift 2
+
+  if command -v "$aikido_cmd" > /dev/null 2>&1; then
+    # If the aikido command is available, just run it with the provided arguments
+    "$aikido_cmd" "$@"
+  else
+    # If the aikido command is not available, print a warning and run the original command
+    printSafeChainWarning "$original_cmd"
+
+    command "$original_cmd" "$@"
+  fi
+}
+
+function npx() {
+  wrapSafeChainCommand "npx" "aikido-npx" "$@"
+}
+
+function yarn() {
+  wrapSafeChainCommand "yarn" "aikido-yarn" "$@"
+}
+
+function pnpm() {
+  wrapSafeChainCommand "pnpm" "aikido-pnpm" "$@"
+}
+
+function pnpx() {
+  wrapSafeChainCommand "pnpx" "aikido-pnpx" "$@"
+}
+
+function bun() {
+  wrapSafeChainCommand "bun" "aikido-bun" "$@"
+}
+
+function bunx() {
+  wrapSafeChainCommand "bunx" "aikido-bunx" "$@"
+}
+
+function npm() {
+  if [[ "$1" == "-v" || "$1" == "--version" ]] && [[ $# -eq 1 ]]; then
+    # If args is just -v or --version and nothing else, just run the npm version command
+    # This is because nvm uses this to check the version of npm
+    command npm "$@"
+    return
+  fi
+
+  wrapSafeChainCommand "npm" "aikido-npm" "$@"
+}
+
+function pip() {
+  wrapSafeChainCommand "pip" "aikido-pip" "$@"
+}
+
+function pip3() {
+  wrapSafeChainCommand "pip3" "aikido-pip3" "$@"
+}
+
+# `python -m pip`, `python -m pip3`.
+function python() {
+  wrapSafeChainCommand "python" "aikido-python" "$@"
+}
+
+# `python3 -m pip`, `python3 -m pip3'.
+function python3() {
+  wrapSafeChainCommand "python3" "aikido-python3" "$@"
+}
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-pwsh.ps1 b/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-pwsh.ps1
new file mode 100644
index 0000000..b692107
--- /dev/null
+++ b/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-pwsh.ps1
@@ -0,0 +1,107 @@
+function Write-SafeChainWarning {
+    param([string]$Command)
+    
+    # PowerShell equivalent of ANSI color codes: yellow background, black text for "Warning:"
+    Write-Host "Warning:" -BackgroundColor Yellow -ForegroundColor Black -NoNewline
+    Write-Host " safe-chain is not available to protect you from installing malware. $Command will run without it."
+    
+    # Cyan text for the install command
+    Write-Host "Install safe-chain by using " -NoNewline
+    Write-Host "npm install -g @aikidosec/safe-chain" -ForegroundColor Cyan -NoNewline
+    Write-Host "."
+}
+
+function Test-CommandAvailable {
+    param([string]$Command)
+    
+    try {
+        Get-Command $Command -ErrorAction Stop | Out-Null
+        return $true
+    }
+    catch {
+        return $false
+    }
+}
+
+function Invoke-RealCommand {
+    param(
+        [string]$Command,
+        [string[]]$Arguments
+    )
+    
+    # Find the real executable to avoid calling our wrapped functions
+    $realCommand = Get-Command -Name $Command -CommandType Application | Select-Object -First 1
+    if ($realCommand) {
+        & $realCommand.Source @Arguments
+    }
+}
+
+function Invoke-WrappedCommand {
+    param(
+        [string]$OriginalCmd,
+        [string]$AikidoCmd,
+        [string[]]$Arguments
+    )
+
+    if (Test-CommandAvailable $AikidoCmd) {
+        & $AikidoCmd @Arguments
+    }
+    else {
+        Write-SafeChainWarning $OriginalCmd
+        Invoke-RealCommand $OriginalCmd $Arguments
+    }
+}
+
+function npx {
+    Invoke-WrappedCommand "npx" "aikido-npx" $args
+}
+
+function yarn {
+    Invoke-WrappedCommand "yarn" "aikido-yarn" $args
+}
+
+function pnpm {
+    Invoke-WrappedCommand "pnpm" "aikido-pnpm" $args
+}
+
+function pnpx {
+    Invoke-WrappedCommand "pnpx" "aikido-pnpx" $args
+}
+
+function bun {
+    Invoke-WrappedCommand "bun" "aikido-bun" $args
+}
+
+function bunx {
+    Invoke-WrappedCommand "bunx" "aikido-bunx" $args
+}
+
+function npm {
+    # If args is just -v or --version and nothing else, just run the npm version command
+    # This is because nvm uses this to check the version of npm
+    if (($args.Length -eq 1) -and (($args[0] -eq "-v") -or ($args[0] -eq "--version"))) {
+        Invoke-RealCommand "npm" $args
+        return
+    }
+    
+    Invoke-WrappedCommand "npm" "aikido-npm" $args
+}
+
+function pip {
+    Invoke-WrappedCommand "pip" "aikido-pip" $args
+}
+
+function pip3 {
+    Invoke-WrappedCommand "pip3" "aikido-pip3" $args
+}
+
+# `python -m pip`, `python -m pip3`.
+function python {
+    Invoke-WrappedCommand 'python' 'aikido-python' $args
+}
+
+# `python3 -m pip`, `python3 -m pip3'.
+function python3 {
+    Invoke-WrappedCommand 'python3' 'aikido-python3' $args
+}
+
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/init-fish.fish b/packages/safe-chain/src/shell-integration/startup-scripts/init-fish.fish
index ebf89ff..29d6bf3 100644
--- a/packages/safe-chain/src/shell-integration/startup-scripts/init-fish.fish
+++ b/packages/safe-chain/src/shell-integration/startup-scripts/init-fish.fish
@@ -68,21 +68,3 @@ function npm
 
