From 9184e7348aed94018e4b57cf0e273ef630aa4339 Mon Sep 17 00:00:00 2001
From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com>
Date: Fri, 11 Oct 2024 13:21:18 +0200
Subject: [PATCH 1/2] switch to src layout

---
 .github/workflows/pylint.yml                       | 6 +++---
 docs/reference/mpes.md                             | 2 +-
 mkdocs.yaml                                        | 2 +-
 pyproject.toml                                     | 8 +++++---
 {pynxtools_mpes => src/pynxtools_mpes}/__init__.py | 0
 {pynxtools_mpes => src/pynxtools_mpes}/mkdocs.py   | 0
 {pynxtools_mpes => src/pynxtools_mpes}/reader.py   | 0
 7 files changed, 10 insertions(+), 8 deletions(-)
 rename {pynxtools_mpes => src/pynxtools_mpes}/__init__.py (100%)
 rename {pynxtools_mpes => src/pynxtools_mpes}/mkdocs.py (100%)
 rename {pynxtools_mpes => src/pynxtools_mpes}/reader.py (100%)

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
index e5696a0..de851dc 100644
--- a/.github/workflows/pylint.yml
+++ b/.github/workflows/pylint.yml
@@ -21,10 +21,10 @@ jobs:
           uv pip install -r dev-requirements.txt
       - name: ruff check
         run: |
-          ruff check pynxtools_mpes tests
+          ruff check src/pynxtools_mpes tests
       - name: ruff format
         run: |
-          ruff format --check pynxtools_mpes tests
+          ruff format --check src/pynxtools_mpes tests
       - name: mypy
         run: |
-          mypy pynxtools_mpes tests
+          mypy src/pynxtools_mpes tests
diff --git a/docs/reference/mpes.md b/docs/reference/mpes.md
index 4d1cb7e..648d694 100644
--- a/docs/reference/mpes.md
+++ b/docs/reference/mpes.md
@@ -2,7 +2,7 @@
 
 The reader supports [HDF5](https://www.hdfgroup.org/solutions/hdf5/) files created using the MPES instruments at the Department of Physical Chemistry of the [Fritz Haber Institute of the Max Planck Society (FHI)](https://pc.fhi-berlin.mpg.de).
 
-The reader for can be found [here](https://github.com/FAIRmat-NFDI/pynxtools-mpes/blob/main/pynxtools_mpes/reader.py).
+The reader for can be found [here](https://github.com/FAIRmat-NFDI/pynxtools-mpes/blob/main/src/pynxtools_mpes/reader.py).
 
 Example data for the MPES reader is available [here](https://github.com/FAIRmat-NFDI/pynxtools-mpes/tree/main/tests/data).
 
diff --git a/mkdocs.yaml b/mkdocs.yaml
index 1dc9de4..4362a0d 100644
--- a/mkdocs.yaml
+++ b/mkdocs.yaml
@@ -20,7 +20,7 @@ nav:
 plugins:
   - search
   - macros:
-      module_name: pynxtools_mpes/mkdocs
+      module_name: src/pynxtools_mpes/mkdocs
 
 theme:
   name: material
diff --git a/pyproject.toml b/pyproject.toml
index c155370..1e3b2a9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,13 +55,15 @@ docs = [
 [project.entry-points."pynxtools.reader"]
 mpes = "pynxtools_mpes.reader:MPESReader"
 
-[tool.setuptools]
-packages = ["pynxtools_mpes"]
+[tool.setuptools.packages.find]
+where = [
+    "src",
+]
 
 [tool.setuptools_scm]
 
 [tool.ruff]
-include = ["pynxtools_mpes/*.py", "tests/*.py"]
+include = ["src/*.py", "tests/*.py"]
 line-length = 88
 indent-width = 4
 
diff --git a/pynxtools_mpes/__init__.py b/src/pynxtools_mpes/__init__.py
similarity index 100%
rename from pynxtools_mpes/__init__.py
rename to src/pynxtools_mpes/__init__.py
diff --git a/pynxtools_mpes/mkdocs.py b/src/pynxtools_mpes/mkdocs.py
similarity index 100%
rename from pynxtools_mpes/mkdocs.py
rename to src/pynxtools_mpes/mkdocs.py
diff --git a/pynxtools_mpes/reader.py b/src/pynxtools_mpes/reader.py
similarity index 100%
rename from pynxtools_mpes/reader.py
rename to src/pynxtools_mpes/reader.py

From 2f81b8dbb892f94cc495826233935daf10d96623 Mon Sep 17 00:00:00 2001
From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com>
Date: Fri, 11 Oct 2024 13:59:08 +0200
Subject: [PATCH 2/2] add src in MANIFEST.IN

---
 MANIFEST.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index 4276f0d..a9131e3 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,4 +1,4 @@
 prune *
 exclude *
-recursive-include pynxtools_mpes *.py
+recursive-include src/pynxtools_mpes *.py
 include pyproject.toml README.md dev-requirements.txt
\ No newline at end of file