esd-spack-installation: fixed passing access token to tests; added log file for spack install step

dedal/tests/spack_from_scratch_test.py

@@ -8,6 +8,10 @@ from esd.spack_manager.factory.SpackManagerCreator import SpackManagerCreator
 from esd.utils.utils import file_exists_and_not_empty
 
 SPACK_ENV_ACCESS_TOKEN = os.getenv("SPACK_ENV_ACCESS_TOKEN")
+test_spack_env_git = f'https://oauth2:{SPACK_ENV_ACCESS_TOKEN}@gitlab.ebrains.eu/ri/projects-and-initiatives/virtualbraintwin/tools/test-spack-env.git'
+ebrains_spack_builds_git = 'https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git'
+
+
 
 def test_spack_repo_exists_1():
     spack_manager = SpackManagerCreator.get_spack_manger(SpackManagerEnum.FROM_SCRATCH)
@@ -32,8 +36,7 @@ def test_spack_repo_exists_3(tmp_path):
 
 def test_spack_from_scratch_setup_1(tmp_path):
     install_dir = tmp_path
-    env = SpackModel('ebrains-spack-builds', install_dir,
-                     'https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git')
+    env = SpackModel('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
     spack_manager = SpackManagerCreator.get_spack_manger(SpackManagerEnum.FROM_SCRATCH, env=env,
                                                          system_name='ebrainslab')
     spack_manager.setup_spack_env()
@@ -42,8 +45,7 @@ def test_spack_from_scratch_setup_1(tmp_path):
 
 def test_spack_from_scratch_setup_2(tmp_path):
     install_dir = tmp_path
-    env = SpackModel('ebrains-spack-builds', install_dir,
-                     'https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git')
+    env = SpackModel('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
     repo = env
     spack_manager = SpackManagerCreator.get_spack_manger(SpackManagerEnum.FROM_SCRATCH, env=env,
                                                          repos=[repo, repo],
@@ -83,8 +85,7 @@ def test_spack_not_a_valid_repo():
 
 def test_spack_from_scratch_concretize_1(tmp_path):
     install_dir = tmp_path
-    env = SpackModel('ebrains-spack-builds', install_dir,
-                     'https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git')
+    env = SpackModel('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
     repo = env
     spack_manager = SpackManagerCreator.get_spack_manger(SpackManagerEnum.FROM_SCRATCH, env=env, repos=[repo, repo],
                                                          system_name='ebrainslab')
@@ -96,8 +97,7 @@ def test_spack_from_scratch_concretize_1(tmp_path):
 
 def test_spack_from_scratch_concretize_2(tmp_path):
     install_dir = tmp_path
-    env = SpackModel('ebrains-spack-builds', install_dir,
-                     'https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git')
+    env = SpackModel('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
     repo = env
     spack_manager = SpackManagerCreator.get_spack_manger(SpackManagerEnum.FROM_SCRATCH, env=env, repos=[repo, repo],
                                                          system_name='ebrainslab')
@@ -109,8 +109,7 @@ def test_spack_from_scratch_concretize_2(tmp_path):
 
 def test_spack_from_scratch_concretize_3(tmp_path):
     install_dir = tmp_path
-    env = SpackModel('ebrains-spack-builds', install_dir,
-                     'https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git')
+    env = SpackModel('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
     repo = env
     spack_manager = SpackManagerCreator.get_spack_manger(SpackManagerEnum.FROM_SCRATCH, env=env,
                                                          repos=[repo, repo],
@@ -122,8 +121,7 @@ def test_spack_from_scratch_concretize_3(tmp_path):
 
 def test_spack_from_scratch_concretize_4(tmp_path):
     install_dir = tmp_path
-    env = SpackModel('test-spack-env', install_dir,
-                     f'https://oauth2:{SPACK_ENV_ACCESS_TOKEN}@gitlab.ebrains.eu/ri/projects-and-initiatives/virtualbraintwin/test-spack-env.git')
+    env = SpackModel('test-spack-env', install_dir, test_spack_env_git)
     spack_manager = SpackManagerCreator.get_spack_manger(SpackManagerEnum.FROM_SCRATCH, env=env)
     spack_manager.setup_spack_env()
     spack_manager.concretize_spack_env(force=False)
@@ -133,8 +131,7 @@ def test_spack_from_scratch_concretize_4(tmp_path):
 
 def test_spack_from_scratch_concretize_5(tmp_path):
     install_dir = tmp_path
-    env = SpackModel('test-spack-env', install_dir,
-                     f'https://oauth2:{SPACK_ENV_ACCESS_TOKEN}@gitlab.ebrains.eu/ri/projects-and-initiatives/virtualbraintwin/test-spack-env.git')
+    env = SpackModel('test-spack-env', install_dir, test_spack_env_git)
     spack_manager = SpackManagerCreator.get_spack_manger(SpackManagerEnum.FROM_SCRATCH, env=env)
     spack_manager.setup_spack_env()
     spack_manager.concretize_spack_env(force=True)
@@ -144,10 +141,8 @@ def test_spack_from_scratch_concretize_5(tmp_path):
 