     wrapSafeChainCommand "npm" "aikido-npm" $argv
 end
-
-function pip
-    wrapSafeChainCommand "pip" "aikido-pip" $argv
-end
-
-function pip3
-    wrapSafeChainCommand "pip3" "aikido-pip3" $argv
-end
-
-# `python -m pip`, `python -m pip3`.
-function python
-    wrapSafeChainCommand "python" "aikido-python" $argv
-end
-
-# `python3 -m pip`, `python3 -m pip3'.
-function python3
-    wrapSafeChainCommand "python3" "aikido-python3" $argv
-end
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/init-posix.sh b/packages/safe-chain/src/shell-integration/startup-scripts/init-posix.sh
index 278b31a..353c6c0 100644
--- a/packages/safe-chain/src/shell-integration/startup-scripts/init-posix.sh
+++ b/packages/safe-chain/src/shell-integration/startup-scripts/init-posix.sh
@@ -60,21 +60,3 @@ function npm() {
 
   wrapSafeChainCommand "npm" "aikido-npm" "$@"
 }
-
-function pip() {
-  wrapSafeChainCommand "pip" "aikido-pip" "$@"
-}
-
-function pip3() {
-  wrapSafeChainCommand "pip3" "aikido-pip3" "$@"
-}
-
-# `python -m pip`, `python -m pip3`.
-function python() {
-  wrapSafeChainCommand "python" "aikido-python" "$@"
-}
-
-# `python3 -m pip`, `python3 -m pip3'.
-function python3() {
-  wrapSafeChainCommand "python3" "aikido-python3" "$@"
-}
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/init-pwsh.ps1 b/packages/safe-chain/src/shell-integration/startup-scripts/init-pwsh.ps1
index b692107..a449405 100644
--- a/packages/safe-chain/src/shell-integration/startup-scripts/init-pwsh.ps1
+++ b/packages/safe-chain/src/shell-integration/startup-scripts/init-pwsh.ps1
@@ -86,22 +86,3 @@ function npm {
     
     Invoke-WrappedCommand "npm" "aikido-npm" $args
 }
-
-function pip {
-    Invoke-WrappedCommand "pip" "aikido-pip" $args
-}
-
-function pip3 {
-    Invoke-WrappedCommand "pip3" "aikido-pip3" $args
-}
-
-# `python -m pip`, `python -m pip3`.
-function python {
-    Invoke-WrappedCommand 'python' 'aikido-python' $args
-}
-
-# `python3 -m pip`, `python3 -m pip3'.
-function python3 {
-    Invoke-WrappedCommand 'python3' 'aikido-python3' $args
-}
-
diff --git a/test/e2e/pip-ci.e2e.spec.js b/test/e2e/pip-ci.e2e.spec.js
index fe013bb..63bfd90 100644
--- a/test/e2e/pip-ci.e2e.spec.js
+++ b/test/e2e/pip-ci.e2e.spec.js
@@ -25,31 +25,55 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
     it("does not intercept python3 --version", async () => {
       const shell = await container.openShell("zsh");
       const result = await shell.runCommand("python3 --version");
-      assert.ok(result.output.match(/Python \d+\.\d+\.\d+/), `Output was: ${result.output}`);
-      assert.ok(!result.output.includes("Safe-chain"), "Safe Chain should not intercept generic python3 command");
+      assert.ok(
+        result.output.match(/Python \d+\.\d+\.\d+/),
+        `Output was: ${result.output}`
+      );
+      assert.ok(
+        !result.output.includes("Safe-chain"),
+        "Safe Chain should not intercept generic python3 command"
+      );
     });
 
     it("does not intercept python3 -c 'print(\"hello\")'", async () => {
       const shell = await container.openShell("zsh");
       const result = await shell.runCommand("python3 -c 'print(\"hello\")'");
-      assert.ok(result.output.includes("hello"), `Output was: ${result.output}`);
-      assert.ok(!result.output.includes("Safe-chain"), "Safe Chain should not intercept generic python3 -c command");
+      assert.ok(
+        result.output.includes("hello"),
+        `Output was: ${result.output}`
+      );
+      assert.ok(
+        !result.output.includes("Safe-chain"),
+        "Safe Chain should not intercept generic python3 -c command"
+      );
     });
 
     it("does not intercept python3 test.py", async () => {
       const shell = await container.openShell("zsh");
       await shell.runCommand("echo 'print(\"Hello from test.py!\")' > test.py");
       const result = await shell.runCommand("python3 test.py");
-      assert.ok(result.output.includes("Hello from test.py!"), `Output was: ${result.output}`);
-      assert.ok(!result.output.includes("Safe-chain"), "Safe Chain should not intercept generic python3 script execution");
+      assert.ok(
+        result.output.includes("Hello from test.py!"),
+        `Output was: ${result.output}`
+      );
+      assert.ok(
+        !result.output.includes("Safe-chain"),
+        "Safe Chain should not intercept generic python3 script execution"
+      );
     });
 
     it("does not intercept python test.py", async () => {
       const shell = await container.openShell("zsh");
       await shell.runCommand("echo 'print(\"Hello from test.py!\")' > test.py");
       const result = await shell.runCommand("python test.py");
-      assert.ok(result.output.includes("Hello from test.py!"), `Output was: ${result.output}`);
-      assert.ok(!result.output.includes("Safe-chain"), "Safe Chain should not intercept generic python script execution");
+      assert.ok(
+        result.output.includes("Hello from test.py!"),
+        `Output was: ${result.output}`
+      );
+      assert.ok(
+        !result.output.includes("Safe-chain"),
+        "Safe Chain should not intercept generic python script execution"
+      );
     });
   });
 
