Merge pull request #344 from FAIRmat-NFDI/300-switch-to-src-layout

Switch to src layout, add default data to package

Author: lukaspie

.github/workflows/check_nexus_version.yml

@@ -16,9 +16,9 @@ jobs:
           git submodule sync --recursive
           git submodule update --init --recursive --jobs=4
           git submodule foreach --recursive 'git fetch --tags'
-          cd pynxtools/definitions
+          cd src/pynxtools/definitions
           git describe --dirty --tags --long --match "*[0-9]*" > ../nexus-ref.txt
           cd ../
       - name: Diff
         run: |
-          diff -w pynxtools/nexus-version.txt pynxtools/nexus-ref.txt
+          diff -w src/pynxtools/nexus-version.txt src/pynxtools/nexus-ref.txt

.github/workflows/pylint.yml

@@ -24,10 +24,10 @@ jobs:
           python -m pip install -r dev-requirements.txt
       - name: ruff
         run: |
-          ruff pynxtools tests
+          ruff src/pynxtools tests
       - name: ruff formatting
         run: |
-          ruff format --check pynxtools tests
+          ruff format --check src/pynxtools tests
       - name: mypy
         run: |
-          mypy pynxtools tests
+          mypy src/pynxtools tests

.gitignore

@@ -88,7 +88,6 @@ cover/
 
 # Django stuff:
 *.log
-!tests/data/dataconverter/readers/mpes/Ref_nexus_mpes.log
 !tests/data/nexus/Ref_nexus_test.log
 local_settings.py
 db.sqlite3
@@ -202,7 +201,7 @@ cython_debug/
 !requirements.txt
 !dev-requirements.txt
 !mkdocs-requirements.txt
-!pynxtools/nexus-version.txt
+!src/pynxtools/nexus-version.txt
 build/
 nexusparser.egg-info/PKG-INFO
 .python-version

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "pynxtools/definitions"]
-	path = pynxtools/definitions
-	url = https://github.com/FAIRmat-NFDI/nexus_definitions.git
+[submodule "src/pynxtools/definitions"]
+	path = src/pynxtools/definitions
+	url = https://github.com/FAIRmat-NFDI/nexus_definitions.git

MANIFEST.in

@@ -1,11 +1,13 @@
 prune *
 exclude *
-recursive-include pynxtools *.py
+recursive-include src/pynxtools *.py
 include pyproject.toml LICENSE README.md TROUBLESHOOTING.md dev-requirements.txt
+include src/pynxtools/data/*
+
+recursive-include src/pynxtools/definitions/base_classes/ *.xml
+recursive-include src/pynxtools/definitions/applications/ *.xml
+recursive-include src/pynxtools/definitions/contributed_definitions/ *.xml
+include src/pynxtools/definitions/*.xsd
+include src/pynxtools/nexus-version.txt
+include src/pynxtools/definitions/NXDL_VERSION
 
-recursive-include pynxtools/definitions/base_classes/ *.xml
-recursive-include pynxtools/definitions/applications/ *.xml
-recursive-include pynxtools/definitions/contributed_definitions/ *.xml
-include pynxtools/definitions/*.xsd
-include pynxtools/nexus-version.txt
-include pynxtools/definitions/NXDL_VERSION

README.md

@@ -25,7 +25,7 @@ nav:
 plugins:
   - search
   - macros:
-      module_name: pynxtools/mkdocs
+      module_name: src/pynxtools/mkdocs
 
 theme:
   name: material