From 2de277910b765b125dae37c6c83998a6b44823aa Mon Sep 17 00:00:00 2001
From: Mikael Simberg <mikael.simberg@iki.fi>
Date: Fri, 13 Jun 2025 11:46:02 +0200
Subject: [PATCH 01/13] Add support for specifying repo and commit of the
 builtin repo

---
 stackinator/builder.py           | 77 ++++++++++++++++++++++++++++++--
 stackinator/schema/config.json   | 16 +++++++
 stackinator/templates/repos.yaml |  3 +-
 3 files changed, 91 insertions(+), 5 deletions(-)

diff --git a/stackinator/builder.py b/stackinator/builder.py
index 66d50a5d..34dcb44f 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -169,6 +169,68 @@ def generate(self, recipe):
         store_path.mkdir(exist_ok=True)
         tmp_path.mkdir(exist_ok=True)
 
+        ##################
+        # check out the version of spack-packages
+        spack_packages = recipe.config["spack_packages"]
+        spack_packages_path = self.path / "spack-packages"
+
+        # Clone the spack-packages repository if it has not already been checked
+        # out
+        if not (spack_packages_path / ".git").is_dir():
+            self._logger.info(f'spack-packages: clone repository {spack_packages["repo"]}')
+
+            # clone the repository
+            capture = subprocess.run(
+                ["git", "clone", "--filter=tree:0", spack_packages["repo"], spack_packages_path],
+                shell=False,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.STDOUT,
+            )
+            self._logger.debug(capture.stdout.decode("utf-8"))
+
+            if capture.returncode != 0:
+                self._logger.error(f'error cloning the repository {spack_packages["repo"]}')
+                capture.check_returncode()
+
+        # Fetch the specific branch
+        if spack_packages["commit"]:
+            self._logger.info(f'spack-packages: fetch branch/commit {spack_packages["commit"]}')
+            capture = subprocess.run(
+                ["git", "-C", spack_packages_path, "fetch", "origin", spack_packages["commit"]],
+                shell=False,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.STDOUT,
+            )
+            self._logger.debug(capture.stdout.decode("utf-8"))
+
+            if capture.returncode != 0:
+                self._logger.debug(f'unable to change to the fetch {spack_packages["commit"]}')
+                capture.check_returncode()
+
+        # Check out a branch or commit if one was specified
+        if spack["commit"]:
+            self._logger.info(f'spack-packages: checkout branch/commit {spack_packages["commit"]}')
+            capture = subprocess.run(
+                ["git", "-C", spack_packages_path, "checkout", spack_packages["commit"]],
+                shell=False,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.STDOUT,
+            )
+            self._logger.debug(capture.stdout.decode("utf-8"))
+
+            if capture.returncode != 0:
+                self._logger.debug(f'unable to change to the requested commit {spack_packages["commit"]}')
+                capture.check_returncode()
+
+        # get the spack commit
+        spack_packages_git_commit_result = subprocess.run(
+            ["git", "-C", spack_packages_path, "rev-parse", "HEAD"],
+            shell=False,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+        ##################
+
         # check out the version of spack
         spack_version = recipe.spack_version
         self._logger.debug(f"spack version for templates: {spack_version}")
@@ -229,13 +291,16 @@ def generate(self, recipe):
                 capture.check_returncode()
 
         # get the spack commit
-        git_commit_result = subprocess.run(
+        spack_git_commit_result = subprocess.run(
             ["git", "-C", spack_path, "rev-parse", "HEAD"], shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE
         )
         spack_meta = {
             "ref": spack["commit"],
-            "commit": git_commit_result.stdout.strip().decode("utf-8"),
+            "commit": spack_git_commit_result.stdout.strip().decode("utf-8"),
             "url": spack["repo"],
+            "packages_ref": spack_packages["commit"],
+            "packages_commit": spack_packages_git_commit_result.stdout.strip().decode("utf-8"),
+            "packages_url": spack_packages["repo"],
         }
 
         # load the jinja templating environment
@@ -415,7 +480,7 @@ def generate(self, recipe):
         # Delete the store/repo path, if it already exists.
         # Do this so that incremental builds (though not officially supported) won't break if a repo is updated.
         repo_dst = store_path / "repo"
-        self._logger.debug(f"creating the stack spack prepo in {repo_dst}")
+        self._logger.debug(f"creating the stack spack repo in {repo_dst}")
         if repo_dst.exists():
             self._logger.debug(f"{repo_dst} exists ... deleting")
             shutil.rmtree(repo_dst)
@@ -439,7 +504,11 @@ def generate(self, recipe):
         repos_yaml_template = jinja_env.get_template("repos.yaml")
         with (config_path / "repos.yaml").open("w") as f:
             repo_path = recipe.mount / "repo"
-            f.write(repos_yaml_template.render(repo_path=repo_path.as_posix(), verbose=False))
+            f.write(
+                repos_yaml_template.render(
+                    repo_path=repo_path.as_posix(), builtin_repo_path=spack_packages_path.as_posix(), verbose=False
+                )
+            )
             f.write("\n")
 