@@ -57,7 +81,9 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
     it(`safe-chain setup-ci wraps pip3 command with PATH shim after installation for ${shell}`, async () => {
       // Setup safe-chain CI shims
       const installationShell = await container.openShell(shell);
-      await installationShell.runCommand("safe-chain setup-ci");
+      await installationShell.runCommand(
+        "safe-chain setup-ci --include-python"
+      );
 
       // Add $HOME/.safe-chain/shims to PATH for subsequent shells
       await installationShell.runCommand(
@@ -73,9 +99,7 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
         "pip3 install --break-system-packages certifi"
       );
 
-      const hasExpectedOutput = result.output.includes(
-        "no malware found."
-      );
+      const hasExpectedOutput = result.output.includes("no malware found.");
       assert.ok(
         hasExpectedOutput,
         hasExpectedOutput
@@ -86,7 +110,9 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
 
     it(`setup-ci routes python -m pip through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
-      await installationShell.runCommand("safe-chain setup-ci");
+      await installationShell.runCommand(
+        "safe-chain setup-ci --include-python"
+      );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
       );
@@ -107,7 +133,9 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
 
     it(`setup-ci routes python3 -m pip through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
-      await installationShell.runCommand("safe-chain setup-ci");
+      await installationShell.runCommand(
+        "safe-chain setup-ci --include-python"
+      );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
       );
@@ -128,7 +156,9 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
 
     it(`setup-ci routes pip through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
-      await installationShell.runCommand("safe-chain setup-ci");
+      await installationShell.runCommand(
+        "safe-chain setup-ci --include-python"
+      );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
       );
@@ -149,7 +179,9 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
 
     it(`setup-ci routes pip3 through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
-      await installationShell.runCommand("safe-chain setup-ci");
+      await installationShell.runCommand(
+        "safe-chain setup-ci --include-python"
+      );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
       );
diff --git a/test/e2e/pip.e2e.spec.js b/test/e2e/pip.e2e.spec.js
index 3d3b4dd..9a1adec 100644
--- a/test/e2e/pip.e2e.spec.js
+++ b/test/e2e/pip.e2e.spec.js
@@ -15,7 +15,7 @@ describe("E2E: pip coverage", () => {
     await container.start();
 
     const installationShell = await container.openShell("zsh");
-    await installationShell.runCommand("safe-chain setup");
+    await installationShell.runCommand("safe-chain setup --include-python");
   });
 
   afterEach(async () => {
@@ -96,7 +96,9 @@ describe("E2E: pip coverage", () => {
 
   it(`python3 -m pip install routes through safe-chain`, async () => {
     const shell = await container.openShell("zsh");
-    const result = await shell.runCommand("python3 -m pip install --break-system-packages requests");
+    const result = await shell.runCommand(
+      "python3 -m pip install --break-system-packages requests"
+    );
 
     assert.ok(
       result.output.includes("no malware found."),
@@ -329,6 +331,9 @@ describe("E2E: pip coverage", () => {
     const result = await shell.runCommand(
       "pip3 install --break-system-packages requests --safe-chain-logging=verbose"
     );
-    assert.ok(result.output.includes("no malware found."), `Output did not include expected text. Output was:\n${result.output}`);
+    assert.ok(
+      result.output.includes("no malware found."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
   });
 });

From 41998dff956f16b68457e391b1740af1d3301dd1 Mon Sep 17 00:00:00 2001
From: Sander Declerck <sander@sdsoftware.be>
Date: Fri, 14 Nov 2025 14:18:12 +0100
Subject: [PATCH 19/25] Describe safe-chain setup --include-python in
 documentation.

