From 29f27392c2bc30f049759aea1c892989bc720bf3 Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Mon, 24 Feb 2025 10:01:37 +0100
Subject: [PATCH 01/14] - Updated .gitlab-ci.yml to include new separate stages
 testing and also for the coverage.

---
 .gitlab-ci.yml | 52 +++++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 45 insertions(+), 7 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8b5459c..7adc146 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,6 +1,7 @@
 stages:
   - test
   - build
+  - coverage_report
 
 variables:
   BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/esd/tmp:latest
@@ -21,23 +22,60 @@ build-wheel:
       - dist/*.tar.gz
     expire_in: 1 week
 
-
-testing-pytest-coverage:
+unit_tests:
   stage: test
   tags:
     - docker-runner
   image: ubuntu:22.04
+  before_script:
+    - chmod +x dedal/utils/bootstrap.sh
+    - ./dedal/utils/bootstrap.sh
+    - pip install -e .[test]
   script:
+    - coverage run s --tb=short --junitxml=test-results.xml -m pytest ./dedal/tests/unit_tests
+    - coverage xml -o coverage_unit.xml
+  artifacts:
+    paths:
+      - coverage_unit.xml
+    expire_in: 1 week
+
+integration_tests:
+  stage: test
+  tags:
+    - docker-runner
+  image: ubuntu:22.04
+  before_script:
     - chmod +x dedal/utils/bootstrap.sh
     - ./dedal/utils/bootstrap.sh
     - pip install -e .[test]
-    - coverage run -m pytest -s --tb=short --junitxml=test-results.xml ./dedal/tests/ && coverage html -i -d htmlcov
+  script:
+    - coverage run s --tb=short --junitxml=test-results.xml -m pytest ./dedal/tests/integration_tests
+    - coverage xml -o coverage_integration.xml
+  artifacts:
+    paths:
+      - coverage_integration.xml
+    expire_in: 1 week
+
+merge_coverage:
+  stage: coverage_report
+  tags:
+    - docker-runner
+  image: ubuntu:22.04
+  before_script:
+    - pip install coverage
+  script:
+    - coverage combine coverage_unit.xml coverage_integration.xml
+    - coverage report
+    - coverage xml -o coverage.xml
+    - coverage html -d coverage_html
   artifacts:
-    when: always
     reports:
-      junit: test-results.xml
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
     paths:
-      - test-results.xml
-      - .dedal.log
+      - coverage.xml
+      - coverage_html
     expire_in: 1 week
+  coverage: '/TOTAL.*?(\d+\%)$/'
 
-- 
GitLab


From ecdff0572d05bf9c714d41c662f2d8815fa7a29e Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Mon, 24 Feb 2025 10:47:59 +0100
Subject: [PATCH 02/14] - Corrected the job sequence within the test stage.

---
 .gitlab-ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7adc146..f35ffbb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -51,6 +51,7 @@ integration_tests:
   script:
     - coverage run s --tb=short --junitxml=test-results.xml -m pytest ./dedal/tests/integration_tests
     - coverage xml -o coverage_integration.xml
+  needs: ["unit_tests"]
   artifacts:
     paths:
       - coverage_integration.xml
-- 
GitLab


From 5957334c899e542b76c7375657c2e9a902c95eee Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Mon, 24 Feb 2025 11:18:00 +0100
Subject: [PATCH 03/14] - Corrected the failing tests.

---
 .gitlab-ci.yml | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f35ffbb..57460e7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -32,10 +32,14 @@ unit_tests:
     - ./dedal/utils/bootstrap.sh
     - pip install -e .[test]
   script:
-    - coverage run s --tb=short --junitxml=test-results.xml -m pytest ./dedal/tests/unit_tests
+    - coverage run -m pytest -s --tb=short --junitxml=test-results.xml ./dedal/tests/unit_tests
     - coverage xml -o coverage_unit.xml
   artifacts:
+    when: always
+    reports:
+      junit: test-results.xml
     paths:
+      - test-results.xml
       - coverage_unit.xml
     expire_in: 1 week
 
@@ -49,11 +53,15 @@ integration_tests:
     - ./dedal/utils/bootstrap.sh
     - pip install -e .[test]
   script:
-    - coverage run s --tb=short --junitxml=test-results.xml -m pytest ./dedal/tests/integration_tests
+    - coverage run -m pytest -s --tb=short --junitxml=test-results.xml ./dedal/tests/integration_tests
     - coverage xml -o coverage_integration.xml
   needs: ["unit_tests"]
   artifacts:
+    when: always
+    reports:
+      junit: test-results.xml
     paths:
+      - test-results.xml
       - coverage_integration.xml
     expire_in: 1 week
 
-- 
GitLab


From 15362bd9a03db9882576a9486a2ff9ffa3a99a7f Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Mon, 24 Feb 2025 15:55:36 +0100
Subject: [PATCH 04/14] - Fixed the failing merge_coverage job by ensuring the
 required coverage package is installed. Moved the common before_script to the
 default section. - Added the test coverage badge to README.md.

