Repository: gammasim/simtools (language: python)

Issue:
Move to src-layout for simtools
Change simtools to src-layout as described in https://setuptools.pypa.io/en/latest/userguide/package_discovery.html#src-layout

simtools is currently organized as [flat layout](https://setuptools.pypa.io/en/latest/userguide/package_discovery.html#flat-layout), which is different to the recommendation from CTAO (see [python-template](https://gitlab.cta-observatory.org/cta-computing/documentation/python-project-template#project-structure--packaging)) and other CTA projects (e.g. [ctapipe](https://github.com/cta-observatory/ctapipe).

Being in sync with those project has the benefits of lowering the maintenance for packaging and deployment, as we can take over one-to-one the settings from other CTAO projects. 

This is triggered by the issues from python building (see  [here](https://github.com/gammasim/simtools/actions/runs/12032739454/job/33545254687#step:5:876)), by the failure of the gammasimtools feedstock (see [here](https://github.com/conda-forge/gammasimtools-feedstock/pull/1/checks?check_run_id=33554392192)), and the failure of solve this issue within a reasonable time scale.

I will make these changes, unless someone wants to become an expert in the whole packaging ecosystem.


Discussion / hints:

Fix patch:
diff --git a/.github/workflows/CI-docs.yml b/.github/workflows/CI-docs.yml
index 203cfd854a..d105c20f17 100644
--- a/.github/workflows/CI-docs.yml
+++ b/.github/workflows/CI-docs.yml
@@ -36,10 +36,10 @@ jobs:
 
       - name: Check for complete API documentation
         run: |-
-          MODULES=$(find simtools -type f -name "*.py" \
-            ! -path "simtools/applications/*" \
+          MODULES=$(find src/simtools -type f -name "*.py" \
+            ! -path "src/simtools/applications/*" \
             ! -name "__init__.py" ! -name "version.py" \
-            ! -path "simtools/_*" -prune)
+            ! -path "src/simtools/_*" -prune)
           FULLY_DOCUMENTED="TRUE"
           for M in "${MODULES[@]}"; do
               module=$(basename "$M" .py)
diff --git a/.github/workflows/CI-linter.yml b/.github/workflows/CI-linter.yml
index d0e40be93d..3b88bb7596 100644
--- a/.github/workflows/CI-linter.yml
+++ b/.github/workflows/CI-linter.yml
@@ -73,7 +73,7 @@ jobs:
 
       - name: pylint
         run: |
-          git ls-files 'simtools/*.py' | xargs pylint -v
+          git ls-files 'src/simtools/*.py' | xargs pylint -v
 
       - name: Pre-commit
         run: |
diff --git a/.github/workflows/CI-schema-validation.yml b/.github/workflows/CI-schema-validation.yml
index 2cbf601a51..ac66bc6f67 100644
--- a/.github/workflows/CI-schema-validation.yml
+++ b/.github/workflows/CI-schema-validation.yml
@@ -4,7 +4,7 @@ on:
   workflow_dispatch:
   pull_request:
     paths:
-      - 'simtools/schemas/model_parameters/*'
+      - 'src/simtools/schemas/model_parameters/*'
       - 'tests/integration_tests/config/*'
 
 jobs:
@@ -35,7 +35,7 @@ jobs:
 
       - name: Check for files without the suffix *.schema.yml
         run: |
-          for file in simtools/schemas/model_parameters/*.yml; do
+          for file in src/simtools/schemas/model_parameters/*.yml; do
             if [[ ! $file =~ .*schema.yml$ ]]; then
               echo "File $file does not have the suffix *.schema.yml"
               exit 1
@@ -44,9 +44,9 @@ jobs:
 
       - name: Model parameter schema validation
         run: |
-          for file in simtools/schemas/model_parameters/*.yml; do
+          for file in src/simtools/schemas/model_parameters/*.yml; do
             echo "Testing schema $file"
-            python simtools/applications/validate_file_using_schema.py \
+            python src/simtools/applications/validate_file_using_schema.py \
             --file_name "$file" \
             --schema model_parameter_and_data_schema.metaschema.yml \
             --data_type "schema" \
@@ -57,7 +57,7 @@ jobs:
         run: |
           for file in tests/integration_tests/config/*.yml; do
             echo "Testing config file $file"
-            python simtools/applications/validate_file_using_schema.py \
+            python src/simtools/applications/validate_file_using_schema.py \
             --file_name "$file" \
             --schema integration_tests_config.metaschema.yml \
             --data_type "schema" \
diff --git a/.gitignore b/.gitignore
index 1d84f9844e..ad439ea189 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,7 +27,7 @@ simtools-output
 
 # Dynamic version file
 # generated by setuptools_scm
-simtools/_version.py
+src/simtools/_version.py
 
 # Coverage files
 coverage*
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2590468bc6..0e88124400 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -37,7 +37,7 @@ repos:
     rev: v2.3.2  # most recent docstr-coverage release or commit sha
     hooks:
       - id: docstr-coverage
-        args: ["--verbose", "2", "--fail-under", "70.", "simtools"]
+        args: ["--verbose", "2", "--fail-under", "70.", "src/simtools"]
   # Github action
   - repo: https://github.com/rhysd/actionlint
     rev: v1.7.4
diff --git a/docs/changes/1264.maintenance.md b/docs/changes/1264.maintenance.md
new file mode 100644
index 0000000000..6871c9de33
--- /dev/null
+++ b/docs/changes/1264.maintenance.md
@@ -0,0 +1,1 @@
+Move simtools package layout to src-layout.
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 5633d9aadf..7ebeca1341 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -14,8 +14,8 @@
 
 import simtools.version
 
-sys.path.insert(0, os.path.abspath("../../simtools"))
-sys.path.insert(0, os.path.abspath("../../simtools/applications"))
+sys.path.insert(0, os.path.abspath("../../src/simtools"))
+sys.path.insert(0, os.path.abspath("../../src/simtools/applications"))
 sys.path.insert(0, os.path.abspath("../.."))
 