---
 README.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/README.md b/README.md
index f169747..5541150 100644
--- a/README.md
+++ b/README.md
@@ -32,6 +32,12 @@ Installing the Aikido Safe Chain is easy. You just need 3 simple steps:
    ```shell
    safe-chain setup
    ```
+
+   To enable Python (pip/pip3) support (beta), use the `--include-python` flag:
+   ```shell
+   safe-chain setup --include-python
+   ```
+
 3. **❗Restart your terminal** to start using the Aikido Safe Chain.
   - This step is crucial as it ensures that the shell aliases for npm, npx, yarn, pnpm, pnpx, bun, bunx, and pip/pip3 are loaded correctly. If you do not restart your terminal, the aliases will not be available.
 4. **Verify the installation** by running one of the following commands:
@@ -120,6 +126,12 @@ To use Aikido Safe Chain in CI/CD environments, run the following command after
 safe-chain setup-ci
 ```
 
+To enable Python (pip/pip3) support (beta) in CI/CD, use the `--include-python` flag:
+
+```shell
+safe-chain setup-ci --include-python
+```
+
 This automatically configures your CI environment to use Aikido Safe Chain for all package manager commands.
 
 ## Supported Platforms

From 87fcb7239a34a19d9fbd65b3f0bf75ec839cb729 Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Mon, 17 Nov 2025 10:03:38 -0800
Subject: [PATCH 20/25] Adapt per review

---
 .../src/packagemanager/pip/runPipCommand.js   | 46 +++++++++----------
 .../packagemanager/pip/runPipCommand.spec.js  | 24 +++++-----
 2 files changed, 34 insertions(+), 36 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 309ee47..f37e9b0 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -32,8 +32,7 @@ export async function runPip(command, args) {
     const tmpDir = os.tmpdir();
     const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
 
-    if (!env.PIP_CONFIG_FILE) {
-      // Build pip config INI
+    if (!env.PIP_CONFIG_FILE) { // Build pip config INI
       /** @type {{ global: { cert: string, proxy?: string } }} */
       const configObj = { global: { cert: combinedCaPath } };
       if (proxy) {
@@ -43,9 +42,7 @@ export async function runPip(command, args) {
       await fs.writeFile(pipConfigPath, pipConfig);
       env.PIP_CONFIG_FILE = pipConfigPath;
 
-    } else if (fsSync.existsSync(env.PIP_CONFIG_FILE)) {
-      // Existing pip config file present and exists on disk.
-      // Lets merge in our cert and proxy settings if not already present
+    } else if (fsSync.existsSync(env.PIP_CONFIG_FILE)) { // Merge pip config INI
       ui.writeVerbose("Safe-chain: Merging user provided PIP_CONFIG_FILE with safe-chain certificate and proxy settings.");
       const userConfig = env.PIP_CONFIG_FILE;
 
@@ -56,24 +53,20 @@ export async function runPip(command, args) {
       // Ensure [global] section exists
       parsed.global = parsed.global || {};
 
-      // Adding CERT and PROXY
-      // If either is already set, there's no neeed to throw an error
-      // MITM might fail and throw later if the proxy config is invalid
-
       // Cert
-      if (typeof parsed.global.cert === "undefined") {
-        ui.writeVerbose("Safe-chain: Adding cert to temporary PIP_CONFIG_FILE.");
-        parsed.global.cert = combinedCaPath;
+      if (typeof parsed.global.cert !== "undefined") {
+        ui.writeWarning("Safe-chain: User defined cert found in PIP_CONFIG_FILE. It will be overwritten in the temporary config.");
       }
+      parsed.global.cert = combinedCaPath;
 
       // Proxy
-      if (typeof parsed.global.proxy === "undefined") {
-        if (proxy) {
-          ui.writeVerbose("Safe-chain: Adding proxy to temporary PIP_CONFIG_FILE.");
-          parsed.global.proxy = proxy;
-        }
+      if (typeof parsed.global.proxy !== "undefined") {
+        ui.writeWarning("Safe-chain: User defined proxy found in PIP_CONFIG_FILE. It will be overwritten in the temporary config.");
       }
-
+      if (proxy) {
+        parsed.global.proxy = proxy;
+      }
+ 
       const updated = ini.stringify(parsed);
 
       // Save to a new temp file to avoid overwriting user's original config
@@ -86,15 +79,20 @@ export async function runPip(command, args) {
     }
 
     // REQUESTS_CA_BUNDLE, SSL_CERT_FILE and PIP_CERT as extra safety nets.
-    if (!env.REQUESTS_CA_BUNDLE) {
-      env.REQUESTS_CA_BUNDLE = combinedCaPath;
+    if (env.REQUESTS_CA_BUNDLE) {
+      ui.writeWarning("Safe-chain: User defined REQUESTS_CA_BUNDLE found in environment. It will be overwritten.");
     }
-    if (!env.SSL_CERT_FILE) {
-      env.SSL_CERT_FILE = combinedCaPath;
+    env.REQUESTS_CA_BUNDLE = combinedCaPath;
+
+    if (env.SSL_CERT_FILE) {
+      ui.writeWarning("Safe-chain: User defined SSL_CERT_FILE found in environment. It will be overwritten.");
     }
-    if (!env.PIP_CERT) {
-      env.PIP_CERT = combinedCaPath;
+    env.SSL_CERT_FILE = combinedCaPath;
+
+    if (env.PIP_CERT) {
+      ui.writeWarning("Safe-chain: User defined PIP_CERT found in environment. It will be overwritten.");
     }
+    env.PIP_CERT = combinedCaPath;
 
     const result = await safeSpawn(command, args, {
       stdio: "inherit",
diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
index ecd8e0f..f67077a 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
@@ -217,10 +217,10 @@ describe("runPipCommand environment variable handling", () => {
     assert.strictEqual(originalParsed.global.cert, undefined, "original file should not gain cert");
     assert.strictEqual(originalParsed.global.proxy, "http://original:9999", "original proxy remains");
 
-    // New file merged: cert added (was missing), proxy preserved (was present)
+    // New file: cert and proxy always overwritten