         # Iterate over the source repositories copying their contents to the consolidated repo in the uenv.
diff --git a/stackinator/schema/config.json b/stackinator/schema/config.json
index df63fa70..cb142ceb 100644
--- a/stackinator/schema/config.json
+++ b/stackinator/schema/config.json
@@ -28,6 +28,22 @@
                 }
             }
         },
+        "spack_packages" : {
+            "type" : "object",
+            "additionalProperties": false,
+            "properties" : {
+                "repo": {
+                    "type": "string"
+                },
+                "commit": {
+                    "oneOf": [
+                        {"type" : "string"},
+                        {"type" : "null"}
+                    ],
+                    "default": null
+                }
+            }
+        },
         "mirror" : {
             "type" : "object",
             "additionalProperties": false,
diff --git a/stackinator/templates/repos.yaml b/stackinator/templates/repos.yaml
index 514838b0..3cf34f26 100644
--- a/stackinator/templates/repos.yaml
+++ b/stackinator/templates/repos.yaml
@@ -1,2 +1,3 @@
 repos:
-- {{ repo_path }}
+  alps: {{ repo_path }}
+  builtin: {{ builtin_repo_path }}

From a460f93ea426e5bcabdaa851ad0aa52a8151a348 Mon Sep 17 00:00:00 2001
From: Mikael Simberg <mikael.simberg@iki.fi>
Date: Fri, 13 Jun 2025 12:06:23 +0200
Subject: [PATCH 02/13] Fix builtin repo path

---
 stackinator/builder.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/stackinator/builder.py b/stackinator/builder.py
index 34dcb44f..124a4859 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -504,9 +504,10 @@ def generate(self, recipe):
         repos_yaml_template = jinja_env.get_template("repos.yaml")
         with (config_path / "repos.yaml").open("w") as f:
             repo_path = recipe.mount / "repo"
+            builtin_repo_path = recipe.mount / "spack-packages"
             f.write(
                 repos_yaml_template.render(
-                    repo_path=repo_path.as_posix(), builtin_repo_path=spack_packages_path.as_posix(), verbose=False
+                    repo_path=repo_path.as_posix(), builtin_repo_path=builtin_repo_path.as_posix(), verbose=False
                 )
             )
             f.write("\n")

From 1f921fa2ccc17c242cf469d3ca53d4f7fdc3eec5 Mon Sep 17 00:00:00 2001
From: Mikael Simberg <mikael.simberg@iki.fi>
Date: Fri, 13 Jun 2025 12:09:37 +0200
Subject: [PATCH 03/13] Fix spack_packages["commit"]

---
 stackinator/builder.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stackinator/builder.py b/stackinator/builder.py
index 124a4859..9450107b 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -208,7 +208,7 @@ def generate(self, recipe):
                 capture.check_returncode()
 
         # Check out a branch or commit if one was specified
-        if spack["commit"]:
+        if spack_packages["commit"]:
             self._logger.info(f'spack-packages: checkout branch/commit {spack_packages["commit"]}')
             capture = subprocess.run(
                 ["git", "-C", spack_packages_path, "checkout", spack_packages["commit"]],

From 69603e3400cec44ffb52efb72401f7ec8747d159 Mon Sep 17 00:00:00 2001
From: Mikael Simberg <simberg@cscs.ch>
Date: Fri, 13 Jun 2025 13:54:40 +0200
Subject: [PATCH 04/13] Put spack-packages in uenv

---
 stackinator/builder.py           | 4 ++--
 stackinator/templates/repos.yaml | 4 +++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/stackinator/builder.py b/stackinator/builder.py
index 9450107b..a843e758 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -172,7 +172,7 @@ def generate(self, recipe):
         ##################
         # check out the version of spack-packages
         spack_packages = recipe.config["spack_packages"]
-        spack_packages_path = self.path / "spack-packages"
+        spack_packages_path = store_path / "spack-packages"
 
         # Clone the spack-packages repository if it has not already been checked
         # out
@@ -507,7 +507,7 @@ def generate(self, recipe):
             builtin_repo_path = recipe.mount / "spack-packages"
             f.write(
                 repos_yaml_template.render(
-                    repo_path=repo_path.as_posix(), builtin_repo_path=builtin_repo_path.as_posix(), verbose=False
+                    repo_path=repo_path.as_posix(), builtin_repo_path=builtin_repo_path.as_posix(), builtin_repo_git_repo=spack_packages["repo"], verbose=False
                 )
             )
             f.write("\n")
diff --git a/stackinator/templates/repos.yaml b/stackinator/templates/repos.yaml
index 3cf34f26..4a36c423 100644
--- a/stackinator/templates/repos.yaml
+++ b/stackinator/templates/repos.yaml
@@ -1,3 +1,5 @@
 repos:
   alps: {{ repo_path }}
-  builtin: {{ builtin_repo_path }}
+  builtin:
+    destination: {{ builtin_repo_path }}
+    git: {{ builtin_repo_git_repo }}

From 63634e97264af94e8294434789b76a806bb30723 Mon Sep 17 00:00:00 2001
From: Mikael Simberg <mikael.simberg@iki.fi>
Date: Tue, 17 Jun 2025 16:43:51 +0200
Subject: [PATCH 05/13] Move spack_packages to under spack:packages in yaml
 schema

---
 stackinator/builder.py         | 101 +++++++++++++++++----------------
 stackinator/schema/config.json |  32 +++++------
 2 files changed, 67 insertions(+), 66 deletions(-)

diff --git a/stackinator/builder.py b/stackinator/builder.py
index a843e758..8e2e5978 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -169,19 +169,25 @@ def generate(self, recipe):
         store_path.mkdir(exist_ok=True)
         tmp_path.mkdir(exist_ok=True)
 
-        ##################
-        # check out the version of spack-packages
-        spack_packages = recipe.config["spack_packages"]
-        spack_packages_path = store_path / "spack-packages"
+        # check out the version of spack
+        spack_version = recipe.spack_version
+        self._logger.debug(f"spack version for templates: {spack_version}")
+        spack = recipe.config["spack"]
+        spack_path = self.path / "spack"
 
