Merge branch 'main' into feature/pipx-2

test/e2e/certbundle.e2e.spec.js

@@ -231,7 +231,7 @@ describe("E2E: NODE_EXTRA_CA_CERTS merging", () => {
   it(`pip install works without NODE_EXTRA_CA_CERTS set`, async () => {
     const shell = await container.openShell("zsh");
     
-    await shell.runCommand("safe-chain setup --include-python");
+    await shell.runCommand("safe-chain setup");
     await shell.runCommand("unset NODE_EXTRA_CA_CERTS");
     
     const result = await shell.runCommand(
@@ -247,7 +247,7 @@ describe("E2E: NODE_EXTRA_CA_CERTS merging", () => {
   it(`pip install works with valid NODE_EXTRA_CA_CERTS set`, async () => {
     const shell = await container.openShell("zsh");
     
-    await shell.runCommand("safe-chain setup --include-python");
+    await shell.runCommand("safe-chain setup");
     
     // Create a temporary valid certificate
     await shell.runCommand("cp /etc/ssl/certs/ca-certificates.crt /tmp/pip-valid-certs.pem");
@@ -265,7 +265,7 @@ describe("E2E: NODE_EXTRA_CA_CERTS merging", () => {
   it(`pip install handles non-existent NODE_EXTRA_CA_CERTS gracefully`, async () => {
     const shell = await container.openShell("zsh");
     
-    await shell.runCommand("safe-chain setup --include-python");
+    await shell.runCommand("safe-chain setup");
     
     const result = await shell.runCommand(
       'export NODE_EXTRA_CA_CERTS="/tmp/nonexistent-pip-certs.pem" && pip3 install --break-system-packages requests'
@@ -281,7 +281,7 @@ describe("E2E: NODE_EXTRA_CA_CERTS merging", () => {
   it(`pip install handles invalid NODE_EXTRA_CA_CERTS gracefully`, async () => {
     const shell = await container.openShell("zsh");
     
-    await shell.runCommand("safe-chain setup --include-python");
+    await shell.runCommand("safe-chain setup");
     
     // Create invalid cert
     await shell.runCommand(

test/e2e/include-python-deprecation.e2e.spec.js

@@ -0,0 +1,45 @@
+import { describe, it, before, beforeEach, afterEach } from "node:test";
+import { DockerTestContainer } from "./DockerTestContainer.js";
+import assert from "node:assert";
+
+describe("E2E: deprecated --include-python handling", () => {
+  let container;
+
+  before(async () => {
+    DockerTestContainer.buildImage();
+  });
+
+  beforeEach(async () => {
+    container = new DockerTestContainer();
+    await container.start();
+  });
+
+  afterEach(async () => {
+    if (container) {
+      await container.stop();
+      container = null;
+    }
+  });
+
+  for (let shell of ["bash", "zsh"]) {
+    it(`safe-chain setup warns and continues for ${shell}`, async () => {
+      const sh = await container.openShell(shell);
+      const result = await sh.runCommand("safe-chain setup --include-python");
+
+      assert.ok(
+        result.output.toLowerCase().includes("deprecated and ignored"),
+        `Expected warning about deprecated --include-python. Output was:\n${result.output}`
+      );
+    });
+
+    it(`safe-chain setup-ci warns and continues for ${shell}`, async () => {
+      const sh = await container.openShell(shell);
+      const result = await sh.runCommand("safe-chain setup-ci --include-python");
+
+      assert.ok(
+        result.output.toLowerCase().includes("deprecated and ignored"),
+        `Expected warning about deprecated --include-python. Output was:\n${result.output}`
+      );
+    });
+  }
+});

test/e2e/pip-ci.e2e.spec.js

@@ -86,7 +86,7 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
       // Setup safe-chain CI shims
       const installationShell = await container.openShell(shell);
       await installationShell.runCommand(
-        "safe-chain setup-ci --include-python"
+        "safe-chain setup-ci"
       );
 