     const newParsed = ini.parse(await fs.readFile(newCfgPath, "utf-8"));
-    assert.strictEqual(newParsed.global.cert, "/tmp/test-combined-ca.pem", "new cert injected");
-    assert.strictEqual(newParsed.global.proxy, "http://original:9999", "existing proxy should be preserved in new file");
+    assert.strictEqual(newParsed.global.cert, "/tmp/test-combined-ca.pem", "cert always overwritten in temp config");
+    assert.strictEqual(newParsed.global.proxy, "http://localhost:8080", "proxy always overwritten in temp config");
     customEnv = null;
   });
 
@@ -247,11 +247,11 @@ describe("runPipCommand environment variable handling", () => {
     assert.strictEqual(originalParsed.global.cert, "/path/to/existing.pem", "original cert preserved");
     assert.strictEqual(originalParsed.global.proxy, "http://original:9999", "original proxy preserved");
 
-    // New temp config preserves existing values (no override when already set)
-    const newContent = await fs.readFile(newCfgPath, "utf-8");
-    const newParsed = ini.parse(newContent);
-    assert.strictEqual(newParsed.global.cert, "/path/to/existing.pem", "existing cert preserved in new temp config");
-    assert.strictEqual(newParsed.global.proxy, "http://original:9999", "existing proxy preserved in new temp config");
+  // New temp config: cert and proxy always overwritten
+  const newContent = await fs.readFile(newCfgPath, "utf-8");
+  const newParsed = ini.parse(newContent);
+  assert.strictEqual(newParsed.global.cert, "/tmp/test-combined-ca.pem", "cert always overwritten in temp config");
+  assert.strictEqual(newParsed.global.proxy, "http://localhost:8080", "proxy always overwritten in temp config");
     customEnv = null;
   });
 
@@ -272,10 +272,10 @@ describe("runPipCommand environment variable handling", () => {
     assert.strictEqual(originalParsed.global.cert, "/path/to/existing.pem", "original cert unchanged");
     assert.strictEqual(originalParsed.global.proxy, undefined, "original proxy still missing");
 
-    // New file preserves existing cert and adds proxy (since it was missing)
-    const newParsed = ini.parse(await fs.readFile(newCfgPath, "utf-8"));
-    assert.strictEqual(newParsed.global.cert, "/path/to/existing.pem", "existing cert preserved (not overridden)");
-    assert.strictEqual(newParsed.global.proxy, "http://localhost:8080", "proxy added from env");
+  // New file: cert and proxy always overwritten
+  const newParsed = ini.parse(await fs.readFile(newCfgPath, "utf-8"));
+  assert.strictEqual(newParsed.global.cert, "/tmp/test-combined-ca.pem", "cert always overwritten in temp config");
+  assert.strictEqual(newParsed.global.proxy, "http://localhost:8080", "proxy always overwritten in temp config");
     customEnv = null;
   });
 });

From 0e5b9b23f16a460631afe9fe27f9edb6bd56d9fd Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Mon, 17 Nov 2025 10:18:47 -0800
Subject: [PATCH 21/25] Fix tests

---
 .../packagemanager/pip/runPipCommand.spec.js  | 50 ++++++++++++-------
 1 file changed, 31 insertions(+), 19 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
index f67077a..4af0b40 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
@@ -52,25 +52,6 @@ describe("runPipCommand environment variable handling", () => {
     mock.reset();
   });
 
-  it("should not overwrite existing env vars for certs and config", async () => {
-    // Set custom env vars before merge
-    customEnv = {
-      REQUESTS_CA_BUNDLE: "/custom/ca-bundle.pem",
-      SSL_CERT_FILE: "/custom/ssl-cert.pem",
-      PIP_CERT: "/custom/pip-cert.pem",
-      PIP_CONFIG_FILE: "/custom/pip.conf"
-    };
-    const res = await runPip("pip3", ["install", "requests"]);
-    assert.strictEqual(res.status, 0);
-    assert.ok(capturedArgs, "safeSpawn should have been called");
-    // Should preserve custom env vars
-    assert.strictEqual(capturedArgs.options.env.REQUESTS_CA_BUNDLE, "/custom/ca-bundle.pem");
-    assert.strictEqual(capturedArgs.options.env.SSL_CERT_FILE, "/custom/ssl-cert.pem");
-    assert.strictEqual(capturedArgs.options.env.PIP_CERT, "/custom/pip-cert.pem");
-    assert.strictEqual(capturedArgs.options.env.PIP_CONFIG_FILE, "/custom/pip.conf");
-    customEnv = null;
-  });
-
   it("should set PIP_CERT env var and create config file", async () => {
     const res = await runPip("pip3", ["install", "requests"]);
     assert.strictEqual(res.status, 0);
@@ -278,4 +259,35 @@ describe("runPipCommand environment variable handling", () => {
   assert.strictEqual(newParsed.global.proxy, "http://localhost:8080", "proxy always overwritten in temp config");
     customEnv = null;
   });
+
+  it("should log warnings when cert and proxy are already set in user config file", async () => {
+    const tmpDir = os.tmpdir();
+    const cfgPath = path.join(tmpDir, `safe-chain-test-pip-warn-${Date.now()}.ini`);
+    const initialIni = [
+      "[global]",
+      "cert = /user/cert.pem",
+      "proxy = http://user-proxy:9999",
+      ""
+    ].join("\n");
+    await fs.writeFile(cfgPath, initialIni, "utf-8");
+
+    process.env.PIP_CONFIG_FILE = cfgPath;
+    const mod = await import("./runPipCommand.js");
+    // Capture stdout/stderr
+    let output = "";
+    const originalWrite = process.stdout.write;
+    const originalError = process.stderr.write;
+    process.stdout.write = (chunk, ...args) => { output += chunk; return originalWrite.apply(process.stdout, [chunk, ...args]); };
+    process.stderr.write = (chunk, ...args) => { output += chunk; return originalError.apply(process.stderr, [chunk, ...args]); };
+
+    await mod.runPip("pip3", ["install", "requests"]);
+
+    process.stdout.write = originalWrite;
+    process.stderr.write = originalError;
