Merge pull request #5 from FAIRmat-NFDI/4-switch-to-src-layout

Use `src` layout

.github/workflows/pylint.yml

@@ -22,10 +22,10 @@ jobs:
           uv pip install --system -r dev-requirements.txt
       - name: ruff
         run: |
-          ruff pynxtools_raman tests
+          ruff check src/pynxtools_raman tests
       - name: ruff formatting
         run: |
-          ruff format --check pynxtools_raman tests
+          ruff format --check src/pynxtools_raman tests
       - name: mypy
         run: |
-          mypy pynxtools_raman tests
+          mypy src/pynxtools_raman tests

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.3.4
+    rev: v0.7.0
     hooks:
       # Run the linter.
       - id: ruff

MANIFEST.in

@@ -0,0 +1,4 @@
+prune *
+exclude *
+recursive-include src/pynxtools_raman *.py
+include pyproject.toml README.md dev-requirements.txt

dev-requirements.txt

@@ -1,22 +1,18 @@
-#
-# This file is autogenerated by pip-compile with Python 3.9
-# by the following command:
-#
-#    pip-compile --extra=dev --extra=docs --output-file=dev-requirements.txt pyproject.toml
-#
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --universal -p 3.11 --extra=dev --extra=docs --output-file=dev-requirements.txt pyproject.toml
 anytree==2.12.1
     # via pynxtools
 ase==3.23.0
     # via pynxtools
-babel==2.15.0
+babel==2.16.0
     # via mkdocs-material
-build==1.2.1
+build==1.2.2.post1
     # via pip-tools
-certifi==2024.7.4
+certifi==2024.8.30
     # via requests
 cfgv==3.4.0
     # via pre-commit
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
     # via requests
 click==8.1.7
     # via
@@ -27,79 +23,79 @@ click==8.1.7
 click-default-group==1.2.4
     # via pynxtools
 colorama==0.4.6
-    # via mkdocs-material
-contourpy==1.2.1
+    # via
+    #   build
+    #   click
+    #   mkdocs
+    #   mkdocs-material
+    #   pytest
+contourpy==1.3.0
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-distlib==0.3.8
+distlib==0.3.9
     # via virtualenv
-exceptiongroup==1.2.1
-    # via pytest
-filelock==3.15.4
+filelock==3.16.1
     # via virtualenv
-fonttools==4.53.0
+fonttools==4.54.1
     # via matplotlib
 ghp-import==2.1.0
     # via mkdocs
-h5py==3.11.0
+h5py==3.12.1
     # via pynxtools
-identify==2.6.0
+hjson==3.1.0
+    # via
+    #   mkdocs-macros-plugin
+    #   super-collections
+identify==2.6.1
     # via pre-commit
-idna==3.7
+idna==3.10
     # via requests
-importlib-metadata==8.0.0
-    # via
-    #   build
-    #   markdown
-    #   mkdocs
-    #   mkdocs-get-deps
-    #   pynxtools
-importlib-resources==6.4.0
-    # via matplotlib
+importlib-metadata==8.5.0
+    # via pynxtools
 iniconfig==2.0.0
     # via pytest
 jinja2==3.1.4
     # via
     #   mkdocs
     #   mkdocs-macros-plugin
     #   mkdocs-material
-kiwisolver==1.4.5
+kiwisolver==1.4.7
     # via matplotlib
-lxml==5.2.2
+lxml==5.3.0
     # via pynxtools
-markdown==3.6
+markdown==3.7
     # via
     #   mkdocs
     #   mkdocs-material
     #   pymdown-extensions
-markupsafe==2.1.5
+markupsafe==3.0.2
     # via
     #   jinja2
     #   mkdocs
-matplotlib==3.9.0
+matplotlib==3.9.2
     # via ase
 mergedeep==1.3.4
     # via
     #   mkdocs
     #   mkdocs-get-deps
     #   pynxtools
-mkdocs==1.6.0
+mkdocs==1.6.1
     # via
+    #   pynxtools-raman (pyproject.toml)
     #   mkdocs-macros-plugin
     #   mkdocs-material
-    #   pynxtools-raman (pyproject.toml)
 mkdocs-get-deps==0.2.0
     # via mkdocs
-mkdocs-macros-plugin==1.0.5
+mkdocs-macros-plugin==1.3.6
     # via pynxtools-raman (pyproject.toml)
-mkdocs-material==9.5.28
+mkdocs-material==9.5.42
     # via pynxtools-raman (pyproject.toml)