---
 .gitlab-ci.yml | 15 +++++----------
 README.md      |  2 ++
 2 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 57460e7..003ac77 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,6 +6,11 @@ stages:
 variables:
   BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/esd/tmp:latest
 
+default:
+  before_script:
+    - chmod +x dedal/utils/bootstrap.sh
+    - ./dedal/utils/bootstrap.sh
+    - pip install -e .[test]
 
 build-wheel:
   stage: build
@@ -27,10 +32,6 @@ unit_tests:
   tags:
     - docker-runner
   image: ubuntu:22.04
-  before_script:
-    - chmod +x dedal/utils/bootstrap.sh
-    - ./dedal/utils/bootstrap.sh
-    - pip install -e .[test]
   script:
     - coverage run -m pytest -s --tb=short --junitxml=test-results.xml ./dedal/tests/unit_tests
     - coverage xml -o coverage_unit.xml
@@ -48,10 +49,6 @@ integration_tests:
   tags:
     - docker-runner
   image: ubuntu:22.04
-  before_script:
-    - chmod +x dedal/utils/bootstrap.sh
-    - ./dedal/utils/bootstrap.sh
-    - pip install -e .[test]
   script:
     - coverage run -m pytest -s --tb=short --junitxml=test-results.xml ./dedal/tests/integration_tests
     - coverage xml -o coverage_integration.xml
@@ -70,8 +67,6 @@ merge_coverage:
   tags:
     - docker-runner
   image: ubuntu:22.04
-  before_script:
-    - pip install coverage
   script:
     - coverage combine coverage_unit.xml coverage_integration.xml
     - coverage report
diff --git a/README.md b/README.md
index dd68dcf..df769fe 100644
--- a/README.md
+++ b/README.md
@@ -51,3 +51,5 @@ The lowest ```spack version``` compatible with this library is ```v0.23.0```.
 
 For both concretization and binary caches, the cache version can be changed via the attributes ```cache_version_concretize``` and ```cache_version_build```. 
 The default values are ```v1```.
+
+![Coverage Badge](https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/yashchiki/badges/koutakia/coverage.svg)
-- 
GitLab


From c3166ff5a440993b99db505b54a8837a0b3cf732 Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Mon, 24 Feb 2025 17:55:58 +0100
Subject: [PATCH 05/14] - coverage combine cannot process Cobertura files.
 Therefore, merge the .coverage folder individually to prevent failures when
 combining the coverage results.

---
 .gitlab-ci.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 003ac77..6bf7c32 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -34,14 +34,14 @@ unit_tests:
   image: ubuntu:22.04
   script:
     - coverage run -m pytest -s --tb=short --junitxml=test-results.xml ./dedal/tests/unit_tests
-    - coverage xml -o coverage_unit.xml
+    - mv .coverage .coverage.unit  # Rename to avoid overwriting
   artifacts:
     when: always
     reports:
       junit: test-results.xml
     paths:
       - test-results.xml
-      - coverage_unit.xml
+      - .coverage.unit
     expire_in: 1 week
 
 integration_tests:
@@ -51,7 +51,7 @@ integration_tests:
   image: ubuntu:22.04
   script:
     - coverage run -m pytest -s --tb=short --junitxml=test-results.xml ./dedal/tests/integration_tests
-    - coverage xml -o coverage_integration.xml
+    - mv .coverage .coverage.integration  # Rename to avoid overwriting
   needs: ["unit_tests"]
   artifacts:
     when: always
@@ -59,7 +59,7 @@ integration_tests:
       junit: test-results.xml
     paths:
       - test-results.xml
-      - coverage_integration.xml
+      - .coverage.integration
     expire_in: 1 week
 
 merge_coverage:
@@ -68,7 +68,7 @@ merge_coverage:
     - docker-runner
   image: ubuntu:22.04
   script:
-    - coverage combine coverage_unit.xml coverage_integration.xml
+    - coverage combine .coverage.unit .coverage.integration
     - coverage report
     - coverage xml -o coverage.xml
     - coverage html -d coverage_html
-- 
GitLab


From 92f210b512e094e1e0ac0685f0d0897d5ffd45c8 Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Tue, 25 Feb 2025 11:43:50 +0100
Subject: [PATCH 06/14] - Added a 10 minute timeout for testing if any specific
 command hangs on subprocess.run command!

---
 dedal/utils/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dedal/utils/utils.py b/dedal/utils/utils.py
index 9fc82ad..de5529d 100644
--- a/dedal/utils/utils.py
+++ b/dedal/utils/utils.py
@@ -30,7 +30,7 @@ def run_command(*args, logger=logging.getLogger(__name__), info_msg: str = '', e
                 exception=None, **kwargs):
     try:
         logger.info(f'{info_msg}: args: {args}')
-        return subprocess.run(args, **kwargs)
+        return subprocess.run(args, **kwargs, timeout=10 * 60)
     except subprocess.CalledProcessError as e:
         if exception_msg is not None:
             logger.error(f"{exception_msg}: {e}")
-- 
GitLab


From ca24dca8bfb424b741d9fe927312f0aec5f38e69 Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Tue, 25 Feb 2025 13:27:04 +0100
Subject: [PATCH 07/14] - Added a 10 minute timeout for testing if any specific
 command hangs on subprocess.run command!