+
+    assert.ok(output.includes("cert found in PIP_CONFIG_FILE"), "Should warn about cert overwrite in output");
+    assert.ok(output.includes("proxy found in PIP_CONFIG_FILE"), "Should warn about proxy overwrite in output");
+    delete process.env.PIP_CONFIG_FILE;
+    customEnv = null;
+  });
 });

From f030b16adf49620202141be8ac435ee1988a27c3 Mon Sep 17 00:00:00 2001
From: bitterpanda <bitterpanda@proton.me>
Date: Fri, 21 Nov 2025 13:33:33 +0100
Subject: [PATCH 22/25] rm obvious comments

---
 packages/safe-chain/src/packagemanager/pip/runPipCommand.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index f37e9b0..cb85c89 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -32,7 +32,7 @@ export async function runPip(command, args) {
     const tmpDir = os.tmpdir();
     const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
 
-    if (!env.PIP_CONFIG_FILE) { // Build pip config INI
+    if (!env.PIP_CONFIG_FILE) {
       /** @type {{ global: { cert: string, proxy?: string } }} */
       const configObj = { global: { cert: combinedCaPath } };
       if (proxy) {
@@ -42,7 +42,7 @@ export async function runPip(command, args) {
       await fs.writeFile(pipConfigPath, pipConfig);
       env.PIP_CONFIG_FILE = pipConfigPath;
 
-    } else if (fsSync.existsSync(env.PIP_CONFIG_FILE)) { // Merge pip config INI
+    } else if (fsSync.existsSync(env.PIP_CONFIG_FILE)) {
       ui.writeVerbose("Safe-chain: Merging user provided PIP_CONFIG_FILE with safe-chain certificate and proxy settings.");
       const userConfig = env.PIP_CONFIG_FILE;
 

From 0a0ac85542ab471e6b6d75e279e46238f9bf734d Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Fri, 21 Nov 2025 09:41:07 -0800
Subject: [PATCH 23/25] Adapt per review

---
 .../src/packagemanager/pip/runPipCommand.js   | 79 ++++++++++++++-----
 .../packagemanager/pip/runPipCommand.spec.js  | 45 +++++++----
 2 files changed, 87 insertions(+), 37 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index cb85c89..8efa000 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -9,10 +9,46 @@ import path from "node:path";
 import ini from "ini";
 
 /**
- * @param {string} command
- * @param {string[]} args
- *
- * @returns {Promise<{status: number}>}
+ * Sets fallback CA bundle environment variables used by Python libraries.
+ * These are applied in addition to the PIP_CONFIG_FILE to ensure all Python
+ * network libraries respect the combined CA bundle, even if they don't read pip's config.
+ * 
+ * @param {NodeJS.ProcessEnv} env - Environment object to modify
+ * @param {string} combinedCaPath - Path to the combined CA bundle
+ */
+function setFallbackCaBundleEnvironmentVariables(env, combinedCaPath) {
+  // REQUESTS_CA_BUNDLE: Used by the popular 'requests' library
+  if (env.REQUESTS_CA_BUNDLE) {
+    ui.writeWarning("Safe-chain: User defined REQUESTS_CA_BUNDLE found in environment. It will be overwritten.");
+  }
+  env.REQUESTS_CA_BUNDLE = combinedCaPath;
+
+  // SSL_CERT_FILE: Used by some Python SSL libraries and urllib
+  if (env.SSL_CERT_FILE) {
+    ui.writeWarning("Safe-chain: User defined SSL_CERT_FILE found in environment. It will be overwritten.");
+  }
+  env.SSL_CERT_FILE = combinedCaPath;
+
+  // PIP_CERT: Pip's own environment variable for certificate verification
+  if (env.PIP_CERT) {
+    ui.writeWarning("Safe-chain: User defined PIP_CERT found in environment. It will be overwritten.");
+  }
+  env.PIP_CERT = combinedCaPath;
+}
+
+/**
+ * Runs a pip command with safe-chain's certificate bundle and proxy configuration.
+ * 
+ * Creates a temporary pip config file (cleaned up automatically after execution) to configure:
+ * - Certificate bundle for HTTPS verification
+ * - Proxy settings if available
+ * 
+ * If the user has an existing PIP_CONFIG_FILE, a new temporary config is created that merges
+ * their settings with safe-chain's, leaving the original file unchanged.
+ * 
+ * @param {string} command - The pip command to execute (e.g., 'pip3')
+ * @param {string[]} args - Command line arguments to pass to pip
+ * @returns {Promise<{status: number}>} Exit status of the pip command
  */
 export async function runPip(command, args) {
   try {
@@ -26,12 +62,15 @@ export async function runPip(command, args) {
     // https://pip.pypa.io/en/stable/topics/https-certificates/ explains that the 'cert' param (which we're providing via INI file)
     // will tell pip to use the provided CA bundle for HTTPS verification.
 
-    // Proxy settings: prefer GLOBAL_AGENT_HTTP_PROXY, then HTTPS_PROXY, then HTTP_PROXY
+    // Proxy settings: GLOBAL_AGENT_HTTP_PROXY is our safe-chain proxy (if active),
+    // otherwise fall back to user-defined HTTPS_PROXY or HTTP_PROXY environment variables
     const proxy = env.GLOBAL_AGENT_HTTP_PROXY || env.HTTPS_PROXY || env.HTTP_PROXY || '';
 
     const tmpDir = os.tmpdir();
     const pipConfigPath = path.join(tmpDir, `safe-chain-pip-${Date.now()}.ini`);
+    let cleanupConfigPath = null; // Track temp file for cleanup
 
+    // Note: Setting PIP_CONFIG_FILE overrides all pip config levels (Global/User/Site) per pip's loading order
     if (!env.PIP_CONFIG_FILE) {
       /** @type {{ global: { cert: string, proxy?: string } }} */
       const configObj = { global: { cert: combinedCaPath } };
@@ -41,6 +80,7 @@ export async function runPip(command, args) {
       const pipConfig = ini.stringify(configObj);
       await fs.writeFile(pipConfigPath, pipConfig);
       env.PIP_CONFIG_FILE = pipConfigPath;
+      cleanupConfigPath = pipConfigPath;
 
     } else if (fsSync.existsSync(env.PIP_CONFIG_FILE)) {
       ui.writeVerbose("Safe-chain: Merging user provided PIP_CONFIG_FILE with safe-chain certificate and proxy settings.");
