Follow standard directory structure (#129) (#133)

* Follow standard directory structure

* fix license

* Update environment.yml

* Update pipeline.yml

* Update environment.yml

* Update pipeline.yml

* Update environment.yml

* Update environment.yml

Author: jan-janssen

.github/workflows/pipeline.yml

@@ -13,7 +13,7 @@ jobs:
     - uses: psf/black@stable
       with:
         options: "--check --diff"
-        src: ./python_workflow_definition/src/python_workflow_definition
+        src: ./src/python_workflow_definition
     - uses: psf/black@stable
       with:
         options: "--check --diff"
@@ -35,7 +35,7 @@ jobs:
     - name: Pip check
       shell: bash -l {0}
       run: |
-        pip install --no-deps --no-build-isolation -e python_workflow_definition
+        pip install --no-deps --no-build-isolation -e .
         pip check
 
   nfdi4ing:
@@ -53,7 +53,7 @@ jobs:
     - name: Installation and setup
       shell: bash -l {0}
       run: |
-        pip install --no-deps --no-build-isolation -e python_workflow_definition
+        pip install --no-deps --no-build-isolation -e .
         conda install -c conda-forge jupyter papermill
         verdi presto --profile-name pwd
         sudo apt-get install -y $(cat binder/apt.txt)
@@ -92,7 +92,7 @@ jobs:
       shell: bash -l {0}
       run: |
         pip install --no-deps --no-build-isolation -e example_workflows/quantum_espresso/qe_xml_parser
-        pip install --no-deps --no-build-isolation -e python_workflow_definition
+        pip install --no-deps --no-build-isolation -e .
         conda install -c conda-forge jupyter papermill
         verdi presto --profile-name pwd
     - name: Tests
@@ -122,7 +122,7 @@ jobs:
     - name: Installation and setup
       shell: bash -l {0}
       run: |
-        pip install --no-deps --no-build-isolation -e python_workflow_definition
+        pip install --no-deps --no-build-isolation -e .
         conda install -c conda-forge jupyter papermill
         verdi presto --profile-name pwd
     - name: Tests

.github/workflows/pypi.yml

@@ -26,9 +26,7 @@ jobs:
         environment-file: binder/environment.yml
     - name: Build
       shell: bash -l {0}
-      run: |
-        cd python_workflow_definition
-        hatch build -t sdist -t wheel
+      run: hatch build -t sdist -t wheel
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

.gitignore

@@ -178,7 +178,7 @@ cython_debug/
 input_tmp.in
 pyiron.log
 pyiron_draw.png
-python_workflow_definition/src/python_workflow_definition/__pycache__/
+src/python_workflow_definition/__pycache__/
 test/
 mini/
 evcurve.png

binder/environment.yml

@@ -2,6 +2,7 @@ channels:
 - conda-forge
 dependencies:
 - python =3.12
+- click =8.1.8
 - pydantic =2.11.4
 - hatch =1.14.1
 - hatchling =1.27.0

python_workflow_definition/pyproject.toml renamed to pyproject.toml

@@ -14,7 +14,7 @@ authors = [
   { name = "Marnik Bercx", email = "marnik.bercx@psi.ch" },
   { name = "Christina Ertural", email = "christina.ertural@bam.de" },
 ]
-license = { file = "../LICENSE" }
+license = { file = "LICENSE" }
 dependencies = [
     "numpy>=1.21,<2",
     "pydantic>=2.7.0,<=2.11.4",