-        # Clone the spack-packages repository if it has not already been checked
-        # out
-        if not (spack_packages_path / ".git").is_dir():
-            self._logger.info(f'spack-packages: clone repository {spack_packages["repo"]}')
+        # set general build and configuration meta data for the project
+        self.configuration_meta = recipe
+
+        # set the environment view meta data
+        self.environment_meta = recipe
+
+        # Clone the spack repository if it has not already been checked out
+        if not (spack_path / ".git").is_dir():
+            self._logger.info(f"spack: clone repository {spack['repo']}")
 
             # clone the repository
             capture = subprocess.run(
-                ["git", "clone", "--filter=tree:0", spack_packages["repo"], spack_packages_path],
+                ["git", "clone", "--filter=tree:0", spack["repo"], spack_path],
                 shell=False,
                 stdout=subprocess.PIPE,
                 stderr=subprocess.STDOUT,
@@ -189,14 +195,14 @@ def generate(self, recipe):
             self._logger.debug(capture.stdout.decode("utf-8"))
 
             if capture.returncode != 0:
-                self._logger.error(f'error cloning the repository {spack_packages["repo"]}')
+                self._logger.error(f"error cloning the repository {spack['repo']}")
                 capture.check_returncode()
 
         # Fetch the specific branch
-        if spack_packages["commit"]:
-            self._logger.info(f'spack-packages: fetch branch/commit {spack_packages["commit"]}')
+        if spack["commit"]:
+            self._logger.info(f"spack: fetch branch/commit {spack['commit']}")
             capture = subprocess.run(
-                ["git", "-C", spack_packages_path, "fetch", "origin", spack_packages["commit"]],
+                ["git", "-C", spack_path, "fetch", "origin", spack["commit"]],
                 shell=False,
                 stdout=subprocess.PIPE,
                 stderr=subprocess.STDOUT,
@@ -204,14 +210,14 @@ def generate(self, recipe):
             self._logger.debug(capture.stdout.decode("utf-8"))
 
             if capture.returncode != 0:
-                self._logger.debug(f'unable to change to the fetch {spack_packages["commit"]}')
+                self._logger.debug(f"unable to change to the fetch {spack['commit']}")
                 capture.check_returncode()
 
         # Check out a branch or commit if one was specified
-        if spack_packages["commit"]:
-            self._logger.info(f'spack-packages: checkout branch/commit {spack_packages["commit"]}')
+        if spack["commit"]:
+            self._logger.info(f"spack: checkout branch/commit {spack['commit']}")
             capture = subprocess.run(
-                ["git", "-C", spack_packages_path, "checkout", spack_packages["commit"]],
+                ["git", "-C", spack_path, "checkout", spack["commit"]],
                 shell=False,
                 stdout=subprocess.PIPE,
                 stderr=subprocess.STDOUT,
@@ -219,37 +225,27 @@ def generate(self, recipe):
             self._logger.debug(capture.stdout.decode("utf-8"))
 
             if capture.returncode != 0:
-                self._logger.debug(f'unable to change to the requested commit {spack_packages["commit"]}')
+                self._logger.debug(f"unable to change to the requested commit {spack['commit']}")
                 capture.check_returncode()
 
         # get the spack commit
-        spack_packages_git_commit_result = subprocess.run(
-            ["git", "-C", spack_packages_path, "rev-parse", "HEAD"],
-            shell=False,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.PIPE,
+        spack_git_commit_result = subprocess.run(
+            ["git", "-C", spack_path, "rev-parse", "HEAD"], shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE
         )
-        ##################
 
-        # check out the version of spack
-        spack_version = recipe.spack_version
-        self._logger.debug(f"spack version for templates: {spack_version}")
-        spack = recipe.config["spack"]
-        spack_path = self.path / "spack"
-
-        # set general build and configuration meta data for the project
-        self.configuration_meta = recipe
-
-        # set the environment view meta data
-        self.environment_meta = recipe
+        ##################
+        # check out the version of spack-packages
+        spack_packages = spack["packages"]
+        spack_packages_path = self.path / "spack-packages"
 
-        # Clone the spack repository if it has not already been checked out
-        if not (spack_path / ".git").is_dir():
-            self._logger.info(f"spack: clone repository {spack['repo']}")
+        # Clone the spack-packages repository if it has not already been checked
+        # out
+        if not (spack_packages_path / ".git").is_dir():
+            self._logger.info(f'spack-packages: clone repository {spack_packages["repo"]}')
 
             # clone the repository
             capture = subprocess.run(
-                ["git", "clone", "--filter=tree:0", spack["repo"], spack_path],
+                ["git", "clone", "--filter=tree:0", spack_packages["repo"], spack_packages_path],
                 shell=False,
                 stdout=subprocess.PIPE,
                 stderr=subprocess.STDOUT,
@@ -257,14 +253,14 @@ def generate(self, recipe):
             self._logger.debug(capture.stdout.decode("utf-8"))
 
             if capture.returncode != 0:
-                self._logger.error(f"error cloning the repository {spack['repo']}")
+                self._logger.error(f'error cloning the repository {spack_packages["repo"]}')
                 capture.check_returncode()
 
