Merge pull request queens-py#174 from gilrrei/move_to_src_layout

refactor: move to src layout

Author: gilrrei

.github/workflows/build_documentation.yml

@@ -29,7 +29,7 @@ jobs:
           PYTHON_PACKAGE_MANAGER: ${{steps.environment.outputs.ppm}}
         run: |
           $PYTHON_PACKAGE_MANAGER activate queens
-          sphinx-apidoc -o doc/source queens -f -M
+          sphinx-apidoc -o doc/source src/queens -f -M
           cd doc
           sphinx-build -b html -d build/doctrees source build/html
       - name: Upload html

.github/workflows/tests_local.yml

@@ -42,23 +42,23 @@ jobs:
           $PYTHON_PACKAGE_MANAGER activate queens
 
           echo "::group::Run isort..."
-          isort --check-only queens tests
+          isort --check-only src/* tests
           echo "::endgroup::"
 
           echo "::group::Run black..."
-          black --check queens tests
+          black --check src/* tests
           echo "::endgroup::"
 
           echo "::group::Run pylint..."
-          pylint --rcfile=.pylintrc --disable=duplicate-code queens tests
+          pylint --rcfile=.pylintrc --disable=duplicate-code src/ tests
           echo "::endgroup::"
 
           echo "::group::Run ruff..."
           ruff check
           echo "::endgroup::"
 
           # echo "::group::Create code quality report..."
-          # pylint queens tests --rcfile=.pylintrc --output-format=json:pylint_warnings.json --fail-under 0
+          # pylint src/ tests --rcfile=.pylintrc --output-format=json:pylint_warnings.json --fail-under 0
           # python .gitlab/pipeline_utils/code_quality_creator.py pylint_warnings.json
           # echo "::endgroup::"
 

.gitlab/.gitlab-ci.yml

@@ -90,7 +90,7 @@ imcs-build_conda_env:
     - $PYTHON_PACKAGE_MANAGER create -y --prefix ./$ENV_PREFIX python=3.11 cloudpickle fabric
     - $PYTHON_PACKAGE_MANAGER activate ./$ENV_PREFIX
     - pip install -e . --no-dependencies
-    - python queens/utils/remote_build.py
+    - python src/queens/utils/remote_build.py
       --host=$REMOTE_ADDRESS --user=queens --remote-python=$REMOTE_PYTHON
       --remote-queens-repository=/home/queens/builds/queens-$CI_PIPELINE_ID --package-manager
       $PYTHON_PACKAGE_MANAGER

.pylintrc

@@ -587,13 +587,7 @@ ignored-checks-for-mixins=no-member,
 ignored-classes=optparse.Values,
                 thread._local,
                 _thread._local,
-                ,argparse.Namespace,
-                queens.visualization.bmfmc_visualization,
-                queens.visualization.bmfia_visualization,
-                queens.visualization.grid_iterator_visualization,
-                queens.visualization.sa_visualization,
-                queens.visualization.surrogate_visualization,
-                queens.visualization.variational_inference_visualization,
+                argparse.Namespace,
                 matplotlib.cm,
                 logging.RootLogger,
 

doc/README.md

@@ -23,9 +23,9 @@
 import requests
 
 from queens.utils.injector import inject
-from queens.utils.path import relative_path_from_queens
+from queens.utils.path import relative_path_from_root
 
-sys.path.insert(1, str(relative_path_from_queens("test_utils").resolve()))
+sys.path.insert(1, str(relative_path_from_root("test_utils").resolve()))
 from get_queens_example_from_readme import (  # pylint: disable=import-error, wrong-import-position,wrong-import-order
     extract_from_markdown_file_by_marker,
     get_queens_example_from_readme,
@@ -54,7 +54,7 @@ def relative_to_doc_source(relative_path):
     Returns:
         pathlib.Path: Path relative from documentation
     """
-    return relative_path_from_queens("doc/source/" + relative_path)
+    return relative_path_from_root("doc/source/" + relative_path)
 
 
 def create_tutorial_from_readme():
@@ -141,7 +141,7 @@ def clean_markdown_file(md_path, new_path):
     Returns:
         str: file name of the new markdown file
     """
-    md_text = clean_markdown(relative_path_from_queens(md_path).read_text())
+    md_text = clean_markdown(relative_path_from_root(md_path).read_text())
     new_path = Path(new_path)
     new_path.write_text(md_text, encoding="utf-8")
     return new_path.name
@@ -155,12 +155,12 @@ def create_development():
     md_paths = []
     md_paths.append(
         clean_markdown_file(
-            relative_path_from_queens("CONTRIBUTING.md"), relative_to_doc_source("contributing.md")
+            relative_path_from_root("CONTRIBUTING.md"), relative_to_doc_source("contributing.md")
         )
     )
     md_paths.append(
         clean_markdown_file(
-            relative_path_from_queens("tests/README.md"), relative_to_doc_source("testing.md")
+            relative_path_from_root("tests/README.md"), relative_to_doc_source("testing.md")
         )
     )
     inject({"md_paths": md_paths}, development_template, development_path)
@@ -176,8 +176,8 @@ def extract_from_markdown_by_marker(marker_name, md_path):
 
     inject(
         {
-            "readme_path": relative_path_from_queens("README.md"),
-            "contributing_path": relative_path_from_queens("CONTRIBUTING.md"),
+            "readme_path": relative_path_from_root("README.md"),
+            "contributing_path": relative_path_from_root("CONTRIBUTING.md"),
             "extract_from_markdown_by_marker": extract_from_markdown_by_marker,
         },
         intro_template,
@@ -190,7 +190,7 @@ def create_overview():
     overview_template = get_template_path_by_name("overview.rst.j2")
     overview_path = relative_to_doc_source("overview.rst")
 
-    queens_base_path = relative_path_from_queens("queens")
+    queens_base_path = relative_path_from_root("src/queens")
 
     def get_module_description(python_file):
         """Get module description.

doc/source/_ext/create_documentation_files.py

@@ -20,9 +20,6 @@ keywords = [
     "bayesian inference",
 ]
 
-[tool.setuptools.packages.find]
-include = ["queens.*", "queens"]
-
 [tool.setuptools.dynamic]
 version = { attr = "queens.__VERSION__" }
 dependencies = { file = ["requirements.in"] }