---
 dedal/tests/unit_tests/utils_test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dedal/tests/unit_tests/utils_test.py b/dedal/tests/unit_tests/utils_test.py
index cd47860..6bb6eda 100644
--- a/dedal/tests/unit_tests/utils_test.py
+++ b/dedal/tests/unit_tests/utils_test.py
@@ -104,7 +104,7 @@ def test_run_command_success(mocker):
     mock_logger = MagicMock()
     result = run_command('bash',  '-c', 'echo hello', logger=mock_logger, info_msg="Running echo")
     mock_logger.info.assert_called_with("Running echo: args: ('bash', '-c', 'echo hello')")
-    mock_subprocess.assert_called_once_with(('bash', '-c', 'echo hello'))
+    mock_subprocess.assert_called_once_with(('bash', '-c', 'echo hello'), timeout=600)
     assert result.returncode == 0
 
 
-- 
GitLab


From e0262adcd32e72102177f4d006664502e04a0fcb Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Tue, 25 Feb 2025 15:51:19 +0100
Subject: [PATCH 08/14] - Commented the failing tests to verify the coverage
 calculation

---
 .../spack_from_scratch_test.py                | 388 +++++++++---------
 1 file changed, 194 insertions(+), 194 deletions(-)

diff --git a/dedal/tests/integration_tests/spack_from_scratch_test.py b/dedal/tests/integration_tests/spack_from_scratch_test.py
index 2fec80f..a85294f 100644
--- a/dedal/tests/integration_tests/spack_from_scratch_test.py
+++ b/dedal/tests/integration_tests/spack_from_scratch_test.py
@@ -8,197 +8,197 @@ from dedal.tests.testing_variables import test_spack_env_git, ebrains_spack_buil
 from dedal.utils.utils import file_exists_and_not_empty
 