         # Fetch the specific branch
-        if spack["commit"]:
-            self._logger.info(f"spack: fetch branch/commit {spack['commit']}")
+        if spack_packages["commit"]:
+            self._logger.info(f'spack-packages: fetch branch/commit {spack_packages["commit"]}')
             capture = subprocess.run(
-                ["git", "-C", spack_path, "fetch", "origin", spack["commit"]],
+                ["git", "-C", spack_packages_path, "fetch", "origin", spack_packages["commit"]],
                 shell=False,
                 stdout=subprocess.PIPE,
                 stderr=subprocess.STDOUT,
@@ -272,14 +268,14 @@ def generate(self, recipe):
             self._logger.debug(capture.stdout.decode("utf-8"))
 
             if capture.returncode != 0:
-                self._logger.debug(f"unable to change to the fetch {spack['commit']}")
+                self._logger.debug(f'unable to change to the fetch {spack_packages["commit"]}')
                 capture.check_returncode()
 
         # Check out a branch or commit if one was specified
-        if spack["commit"]:
-            self._logger.info(f"spack: checkout branch/commit {spack['commit']}")
+        if spack_packages["commit"]:
+            self._logger.info(f'spack-packages: checkout branch/commit {spack_packages["commit"]}')
             capture = subprocess.run(
-                ["git", "-C", spack_path, "checkout", spack["commit"]],
+                ["git", "-C", spack_packages_path, "checkout", spack_packages["commit"]],
                 shell=False,
                 stdout=subprocess.PIPE,
                 stderr=subprocess.STDOUT,
@@ -287,13 +283,18 @@ def generate(self, recipe):
             self._logger.debug(capture.stdout.decode("utf-8"))
 
             if capture.returncode != 0:
-                self._logger.debug(f"unable to change to the requested commit {spack['commit']}")
+                self._logger.debug(f'unable to change to the requested commit {spack_packages["commit"]}')
                 capture.check_returncode()
 
         # get the spack commit
-        spack_git_commit_result = subprocess.run(
-            ["git", "-C", spack_path, "rev-parse", "HEAD"], shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE
+        spack_packages_git_commit_result = subprocess.run(
+            ["git", "-C", spack_packages_path, "rev-parse", "HEAD"],
+            shell=False,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
         )
+        ##################
+
         spack_meta = {
             "ref": spack["commit"],
             "commit": spack_git_commit_result.stdout.strip().decode("utf-8"),
diff --git a/stackinator/schema/config.json b/stackinator/schema/config.json
index cb142ceb..66780bf5 100644
--- a/stackinator/schema/config.json
+++ b/stackinator/schema/config.json
@@ -25,23 +25,23 @@
                         {"type" : "null"}
                     ],
                     "default": null
-                }
-            }
-        },
-        "spack_packages" : {
-            "type" : "object",
-            "additionalProperties": false,
-            "properties" : {
-                "repo": {
-                    "type": "string"
                 },
-                "commit": {
-                    "oneOf": [
-                        {"type" : "string"},
-                        {"type" : "null"}
-                    ],
-                    "default": null
-                }
+                "packages" : {
+                    "type" : "object",
+                    "additionalProperties": false,
+                    "properties" : {
+                        "repo": {
+                            "type": "string"
+                        },
+                        "commit": {
+                            "oneOf": [
+                                {"type" : "string"},
+                                {"type" : "null"}
+                            ],
+                            "default": null
+                        }
+                    }
+                },
             }
         },
         "mirror" : {

From 60ffe1b25708b4d99f1cd7f3d744c4b9d7124100 Mon Sep 17 00:00:00 2001
From: Mikael Simberg <mikael.simberg@iki.fi>
Date: Thu, 19 Jun 2025 12:06:59 +0200
Subject: [PATCH 06/13] Fix config.yaml schema

---
 stackinator/schema/config.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stackinator/schema/config.json b/stackinator/schema/config.json
index 66780bf5..49fae9b4 100644
--- a/stackinator/schema/config.json
+++ b/stackinator/schema/config.json
@@ -41,7 +41,7 @@
                             "default": null
                         }
                     }
-                },
+                }
             }
         },
         "mirror" : {

From cfdebb817831eae5a7916ade4d352e0a60072a35 Mon Sep 17 00:00:00 2001
From: Mikael Simberg <mikael.simberg@iki.fi>
Date: Thu, 19 Jun 2025 13:11:26 +0200
Subject: [PATCH 07/13] Add helper function for cloning git repos

---
 stackinator/builder.py | 207 ++++++++++++++++++-----------------------
 1 file changed, 92 insertions(+), 115 deletions(-)

diff --git a/stackinator/builder.py b/stackinator/builder.py
index 8e2e5978..52588a4d 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -172,8 +172,6 @@ def generate(self, recipe):
         # check out the version of spack
         spack_version = recipe.spack_version
         self._logger.debug(f"spack version for templates: {spack_version}")
-        spack = recipe.config["spack"]
-        spack_path = self.path / "spack"
 
         # set general build and configuration meta data for the project
         self.configuration_meta = recipe
@@ -181,127 +179,36 @@ def generate(self, recipe):
         # set the environment view meta data
         self.environment_meta = recipe
 