 
diff --git a/pyproject.toml b/pyproject.toml
index 72386bc937..d29f2d588f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,8 +1,8 @@
 [build-system]
 build-backend = "setuptools.build_meta"
 requires = [
-  "setuptools>=65",
-  "setuptools-scm[toml]>=6.2",
+  "setuptools>=64",
+  "setuptools-scm[toml]>=8",
 ]
 
 [project]
@@ -100,13 +100,14 @@ scripts.simtools-validate-file-using-schema = "simtools.applications.validate_fi
 scripts.simtools-validate-optics = "simtools.applications.validate_optics:main"
 
 [tool.setuptools]
-packages = [
-  "simtools",
-]
-include-package-data = true
+package-dir = { "" = "src" }
+
+[tool.setuptools.packages.find]
+where = [ "src" ]
+exclude = [ "simtools._dev_version.*" ]
 
 [tool.setuptools_scm]
-write_to = "simtools/_version.py"
+write_to = "src/simtools/_version.py"
 
 [tool.black]
 line-length = 100
@@ -260,7 +261,7 @@ minversion = "6.0"
 norecursedirs = [
   "build",
   "docs/_build",
-  "simtools/applications",
+  "src/simtools/applications",
 ]
 addopts = "-v --cov=simtools --cov-report=xml --cov-report=term"
 testpaths = "tests/unit_tests/"
@@ -273,10 +274,8 @@ exclude_also = [
 ]
 
 [tool.coverage.run]
+omit = [ "src/simtools/_version.py", "*__init__*", "src/simtools/applications/**" ]
 relative_files = true
-source = [
-  "simtools",
-]
 