 mkdocs-material-extensions==1.3.1
     # via
-    #   mkdocs-material
     #   pynxtools-raman (pyproject.toml)
-mypy==1.10.1
+    #   mkdocs-material
+mypy==1.12.1
     # via pynxtools-raman (pyproject.toml)
 mypy-extensions==1.0.0
     # via mypy
@@ -120,51 +116,56 @@ packaging==24.1
     #   build
     #   matplotlib
     #   mkdocs
+    #   mkdocs-macros-plugin
     #   pytest
     #   xarray
-paginate==0.5.6
+paginate==0.5.7
     # via mkdocs-material
-pandas==2.2.2
+pandas==2.2.3
     # via
     #   pynxtools
     #   xarray
 pathspec==0.12.1
-    # via mkdocs
-pillow==10.4.0
+    # via
+    #   mkdocs
+    #   mkdocs-macros-plugin
+pillow==11.0.0
     # via matplotlib
+pip==24.2
+    # via pip-tools
 pip-tools==7.4.1
     # via pynxtools-raman (pyproject.toml)
-platformdirs==4.2.2
+platformdirs==4.3.6
     # via
     #   mkdocs-get-deps
     #   virtualenv
 pluggy==1.5.0
     # via pytest
-pre-commit==3.7.1
+pre-commit==4.0.1
     # via pynxtools-raman (pyproject.toml)
 pygments==2.18.0
     # via mkdocs-material
-pymdown-extensions==10.8.1
+pymdown-extensions==10.11.2
     # via mkdocs-material
-pynxtools==0.4.0
+pynxtools==0.7.4
     # via pynxtools-raman (pyproject.toml)
-pyparsing==3.1.2
+pyparsing==3.2.0
     # via matplotlib
-pyproject-hooks==1.1.0
+pyproject-hooks==1.2.0
     # via
     #   build
     #   pip-tools
-pytest==8.2.2
+pytest==8.3.3
     # via pynxtools-raman (pyproject.toml)
 python-dateutil==2.9.0.post0
     # via
     #   ghp-import
     #   matplotlib
     #   mkdocs-macros-plugin
     #   pandas
-pytz==2024.1
+pytz==2024.2
     # via pandas
-pyyaml==6.0.1
+pyyaml==6.0.2
     # via
     #   mkdocs
     #   mkdocs-get-deps
@@ -175,47 +176,39 @@ pyyaml==6.0.1
     #   pyyaml-env-tag
 pyyaml-env-tag==0.1
     # via mkdocs
-regex==2024.5.15
+regex==2024.9.11
     # via mkdocs-material
 requests==2.32.3
     # via mkdocs-material
-ruff==0.3.4
+ruff==0.7.0
     # via pynxtools-raman (pyproject.toml)
-scipy==1.13.1
+scipy==1.14.1
     # via ase
+setuptools==75.2.0
+    # via pip-tools
 six==1.16.0
     # via
     #   anytree
     #   python-dateutil
-termcolor==2.4.0
+super-collections==0.5.3
     # via mkdocs-macros-plugin
-tomli==2.0.1
-    # via
-    #   build
-    #   mypy
-    #   pip-tools
-    #   pytest
-types-pyyaml==6.0.12.20240311
+termcolor==2.5.0
+    # via mkdocs-macros-plugin
+types-pyyaml==6.0.12.20240917
     # via pynxtools-raman (pyproject.toml)
 typing-extensions==4.12.2
     # via mypy
-tzdata==2024.1
+tzdata==2024.2
     # via pandas
-urllib3==2.2.2
+urllib3==2.2.3
     # via requests
-virtualenv==20.26.3
+virtualenv==20.27.0
     # via pre-commit
-watchdog==4.0.1
+watchdog==5.0.3
     # via mkdocs
-wheel==0.43.0
+wheel==0.44.0
     # via pip-tools
-xarray==2024.6.0
+xarray==2024.9.0
     # via pynxtools
-zipp==3.19.2
-    # via
-    #   importlib-metadata
-    #   importlib-resources
-
-# The following packages are considered to be unsafe in a requirements file:
-# pip
-# setuptools
+zipp==3.20.2
+    # via importlib-metadata

pyproject.toml

@@ -22,7 +22,7 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "pynxtools>=0.4.0"
+    "pynxtools>=0.7.0"
 ]
 
 [project.entry-points."pynxtools.reader"]
@@ -34,7 +34,7 @@ raman = "pynxtools_raman.reader:RamanReader"
 [project.optional-dependencies]
 dev = [
     "mypy",
-    "ruff==0.3.4",
+    "ruff>=0.6",
     "pytest",
     "types-pyyaml",
     "pip-tools",
@@ -52,7 +52,7 @@ version_scheme = "no-guess-dev"
 local_scheme = "node-and-date"
 
 [tool.ruff]
-include = ["pynxtools_raman/*.py", "tests/*.py"]
+include = ["src/pynxtools_raman/*.py", "tests/*.py"]
 line-length = 88
 indent-width = 4