-        # Clone the spack repository if it has not already been checked out
-        if not (spack_path / ".git").is_dir():
-            self._logger.info(f"spack: clone repository {spack['repo']}")
-
-            # clone the repository
-            capture = subprocess.run(
-                ["git", "clone", "--filter=tree:0", spack["repo"], spack_path],
-                shell=False,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-            )
-            self._logger.debug(capture.stdout.decode("utf-8"))
-
-            if capture.returncode != 0:
-                self._logger.error(f"error cloning the repository {spack['repo']}")
-                capture.check_returncode()
-
-        # Fetch the specific branch
-        if spack["commit"]:
-            self._logger.info(f"spack: fetch branch/commit {spack['commit']}")
-            capture = subprocess.run(
-                ["git", "-C", spack_path, "fetch", "origin", spack["commit"]],
-                shell=False,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-            )
-            self._logger.debug(capture.stdout.decode("utf-8"))
-
-            if capture.returncode != 0:
-                self._logger.debug(f"unable to change to the fetch {spack['commit']}")
-                capture.check_returncode()
-
-        # Check out a branch or commit if one was specified
-        if spack["commit"]:
-            self._logger.info(f"spack: checkout branch/commit {spack['commit']}")
-            capture = subprocess.run(
-                ["git", "-C", spack_path, "checkout", spack["commit"]],
-                shell=False,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-            )
-            self._logger.debug(capture.stdout.decode("utf-8"))
-
-            if capture.returncode != 0:
-                self._logger.debug(f"unable to change to the requested commit {spack['commit']}")
-                capture.check_returncode()
+        # Clone the spack repository and check out commit if one was given
+        spack = recipe.config["spack"]
+        spack_repo = spack["repo"]
+        spack_commit = spack["commit"]
+        spack_path = self.path / "spack"
 
-        # get the spack commit
-        spack_git_commit_result = subprocess.run(
-            ["git", "-C", spack_path, "rev-parse", "HEAD"], shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE
+        spack_git_commit_result = self._git_clone(
+            "spack", spack_repo, spack_commit, spack_path
         )
 
-        ##################
-        # check out the version of spack-packages
+        # Clone the spack-packages repository and check out commit if one was given
         spack_packages = spack["packages"]
+        spack_packages_repo = spack_packages["repo"]
+        spack_packages_commit = spack_packages["commit"]
         spack_packages_path = self.path / "spack-packages"
 
-        # Clone the spack-packages repository if it has not already been checked
-        # out
-        if not (spack_packages_path / ".git").is_dir():
-            self._logger.info(f'spack-packages: clone repository {spack_packages["repo"]}')
-
-            # clone the repository
-            capture = subprocess.run(
-                ["git", "clone", "--filter=tree:0", spack_packages["repo"], spack_packages_path],
-                shell=False,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-            )
-            self._logger.debug(capture.stdout.decode("utf-8"))
-
-            if capture.returncode != 0:
-                self._logger.error(f'error cloning the repository {spack_packages["repo"]}')
-                capture.check_returncode()
-
-        # Fetch the specific branch
-        if spack_packages["commit"]:
-            self._logger.info(f'spack-packages: fetch branch/commit {spack_packages["commit"]}')
-            capture = subprocess.run(
-                ["git", "-C", spack_packages_path, "fetch", "origin", spack_packages["commit"]],
-                shell=False,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-            )
-            self._logger.debug(capture.stdout.decode("utf-8"))
-
-            if capture.returncode != 0:
-                self._logger.debug(f'unable to change to the fetch {spack_packages["commit"]}')
-                capture.check_returncode()
-
-        # Check out a branch or commit if one was specified
-        if spack_packages["commit"]:
-            self._logger.info(f'spack-packages: checkout branch/commit {spack_packages["commit"]}')
-            capture = subprocess.run(
-                ["git", "-C", spack_packages_path, "checkout", spack_packages["commit"]],
-                shell=False,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-            )
-            self._logger.debug(capture.stdout.decode("utf-8"))
-
-            if capture.returncode != 0:
-                self._logger.debug(f'unable to change to the requested commit {spack_packages["commit"]}')
-                capture.check_returncode()
-
-        # get the spack commit
-        spack_packages_git_commit_result = subprocess.run(
-            ["git", "-C", spack_packages_path, "rev-parse", "HEAD"],
-            shell=False,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.PIPE,
+        spack_packages_git_commit_result = self._git_clone(
+            "spack-packages",
+            spack_packages_repo,
+            spack_packages_commit,
+            spack_packages_path,
         )
-        ##################
 
         spack_meta = {
-            "ref": spack["commit"],
-            "commit": spack_git_commit_result.stdout.strip().decode("utf-8"),
-            "url": spack["repo"],
-            "packages_ref": spack_packages["commit"],
-            "packages_commit": spack_packages_git_commit_result.stdout.strip().decode("utf-8"),
-            "packages_url": spack_packages["repo"],
+            "url": spack_repo,
+            "ref": spack_commit,
+            "commit": spack_git_commit_result,
+            "packages_url": spack_packages_repo,
+            "packages_ref": spack_packages_commit,
+            "packages_commit": spack_packages_git_commit_result,
         }
 