 [tool.towncrier]
 package = "simtools"
diff --git a/simtools/_dev_version/scm_version.py b/simtools/_dev_version/scm_version.py
deleted file mode 100644
index 15876487ec..0000000000
--- a/simtools/_dev_version/scm_version.py
+++ /dev/null
@@ -1,10 +0,0 @@
-# Try to use setuptools_scm to get the current version; this is only used
-# in development installations from the git repository.
-import os.path as pth
-
-try:
-    from setuptools_scm import get_version
-
-    version = get_version(root=pth.join("..", ".."), relative_to=__file__)
-except Exception as exc:
-    raise ImportError("setuptools_scm broken or not installed") from exc
diff --git a/simtools/constants.py b/simtools/constants.py
deleted file mode 100644
index a95c732e25..0000000000
--- a/simtools/constants.py
+++ /dev/null
@@ -1,9 +0,0 @@
-"""Project wide constants."""
-
-from pathlib import Path
-
-# Path to metadata jsonschema
-METADATA_JSON_SCHEMA = Path(__file__).parent / "../simtools/schemas/metadata.metaschema.yml"
-
-# Path to model parameter schema files
-MODEL_PARAMETER_SCHEMA_PATH = Path(__file__).parent / "../simtools/schemas/model_parameters"
diff --git a/simtools/visualization/__init__.py b/simtools/visualization/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/sonar-project.properties b/sonar-project.properties
index 7f2d995841..87db44e0ef 100644
--- a/sonar-project.properties
+++ b/sonar-project.properties
@@ -3,5 +3,5 @@ sonar.host.url=https://sonar-cta-dpps.zeuthen.desy.de
 sonar.qualitygate.wait=true
 sonar.python.coverage.reportPaths=coverage.xml
 sonar.python.version=3.11
-sonar.exclusions=**/docs/**,simtools/applications/*
+sonar.exclusions=**/docs/**,src/simtools/applications/*,**__init__.py
 sonar.coverage.exclusions=**/tests/**
diff --git a/simtools/__init__.py b/src/simtools/__init__.py
similarity index 100%
rename from simtools/__init__.py
rename to src/simtools/__init__.py
diff --git a/src/simtools/_dev_version/__init__.py b/src/simtools/_dev_version/__init__.py
new file mode 100644
index 0000000000..0604e0ec47
--- /dev/null
+++ b/src/simtools/_dev_version/__init__.py
@@ -0,0 +1,9 @@
+# Try to use setuptools_scm to get the current version; this is only used
+# in development installations from the git repository.
+# see src/simtools/version.py for details
+try:
+    from setuptools_scm import get_version
+
+    version = get_version(root="../../..", relative_to=__file__)
+except Exception as e:
+    raise ImportError(f"setuptools_scm broken or not installed: {e}")
diff --git a/simtools/_dev_version/__init__.py b/src/simtools/applications/__init__.py
similarity index 100%
rename from simtools/_dev_version/__init__.py
rename to src/simtools/applications/__init__.py
diff --git a/simtools/applications/calculate_trigger_rate.py b/src/simtools/applications/calculate_trigger_rate.py
similarity index 100%
rename from simtools/applications/calculate_trigger_rate.py
rename to src/simtools/applications/calculate_trigger_rate.py
diff --git a/simtools/applications/convert_all_model_parameters_from_simtel.py b/src/simtools/applications/convert_all_model_parameters_from_simtel.py
similarity index 100%
rename from simtools/applications/convert_all_model_parameters_from_simtel.py
rename to src/simtools/applications/convert_all_model_parameters_from_simtel.py
diff --git a/simtools/applications/convert_geo_coordinates_of_array_elements.py b/src/simtools/applications/convert_geo_coordinates_of_array_elements.py
similarity index 100%
rename from simtools/applications/convert_geo_coordinates_of_array_elements.py
rename to src/simtools/applications/convert_geo_coordinates_of_array_elements.py
diff --git a/simtools/applications/convert_model_parameter_from_simtel.py b/src/simtools/applications/convert_model_parameter_from_simtel.py
similarity index 100%
rename from simtools/applications/convert_model_parameter_from_simtel.py
rename to src/simtools/applications/convert_model_parameter_from_simtel.py
diff --git a/simtools/applications/db_add_file_to_db.py b/src/simtools/applications/db_add_file_to_db.py
similarity index 100%
rename from simtools/applications/db_add_file_to_db.py
rename to src/simtools/applications/db_add_file_to_db.py
diff --git a/simtools/applications/db_add_model_parameters_from_repository_to_db.py b/src/simtools/applications/db_add_model_parameters_from_repository_to_db.py
similarity index 100%
rename from simtools/applications/db_add_model_parameters_from_repository_to_db.py
rename to src/simtools/applications/db_add_model_parameters_from_repository_to_db.py
diff --git a/simtools/applications/db_add_value_from_json_to_db.py b/src/simtools/applications/db_add_value_from_json_to_db.py
similarity index 100%
rename from simtools/applications/db_add_value_from_json_to_db.py
rename to src/simtools/applications/db_add_value_from_json_to_db.py
diff --git a/simtools/applications/db_development_tools/write_array_elements_positions_to_repository.py b/src/simtools/applications/db_development_tools/write_array_elements_positions_to_repository.py
similarity index 100%
rename from simtools/applications/db_development_tools/write_array_elements_positions_to_repository.py
rename to src/simtools/applications/db_development_tools/write_array_elements_positions_to_repository.py
diff --git a/simtools/applications/db_get_array_layouts_from_db.py b/src/simtools/applications/db_get_array_layouts_from_db.py
similarity index 100%
rename from simtools/applications/db_get_array_layouts_from_db.py
rename to src/simtools/applications/db_get_array_layouts_from_db.py
diff --git a/simtools/applications/db_get_file_from_db.py b/src/simtools/applications/db_get_file_from_db.py