 def test_spack_from_scratch_concretize_6(tmp_path):
     install_dir = tmp_path
-    env = SpackModel('test-spack-env', install_dir,
-                     f'https://oauth2:{SPACK_ENV_ACCESS_TOKEN}@gitlab.ebrains.eu/ri/projects-and-initiatives/virtualbraintwin/test-spack-env.git')
-    repo = SpackModel('ebrains-spack-builds', install_dir,
-                      'https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git')
+    env = SpackModel('test-spack-env', install_dir, test_spack_env_git)
+    repo = SpackModel('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
     spack_manager = SpackManagerCreator.get_spack_manger(SpackManagerEnum.FROM_SCRATCH, env=env, repos=[repo])
     spack_manager.setup_spack_env()
     spack_manager.concretize_spack_env(force=False)
@@ -157,10 +152,8 @@ def test_spack_from_scratch_concretize_6(tmp_path):
 
 def test_spack_from_scratch_concretize_7(tmp_path):
     install_dir = tmp_path
-    env = SpackModel('test-spack-env', install_dir,
-                     'https://gitlab.ebrains.eu/ri/projects-and-initiatives/virtualbraintwin/test-spack-env.git')
-    repo = SpackModel('ebrains-spack-builds', install_dir,
-                      'https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git')
+    env = SpackModel('test-spack-env', install_dir, test_spack_env_git)
+    repo = SpackModel('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
     spack_manager = SpackManagerCreator.get_spack_manger(SpackManagerEnum.FROM_SCRATCH, env=env, repos=[repo])
     spack_manager.setup_spack_env()
     spack_manager.concretize_spack_env(force=True)

esd/spack_manager/SpackManager.py

@@ -2,12 +2,13 @@ import os
 import re
 from abc import ABC, abstractmethod
 from pathlib import Path
+from tabnanny import check
 
 from esd.error_handling.exceptions import BashCommandException, NoSpackEnvironmentException, \
     SpackInstallPackagesException
 from esd.logger.logger_builder import get_logger
 from esd.model.SpackModel import SpackModel
-from esd.spack_manager.wrapper.spack_wrapper import no_spack_env
+from esd.spack_manager.wrapper.spack_wrapper import check_spack_env
 from esd.utils.utils import run_command, git_clone_repo
 
 
@@ -53,7 +54,6 @@ class SpackManager(ABC):
         pass
 
     def create_fetch_spack_environment(self):
-
         if self.env.git_path:
             git_clone_repo(self.env.env_name, self.env.path / self.env.env_name, self.env.git_path, logger=self.logger)
         else:
@@ -127,7 +127,7 @@ class SpackManager(ABC):
             return False
         return True
 
-    @no_spack_env
+    @check_spack_env
     def add_spack_repo(self, repo_path: Path, repo_name: str):
         """Add the Spack repository if it does not exist."""
         run_command("bash", "-c",
@@ -137,7 +137,7 @@ class SpackManager(ABC):
                     exception_msg=f"Failed to add {repo_name} to spack environment {self.env.env_name}",
                     exception=BashCommandException)
 
-    @no_spack_env
+    @check_spack_env
     def get_compiler_version(self):
         result = run_command("bash", "-c",
                              f'source {self.spack_setup_script} && spack env activate -p {self.env_path} && spack compiler list',
@@ -167,8 +167,21 @@ class SpackManager(ABC):
             return spack_version.stdout.strip().split()[0]
         return None
 
-
-    def install_spack(self, spack_version="v0.21.1", spack_repo='https://github.com/spack/spack'):
+    @check_spack_env
+    def install_packages(self, jobs: int, signed=True, fresh=False):
+        signed = '' if signed else '--no-check-signature'
+        fresh = '--fresh' if fresh else ''
+        with open(str(Path(os.getcwd()).resolve() / ".generate_cache.log"), "w") as log_file:
+            run_command("bash", "-c",
+                        f'source {self.spack_setup_script} && spack install --env {self.env.env_name} -v {signed} --j {jobs} {fresh}',
+                        stdout=log_file,
+                        capture_output=True, text=True, check=True,
+                        logger=self.logger,
+                        debug_msg=f"Installing spack packages for {self.env.env_name}",
+                        exception_msg=f"Error installing spack packages for {self.env.env_name}",
+                        exception=SpackInstallPackagesException)
+
+    def install_spack(self, spack_version="v0.22.0", spack_repo='https://github.com/spack/spack'):
         try:
             user = os.getlogin()
         except OSError:

esd/spack_manager/wrapper/spack_wrapper.py

@@ -3,7 +3,7 @@ import functools
 from esd.error_handling.exceptions import NoSpackEnvironmentException
 
 
-def no_spack_env(method):
+def check_spack_env(method):
     @functools.wraps(method)
     def wrapper(self, *args, **kwargs):
         if self.spack_env_exists():