       // Add $HOME/.safe-chain/shims to PATH for subsequent shells
@@ -115,7 +115,7 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
     it(`setup-ci routes python -m pip through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
       await installationShell.runCommand(
-        "safe-chain setup-ci --include-python"
+        "safe-chain setup-ci"
       );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
@@ -138,7 +138,7 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
     it(`setup-ci routes python3 -m pip through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
       await installationShell.runCommand(
-        "safe-chain setup-ci --include-python"
+        "safe-chain setup-ci"
       );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
@@ -161,7 +161,7 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
     it(`setup-ci routes pip through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
       await installationShell.runCommand(
-        "safe-chain setup-ci --include-python"
+        "safe-chain setup-ci"
       );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
@@ -184,7 +184,7 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
     it(`setup-ci routes pip3 through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
       await installationShell.runCommand(
-        "safe-chain setup-ci --include-python"
+        "safe-chain setup-ci"
       );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"

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 --include-python");
+    await installationShell.runCommand("safe-chain setup");
 
     // Clear pip cache before each test to ensure fresh downloads through proxy
     await installationShell.runCommand("pip3 cache purge");

test/e2e/poetry.e2e.spec.js

@@ -15,7 +15,7 @@ describe("E2E: poetry coverage", () => {
     await container.start();
 
     const installationShell = await container.openShell("zsh");
-    await installationShell.runCommand("safe-chain setup --include-python");
+    await installationShell.runCommand("safe-chain setup");
     
     // Clear poetry cache
     await installationShell.runCommand("command poetry cache clear pypi --all -n");

test/e2e/teardown-dirs.e2e.spec.js

@@ -57,20 +57,18 @@ describe("E2E: safe-chain teardown command", () => {
     assert.ok(checkScriptsGone.output.includes("missing"), "Scripts directory should be removed after teardown");
   });
 
-  it("safe-chain teardown removes shims directory created by setup-ci --include-python", async () => {
+  it("safe-chain teardown removes shims directory created by setup-ci", async () => {
     const shell = await container.openShell("bash");
 
-    // Run setup-ci with --include-python
-    await shell.runCommand("safe-chain setup-ci --include-python");
-
+    // Run setup-ci
+    await shell.runCommand("safe-chain setup-ci");
     // Verify shims directory exists
     const checkShimsExist = await shell.runCommand("test -d ~/.safe-chain/shims && echo 'exists' || echo 'missing'");
-    assert.ok(checkShimsExist.output.includes("exists"), "Shims directory should exist after setup-ci --include-python");
+    assert.ok(checkShimsExist.output.includes("exists"), "Shims directory should exist after setup-ci");
 
     // Verify Python shims were created
     const checkPythonShims = await shell.runCommand("test -f ~/.safe-chain/shims/pip && echo 'exists' || echo 'missing'");
-    assert.ok(checkPythonShims.output.includes("exists"), "Python shims should exist after setup-ci --include-python");
-
+    assert.ok(checkPythonShims.output.includes("exists"), "Python shims should exist after setup-ci");
     // Run teardown
     await shell.runCommand("safe-chain teardown");
 
@@ -79,15 +77,14 @@ describe("E2E: safe-chain teardown command", () => {
     assert.ok(checkShimsGone.output.includes("missing"), "Shims directory should be removed after teardown");
   });
 
-  it("safe-chain teardown removes scripts directory created by setup --include-python", async () => {
+  it("safe-chain teardown removes scripts directory created by setup", async () => {
     const shell = await container.openShell("bash");
 
-    // Run setup with --include-python
-    await shell.runCommand("safe-chain setup --include-python");
-
+    // Run setup
+    await shell.runCommand("safe-chain setup");
     // Verify scripts directory exists
     const checkScriptsExist = await shell.runCommand("test -d ~/.safe-chain/scripts && echo 'exists' || echo 'missing'");
-    assert.ok(checkScriptsExist.output.includes("exists"), "Scripts directory should exist after setup --include-python");
+    assert.ok(checkScriptsExist.output.includes("exists"), "Scripts directory should exist after setup");
 
     // Run teardown
     await shell.runCommand("safe-chain teardown");

test/e2e/uv.e2e.spec.js

@@ -15,7 +15,7 @@ describe("E2E: uv coverage", () => {
     await container.start();
 
     const installationShell = await container.openShell("zsh");
-    await installationShell.runCommand("safe-chain setup --include-python");
+    await installationShell.runCommand("safe-chain setup");
 
     // Clear uv cache
     await installationShell.runCommand("uv cache clean");