 
-def test_spack_repo_exists_1():
-    spack_operation = SpackOperationCreator.get_spack_operator()
-    spack_operation.install_spack()
-    assert spack_operation.spack_repo_exists('ebrains-spack-builds') == False
-
-
-def test_spack_repo_exists_2(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('ebrains-spack-builds', install_dir)
-    config = SpackConfig(env=env, install_dir=install_dir)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    with pytest.raises(NoSpackEnvironmentException):
-        spack_operation.spack_repo_exists(env.env_name)
-
-
-def test_spack_repo_exists_3(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('ebrains-spack-builds', install_dir)
-    config = SpackConfig(env=env, install_dir=install_dir)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    print(spack_operation.get_spack_installed_version())
-    spack_operation.setup_spack_env()
-    assert spack_operation.spack_repo_exists(env.env_name) == False
-
-
-def test_spack_from_scratch_setup_1(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    spack_operation.setup_spack_env()
-    assert spack_operation.spack_repo_exists(env.env_name) == False
-
-
-def test_spack_from_scratch_setup_2(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-    repo = env
-    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-    config.add_repo(repo)
-    config.add_repo(repo)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    spack_operation.setup_spack_env()
-    assert spack_operation.spack_repo_exists(env.env_name) == True
-
-
-def test_spack_from_scratch_setup_3(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('new_env1', install_dir)
-    repo = env
-    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-    config.add_repo(repo)
-    config.add_repo(repo)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    with pytest.raises(BashCommandException):
-        spack_operation.setup_spack_env()
-
-
-def test_spack_from_scratch_setup_4(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('new_env2', install_dir)
-    config = SpackConfig(env=env, install_dir=install_dir)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    spack_operation.setup_spack_env()
-    assert spack_operation.spack_env_exists() == True
-
-
-def test_spack_not_a_valid_repo():
-    env = SpackDescriptor('ebrains-spack-builds', Path(), None)
-    repo = env
-    config = SpackConfig(env=env, system_name='ebrainslab')
-    config.add_repo(repo)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    with pytest.raises(BashCommandException):
-        spack_operation.add_spack_repo(repo.path, repo.env_name)
-
-
-def test_spack_from_scratch_concretize_1(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-    repo = env
-    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-    config.add_repo(repo)
-    config.add_repo(repo)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    spack_operation.install_spack()
-    spack_operation.setup_spack_env()
-    spack_operation.concretize_spack_env(force=True)
-    concretization_file_path = spack_operation.env_path / 'spack.lock'
-    assert file_exists_and_not_empty(concretization_file_path) == True
-
-
-def test_spack_from_scratch_concretize_2(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-    repo = env
-    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-    config.add_repo(repo)
-    config.add_repo(repo)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    spack_operation.setup_spack_env()
-    spack_operation.concretize_spack_env(force=False)
-    concretization_file_path = spack_operation.env_path / 'spack.lock'
-    assert file_exists_and_not_empty(concretization_file_path) == True
-
-
-def test_spack_from_scratch_concretize_3(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-    repo = env
-    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-    config.add_repo(repo)
-    config.add_repo(repo)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    spack_operation.setup_spack_env()
-    concretization_file_path = spack_operation.env_path / 'spack.lock'
-    assert file_exists_and_not_empty(concretization_file_path) == False
-
-
-def test_spack_from_scratch_concretize_4(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
-    config = SpackConfig(env=env, install_dir=install_dir)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    spack_operation.setup_spack_env()
-    spack_operation.concretize_spack_env(force=False)
-    concretization_file_path = spack_operation.env_path / 'spack.lock'
-    assert file_exists_and_not_empty(concretization_file_path) == True
-
-
-def test_spack_from_scratch_concretize_5(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
-    config = SpackConfig(env=env, install_dir=install_dir)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    spack_operation.setup_spack_env()
-    spack_operation.concretize_spack_env(force=True)
-    concretization_file_path = spack_operation.env_path / 'spack.lock'
-    assert file_exists_and_not_empty(concretization_file_path) == True
-
-
-def test_spack_from_scratch_concretize_6(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
-    repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-    config = SpackConfig(env=env, install_dir=install_dir)
-    config.add_repo(repo)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    spack_operation.setup_spack_env()
-    spack_operation.concretize_spack_env(force=False)
-    concretization_file_path = spack_operation.env_path / 'spack.lock'
-    assert file_exists_and_not_empty(concretization_file_path) == True
-
-
-def test_spack_from_scratch_concretize_7(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
-    repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-    config = SpackConfig(env=env)
-    config.add_repo(repo)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    spack_operation.setup_spack_env()
-    spack_operation.concretize_spack_env(force=True)
-    concretization_file_path = spack_operation.env_path / 'spack.lock'
-    assert file_exists_and_not_empty(concretization_file_path) == True
-
-
-def test_spack_from_scratch_install(tmp_path):
-    install_dir = tmp_path
-    env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
-    repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-    config = SpackConfig(env=env)
-    config.add_repo(repo)
-    spack_operation = SpackOperationCreator.get_spack_operator(config)
-    spack_operation.install_spack()
-    spack_operation.setup_spack_env()
-    spack_operation.concretize_spack_env(force=True)
-    concretization_file_path = spack_operation.env_path / 'spack.lock'
-    assert file_exists_and_not_empty(concretization_file_path) == True
-    install_result = spack_operation.install_packages(jobs=2, signed=False, fresh=True, debug=False)
-    assert install_result.returncode == 0
+# def test_spack_repo_exists_1():
+#     spack_operation = SpackOperationCreator.get_spack_operator()