similarity index 100%
rename from simtools/applications/db_get_file_from_db.py
rename to src/simtools/applications/db_get_file_from_db.py
diff --git a/simtools/applications/db_get_parameter_from_db.py b/src/simtools/applications/db_get_parameter_from_db.py
similarity index 100%
rename from simtools/applications/db_get_parameter_from_db.py
rename to src/simtools/applications/db_get_parameter_from_db.py
diff --git a/simtools/applications/db_inspect_databases.py b/src/simtools/applications/db_inspect_databases.py
similarity index 100%
rename from simtools/applications/db_inspect_databases.py
rename to src/simtools/applications/db_inspect_databases.py
diff --git a/simtools/applications/derive_mirror_rnda.py b/src/simtools/applications/derive_mirror_rnda.py
similarity index 100%
rename from simtools/applications/derive_mirror_rnda.py
rename to src/simtools/applications/derive_mirror_rnda.py
diff --git a/simtools/applications/derive_psf_parameters.py b/src/simtools/applications/derive_psf_parameters.py
similarity index 100%
rename from simtools/applications/derive_psf_parameters.py
rename to src/simtools/applications/derive_psf_parameters.py
diff --git a/simtools/applications/generate_array_config.py b/src/simtools/applications/generate_array_config.py
similarity index 100%
rename from simtools/applications/generate_array_config.py
rename to src/simtools/applications/generate_array_config.py
diff --git a/simtools/applications/generate_corsika_histograms.py b/src/simtools/applications/generate_corsika_histograms.py
similarity index 100%
rename from simtools/applications/generate_corsika_histograms.py
rename to src/simtools/applications/generate_corsika_histograms.py
diff --git a/simtools/applications/generate_default_metadata.py b/src/simtools/applications/generate_default_metadata.py
similarity index 100%
rename from simtools/applications/generate_default_metadata.py
rename to src/simtools/applications/generate_default_metadata.py
diff --git a/simtools/applications/generate_regular_arrays.py b/src/simtools/applications/generate_regular_arrays.py
similarity index 100%
rename from simtools/applications/generate_regular_arrays.py
rename to src/simtools/applications/generate_regular_arrays.py
diff --git a/simtools/applications/generate_simtel_array_histograms.py b/src/simtools/applications/generate_simtel_array_histograms.py
similarity index 100%
rename from simtools/applications/generate_simtel_array_histograms.py
rename to src/simtools/applications/generate_simtel_array_histograms.py
diff --git a/simtools/applications/plot_array_layout.py b/src/simtools/applications/plot_array_layout.py
similarity index 100%
rename from simtools/applications/plot_array_layout.py
rename to src/simtools/applications/plot_array_layout.py
diff --git a/simtools/applications/production_generate_simulation_config.py b/src/simtools/applications/production_generate_simulation_config.py
similarity index 100%
rename from simtools/applications/production_generate_simulation_config.py
rename to src/simtools/applications/production_generate_simulation_config.py
diff --git a/simtools/applications/production_scale_events.py b/src/simtools/applications/production_scale_events.py
similarity index 100%
rename from simtools/applications/production_scale_events.py
rename to src/simtools/applications/production_scale_events.py
diff --git a/simtools/applications/simulate_light_emission.py b/src/simtools/applications/simulate_light_emission.py
similarity index 100%
rename from simtools/applications/simulate_light_emission.py
rename to src/simtools/applications/simulate_light_emission.py
diff --git a/simtools/applications/simulate_prod.py b/src/simtools/applications/simulate_prod.py
similarity index 100%
rename from simtools/applications/simulate_prod.py
rename to src/simtools/applications/simulate_prod.py
diff --git a/simtools/applications/submit_data_from_external.py b/src/simtools/applications/submit_data_from_external.py
similarity index 100%
rename from simtools/applications/submit_data_from_external.py
rename to src/simtools/applications/submit_data_from_external.py
diff --git a/simtools/applications/submit_model_parameter_from_external.py b/src/simtools/applications/submit_model_parameter_from_external.py
similarity index 100%
rename from simtools/applications/submit_model_parameter_from_external.py
rename to src/simtools/applications/submit_model_parameter_from_external.py
diff --git a/simtools/applications/validate_camera_efficiency.py b/src/simtools/applications/validate_camera_efficiency.py
similarity index 100%
rename from simtools/applications/validate_camera_efficiency.py
rename to src/simtools/applications/validate_camera_efficiency.py
diff --git a/simtools/applications/validate_camera_fov.py b/src/simtools/applications/validate_camera_fov.py
similarity index 100%
rename from simtools/applications/validate_camera_fov.py
rename to src/simtools/applications/validate_camera_fov.py
diff --git a/simtools/applications/validate_cumulative_psf.py b/src/simtools/applications/validate_cumulative_psf.py
similarity index 100%
rename from simtools/applications/validate_cumulative_psf.py
rename to src/simtools/applications/validate_cumulative_psf.py
diff --git a/simtools/applications/validate_file_using_schema.py b/src/simtools/applications/validate_file_using_schema.py
similarity index 97%
rename from simtools/applications/validate_file_using_schema.py
rename to src/simtools/applications/validate_file_using_schema.py
index 1127766f5a..a587ef9546 100644
--- a/simtools/applications/validate_file_using_schema.py
+++ b/src/simtools/applications/validate_file_using_schema.py
@@ -33,6 +33,7 @@
 """
 