@@ -72,32 +112,31 @@ export async function runPip(command, args) {
       // Save to a new temp file to avoid overwriting user's original config
       await fs.writeFile(pipConfigPath, updated, "utf-8");
       env.PIP_CONFIG_FILE = pipConfigPath;
+      cleanupConfigPath = pipConfigPath;
 
     } else {
       // The user provided PIP_CONFIG_FILE does not exist on disk
       // PIP will handle this as an error and inform the user
     }
 
-    // REQUESTS_CA_BUNDLE, SSL_CERT_FILE and PIP_CERT as extra safety nets.
-    if (env.REQUESTS_CA_BUNDLE) {
-      ui.writeWarning("Safe-chain: User defined REQUESTS_CA_BUNDLE found in environment. It will be overwritten.");
-    }
-    env.REQUESTS_CA_BUNDLE = combinedCaPath;
-
-    if (env.SSL_CERT_FILE) {
-      ui.writeWarning("Safe-chain: User defined SSL_CERT_FILE found in environment. It will be overwritten.");
-    }
-    env.SSL_CERT_FILE = combinedCaPath;
-
-    if (env.PIP_CERT) {
-      ui.writeWarning("Safe-chain: User defined PIP_CERT found in environment. It will be overwritten.");
-    }
-    env.PIP_CERT = combinedCaPath;
+    // Set fallback CA bundle environment variables for Python libraries that don't read pip config
+    setFallbackCaBundleEnvironmentVariables(env, combinedCaPath);
 
     const result = await safeSpawn(command, args, {
       stdio: "inherit",
       env,
     });
+
+    // Cleanup temporary config file if we created one
+    if (cleanupConfigPath) {
+      try {
+        await fs.unlink(cleanupConfigPath);
+      } catch (error) {
+        // Ignore cleanup errors - the file may have already been deleted or is inaccessible
+        // Temp files in os.tmpdir() may eventually be cleaned by the OS, but timing varies by platform
+      }
+    }
+
     return { status: result.status };
   } catch (/** @type any */ error) {
     if (error.status) {
diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
index 4af0b40..5d88b0e 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
@@ -9,15 +9,25 @@ describe("runPipCommand environment variable handling", () => {
   let runPip;
   let capturedArgs = null;
   let customEnv = null;
+  let capturedConfigContent = null; // Capture config file content before cleanup
 
   beforeEach(async () => {
     capturedArgs = null;
+    capturedConfigContent = null;
 
-    // Mock safeSpawn to capture args
+    // Mock safeSpawn to capture args and config file content before cleanup
     mock.module("../../utils/safeSpawn.js", {
       namedExports: {
         safeSpawn: async (command, args, options) => {
           capturedArgs = { command, args, options };
+          // Capture the config file content before the function cleans it up
+          if (options.env.PIP_CONFIG_FILE) {
+            try {
+              capturedConfigContent = await fs.readFile(options.env.PIP_CONFIG_FILE, "utf-8");
+            } catch (e) {
+              // Ignore if file doesn't exist or can't be read
+            }
+          }
           return { status: 0 };
         },
       },
@@ -151,9 +161,9 @@ describe("runPipCommand environment variable handling", () => {
     const originalParsed = ini.parse(originalContent);
     assert.strictEqual(originalParsed.global.cert, undefined, "original file should not gain cert");
 
-    // New file has merged settings
-    const newContent = await fs.readFile(newCfgPath, "utf-8");
-    const newParsed = ini.parse(newContent);
+    // New file has merged settings (read from captured content before cleanup)
+    assert.ok(capturedConfigContent, "config content should have been captured");
+    const newParsed = ini.parse(capturedConfigContent);
     assert.strictEqual(newParsed.global.cert, "/tmp/test-combined-ca.pem", "new config should include cert");
     assert.strictEqual(newParsed.global.proxy, "http://localhost:8080", "new config should include proxy from env");
     assert.strictEqual(newParsed.global["index-url"], "https://example.com/simple", "index-url should be preserved");
@@ -166,8 +176,8 @@ describe("runPipCommand environment variable handling", () => {
     assert.strictEqual(res.status, 0);
 
     const configPath = capturedArgs.options.env.PIP_CONFIG_FILE;
-    const content = await fs.readFile(configPath, "utf-8");
-    const parsed = ini.parse(content);
+    assert.ok(capturedConfigContent, "config content should have been captured");
+    const parsed = ini.parse(capturedConfigContent);
     assert.ok(parsed.global, "[global] should exist after creation");
     assert.strictEqual(
       parsed.global.proxy,
@@ -198,8 +208,9 @@ describe("runPipCommand environment variable handling", () => {
     assert.strictEqual(originalParsed.global.cert, undefined, "original file should not gain cert");
     assert.strictEqual(originalParsed.global.proxy, "http://original:9999", "original proxy remains");
 
-    // New file: cert and proxy always overwritten
-    const newParsed = ini.parse(await fs.readFile(newCfgPath, "utf-8"));
+    // New file: cert and proxy always overwritten (read from captured content)
+    assert.ok(capturedConfigContent, "config content should have been captured");
+    const newParsed = ini.parse(capturedConfigContent);
     assert.strictEqual(newParsed.global.cert, "/tmp/test-combined-ca.pem", "cert always overwritten in temp config");
     assert.strictEqual(newParsed.global.proxy, "http://localhost:8080", "proxy always overwritten in temp config");
     customEnv = null;
@@ -228,9 +239,9 @@ describe("runPipCommand environment variable handling", () => {
     assert.strictEqual(originalParsed.global.cert, "/path/to/existing.pem", "original cert preserved");