+#     spack_operation.install_spack()
+#     assert spack_operation.spack_repo_exists('ebrains-spack-builds') == False
+#
+#
+# def test_spack_repo_exists_2(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('ebrains-spack-builds', install_dir)
+#     config = SpackConfig(env=env, install_dir=install_dir)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     with pytest.raises(NoSpackEnvironmentException):
+#         spack_operation.spack_repo_exists(env.env_name)
+#
+#
+# def test_spack_repo_exists_3(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('ebrains-spack-builds', install_dir)
+#     config = SpackConfig(env=env, install_dir=install_dir)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     print(spack_operation.get_spack_installed_version())
+#     spack_operation.setup_spack_env()
+#     assert spack_operation.spack_repo_exists(env.env_name) == False
+#
+#
+# def test_spack_from_scratch_setup_1(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     spack_operation.setup_spack_env()
+#     assert spack_operation.spack_repo_exists(env.env_name) == False
+#
+#
+# def test_spack_from_scratch_setup_2(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+#     repo = env
+#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+#     config.add_repo(repo)
+#     config.add_repo(repo)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     spack_operation.setup_spack_env()
+#     assert spack_operation.spack_repo_exists(env.env_name) == True
+#
+#
+# def test_spack_from_scratch_setup_3(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('new_env1', install_dir)
+#     repo = env
+#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+#     config.add_repo(repo)
+#     config.add_repo(repo)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     with pytest.raises(BashCommandException):
+#         spack_operation.setup_spack_env()
+#
+#
+# def test_spack_from_scratch_setup_4(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('new_env2', install_dir)
+#     config = SpackConfig(env=env, install_dir=install_dir)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     spack_operation.setup_spack_env()
+#     assert spack_operation.spack_env_exists() == True
+#
+#
+# def test_spack_not_a_valid_repo():
+#     env = SpackDescriptor('ebrains-spack-builds', Path(), None)
+#     repo = env
+#     config = SpackConfig(env=env, system_name='ebrainslab')
+#     config.add_repo(repo)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     with pytest.raises(BashCommandException):
+#         spack_operation.add_spack_repo(repo.path, repo.env_name)
+#
+#
+# def test_spack_from_scratch_concretize_1(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+#     repo = env
+#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+#     config.add_repo(repo)
+#     config.add_repo(repo)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     spack_operation.install_spack()
+#     spack_operation.setup_spack_env()
+#     spack_operation.concretize_spack_env(force=True)
+#     concretization_file_path = spack_operation.env_path / 'spack.lock'
+#     assert file_exists_and_not_empty(concretization_file_path) == True
+#
+#
+# def test_spack_from_scratch_concretize_2(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+#     repo = env
+#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+#     config.add_repo(repo)
+#     config.add_repo(repo)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     spack_operation.setup_spack_env()
+#     spack_operation.concretize_spack_env(force=False)
+#     concretization_file_path = spack_operation.env_path / 'spack.lock'
+#     assert file_exists_and_not_empty(concretization_file_path) == True
+#
+#
+# def test_spack_from_scratch_concretize_3(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+#     repo = env
+#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+#     config.add_repo(repo)
+#     config.add_repo(repo)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     spack_operation.setup_spack_env()
+#     concretization_file_path = spack_operation.env_path / 'spack.lock'
+#     assert file_exists_and_not_empty(concretization_file_path) == False
+#
+#
+# def test_spack_from_scratch_concretize_4(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
+#     config = SpackConfig(env=env, install_dir=install_dir)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     spack_operation.setup_spack_env()
+#     spack_operation.concretize_spack_env(force=False)
+#     concretization_file_path = spack_operation.env_path / 'spack.lock'
+#     assert file_exists_and_not_empty(concretization_file_path) == True
+#
+#
+# def test_spack_from_scratch_concretize_5(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
+#     config = SpackConfig(env=env, install_dir=install_dir)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     spack_operation.setup_spack_env()
+#     spack_operation.concretize_spack_env(force=True)
+#     concretization_file_path = spack_operation.env_path / 'spack.lock'
+#     assert file_exists_and_not_empty(concretization_file_path) == True
+#
+#
+# def test_spack_from_scratch_concretize_6(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
+#     repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+#     config = SpackConfig(env=env, install_dir=install_dir)
+#     config.add_repo(repo)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     spack_operation.setup_spack_env()
+#     spack_operation.concretize_spack_env(force=False)
+#     concretization_file_path = spack_operation.env_path / 'spack.lock'
+#     assert file_exists_and_not_empty(concretization_file_path) == True
+#
+#
+# def test_spack_from_scratch_concretize_7(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
+#     repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+#     config = SpackConfig(env=env)
+#     config.add_repo(repo)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     spack_operation.setup_spack_env()
+#     spack_operation.concretize_spack_env(force=True)
+#     concretization_file_path = spack_operation.env_path / 'spack.lock'
+#     assert file_exists_and_not_empty(concretization_file_path) == True
+#
+#
+# def test_spack_from_scratch_install(tmp_path):
+#     install_dir = tmp_path
+#     env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
+#     repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+#     config = SpackConfig(env=env)
+#     config.add_repo(repo)
+#     spack_operation = SpackOperationCreator.get_spack_operator(config)
+#     spack_operation.install_spack()
+#     spack_operation.setup_spack_env()
+#     spack_operation.concretize_spack_env(force=True)
+#     concretization_file_path = spack_operation.env_path / 'spack.lock'
+#     assert file_exists_and_not_empty(concretization_file_path) == True
+#     install_result = spack_operation.install_packages(jobs=2, signed=False, fresh=True, debug=False)
+#     assert install_result.returncode == 0
-- 
GitLab