 import logging
+from importlib.resources import files
 from pathlib import Path
 
 import simtools.utils.general as gen
@@ -138,10 +139,7 @@ def validate_data_files(args_dict, logger):
         for file_name in Path(model_parameters_directory).rglob("*.json"):
             tmp_args_dict["file_name"] = file_name
             schema_file = (
-                Path(__file__).parent
-                / "../schemas"
-                / "model_parameters"
-                / f"{file_name.stem}.schema.yml"
+                files("simtools") / "schemas/model_parameters" / f"{file_name.stem}.schema.yml"
             )
             tmp_args_dict["schema"] = schema_file
             tmp_args_dict["data_type"] = "model_parameter"
diff --git a/simtools/applications/validate_optics.py b/src/simtools/applications/validate_optics.py
similarity index 100%
rename from simtools/applications/validate_optics.py
rename to src/simtools/applications/validate_optics.py
diff --git a/simtools/camera_efficiency.py b/src/simtools/camera_efficiency.py
similarity index 100%
rename from simtools/camera_efficiency.py
rename to src/simtools/camera_efficiency.py
diff --git a/simtools/applications/__init__.py b/src/simtools/configuration/__init__.py
similarity index 100%
rename from simtools/applications/__init__.py
rename to src/simtools/configuration/__init__.py
diff --git a/simtools/configuration/commandline_parser.py b/src/simtools/configuration/commandline_parser.py
similarity index 100%
rename from simtools/configuration/commandline_parser.py
rename to src/simtools/configuration/commandline_parser.py
diff --git a/simtools/configuration/configurator.py b/src/simtools/configuration/configurator.py
similarity index 100%
rename from simtools/configuration/configurator.py
rename to src/simtools/configuration/configurator.py
diff --git a/src/simtools/constants.py b/src/simtools/constants.py
new file mode 100644
index 0000000000..b5185b218d
--- /dev/null
+++ b/src/simtools/constants.py
@@ -0,0 +1,9 @@
+"""Project wide constants."""
+
+from importlib.resources import files
+
+# Path to metadata jsonschema
+METADATA_JSON_SCHEMA = files("simtools") / "schemas/metadata.metaschema.yml"
+
+# Path to model parameter schema files
+MODEL_PARAMETER_SCHEMA_PATH = files("simtools") / "schemas/model_parameters"
diff --git a/simtools/configuration/__init__.py b/src/simtools/corsika/__init__.py
similarity index 100%
rename from simtools/configuration/__init__.py
rename to src/simtools/corsika/__init__.py
diff --git a/simtools/corsika/corsika_config.py b/src/simtools/corsika/corsika_config.py
similarity index 100%
rename from simtools/corsika/corsika_config.py
rename to src/simtools/corsika/corsika_config.py
diff --git a/simtools/corsika/corsika_histograms.py b/src/simtools/corsika/corsika_histograms.py
similarity index 100%
rename from simtools/corsika/corsika_histograms.py
rename to src/simtools/corsika/corsika_histograms.py
diff --git a/simtools/corsika/corsika_histograms_visualize.py b/src/simtools/corsika/corsika_histograms_visualize.py
similarity index 100%
rename from simtools/corsika/corsika_histograms_visualize.py
rename to src/simtools/corsika/corsika_histograms_visualize.py
diff --git a/simtools/corsika/primary_particle.py b/src/simtools/corsika/primary_particle.py
similarity index 100%
rename from simtools/corsika/primary_particle.py
rename to src/simtools/corsika/primary_particle.py
diff --git a/simtools/corsika/__init__.py b/src/simtools/data_model/__init__.py
similarity index 100%
rename from simtools/corsika/__init__.py
rename to src/simtools/data_model/__init__.py
diff --git a/simtools/data_model/data_reader.py b/src/simtools/data_model/data_reader.py
similarity index 100%
rename from simtools/data_model/data_reader.py
rename to src/simtools/data_model/data_reader.py
diff --git a/simtools/data_model/format_checkers.py b/src/simtools/data_model/format_checkers.py
similarity index 100%
rename from simtools/data_model/format_checkers.py
rename to src/simtools/data_model/format_checkers.py
diff --git a/simtools/data_model/metadata_collector.py b/src/simtools/data_model/metadata_collector.py
similarity index 100%
rename from simtools/data_model/metadata_collector.py
rename to src/simtools/data_model/metadata_collector.py
diff --git a/simtools/data_model/metadata_model.py b/src/simtools/data_model/metadata_model.py
similarity index 100%
rename from simtools/data_model/metadata_model.py
rename to src/simtools/data_model/metadata_model.py
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rename from simtools/schemas/model_parameters/secondary_mirror_degraded_reflection.schema.yml
rename to src/simtools/schemas/model_parameters/secondary_mirror_degraded_reflection.schema.yml
diff --git a/simtools/schemas/model_parameters/secondary_mirror_diameter.schema.yml b/src/simtools/schemas/model_parameters/secondary_mirror_diameter.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/secondary_mirror_diameter.schema.yml
rename to src/simtools/schemas/model_parameters/secondary_mirror_diameter.schema.yml
diff --git a/simtools/schemas/model_parameters/secondary_mirror_hole_diameter.schema.yml b/src/simtools/schemas/model_parameters/secondary_mirror_hole_diameter.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/secondary_mirror_hole_diameter.schema.yml
rename to src/simtools/schemas/model_parameters/secondary_mirror_hole_diameter.schema.yml
diff --git a/simtools/schemas/model_parameters/secondary_mirror_incidence_angle.schema.yml b/src/simtools/schemas/model_parameters/secondary_mirror_incidence_angle.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/secondary_mirror_incidence_angle.schema.yml
rename to src/simtools/schemas/model_parameters/secondary_mirror_incidence_angle.schema.yml
diff --git a/simtools/schemas/model_parameters/secondary_mirror_parameters.schema.yml b/src/simtools/schemas/model_parameters/secondary_mirror_parameters.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/secondary_mirror_parameters.schema.yml
rename to src/simtools/schemas/model_parameters/secondary_mirror_parameters.schema.yml
diff --git a/simtools/schemas/model_parameters/secondary_mirror_ref_radius.schema.yml b/src/simtools/schemas/model_parameters/secondary_mirror_ref_radius.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/secondary_mirror_ref_radius.schema.yml
rename to src/simtools/schemas/model_parameters/secondary_mirror_ref_radius.schema.yml
diff --git a/simtools/schemas/model_parameters/secondary_mirror_reflectivity.schema.yml b/src/simtools/schemas/model_parameters/secondary_mirror_reflectivity.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/secondary_mirror_reflectivity.schema.yml
rename to src/simtools/schemas/model_parameters/secondary_mirror_reflectivity.schema.yml
diff --git a/simtools/schemas/model_parameters/secondary_mirror_segmentation.schema.yml b/src/simtools/schemas/model_parameters/secondary_mirror_segmentation.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/secondary_mirror_segmentation.schema.yml
rename to src/simtools/schemas/model_parameters/secondary_mirror_segmentation.schema.yml
diff --git a/simtools/schemas/model_parameters/secondary_mirror_shadow_diameter.schema.yml b/src/simtools/schemas/model_parameters/secondary_mirror_shadow_diameter.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/secondary_mirror_shadow_diameter.schema.yml
rename to src/simtools/schemas/model_parameters/secondary_mirror_shadow_diameter.schema.yml
diff --git a/simtools/schemas/model_parameters/secondary_mirror_shadow_offset.schema.yml b/src/simtools/schemas/model_parameters/secondary_mirror_shadow_offset.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/secondary_mirror_shadow_offset.schema.yml
rename to src/simtools/schemas/model_parameters/secondary_mirror_shadow_offset.schema.yml
diff --git a/simtools/schemas/model_parameters/store_photoelectrons.schema.yml b/src/simtools/schemas/model_parameters/store_photoelectrons.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/store_photoelectrons.schema.yml
rename to src/simtools/schemas/model_parameters/store_photoelectrons.schema.yml