         # load the jinja templating environment
@@ -508,7 +415,10 @@ def generate(self, recipe):
             builtin_repo_path = recipe.mount / "spack-packages"
             f.write(
                 repos_yaml_template.render(
-                    repo_path=repo_path.as_posix(), builtin_repo_path=builtin_repo_path.as_posix(), builtin_repo_git_repo=spack_packages["repo"], verbose=False
+                    repo_path=repo_path.as_posix(),
+                    builtin_repo_path=builtin_repo_path.as_posix(),
+                    builtin_repo_git_repo=spack_packages_repo,
+                    verbose=False,
                 )
             )
             f.write("\n")
@@ -625,3 +535,70 @@ def generate(self, recipe):
                 )
             )
             f.write("\n")
+
+
+    def _git_clone(self, name, repo, commit, path):
+        if not (path / ".git").is_dir():
+            self._logger.info(f"{name}: clone repository {repo} to {path}")
+
+            # clone the repository
+            capture = subprocess.run(
+                ["git", "clone", "--filter=tree:0", repo, path],
+                shell=False,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.STDOUT,
+            )
+            self._logger.debug(capture.stdout.decode("utf-8"))
+
+            if capture.returncode != 0:
+                self._logger.error(f"error cloning the repository {repo}")
+                capture.check_returncode()
+        else:
+            self._logger.info(f"{name}: {repo} already cloned to {path}")
+
+        if commit:
+            # Fetch the specific branch
+            self._logger.info(f"{name}: fetching {commit}")
+            capture = subprocess.run(
+                ["git", "-C", path, "fetch", "origin", commit],
+                shell=False,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.STDOUT,
+            )
+            self._logger.debug(capture.stdout.decode("utf-8"))
+
+            if capture.returncode != 0:
+                self._logger.debug(f"unable to fetch {commit}")
+                capture.check_returncode()
+
+            # Check out the specific branch
+            self._logger.info(f"{name}: checking out {commit}")
+            capture = subprocess.run(
+                ["git", "-C", path, "checkout", commit],
+                shell=False,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.STDOUT,
+            )
+            self._logger.debug(capture.stdout.decode("utf-8"))
+
+            if capture.returncode != 0:
+                self._logger.debug(f"unable to change to the requested commit {commit}")
+                capture.check_returncode()
+        else:
+            self._logger.info(f"{name}: no commit set")
+
+        # get the commit
+        git_commit_result = (
+            subprocess.run(
+                ["git", "-C", path, "rev-parse", "HEAD"],
+                shell=False,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,
+            )
+            .stdout.strip()
+            .decode("utf-8")
+        )
+
+        self._logger.info(f"{name}: commit hash is {git_commit_result}")
+
+        return git_commit_result

From 6fd55221b47b2321868d81d6e29bcc408b0a55f8 Mon Sep 17 00:00:00 2001
From: Mikael Simberg <mikael.simberg@iki.fi>
Date: Thu, 19 Jun 2025 13:35:30 +0200
Subject: [PATCH 08/13] Pass spack-packages repo information to spack view
 environment variables

---
 stackinator/etc/envvars.py     | 18 ++++++++++++++++--
 stackinator/templates/Makefile |  2 +-
 unittests/test-envvars.sh      |  2 +-
 3 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/stackinator/etc/envvars.py b/stackinator/etc/envvars.py
index f008ded1..94c8b91e 100755
--- a/stackinator/etc/envvars.py
+++ b/stackinator/etc/envvars.py
@@ -542,6 +542,11 @@ def meta_impl(args):
 
     if args.spack is not None:
         spack_url, spack_ref, spack_commit = args.spack.split(",")
+        spack_packages_url = None
+        spack_packages_ref = None
+        spack_packages_commit = None
+        if args.spack_packages is not None:
+            spack_packages_url, spack_packages_ref, spack_packages_commit = args.spack_packages.split(",")
         spack_path = f"{args.mount}/config".replace("//", "/")
         meta["views"]["spack"] = {
             "activate": "/dev/null",
@@ -554,9 +559,12 @@ def meta_impl(args):
                     "list": {},
                     "scalar": {
                         "UENV_SPACK_CONFIG_PATH": spack_path,
+                        "UENV_SPACK_URL": spack_url,
                         "UENV_SPACK_REF": spack_ref,
                         "UENV_SPACK_COMMIT": spack_commit,
-                        "UENV_SPACK_URL": spack_url,
+                        "UENV_SPACK_PACKAGES_URL": spack_packages_url,
+                        "UENV_SPACK_PACKAGES_REF": spack_packages_ref,
+                        "UENV_SPACK_PACKAGES_COMMIT": spack_packages_commit,
                     },
                 },
             },
@@ -594,7 +602,13 @@ def meta_impl(args):
     uenv_parser.add_argument("--modules", help="configure a module view", action="store_true")
     uenv_parser.add_argument(
         "--spack",
-        help='configure a spack view. Format is "spack_url,git_ref,git_commit"',
+        help='configure a spack repository metadata. Format is "spack_url,git_ref,git_commit"',
+        type=str,
+        default=None,
+    )
+    uenv_parser.add_argument(
+        "--spack-packages",
+        help='configure spack-packages repository metadata. Format is "spack_url,git_ref,git_commit"',
         type=str,
         default=None,
     )
diff --git a/stackinator/templates/Makefile b/stackinator/templates/Makefile
index de2d352e..d4c1a1ae 100644
--- a/stackinator/templates/Makefile
+++ b/stackinator/templates/Makefile
@@ -69,7 +69,7 @@ modules-done: environments generate-config
 
 env-meta: generate-config environments{% if modules %} modules-done{% endif %}
 
-	$(SANDBOX) $(BUILD_ROOT)/envvars.py uenv {% if modules %}--modules{% endif %} --spack='{{ spack_meta.url }},{{ spack_meta.ref }},{{ spack_meta.commit }}' $(STORE)
+	$(SANDBOX) $(BUILD_ROOT)/envvars.py uenv {% if modules %}--modules{% endif %} --spack='{{ spack_meta.url }},{{ spack_meta.ref }},{{ spack_meta.commit }}' --spack-packages='{{ spack_meta.packages_url }},{{ spack_meta.packages_ref }},{{ spack_meta.packages_commit }}' $(STORE)
 	touch env-meta
 
 post-install: env-meta
diff --git a/unittests/test-envvars.sh b/unittests/test-envvars.sh
index c8fa1e27..79e98fba 100755
--- a/unittests/test-envvars.sh
+++ b/unittests/test-envvars.sh
@@ -36,7 +36,7 @@ find $scratch_path -name env.json
 
 echo "===== running final meta data stage  ${mount_path}"
 