From 6e2f574f12c83206a44c8239f81f7154bce9e594 Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Tue, 25 Feb 2025 16:18:33 +0100
Subject: [PATCH 09/14] Revert "- Commented the failing tests to verify the
 coverage calculation"

This reverts commit e0262adcd32e72102177f4d006664502e04a0fcb.
---
 .../spack_from_scratch_test.py                | 388 +++++++++---------
 1 file changed, 194 insertions(+), 194 deletions(-)

diff --git a/dedal/tests/integration_tests/spack_from_scratch_test.py b/dedal/tests/integration_tests/spack_from_scratch_test.py
index a85294f..2fec80f 100644
--- a/dedal/tests/integration_tests/spack_from_scratch_test.py
+++ b/dedal/tests/integration_tests/spack_from_scratch_test.py
@@ -8,197 +8,197 @@ from dedal.tests.testing_variables import test_spack_env_git, ebrains_spack_buil
 from dedal.utils.utils import file_exists_and_not_empty
 
 
-# def test_spack_repo_exists_1():
-#     spack_operation = SpackOperationCreator.get_spack_operator()
-#     spack_operation.install_spack()
-#     assert spack_operation.spack_repo_exists('ebrains-spack-builds') == False
-#
-#
-# def test_spack_repo_exists_2(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('ebrains-spack-builds', install_dir)
-#     config = SpackConfig(env=env, install_dir=install_dir)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     with pytest.raises(NoSpackEnvironmentException):
-#         spack_operation.spack_repo_exists(env.env_name)
-#
-#
-# def test_spack_repo_exists_3(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('ebrains-spack-builds', install_dir)
-#     config = SpackConfig(env=env, install_dir=install_dir)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     print(spack_operation.get_spack_installed_version())
-#     spack_operation.setup_spack_env()
-#     assert spack_operation.spack_repo_exists(env.env_name) == False
-#
-#
-# def test_spack_from_scratch_setup_1(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     spack_operation.setup_spack_env()
-#     assert spack_operation.spack_repo_exists(env.env_name) == False
-#
-#
-# def test_spack_from_scratch_setup_2(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-#     repo = env
-#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-#     config.add_repo(repo)
-#     config.add_repo(repo)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     spack_operation.setup_spack_env()
-#     assert spack_operation.spack_repo_exists(env.env_name) == True
-#
-#
-# def test_spack_from_scratch_setup_3(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('new_env1', install_dir)
-#     repo = env
-#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-#     config.add_repo(repo)
-#     config.add_repo(repo)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     with pytest.raises(BashCommandException):
-#         spack_operation.setup_spack_env()
-#
-#
-# def test_spack_from_scratch_setup_4(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('new_env2', install_dir)
-#     config = SpackConfig(env=env, install_dir=install_dir)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     spack_operation.setup_spack_env()
-#     assert spack_operation.spack_env_exists() == True
-#
-#
-# def test_spack_not_a_valid_repo():
-#     env = SpackDescriptor('ebrains-spack-builds', Path(), None)
-#     repo = env
-#     config = SpackConfig(env=env, system_name='ebrainslab')
-#     config.add_repo(repo)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     with pytest.raises(BashCommandException):
-#         spack_operation.add_spack_repo(repo.path, repo.env_name)
-#
-#
-# def test_spack_from_scratch_concretize_1(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-#     repo = env
-#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-#     config.add_repo(repo)
-#     config.add_repo(repo)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     spack_operation.install_spack()
-#     spack_operation.setup_spack_env()
-#     spack_operation.concretize_spack_env(force=True)
-#     concretization_file_path = spack_operation.env_path / 'spack.lock'
-#     assert file_exists_and_not_empty(concretization_file_path) == True
-#
-#
-# def test_spack_from_scratch_concretize_2(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-#     repo = env
-#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-#     config.add_repo(repo)
-#     config.add_repo(repo)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     spack_operation.setup_spack_env()
-#     spack_operation.concretize_spack_env(force=False)
-#     concretization_file_path = spack_operation.env_path / 'spack.lock'
-#     assert file_exists_and_not_empty(concretization_file_path) == True
-#
-#
-# def test_spack_from_scratch_concretize_3(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-#     repo = env
-#     config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
-#     config.add_repo(repo)
-#     config.add_repo(repo)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     spack_operation.setup_spack_env()
-#     concretization_file_path = spack_operation.env_path / 'spack.lock'
-#     assert file_exists_and_not_empty(concretization_file_path) == False
-#
-#
-# def test_spack_from_scratch_concretize_4(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
-#     config = SpackConfig(env=env, install_dir=install_dir)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     spack_operation.setup_spack_env()
-#     spack_operation.concretize_spack_env(force=False)
-#     concretization_file_path = spack_operation.env_path / 'spack.lock'
-#     assert file_exists_and_not_empty(concretization_file_path) == True
-#
-#
-# def test_spack_from_scratch_concretize_5(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
-#     config = SpackConfig(env=env, install_dir=install_dir)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     spack_operation.setup_spack_env()
-#     spack_operation.concretize_spack_env(force=True)
-#     concretization_file_path = spack_operation.env_path / 'spack.lock'
-#     assert file_exists_and_not_empty(concretization_file_path) == True
-#
-#
-# def test_spack_from_scratch_concretize_6(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
-#     repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-#     config = SpackConfig(env=env, install_dir=install_dir)
-#     config.add_repo(repo)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     spack_operation.setup_spack_env()
-#     spack_operation.concretize_spack_env(force=False)
-#     concretization_file_path = spack_operation.env_path / 'spack.lock'
-#     assert file_exists_and_not_empty(concretization_file_path) == True
-#
-#
-# def test_spack_from_scratch_concretize_7(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
-#     repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-#     config = SpackConfig(env=env)
-#     config.add_repo(repo)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     spack_operation.setup_spack_env()
-#     spack_operation.concretize_spack_env(force=True)
-#     concretization_file_path = spack_operation.env_path / 'spack.lock'
-#     assert file_exists_and_not_empty(concretization_file_path) == True
-#
-#
-# def test_spack_from_scratch_install(tmp_path):
-#     install_dir = tmp_path
-#     env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
-#     repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
-#     config = SpackConfig(env=env)
-#     config.add_repo(repo)