diff --git a/simtools/schemas/model_parameters/tailcut_scale.schema.yml b/src/simtools/schemas/model_parameters/tailcut_scale.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/tailcut_scale.schema.yml
rename to src/simtools/schemas/model_parameters/tailcut_scale.schema.yml
diff --git a/simtools/schemas/model_parameters/telescope_axis_height.schema.yml b/src/simtools/schemas/model_parameters/telescope_axis_height.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/telescope_axis_height.schema.yml
rename to src/simtools/schemas/model_parameters/telescope_axis_height.schema.yml
diff --git a/simtools/schemas/model_parameters/telescope_random_angle.schema.yml b/src/simtools/schemas/model_parameters/telescope_random_angle.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/telescope_random_angle.schema.yml
rename to src/simtools/schemas/model_parameters/telescope_random_angle.schema.yml
diff --git a/simtools/schemas/model_parameters/telescope_random_error.schema.yml b/src/simtools/schemas/model_parameters/telescope_random_error.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/telescope_random_error.schema.yml
rename to src/simtools/schemas/model_parameters/telescope_random_error.schema.yml
diff --git a/simtools/schemas/model_parameters/telescope_sphere_radius.schema.yml b/src/simtools/schemas/model_parameters/telescope_sphere_radius.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/telescope_sphere_radius.schema.yml
rename to src/simtools/schemas/model_parameters/telescope_sphere_radius.schema.yml
diff --git a/simtools/schemas/model_parameters/telescope_transmission.schema.yml b/src/simtools/schemas/model_parameters/telescope_transmission.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/telescope_transmission.schema.yml
rename to src/simtools/schemas/model_parameters/telescope_transmission.schema.yml
diff --git a/simtools/schemas/model_parameters/teltrig_min_sigsum.schema.yml b/src/simtools/schemas/model_parameters/teltrig_min_sigsum.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/teltrig_min_sigsum.schema.yml
rename to src/simtools/schemas/model_parameters/teltrig_min_sigsum.schema.yml
diff --git a/simtools/schemas/model_parameters/teltrig_min_time.schema.yml b/src/simtools/schemas/model_parameters/teltrig_min_time.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/teltrig_min_time.schema.yml
rename to src/simtools/schemas/model_parameters/teltrig_min_time.schema.yml
diff --git a/simtools/schemas/model_parameters/transit_time_calib_error.schema.yml b/src/simtools/schemas/model_parameters/transit_time_calib_error.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/transit_time_calib_error.schema.yml
rename to src/simtools/schemas/model_parameters/transit_time_calib_error.schema.yml
diff --git a/simtools/schemas/model_parameters/transit_time_compensate_error.schema.yml b/src/simtools/schemas/model_parameters/transit_time_compensate_error.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/transit_time_compensate_error.schema.yml
rename to src/simtools/schemas/model_parameters/transit_time_compensate_error.schema.yml
diff --git a/simtools/schemas/model_parameters/transit_time_compensate_step.schema.yml b/src/simtools/schemas/model_parameters/transit_time_compensate_step.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/transit_time_compensate_step.schema.yml
rename to src/simtools/schemas/model_parameters/transit_time_compensate_step.schema.yml
diff --git a/simtools/schemas/model_parameters/transit_time_error.schema.yml b/src/simtools/schemas/model_parameters/transit_time_error.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/transit_time_error.schema.yml
rename to src/simtools/schemas/model_parameters/transit_time_error.schema.yml
diff --git a/simtools/schemas/model_parameters/transit_time_jitter.schema.yml b/src/simtools/schemas/model_parameters/transit_time_jitter.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/transit_time_jitter.schema.yml
rename to src/simtools/schemas/model_parameters/transit_time_jitter.schema.yml
diff --git a/simtools/schemas/model_parameters/trigger_current_limit.schema.yml b/src/simtools/schemas/model_parameters/trigger_current_limit.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/trigger_current_limit.schema.yml
rename to src/simtools/schemas/model_parameters/trigger_current_limit.schema.yml
diff --git a/simtools/schemas/model_parameters/trigger_delay_compensation.schema.yml b/src/simtools/schemas/model_parameters/trigger_delay_compensation.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/trigger_delay_compensation.schema.yml
rename to src/simtools/schemas/model_parameters/trigger_delay_compensation.schema.yml
diff --git a/simtools/schemas/model_parameters/trigger_pixels.schema.yml b/src/simtools/schemas/model_parameters/trigger_pixels.schema.yml
similarity index 100%
rename from simtools/schemas/model_parameters/trigger_pixels.schema.yml
rename to src/simtools/schemas/model_parameters/trigger_pixels.schema.yml
diff --git a/simtools/runners/__init__.py b/src/simtools/simtel/__init__.py
similarity index 100%
rename from simtools/runners/__init__.py
rename to src/simtools/simtel/__init__.py
diff --git a/simtools/simtel/simtel_config_reader.py b/src/simtools/simtel/simtel_config_reader.py
similarity index 100%
rename from simtools/simtel/simtel_config_reader.py
rename to src/simtools/simtel/simtel_config_reader.py
diff --git a/simtools/simtel/simtel_config_writer.py b/src/simtools/simtel/simtel_config_writer.py
similarity index 100%
rename from simtools/simtel/simtel_config_writer.py
rename to src/simtools/simtel/simtel_config_writer.py
diff --git a/simtools/simtel/simtel_io_events.py b/src/simtools/simtel/simtel_io_events.py
similarity index 100%
rename from simtools/simtel/simtel_io_events.py
rename to src/simtools/simtel/simtel_io_events.py
diff --git a/simtools/simtel/simtel_io_histogram.py b/src/simtools/simtel/simtel_io_histogram.py
similarity index 100%
rename from simtools/simtel/simtel_io_histogram.py
rename to src/simtools/simtel/simtel_io_histogram.py
diff --git a/simtools/simtel/simtel_io_histograms.py b/src/simtools/simtel/simtel_io_histograms.py
similarity index 100%
rename from simtools/simtel/simtel_io_histograms.py
rename to src/simtools/simtel/simtel_io_histograms.py
diff --git a/simtools/simtel/simulator_array.py b/src/simtools/simtel/simulator_array.py
similarity index 100%
rename from simtools/simtel/simulator_array.py
rename to src/simtools/simtel/simulator_array.py
diff --git a/simtools/simtel/simulator_camera_efficiency.py b/src/simtools/simtel/simulator_camera_efficiency.py
similarity index 100%
rename from simtools/simtel/simulator_camera_efficiency.py
rename to src/simtools/simtel/simulator_camera_efficiency.py
diff --git a/simtools/simtel/simulator_light_emission.py b/src/simtools/simtel/simulator_light_emission.py
similarity index 100%
rename from simtools/simtel/simulator_light_emission.py
rename to src/simtools/simtel/simulator_light_emission.py
diff --git a/simtools/simtel/simulator_ray_tracing.py b/src/simtools/simtel/simulator_ray_tracing.py
similarity index 100%
rename from simtools/simtel/simulator_ray_tracing.py
rename to src/simtools/simtel/simulator_ray_tracing.py
diff --git a/simtools/simulator.py b/src/simtools/simulator.py
similarity index 100%
rename from simtools/simulator.py
rename to src/simtools/simulator.py
diff --git a/simtools/testing/__init__.py b/src/simtools/utils/__init__.py
similarity index 100%
rename from simtools/testing/__init__.py
rename to src/simtools/utils/__init__.py
diff --git a/simtools/utils/general.py b/src/simtools/utils/general.py
similarity index 100%
rename from simtools/utils/general.py
rename to src/simtools/utils/general.py
diff --git a/simtools/utils/geometry.py b/src/simtools/utils/geometry.py
similarity index 100%
rename from simtools/utils/geometry.py
rename to src/simtools/utils/geometry.py
diff --git a/simtools/utils/names.py b/src/simtools/utils/names.py
similarity index 98%
rename from simtools/utils/names.py
rename to src/simtools/utils/names.py
index acc7a5c681..05f4832a15 100644
--- a/simtools/utils/names.py
+++ b/src/simtools/utils/names.py
@@ -4,7 +4,7 @@
 import logging
 import re
 from functools import cache
-from pathlib import Path
+from importlib.resources import files
 