     assert.strictEqual(originalParsed.global.proxy, "http://original:9999", "original proxy preserved");
 
-  // New temp config: cert and proxy always overwritten
-  const newContent = await fs.readFile(newCfgPath, "utf-8");
-  const newParsed = ini.parse(newContent);
+  // New temp config: cert and proxy always overwritten (read from captured content)
+  assert.ok(capturedConfigContent, "config content should have been captured");
+  const newParsed = ini.parse(capturedConfigContent);
   assert.strictEqual(newParsed.global.cert, "/tmp/test-combined-ca.pem", "cert always overwritten in temp config");
   assert.strictEqual(newParsed.global.proxy, "http://localhost:8080", "proxy always overwritten in temp config");
     customEnv = null;
@@ -253,8 +264,9 @@ describe("runPipCommand environment variable handling", () => {
     assert.strictEqual(originalParsed.global.cert, "/path/to/existing.pem", "original cert unchanged");
     assert.strictEqual(originalParsed.global.proxy, undefined, "original proxy still missing");
 
-  // New file: cert and proxy always overwritten
-  const newParsed = ini.parse(await fs.readFile(newCfgPath, "utf-8"));
+  // New file: cert and proxy always overwritten (read from captured content)
+  assert.ok(capturedConfigContent, "config content should have been captured");
+  const newParsed = ini.parse(capturedConfigContent);
   assert.strictEqual(newParsed.global.cert, "/tmp/test-combined-ca.pem", "cert always overwritten in temp config");
   assert.strictEqual(newParsed.global.proxy, "http://localhost:8080", "proxy always overwritten in temp config");
     customEnv = null;
@@ -271,8 +283,8 @@ describe("runPipCommand environment variable handling", () => {
     ].join("\n");
     await fs.writeFile(cfgPath, initialIni, "utf-8");
 
-    process.env.PIP_CONFIG_FILE = cfgPath;
-    const mod = await import("./runPipCommand.js");
+    customEnv = { PIP_CONFIG_FILE: cfgPath };
+    
     // Capture stdout/stderr
     let output = "";
     const originalWrite = process.stdout.write;
@@ -280,14 +292,13 @@ describe("runPipCommand environment variable handling", () => {
     process.stdout.write = (chunk, ...args) => { output += chunk; return originalWrite.apply(process.stdout, [chunk, ...args]); };
     process.stderr.write = (chunk, ...args) => { output += chunk; return originalError.apply(process.stderr, [chunk, ...args]); };
 
-    await mod.runPip("pip3", ["install", "requests"]);
+    await runPip("pip3", ["install", "requests"]);
 
     process.stdout.write = originalWrite;
     process.stderr.write = originalError;
 
     assert.ok(output.includes("cert found in PIP_CONFIG_FILE"), "Should warn about cert overwrite in output");
     assert.ok(output.includes("proxy found in PIP_CONFIG_FILE"), "Should warn about proxy overwrite in output");
-    delete process.env.PIP_CONFIG_FILE;
     customEnv = null;
   });
 });

From ab1aa0dce9f0f72a94b2d472694290288d1513b7 Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Fri, 21 Nov 2025 09:58:43 -0800
Subject: [PATCH 24/25] Little cleanup

---
 packages/safe-chain/src/packagemanager/pip/runPipCommand.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 8efa000..3e83346 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -39,9 +39,9 @@ function setFallbackCaBundleEnvironmentVariables(env, combinedCaPath) {
 /**
  * Runs a pip command with safe-chain's certificate bundle and proxy configuration.
  * 
- * Creates a temporary pip config file (cleaned up automatically after execution) to configure:
- * - Certificate bundle for HTTPS verification
- * - Proxy settings if available
+ * Creates a temporary pip config file to configure:
+ * - Cert bundle for HTTPS verification
+ * - Proxy settings
  * 
  * If the user has an existing PIP_CONFIG_FILE, a new temporary config is created that merges
  * their settings with safe-chain's, leaving the original file unchanged.

From 72bf44cb6d5b1f92a025605d757a20deb77095a0 Mon Sep 17 00:00:00 2001
From: Reinier Criel <reinier.criel@gmail.com>
Date: Fri, 21 Nov 2025 10:31:57 -0800
Subject: [PATCH 25/25] Fix linting issue

---
 packages/safe-chain/src/packagemanager/pip/runPipCommand.js    | 2 +-
 .../safe-chain/src/packagemanager/pip/runPipCommand.spec.js    | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 3e83346..23485ff 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -131,7 +131,7 @@ export async function runPip(command, args) {
     if (cleanupConfigPath) {
       try {
         await fs.unlink(cleanupConfigPath);
-      } catch (error) {
+      } catch {
         // Ignore cleanup errors - the file may have already been deleted or is inaccessible
         // Temp files in os.tmpdir() may eventually be cleaned by the OS, but timing varies by platform
       }
diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
index 5d88b0e..d0df961 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
@@ -24,7 +24,7 @@ describe("runPipCommand environment variable handling", () => {
           if (options.env.PIP_CONFIG_FILE) {
             try {
               capturedConfigContent = await fs.readFile(options.env.PIP_CONFIG_FILE, "utf-8");
-            } catch (e) {
+            } catch {
               // Ignore if file doesn't exist or can't be read
             }
           }
@@ -175,7 +175,6 @@ describe("runPipCommand environment variable handling", () => {
     const res = await runPip("pip3", ["install", "requests"]);
     assert.strictEqual(res.status, 0);
 
-    const configPath = capturedArgs.options.env.PIP_CONFIG_FILE;
     assert.ok(capturedConfigContent, "config content should have been captured");
     const parsed = ini.parse(capturedConfigContent);
     assert.ok(parsed.global, "[global] should exist after creation");