-#     spack_operation = SpackOperationCreator.get_spack_operator(config)
-#     spack_operation.install_spack()
-#     spack_operation.setup_spack_env()
-#     spack_operation.concretize_spack_env(force=True)
-#     concretization_file_path = spack_operation.env_path / 'spack.lock'
-#     assert file_exists_and_not_empty(concretization_file_path) == True
-#     install_result = spack_operation.install_packages(jobs=2, signed=False, fresh=True, debug=False)
-#     assert install_result.returncode == 0
+def test_spack_repo_exists_1():
+    spack_operation = SpackOperationCreator.get_spack_operator()
+    spack_operation.install_spack()
+    assert spack_operation.spack_repo_exists('ebrains-spack-builds') == False
+
+
+def test_spack_repo_exists_2(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('ebrains-spack-builds', install_dir)
+    config = SpackConfig(env=env, install_dir=install_dir)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    with pytest.raises(NoSpackEnvironmentException):
+        spack_operation.spack_repo_exists(env.env_name)
+
+
+def test_spack_repo_exists_3(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('ebrains-spack-builds', install_dir)
+    config = SpackConfig(env=env, install_dir=install_dir)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    print(spack_operation.get_spack_installed_version())
+    spack_operation.setup_spack_env()
+    assert spack_operation.spack_repo_exists(env.env_name) == False
+
+
+def test_spack_from_scratch_setup_1(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    spack_operation.setup_spack_env()
+    assert spack_operation.spack_repo_exists(env.env_name) == False
+
+
+def test_spack_from_scratch_setup_2(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+    repo = env
+    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+    config.add_repo(repo)
+    config.add_repo(repo)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    spack_operation.setup_spack_env()
+    assert spack_operation.spack_repo_exists(env.env_name) == True
+
+
+def test_spack_from_scratch_setup_3(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('new_env1', install_dir)
+    repo = env
+    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+    config.add_repo(repo)
+    config.add_repo(repo)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    with pytest.raises(BashCommandException):
+        spack_operation.setup_spack_env()
+
+
+def test_spack_from_scratch_setup_4(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('new_env2', install_dir)
+    config = SpackConfig(env=env, install_dir=install_dir)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    spack_operation.setup_spack_env()
+    assert spack_operation.spack_env_exists() == True
+
+
+def test_spack_not_a_valid_repo():
+    env = SpackDescriptor('ebrains-spack-builds', Path(), None)
+    repo = env
+    config = SpackConfig(env=env, system_name='ebrainslab')
+    config.add_repo(repo)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    with pytest.raises(BashCommandException):
+        spack_operation.add_spack_repo(repo.path, repo.env_name)
+
+
+def test_spack_from_scratch_concretize_1(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+    repo = env
+    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+    config.add_repo(repo)
+    config.add_repo(repo)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    spack_operation.install_spack()
+    spack_operation.setup_spack_env()
+    spack_operation.concretize_spack_env(force=True)
+    concretization_file_path = spack_operation.env_path / 'spack.lock'
+    assert file_exists_and_not_empty(concretization_file_path) == True
+
+
+def test_spack_from_scratch_concretize_2(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+    repo = env
+    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+    config.add_repo(repo)
+    config.add_repo(repo)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    spack_operation.setup_spack_env()
+    spack_operation.concretize_spack_env(force=False)
+    concretization_file_path = spack_operation.env_path / 'spack.lock'
+    assert file_exists_and_not_empty(concretization_file_path) == True
+
+
+def test_spack_from_scratch_concretize_3(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+    repo = env
+    config = SpackConfig(env=env, system_name='ebrainslab', install_dir=install_dir)
+    config.add_repo(repo)
+    config.add_repo(repo)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    spack_operation.setup_spack_env()
+    concretization_file_path = spack_operation.env_path / 'spack.lock'
+    assert file_exists_and_not_empty(concretization_file_path) == False
+
+
+def test_spack_from_scratch_concretize_4(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
+    config = SpackConfig(env=env, install_dir=install_dir)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    spack_operation.setup_spack_env()
+    spack_operation.concretize_spack_env(force=False)
+    concretization_file_path = spack_operation.env_path / 'spack.lock'
+    assert file_exists_and_not_empty(concretization_file_path) == True
+
+
+def test_spack_from_scratch_concretize_5(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
+    config = SpackConfig(env=env, install_dir=install_dir)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    spack_operation.setup_spack_env()
+    spack_operation.concretize_spack_env(force=True)
+    concretization_file_path = spack_operation.env_path / 'spack.lock'
+    assert file_exists_and_not_empty(concretization_file_path) == True
+
+
+def test_spack_from_scratch_concretize_6(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
+    repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+    config = SpackConfig(env=env, install_dir=install_dir)
+    config.add_repo(repo)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    spack_operation.setup_spack_env()
+    spack_operation.concretize_spack_env(force=False)
+    concretization_file_path = spack_operation.env_path / 'spack.lock'
+    assert file_exists_and_not_empty(concretization_file_path) == True
+
+
+def test_spack_from_scratch_concretize_7(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
+    repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+    config = SpackConfig(env=env)
+    config.add_repo(repo)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    spack_operation.setup_spack_env()
+    spack_operation.concretize_spack_env(force=True)
+    concretization_file_path = spack_operation.env_path / 'spack.lock'
+    assert file_exists_and_not_empty(concretization_file_path) == True
+
+
+def test_spack_from_scratch_install(tmp_path):
+    install_dir = tmp_path
+    env = SpackDescriptor('test-spack-env', install_dir, test_spack_env_git)
+    repo = SpackDescriptor('ebrains-spack-builds', install_dir, ebrains_spack_builds_git)
+    config = SpackConfig(env=env)
+    config.add_repo(repo)
+    spack_operation = SpackOperationCreator.get_spack_operator(config)
+    spack_operation.install_spack()
+    spack_operation.setup_spack_env()
+    spack_operation.concretize_spack_env(force=True)
+    concretization_file_path = spack_operation.env_path / 'spack.lock'
+    assert file_exists_and_not_empty(concretization_file_path) == True
+    install_result = spack_operation.install_packages(jobs=2, signed=False, fresh=True, debug=False)
+    assert install_result.returncode == 0
-- 
GitLab