 import yaml
 
@@ -34,8 +34,7 @@ def array_elements():
     dict
         Array elements.
     """
-    base_path = Path(__file__).parent
-    with open(base_path / "../schemas/array_elements.yml", encoding="utf-8") as file:
+    with open(files("simtools") / "schemas/array_elements.yml", encoding="utf-8") as file:
         return yaml.safe_load(file)["data"]
 
 
@@ -60,7 +59,7 @@ def site_names():
 @cache
 def load_model_parameters(class_key_list):
     model_parameters = {}
-    schema_files = glob.glob(str(Path(__file__).parent / "../schemas/model_parameters") + "/*.yml")
+    schema_files = glob.glob(str(files("simtools") / "schemas/model_parameters") + "/*.yml")
     for schema_file in schema_files:
         with open(schema_file, encoding="utf-8") as f:
             data = yaml.safe_load(f)
diff --git a/simtools/utils/value_conversion.py b/src/simtools/utils/value_conversion.py
similarity index 100%
rename from simtools/utils/value_conversion.py
rename to src/simtools/utils/value_conversion.py
diff --git a/simtools/version.py b/src/simtools/version.py
similarity index 92%
rename from simtools/version.py
rename to src/simtools/version.py
index bda02a7682..669c1f4b84 100644
--- a/simtools/version.py
+++ b/src/simtools/version.py
@@ -6,7 +6,7 @@
 
 try:
     try:
-        from ._dev.scm_version import version
+        from ._dev_version import version
     except ImportError:
         from ._version import version
 except Exception:
diff --git a/simtools/utils/__init__.py b/src/simtools/visualization/__init__.py
similarity index 100%
rename from simtools/utils/__init__.py
rename to src/simtools/visualization/__init__.py
diff --git a/simtools/visualization/legend_handlers.py b/src/simtools/visualization/legend_handlers.py
similarity index 100%
rename from simtools/visualization/legend_handlers.py
rename to src/simtools/visualization/legend_handlers.py
diff --git a/simtools/visualization/plot_camera.py b/src/simtools/visualization/plot_camera.py
similarity index 100%
rename from simtools/visualization/plot_camera.py
rename to src/simtools/visualization/plot_camera.py
diff --git a/simtools/visualization/visualize.py b/src/simtools/visualization/visualize.py
similarity index 100%
rename from simtools/visualization/visualize.py
rename to src/simtools/visualization/visualize.py


Test patch:
diff --git a/.github/workflows/CI-integrationtests.yml b/.github/workflows/CI-integrationtests.yml
index 82f8b6008d..a9dc67e1a2 100644
--- a/.github/workflows/CI-integrationtests.yml
+++ b/.github/workflows/CI-integrationtests.yml
@@ -90,6 +90,5 @@ jobs:
         shell: bash -l {0}
         run: |
           source /workdir/env/bin/activate
-          pip install '.[tests,dev,doc]'
-          export PYTHONPATH=$PYTHONPATH:.
+          pip install -e '.[tests,dev,doc]'
           pytest --model_version=${{ matrix.type }} --color=yes --durations=20 -n auto --dist loadscope --no-cov tests/integration_tests/
diff --git a/.github/workflows/CI-unittests.yml b/.github/workflows/CI-unittests.yml
index b0cb9446b0..62a7cff416 100644
--- a/.github/workflows/CI-unittests.yml
+++ b/.github/workflows/CI-unittests.yml
@@ -99,7 +99,7 @@ jobs:
         shell: bash -l {0}
         run: |
           pytest --durations=10 --color=yes -n auto --dist loadscope \
-            --cov --cov-report=xml
+            --cov=simtools --cov-report=xml
 
