Don't cache git credentials in workflows

.github/workflows/docs.yml

@@ -31,6 +31,8 @@ jobs:
     # for latest versions if the standard actions start emitting warnings
     steps:
     - uses: actions/checkout@v4
+      with:
+        persist-credentials: false
 
     # sphinx-action uses docker under the hood and doesn't play nice with the
     # dependency caching, so it may be better to switch to using `tox -e docs`

.github/workflows/publish.yml

@@ -15,6 +15,8 @@ jobs:
       id-token: write
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
 
       - uses: pdm-project/setup-pdm@v4
         with:

.github/workflows/scan-workflows.yml

@@ -0,0 +1,41 @@
+name: "Scan workflows"
+
+on:
+    pull_request:
+      branches:
+        - "**"
+      paths:
+        # Run for changes to *any* workflow file
+        - ".github/workflows/*.yml"
+    push:
+      branches:
+        - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      # required for all workflows
+      security-events: write
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Install zizmor
+        run: cargo install zizmor
+
+      - name: Scan workflows
+        run:
+          zizmor --format=sarif . | tee workflow-scan.sarif
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: github/codeql-action/upload-sarif@v3
+        if: always()
+        with:
+          # Path to SARIF file relative to the root of the repository
+          sarif_file: workflow-scan.sarif

.github/workflows/test.yml

@@ -48,6 +48,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        persist-credentials: false
 
     - name: Capture timestamp for debugging artifacts
       id: timestamp
@@ -149,6 +151,9 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
       - uses: actions/setup-python@v5
         with:
           # Use latest Python, so it understands all syntax.

.github/workflows/update-expected-output.yml

@@ -65,6 +65,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        persist-credentials: false
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
@@ -183,6 +185,8 @@ jobs:
       uses: actions/checkout@v4
       with:
         ref: ${{ github.head_ref }}
+        # The PR creation step below needs git push credentials
+        persist-credentials: true
 
     - name: Download all updated output files
       uses: actions/download-artifact@v4

.gitignore

@@ -1,5 +1,6 @@
 # Artifacts exported from CI by test suite
 /export/
+*.sarif
 
 # VSCode config is platform specific
 .vscode

tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json

@@ -1,12 +1,12 @@
 {
   "app_launch_module": "scipy_client",
-  "app_launch_module_hash": "sha256/344b1be70920bd9635ce38fa14fca86b531ce2e334f54968321469c5fbb5b608",
+  "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "737a6b60e3be2fed00a8d1385973bf9526b25250a8fa2dd65d288925fcfa341b"
+    "sha256": "84c38c5717c3ff4e5fc9a13b22045b8c7fa2a96682648e419e22983e9023f554"
   },
   "archive_name": "app-scipy-client.tar.xz",
-  "archive_size": 1424,
+  "archive_size": 1504,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,

tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json

@@ -1,12 +1,12 @@
 {
   "app_launch_module": "scipy_import",
-  "app_launch_module_hash": "sha256:6278ff255372146d752518ffdf49f3432667d7c93997ed980b3676fdc75406ee",
+  "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "2d8d19d109288cdc91a643e7b3fd9bcbc9fa38d40bbafe631074878245cb038f"
+    "sha256": "4c30fb1472a1905d0369b700bd922f317f8ab4875e7b02a9c997dedf5cb0b175"
   },
   "archive_name": "app-scipy-import.tar.xz",
-  "archive_size": 1336,
+  "archive_size": 1412,
   "install_target": "app-scipy-import",
   "layer_name": "app-scipy-import",
   "lock_version": 1,

tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-sklearn-import.json

@@ -1,12 +1,12 @@
 {
   "app_launch_module": "sklearn_import",
-  "app_launch_module_hash": "sha256:b6de2b52093004bcc39df16d115929021937f77b5feda45d090b06116ea34f49",
+  "app_launch_module_hash": "sha256:f66c01bbcca47cd31d79d2fb5377de0de18631ffc3c904629d46f6cad2918694",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "dd778c5f82c1c1ee62765d876a063dba4b374b6f4e06842104c8945e66663748"
+    "sha256": "ba0b38bb3c8539b9882bdfd752f1407961f26fe8a2c1af3d1bed62d83478b8e7"
   },
   "archive_name": "app-sklearn-import.tar.xz",
-  "archive_size": 1332,
+  "archive_size": 1420,
   "install_target": "app-sklearn-import",
   "layer_name": "app-sklearn-import",
   "lock_version": 1,

tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json

@@ -3,13 +3,13 @@
     "applications": [
       {
         "app_launch_module": "scipy_import",
-        "app_launch_module_hash": "sha256:6278ff255372146d752518ffdf49f3432667d7c93997ed980b3676fdc75406ee",
+        "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "2d8d19d109288cdc91a643e7b3fd9bcbc9fa38d40bbafe631074878245cb038f"
+          "sha256": "4c30fb1472a1905d0369b700bd922f317f8ab4875e7b02a9c997dedf5cb0b175"
         },
         "archive_name": "app-scipy-import.tar.xz",
-        "archive_size": 1336,
+        "archive_size": 1412,
         "install_target": "app-scipy-import",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
@@ -23,13 +23,13 @@
       },
       {
         "app_launch_module": "scipy_client",
-        "app_launch_module_hash": "sha256/344b1be70920bd9635ce38fa14fca86b531ce2e334f54968321469c5fbb5b608",
+        "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "737a6b60e3be2fed00a8d1385973bf9526b25250a8fa2dd65d288925fcfa341b"
+          "sha256": "84c38c5717c3ff4e5fc9a13b22045b8c7fa2a96682648e419e22983e9023f554"
         },
         "archive_name": "app-scipy-client.tar.xz",
-        "archive_size": 1424,
+        "archive_size": 1504,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,
@@ -44,13 +44,13 @@
       },
       {
         "app_launch_module": "sklearn_import",
-        "app_launch_module_hash": "sha256:b6de2b52093004bcc39df16d115929021937f77b5feda45d090b06116ea34f49",
+        "app_launch_module_hash": "sha256:f66c01bbcca47cd31d79d2fb5377de0de18631ffc3c904629d46f6cad2918694",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "dd778c5f82c1c1ee62765d876a063dba4b374b6f4e06842104c8945e66663748"
+          "sha256": "ba0b38bb3c8539b9882bdfd752f1407961f26fe8a2c1af3d1bed62d83478b8e7"
         },
         "archive_name": "app-sklearn-import.tar.xz",
-        "archive_size": 1332,
+        "archive_size": 1420,
         "install_target": "app-sklearn-import",
         "layer_name": "app-sklearn-import",
         "lock_version": 1,

tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json

@@ -1,12 +1,12 @@
 {
   "app_launch_module": "scipy_client",
-  "app_launch_module_hash": "sha256/344b1be70920bd9635ce38fa14fca86b531ce2e334f54968321469c5fbb5b608",
+  "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "b4f061f14023391f588940cb8f509ae8c46dd8fca552346c15df153f09eeb85d"
+    "sha256": "2cdf88d7a5ed2dca88d7a59e2b5d9744503cf824218371948000f1b08486df4e"
   },
   "archive_name": "app-scipy-client.tar.xz",
-  "archive_size": 1400,
+  "archive_size": 1484,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,

tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json

@@ -1,12 +1,12 @@
 {
   "app_launch_module": "scipy_import",
-  "app_launch_module_hash": "sha256:6278ff255372146d752518ffdf49f3432667d7c93997ed980b3676fdc75406ee",
+  "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "a7d51a74e9c5b370af3038bb5abb08fd81b49b446c02e6c16ff6b1fd9ac9025b"
+    "sha256": "5034f1fa0a0731af9e88699519a508e72662b003c30e14814ce72e00ef8a6223"
   },
   "archive_name": "app-scipy-import.tar.xz",
-  "archive_size": 1284,
+  "archive_size": 1392,
   "install_target": "app-scipy-import",
   "layer_name": "app-scipy-import",
   "lock_version": 1,

tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json

@@ -3,13 +3,13 @@
     "applications": [
       {
         "app_launch_module": "scipy_import",
-        "app_launch_module_hash": "sha256:6278ff255372146d752518ffdf49f3432667d7c93997ed980b3676fdc75406ee",
+        "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "a7d51a74e9c5b370af3038bb5abb08fd81b49b446c02e6c16ff6b1fd9ac9025b"
+          "sha256": "5034f1fa0a0731af9e88699519a508e72662b003c30e14814ce72e00ef8a6223"
         },
         "archive_name": "app-scipy-import.tar.xz",
-        "archive_size": 1284,
+        "archive_size": 1392,
         "install_target": "app-scipy-import",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
@@ -23,13 +23,13 @@
       },
       {
         "app_launch_module": "scipy_client",
-        "app_launch_module_hash": "sha256/344b1be70920bd9635ce38fa14fca86b531ce2e334f54968321469c5fbb5b608",
+        "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "b4f061f14023391f588940cb8f509ae8c46dd8fca552346c15df153f09eeb85d"
+          "sha256": "2cdf88d7a5ed2dca88d7a59e2b5d9744503cf824218371948000f1b08486df4e"
         },
         "archive_name": "app-scipy-client.tar.xz",
-        "archive_size": 1400,
+        "archive_size": 1484,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,

tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json

@@ -1,12 +1,12 @@
 {
   "app_launch_module": "scipy_client",
-  "app_launch_module_hash": "sha256/344b1be70920bd9635ce38fa14fca86b531ce2e334f54968321469c5fbb5b608",
+  "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "a4229a9be2b24b0739b11729278d9acb68320b1d36b1f2a7d46191b359f4df74"
+    "sha256": "69060c0e0a74290723c5e65a343e463112a249da960d8bf29997933cd1565787"
   },
   "archive_name": "app-scipy-client.zip",
-  "archive_size": 255062,
+  "archive_size": 255147,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,

tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json

@@ -1,12 +1,12 @@
 {
   "app_launch_module": "scipy_import",
-  "app_launch_module_hash": "sha256:6278ff255372146d752518ffdf49f3432667d7c93997ed980b3676fdc75406ee",
+  "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "3ebb818738bdd10e5eebdb48fda4be41ac73af88890ba9f749c7dbb23ce2aaa8"
+    "sha256": "1907700fc74c6a0bc62d851dce87bfed6a0ad52d0fec5863c9eadd1e26c029ff"
   },
   "archive_name": "app-scipy-import.zip",
-  "archive_size": 254578,
+  "archive_size": 254658,
   "install_target": "app-scipy-import",
   "layer_name": "app-scipy-import",
   "lock_version": 1,

tests/sample_project/expected_manifests/win_amd64/venvstacks.json

@@ -3,13 +3,13 @@
     "applications": [
       {
         "app_launch_module": "scipy_import",
-        "app_launch_module_hash": "sha256:6278ff255372146d752518ffdf49f3432667d7c93997ed980b3676fdc75406ee",
+        "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "3ebb818738bdd10e5eebdb48fda4be41ac73af88890ba9f749c7dbb23ce2aaa8"
+          "sha256": "1907700fc74c6a0bc62d851dce87bfed6a0ad52d0fec5863c9eadd1e26c029ff"
         },
         "archive_name": "app-scipy-import.zip",
-        "archive_size": 254578,
+        "archive_size": 254658,
         "install_target": "app-scipy-import",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
@@ -23,13 +23,13 @@
       },
       {
         "app_launch_module": "scipy_client",
-        "app_launch_module_hash": "sha256/344b1be70920bd9635ce38fa14fca86b531ce2e334f54968321469c5fbb5b608",
+        "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "a4229a9be2b24b0739b11729278d9acb68320b1d36b1f2a7d46191b359f4df74"
+          "sha256": "69060c0e0a74290723c5e65a343e463112a249da960d8bf29997933cd1565787"
         },
         "archive_name": "app-scipy-client.zip",
-        "archive_size": 255062,
+        "archive_size": 255147,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,

tests/sample_project/launch_modules/scipy_client/cli.py

@@ -1,5 +1,6 @@
 """Sample CLI helper module importing scipy and httpx"""
 
+import numpy
 import scipy
 import httpx
 
@@ -11,4 +12,10 @@ def main():
     for disallowed in ("pip", "sklearn"):
         if find_spec(disallowed):
             raise RuntimeError(f"Should not be able to import {disallowed!r}!")
+
+    for module in (numpy, scipy, httpx):
+        # This is just here to allow the launch modules to pass lint checks
+        assert module.__spec__ is not None
+        assert find_spec(module.__spec__.name) is not None
+
     print("Environment launch module executed successfully")

tests/sample_project/launch_modules/scipy_import.py

@@ -1,5 +1,6 @@
 """Sample launch module importing scipy"""
 
+import numpy
 import scipy
 
 if __name__ == "__main__":
@@ -10,4 +11,9 @@
         if find_spec(disallowed):
             raise RuntimeError(f"Should not be able to import {disallowed!r}!")
 
+    for module in (numpy, scipy):
+        # This is just here to allow the launch modules to pass lint checks
+        assert module.__spec__ is not None
+        assert find_spec(module.__spec__.name) is not None
+
     print("Environment launch module executed successfully")

tests/sample_project/launch_modules/sklearn_import.py

@@ -1,5 +1,7 @@
 """Sample launch module importing sklearn"""
 
+import numpy
+import scipy
 import sklearn
 
 if __name__ == "__main__":
@@ -10,4 +12,9 @@
         if find_spec(disallowed):
             raise RuntimeError(f"Should not be able to import {disallowed!r}!")
 
+    for module in (numpy, scipy, sklearn):
+        # This is just here to allow the launch modules to pass lint checks
+        assert module.__spec__ is not None
+        assert find_spec(module.__spec__.name) is not None
+
     print("Environment launch module executed successfully")