From 4491132f703b9654758705795e8797601c20ab96 Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Tue, 25 Feb 2025 16:19:01 +0100
Subject: [PATCH 10/14] Revert "- Added a 10 minute timeout for testing if any
 specific command hangs on subprocess.run command!"

This reverts commit ca24dca8bfb424b741d9fe927312f0aec5f38e69.
---
 dedal/tests/unit_tests/utils_test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dedal/tests/unit_tests/utils_test.py b/dedal/tests/unit_tests/utils_test.py
index 6bb6eda..cd47860 100644
--- a/dedal/tests/unit_tests/utils_test.py
+++ b/dedal/tests/unit_tests/utils_test.py
@@ -104,7 +104,7 @@ def test_run_command_success(mocker):
     mock_logger = MagicMock()
     result = run_command('bash',  '-c', 'echo hello', logger=mock_logger, info_msg="Running echo")
     mock_logger.info.assert_called_with("Running echo: args: ('bash', '-c', 'echo hello')")
-    mock_subprocess.assert_called_once_with(('bash', '-c', 'echo hello'), timeout=600)
+    mock_subprocess.assert_called_once_with(('bash', '-c', 'echo hello'))
     assert result.returncode == 0
 
 
-- 
GitLab


From 997d22b052d32246d67b4f702c0e816a88029618 Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Tue, 25 Feb 2025 16:19:12 +0100
Subject: [PATCH 11/14] Revert "- Added a 10 minute timeout for testing if any
 specific command hangs on subprocess.run command!"

This reverts commit 92f210b512e094e1e0ac0685f0d0897d5ffd45c8.
---
 dedal/utils/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dedal/utils/utils.py b/dedal/utils/utils.py
index de5529d..9fc82ad 100644
--- a/dedal/utils/utils.py
+++ b/dedal/utils/utils.py
@@ -30,7 +30,7 @@ def run_command(*args, logger=logging.getLogger(__name__), info_msg: str = '', e
                 exception=None, **kwargs):
     try:
         logger.info(f'{info_msg}: args: {args}')
-        return subprocess.run(args, **kwargs, timeout=10 * 60)
+        return subprocess.run(args, **kwargs)
     except subprocess.CalledProcessError as e:
         if exception_msg is not None:
             logger.error(f"{exception_msg}: {e}")
-- 
GitLab


From 84d30a756b71eaac291a6c77d448dd397e8badc6 Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Wed, 5 Mar 2025 10:32:41 +0100
Subject: [PATCH 12/14] - Added .dedal.log also as a job artefact

---
 .gitlab-ci.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6bf7c32..0ce0289 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -41,6 +41,7 @@ unit_tests:
       junit: test-results.xml
     paths:
       - test-results.xml
+      - .dedal.log
       - .coverage.unit
     expire_in: 1 week
 
@@ -59,6 +60,7 @@ integration_tests:
       junit: test-results.xml
     paths:
       - test-results.xml
+      - .dedal.log
       - .coverage.integration
     expire_in: 1 week
 
-- 
GitLab


From 54c811b9e959031207ec1caaf6e51d477784a7c0 Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Wed, 5 Mar 2025 14:51:01 +0100
Subject: [PATCH 13/14] - Corrected the failing tests.

---
 dedal/spack_factory/SpackOperationCreateCache.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/dedal/spack_factory/SpackOperationCreateCache.py b/dedal/spack_factory/SpackOperationCreateCache.py
index 41cfc84..8d6125f 100644
--- a/dedal/spack_factory/SpackOperationCreateCache.py
+++ b/dedal/spack_factory/SpackOperationCreateCache.py
@@ -42,7 +42,10 @@ class SpackOperationCreateCache(SpackOperation):
         if self.spack_config.gpg:
             signed = True
             self.create_gpg_keys()
-        self.add_mirror('local_cache', self.spack_config.buildcache_dir, signed=signed, autopush=signed,
+        self.add_mirror('local_cache',
+                        str(self.spack_config.buildcache_dir),
+                        signed=signed,
+                        autopush=signed,
                         global_mirror=False)
         self.logger.info(f'Added mirror for {self.spack_config.env.name}')
         super().install_packages(jobs=jobs, signed=signed, debug=debug, fresh=True)
-- 
GitLab


From 14474dd656100116d2763662ba27b1437e5543bf Mon Sep 17 00:00:00 2001
From: Jithu Murugan <j.murugan@fz-juelich.de>
Date: Thu, 6 Mar 2025 11:38:59 +0100
Subject: [PATCH 14/14] - Moved the coverage badge to the top.

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index c8a01e8..55080aa 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,5 @@
 # Dedal
+![Coverage Badge](https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/yashchiki/badges/koutakia/coverage.svg)
 
 This repository provides functionalities to easily ```managed spack environments``` and
 ```helpers for the container image build flow```.
@@ -140,4 +141,4 @@ Installs spack packages present in the spack environment defined in configuratio
 # Dedal's UML diagram
 
 ![screenshot](dedal/docs/resources/dedal_UML.png)
-![Coverage Badge](https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/yashchiki/badges/koutakia/coverage.svg)
+
-- 
GitLab