Reorganise the data files and corresponging changes.

Author: RubelMozumder

.github/workflows/publish-north.yaml

@@ -11,18 +11,22 @@ on:
 
 env:
   REGISTRY: ghcr.io
-  UV_VERSION: 0.7
+  UV_VERSION: 0.9
   PYTHON_VERSION: 3.12
-  JUPYTER_VERSION: "2025-04-14"
+  JUPYTER_VERSION: 2025-04-14
   IMAGE_PREFIX: /jupyter
   SERVICES: jupyter
   SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYNXTOOLS_SPM: "0.0.0+0.UNKNOWN"
-  TEST_DATA_DIR: $(pwd)/src/pynxtools_spm/nomad/example_uploads
-
+  # Upload to Jupyter image build
+  EXAMPLES_DIR: $(pwd)/src/pynxtools_spm/north_tools/spm_jupyter/examples
+  # Data for testing notebooks in Jupyter image
+  TEST_DATA_DIR: $(pwd)/src/pynxtools_spm
   # Path w.r.t. TEST_DATA_DIR multi-line in single string
-  TEST_NOTEBOOKS: afm/AFMExampleWithCustomization/CommandLineDataconverter.ipynb
-    stm/STMExampleWithCustomization/CommandLineDataconverter.ipynb
-    sts/STSExampleWithCustomization/CommandLineDataconverter.ipynb
+  TEST_NOTEBOOKS:
+    nomad/example_uploads/afm/AFMExampleWithCustomization/CommandLineDataconverter.ipynb
+    nomad/example_uploads/stm/STMExampleWithCustomization/CommandLineDataconverter.ipynb
+    nomad/example_uploads/sts/STSExampleWithCustomization/CommandLineDataconverter.ipynb
+    north_tools/spm_jupyter/examples/stm/CommandLineDataconverter_STM.ipynb
 
 permissions:
   packages: write
@@ -63,13 +67,6 @@ jobs:
           VERSION=$(./scripts/get_git_version.sh)
           echo "Computed version: $VERSION"
           echo "SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYNXTOOLS_SPM=$VERSION" >> "$GITHUB_ENV"
-          echo "Env variable: ${{ env.SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYNXTOOLS_SPM }}"
-      - name: All the available variables from env
-        run: |
-          echo "UV_VERSION=${{ env.UV_VERSION }}"
-          echo "PYTHON_VERSION=${{ env.PYTHON_VERSION }}"
-          echo "JUPYTER_VERSION=${{ env.JUPYTER_VERSION }}"
-          echo "SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYNXTOOLS_SPM=${{ env.SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYNXTOOLS_SPM }}"
       - uses: docker/setup-buildx-action@v3
       # https://github.com/docker/metadata-action
       - name: Extract Docker metadata
@@ -92,12 +89,13 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           context: .
-          file: Dockerfile
+          file: docker/Dockerfile.jupyter
           build-args: |
             UV_VERSION=${{ env.UV_VERSION }}
             PYTHON_VERSION=${{ env.PYTHON_VERSION }}
             JUPYTER_VERSION=${{ env.JUPYTER_VERSION }}
             SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYNXTOOLS_SPM=${{ env.SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYNXTOOLS_SPM }}
+            EXAMPLES_DIR=${{ env.EXAMPLES_DIR }}
           cache-from: type=gha
           cache-to: type=gha,mode=max
           push: false

Dockerfile docker/Dockerfile.jupyterDockerfile renamed to docker/Dockerfile.jupyter

@@ -1,9 +1,9 @@
-
 ARG JUPYTER_TAG=2025-10-20
 ARG UV_VERSION=0.9
 ARG PLUGIN_NAME="PLUGIN"
 ARG PYTHON_VERSION=3.12
 ARG SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYNXTOOLS_SPM="0.0.0+0.gunknown"
+ARG EXAMPLES_DIR="./src/test_north/north_tools/spm_jupyter/examples"
 FROM ghcr.io/astral-sh/uv:${UV_VERSION} AS uv_stage
 
 FROM quay.io/jupyter/scipy-notebook:${JUPYTER_TAG} AS scipy_notebook
@@ -58,28 +58,28 @@ ENV UV_PROJECT_ENVIRONMENT=${CONDA_DIR} \
     UV_SYSTEM_PYTHON=1 \
     SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYNXTOOLS_SPM=${SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYNXTOOLS_SPM}
 
-COPY --chown=${NB_USER}:${NB_GID} . $HOME/$PLUGIN_NAME
+COPY --chown=${NB_USER}:${NB_GID} . ${HOME}/${PLUGIN_NAME}
 
-WORKDIR $HOME/$PLUGIN_NAME
+WORKDIR ${HOME}/${PLUGIN_NAME}
 
 # RUN export SETUPTOOLS_SCM_PRETEND_VERSION=${SETUPTOOLS_SCM_PRETEND_VERSION}
 # https://docs.astral.sh/uv/guides/integration/docker/#intermediate-layers
 # Install dependencies
 RUN --mount=type=cache,target=/root/.cache/uv \
     uv sync --locked --no-editable --extra=north --extra=nomad --inexact
 
-WORKDIR $HOME
+WORKDIR ${HOME}
 RUN rm -rf ${HOME}/${PLUGIN_NAME}
 
 RUN jupyter lab build --dev-build=False --minimize=False && \
     fix-permissions "/home/${NB_USER}" \ 
     && fix-permissions "${CONDA_DIR}"
 
-WORKDIR $HOME
+WORKDIR ${HOME}
 
+ARG EXAMPLES_DIR
 # copy north examples
-COPY --chown=${NB_UID}:${NB_GID}  ./src/pynxtools_spm/nomad/example_uploads ${HOME}/examples
-
+COPY --chown=${NB_UID}:${NB_GID}  ${EXAMPLES_DIR} ${HOME}/examples
 
 RUN touch ${HOME}/.hushlogin
 

pyproject.toml

@@ -73,7 +73,7 @@ sts_example = "pynxtools_spm.nomad.entrypoints:sts_example"
 stm_example = "pynxtools_spm.nomad.entrypoints:stm_example"
 afm_example = "pynxtools_spm.nomad.entrypoints:afm_example"
 spm_app = "pynxtools_spm.nomad.apps:spm_app"
-spm_tool = "pynxtools_spm.north_tools.jupyter_nb:spm_jupyter"
+spm_tool = "pynxtools_spm.north_tools.spm_jupyter:spm_jupyter"
 
 
 [tool.setuptools.packages.find]

…s_spm/north_tools/jupyter_nb/__init__.py …_spm/north_tools/spm_jupyter/__init__.pysrc/pynxtools_spm/north_tools/jupyter_nb/__init__.py renamed to src/pynxtools_spm/north_tools/spm_jupyter/__init__.py src/pynxtools_spm/north_tools/jupyter_nb/__init__.py renamed to src/pynxtools_spm/north_tools/spm_jupyter/__init__.py

@@ -17,7 +17,7 @@
     path_prefix="lab/tree",
     privileged=False,
     with_path=True,
-    display_name="SPM",
+    display_name="SPM-Jupyter",
 )
 
 spm_jupyter = NorthToolEntryPoint(id_url_safe="spm_jupyter", north_tool=tool)