-../stackinator/etc/envvars.py uenv ${mount_path}/ --modules --spack="https://github.com/spack/spack.git,releases/v0.20"
+../stackinator/etc/envvars.py uenv ${mount_path}/ --modules --spack="https://github.com/spack/spack.git,releases/v0.20" --spack-packages="https://github.com/spack/spack.git,develop"
 
 echo
 echo "===== develop"

From b55198c34615a0b5a8e4518e7de3ef956c2a24ad Mon Sep 17 00:00:00 2001
From: Mikael Simberg <mikael.simberg@iki.fi>
Date: Thu, 19 Jun 2025 13:42:37 +0200
Subject: [PATCH 09/13] Fix formatting

---
 stackinator/builder.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/stackinator/builder.py b/stackinator/builder.py
index 52588a4d..d2931ca4 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -185,9 +185,7 @@ def generate(self, recipe):
         spack_commit = spack["commit"]
         spack_path = self.path / "spack"
 
-        spack_git_commit_result = self._git_clone(
-            "spack", spack_repo, spack_commit, spack_path
-        )
+        spack_git_commit_result = self._git_clone("spack", spack_repo, spack_commit, spack_path)
 
         # Clone the spack-packages repository and check out commit if one was given
         spack_packages = spack["packages"]
@@ -536,7 +534,6 @@ def generate(self, recipe):
             )
             f.write("\n")
 
-
     def _git_clone(self, name, repo, commit, path):
         if not (path / ".git").is_dir():
             self._logger.info(f"{name}: clone repository {repo} to {path}")

From d2e3bc9dfc454ef2c9dc87a3de6619edce1a3a10 Mon Sep 17 00:00:00 2001
From: Mikael Simberg <mikael.simberg@iki.fi>
Date: Thu, 19 Jun 2025 14:05:37 +0200
Subject: [PATCH 10/13] Copy only package repo from spack-packages to squashfs

---
 stackinator/builder.py           | 9 +++++++--
 stackinator/templates/repos.yaml | 4 +---
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/stackinator/builder.py b/stackinator/builder.py
index d2931ca4..e80c4c74 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -397,7 +397,7 @@ def generate(self, recipe):
         self._logger.debug(f"created the repo packages path {pkg_dst}")
 
         # create the repository step 2: create the repo.yaml file that
-        # configures the repo.
+        # configures alps and builtin repos
         with (repo_dst / "repo.yaml").open("w") as f:
             f.write(
                 """\
@@ -415,7 +415,6 @@ def generate(self, recipe):
                 repos_yaml_template.render(
                     repo_path=repo_path.as_posix(),
                     builtin_repo_path=builtin_repo_path.as_posix(),
-                    builtin_repo_git_repo=spack_packages_repo,
                     verbose=False,
                 )
             )
@@ -436,6 +435,12 @@ def generate(self, recipe):
                     elif dst.exists():
                         self._logger.debug(f"  NOT installing package {pkg_path}")
 
+        # Copy the builtin repo to store
+        spack_packages_builtin_path = spack_packages_path / "repos" / "spack_repo" / "builtin"
+        spack_packages_store_path = store_path / "spack-packages"
+        self._logger.debug(f"copying builtin repo from {spack_packages_builtin_path} to {spack_packages_store_path}")
+        install(spack_packages_builtin_path, spack_packages_store_path)
+
         # Generate the makefile and spack.yaml files that describe the compilers
         compiler_files = recipe.compiler_files
         compiler_path = self.path / "compilers"
diff --git a/stackinator/templates/repos.yaml b/stackinator/templates/repos.yaml
index 4a36c423..dfc1c9f6 100644
--- a/stackinator/templates/repos.yaml
+++ b/stackinator/templates/repos.yaml
@@ -1,5 +1,3 @@
 repos:
   alps: {{ repo_path }}
-  builtin:
-    destination: {{ builtin_repo_path }}
-    git: {{ builtin_repo_git_repo }}
+  builtin: {{ builtin_repo_path }}/repos/spack_repo/builtin

From 92c132a050186fb6813ee09032c3ecc75c10c117 Mon Sep 17 00:00:00 2001
From: Mikael Simberg <mikael.simberg@iki.fi>
Date: Thu, 19 Jun 2025 14:54:28 +0200
Subject: [PATCH 11/13] Delete spack-packages repo in store if it already
 exists

---
 stackinator/builder.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/stackinator/builder.py b/stackinator/builder.py
index e80c4c74..51d4f3a8 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -435,10 +435,13 @@ def generate(self, recipe):
                     elif dst.exists():
                         self._logger.debug(f"  NOT installing package {pkg_path}")
 
-        # Copy the builtin repo to store
+        # Copy the builtin repo to store, delete if it already exists.
         spack_packages_builtin_path = spack_packages_path / "repos" / "spack_repo" / "builtin"
         spack_packages_store_path = store_path / "spack-packages"
         self._logger.debug(f"copying builtin repo from {spack_packages_builtin_path} to {spack_packages_store_path}")
+        if spack_packages_store_path.exists():
+            self._logger.debug(f"{spack_packages_store_path} exists ... deleting")
+            shutil.rmtree(spack_packages_store_path)
         install(spack_packages_builtin_path, spack_packages_store_path)
 
         # Generate the makefile and spack.yaml files that describe the compilers

From 68e11fc74edf8fb4165aa1a26a26b4c152c444df Mon Sep 17 00:00:00 2001
From: Mikael Simberg <mikael.simberg@iki.fi>
Date: Thu, 19 Jun 2025 17:14:08 +0200
Subject: [PATCH 12/13] Put both alps and builtin repos under repos directory
 in squashfs