       # CTAO-DPPS-SonarQube
       - uses: SonarSource/sonarqube-scan-action@v4.1.0
diff --git a/simtools/schemas/integration_tests_config.metaschema.yml b/src/simtools/schemas/integration_tests_config.metaschema.yml
similarity index 100%
rename from simtools/schemas/integration_tests_config.metaschema.yml
rename to src/simtools/schemas/integration_tests_config.metaschema.yml
diff --git a/simtools/simtel/__init__.py b/src/simtools/testing/__init__.py
similarity index 100%
rename from simtools/simtel/__init__.py
rename to src/simtools/testing/__init__.py
diff --git a/simtools/testing/assertions.py b/src/simtools/testing/assertions.py
similarity index 100%
rename from simtools/testing/assertions.py
rename to src/simtools/testing/assertions.py
diff --git a/simtools/testing/configuration.py b/src/simtools/testing/configuration.py
similarity index 100%
rename from simtools/testing/configuration.py
rename to src/simtools/testing/configuration.py
diff --git a/simtools/testing/helpers.py b/src/simtools/testing/helpers.py
similarity index 100%
rename from simtools/testing/helpers.py
rename to src/simtools/testing/helpers.py
diff --git a/simtools/testing/validate_output.py b/src/simtools/testing/validate_output.py
similarity index 100%
rename from simtools/testing/validate_output.py
rename to src/simtools/testing/validate_output.py
diff --git a/tests/integration_tests/config/generate_default_metadata_to_json_file.yml b/tests/integration_tests/config/generate_default_metadata_to_json_file.yml
index a0f6c04fc6..6f5a44cc4b 100644
--- a/tests/integration_tests/config/generate_default_metadata_to_json_file.yml
+++ b/tests/integration_tests/config/generate_default_metadata_to_json_file.yml
@@ -4,7 +4,7 @@ CTA_SIMPIPE:
   CONFIGURATION:
     OUTPUT_FILE: test.json
     OUTPUT_PATH: simtools-output
-    SCHEMA: simtools/schemas/metadata.metaschema.yml
+    SCHEMA: src/simtools/schemas/metadata.metaschema.yml
   INTEGRATION_TESTS:
     - OUTPUT_FILE: test.json
     - FILE_TYPE: json
diff --git a/tests/integration_tests/config/generate_default_metadata_to_yml_file.yml b/tests/integration_tests/config/generate_default_metadata_to_yml_file.yml
index 6ce65478ac..324232a0de 100644
--- a/tests/integration_tests/config/generate_default_metadata_to_yml_file.yml
+++ b/tests/integration_tests/config/generate_default_metadata_to_yml_file.yml
@@ -4,7 +4,7 @@ CTA_SIMPIPE:
   CONFIGURATION:
     OUTPUT_FILE: test.yml
     OUTPUT_PATH: simtools-output
-    SCHEMA: simtools/schemas/metadata.metaschema.yml
+    SCHEMA: src/simtools/schemas/metadata.metaschema.yml
   INTEGRATION_TESTS:
     - OUTPUT_FILE: test.yml
     - FILE_TYPE: yml
diff --git a/tests/integration_tests/config/validate_file_using_schema_yml_validate_schema.yml b/tests/integration_tests/config/validate_file_using_schema_yml_validate_schema.yml
index c0d315cc4a..df118930f7 100644
--- a/tests/integration_tests/config/validate_file_using_schema_yml_validate_schema.yml
+++ b/tests/integration_tests/config/validate_file_using_schema_yml_validate_schema.yml
@@ -2,6 +2,6 @@ CTA_SIMPIPE:
   APPLICATION: simtools-validate-file-using-schema
   TEST_NAME: yml_validate_schema
   CONFIGURATION:
-    SCHEMA: simtools/schemas/model_parameter_and_data_schema.metaschema.yml
+    SCHEMA: src/simtools/schemas/model_parameter_and_data_schema.metaschema.yml
     FILE_NAME: tests/resources/MST_mirror_2f_measurements.schema.yml
     DATA_TYPE: schema
diff --git a/tests/unit_tests/data_model/test_metadata_collector.py b/tests/unit_tests/data_model/test_metadata_collector.py
index 454090d199..bd7f125e4d 100644
--- a/tests/unit_tests/data_model/test_metadata_collector.py
+++ b/tests/unit_tests/data_model/test_metadata_collector.py
@@ -18,27 +18,28 @@
 
 
 def test_get_data_model_schema_file_name():
+    schema_file_path = files("simtools") / "schemas"
     # from args_dict / command line
     args_dict = {"no_schema": "schema_file.yml"}
     _collector = metadata_collector.MetadataCollector(args_dict)
     schema_file = _collector.get_data_model_schema_file_name()
     assert schema_file is None
 
-    args_dict = {"schema": "simtools/schemas/metadata.metaschema.yml"}
+    args_dict = {"schema": str(schema_file_path / "metadata.metaschema.yml")}
     _collector = metadata_collector.MetadataCollector(args_dict)
     schema_file = _collector.get_data_model_schema_file_name()
     assert schema_file == args_dict["schema"]
 
     # from metadata
-    _collector.top_level_meta["cta"]["product"]["data"]["model"][
-        "url"
-    ] = "simtools/schemas/top_level_meta.schema.yml"
+    _collector.top_level_meta["cta"]["product"]["data"]["model"]["url"] = str(
+        schema_file_path / "top_level_meta.schema.yml"
+    )
     schema_file = _collector.get_data_model_schema_file_name()
     # test that priority is given to args_dict (if not none)
     assert schema_file == args_dict["schema"]
     _collector.args_dict["schema"] = None
     schema_file = _collector.get_data_model_schema_file_name()
-    assert schema_file == "simtools/schemas/top_level_meta.schema.yml"
+    assert schema_file == str(schema_file_path / "top_level_meta.schema.yml")
 
     _collector.top_level_meta["cta"]["product"]["data"]["model"].pop("url")
     schema_file = _collector.get_data_model_schema_file_name()
@@ -264,7 +265,7 @@ def test_process_metadata_from_file():
     assert _collector._process_metadata_from_file(meta_dict_4) == meta_dict_4
 
 
-def test__remove_line_feed():
+def test_remove_line_feed():
     collector = metadata_collector.MetadataCollector({})
     input_string = "This is a string without line feeds."
     result = collector._remove_line_feed(input_string)
diff --git a/tests/unit_tests/data_model/test_metadata_model.py b/tests/unit_tests/data_model/test_metadata_model.py
index 28f12f5fe8..7308e70843 100644
--- a/tests/unit_tests/data_model/test_metadata_model.py
+++ b/tests/unit_tests/data_model/test_metadata_model.py
@@ -1,5 +1,6 @@
 import logging
 import os
+from importlib.resources import files
 
 import jsonschema
 import pytest
@@ -51,7 +52,7 @@ def test_validate_schema(tmp_test_directory):
 
 
 def test_validate_schema_astropy_units(caplog):
-    _schema = "simtools/schemas/model_parameter_and_data_schema.metaschema.yml"
+    _schema = files("simtools") / "schemas" / "model_parameter_and_data_schema.metaschema.yml"
 
     success_string = "Successful validation of data using schema from"