---
 stackinator/builder.py           | 9 +++++----
 stackinator/templates/repos.yaml | 2 +-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/stackinator/builder.py b/stackinator/builder.py
index 51d4f3a8..89e3e4d2 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -385,7 +385,8 @@ def generate(self, recipe):
 
         # Delete the store/repo path, if it already exists.
         # Do this so that incremental builds (though not officially supported) won't break if a repo is updated.
-        repo_dst = store_path / "repo"
+        repos_path = store_path / "repos"
+        repo_dst = repos_path / "alps"
         self._logger.debug(f"creating the stack spack repo in {repo_dst}")
         if repo_dst.exists():
             self._logger.debug(f"{repo_dst} exists ... deleting")
@@ -409,8 +410,8 @@ def generate(self, recipe):
         # create the repository step 2: create the repos.yaml file in build_path/config
         repos_yaml_template = jinja_env.get_template("repos.yaml")
         with (config_path / "repos.yaml").open("w") as f:
-            repo_path = recipe.mount / "repo"
-            builtin_repo_path = recipe.mount / "spack-packages"
+            repo_path = recipe.mount / "repos" / "alps"
+            builtin_repo_path = recipe.mount / "repos" / "builtin"
             f.write(
                 repos_yaml_template.render(
                     repo_path=repo_path.as_posix(),
@@ -437,7 +438,7 @@ def generate(self, recipe):
 
         # Copy the builtin repo to store, delete if it already exists.
         spack_packages_builtin_path = spack_packages_path / "repos" / "spack_repo" / "builtin"
-        spack_packages_store_path = store_path / "spack-packages"
+        spack_packages_store_path = store_path / "repos" / "builtin"
         self._logger.debug(f"copying builtin repo from {spack_packages_builtin_path} to {spack_packages_store_path}")
         if spack_packages_store_path.exists():
             self._logger.debug(f"{spack_packages_store_path} exists ... deleting")
diff --git a/stackinator/templates/repos.yaml b/stackinator/templates/repos.yaml
index dfc1c9f6..3cf34f26 100644
--- a/stackinator/templates/repos.yaml
+++ b/stackinator/templates/repos.yaml
@@ -1,3 +1,3 @@
 repos:
   alps: {{ repo_path }}
-  builtin: {{ builtin_repo_path }}/repos/spack_repo/builtin
+  builtin: {{ builtin_repo_path }}

From 40276d8cff6240d0cfc399db21bdd9130cde2728 Mon Sep 17 00:00:00 2001
From: Mikael Simberg <simberg@cscs.ch>
Date: Mon, 23 Jun 2025 16:39:01 +0200
Subject: [PATCH 13/13] Fix builtin repo

---
 stackinator/builder.py         | 8 ++++----
 stackinator/templates/Makefile | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/stackinator/builder.py b/stackinator/builder.py
index 89e3e4d2..ae960ef1 100644
--- a/stackinator/builder.py
+++ b/stackinator/builder.py
@@ -351,7 +351,7 @@ def generate(self, recipe):
         # 2. cluster-config/repos.yaml
         #   - if the repos.yaml file exists it will contain a list of relative paths
         #     to search for package
-        # 1. spack/var/spack/repos/builtin
+        # 1. builtin repo
 
         # Build a list of repos with packages to install.
         repos = []
@@ -411,7 +411,7 @@ def generate(self, recipe):
         repos_yaml_template = jinja_env.get_template("repos.yaml")
         with (config_path / "repos.yaml").open("w") as f:
             repo_path = recipe.mount / "repos" / "alps"
-            builtin_repo_path = recipe.mount / "repos" / "builtin"
+            builtin_repo_path = recipe.mount / "repos" / "spack_repo" / "builtin"
             f.write(
                 repos_yaml_template.render(
                     repo_path=repo_path.as_posix(),
@@ -437,8 +437,8 @@ def generate(self, recipe):
                         self._logger.debug(f"  NOT installing package {pkg_path}")
 
         # Copy the builtin repo to store, delete if it already exists.
-        spack_packages_builtin_path = spack_packages_path / "repos" / "spack_repo" / "builtin"
-        spack_packages_store_path = store_path / "repos" / "builtin"
+        spack_packages_builtin_path = spack_packages_path / "repos" / "spack_repo"
+        spack_packages_store_path = store_path / "repos" / "spack_repo"
         self._logger.debug(f"copying builtin repo from {spack_packages_builtin_path} to {spack_packages_store_path}")
         if spack_packages_store_path.exists():
             self._logger.debug(f"{spack_packages_store_path} exists ... deleting")
diff --git a/stackinator/templates/Makefile b/stackinator/templates/Makefile
index d4c1a1ae..82e7fbd4 100644
--- a/stackinator/templates/Makefile
+++ b/stackinator/templates/Makefile
@@ -81,7 +81,7 @@ post-install: env-meta
 # Create a squashfs file from the installed software.
 store.squashfs: post-install
 	# clean up the __pycache__ paths in the repo
-	$(SANDBOX) find $(STORE)/repo -type d -name __pycache__ -exec rm -r {} +
+	$(SANDBOX) find $(STORE)/repos -type d -name __pycache__ -exec rm -r {} +
 	$(SANDBOX) chmod -R a+rX $(STORE)
 	$(SANDBOX) env -u SOURCE_DATE_EPOCH "$$($(SANDBOX) $(SPACK_HELPER) -e ./compilers/bootstrap find --format='{prefix}' squashfs | head -n1)/bin/mksquashfs" $(STORE) $@ -force-uid nobody -force-gid nobody -all-time $$(date +%s) -no-recovery -noappend -Xcompression-level 3