Merge branch 'main' of https://github.com/artorg-unibe-ch/HFE

.github/workflows/build-gcc.yml

@@ -1,4 +1,4 @@
-name: Build Docker Container
+name: Build Docker Container - gcc
 
 on:
   push:
@@ -10,6 +10,9 @@ jobs:
   docker:
     runs-on: ubuntu-latest
     steps:
+      -
+        name: Delete huge unnecessary tools folder
+        run: rm -rf /opt/hostedtoolcache
       -
         name: Set up QEMU
         uses: docker/setup-qemu-action@v2
@@ -26,12 +29,11 @@ jobs:
         name: Build and push
         uses: docker/build-push-action@v5
         with:
-            context: "{{defaultContext}}:02_CODE"
+            context: "{{defaultContext}}:02_CODE/docker_apptainer_hpc"
             file: Dockerfile.ubuntu24.04.gcc
             push: true
             tags: ${{ secrets.DOCKERHUB_USERNAME }}/hfe_development_gcc:latest
             build-args: |
                 GITHUB_USERNAME=${{ secrets.USERNAME_ADMIN }}
-                GITHUB_TOKEN=${{ secrets.TOKEN_ADMIN }}
                 USER_UID=1000
                 USER_GID=1000

.github/workflows/build-ifort.yml

@@ -1,4 +1,4 @@
-name: Build Docker Container
+name: Build Docker Container - ifort
 
 on:
   push:
@@ -10,6 +10,9 @@ jobs:
   docker:
     runs-on: ubuntu-latest
     steps:
+      -
+        name: Delete huge unnecessary tools folder
+        run: rm -rf /opt/hostedtoolcache
       -
         name: Set up QEMU
         uses: docker/setup-qemu-action@v2
@@ -26,12 +29,11 @@ jobs:
         name: Build and push
         uses: docker/build-push-action@v5
         with:
-            context: "{{defaultContext}}:02_CODE"
+            context: "{{defaultContext}}:02_CODE/docker_apptainer_hpc"
             file: Dockerfile.ubuntu24.04.ifort
             push: true
             tags: ${{ secrets.DOCKERHUB_USERNAME }}/hfe_development_ifort:latest
             build-args: |
                 GITHUB_USERNAME=${{ secrets.USERNAME_ADMIN }}
-                GITHUB_TOKEN=${{ secrets.TOKEN_ADMIN }}
                 USER_UID=1000
                 USER_GID=1000

.github/workflows/docs.yml

@@ -0,0 +1,53 @@
+name: Documentation
+
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+
+      - name: Set up Python virtual environment
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+          pip install --upgrade pip
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libglu1-mesa
+
+      - name: Clone and install pyhexspline
+        run: |
+          git clone https://github.com/artorg-unibe-ch/spline_mesher.git
+          cd spline_mesher
+          ../venv/bin/pip install -e .
+
+      - name: Install Python dependencies
+        run: |
+          source venv/bin/activate
+          pip install sphinx sphinx_rtd_theme myst_parser matplotlib numpy gmsh vtk coloredlogs fast_simplification SimpleITK hydra-core pyvista pandas psutil scipy numba
+
+      - name: Sphinx build
+        run: |
+          source venv/bin/activate
+          sphinx-build 02_CODE/src/docs/ 02_CODE/src/docs/_build
+
+      - name: Create .nojekyll file
+        run: |
+          touch 02_CODE/src/docs/_build/.nojekyll
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: 02_CODE/src/docs/_build
+          force_orphan: true

.github/workflows/todo_to_issue.yml

@@ -1,4 +1,4 @@
-name: "Run TODO to Issue"
+name: "TODO to Issue"
 on: ["push"]
 jobs:
   build:

.gitignore

@@ -21,8 +21,8 @@ outputs/
 04_SIMULATIONS/
 !04_SIMULATIONS/simulations_directory.text
 99_TEMP/
-QMSKI/DSC_PAPER/
-out/
+QMSKI/*
+out/*
 
 multirun/
 

02_CODE/docker_apptainer_hpc/Dockerfile.ubuntu24.04.gcc

@@ -27,19 +27,18 @@ ENV PATH="/opt/miniconda/bin:$PATH"
 RUN conda create -n hfe-essentials python=3.12
 SHELL ["conda", "run", "-n", "hfe-essentials", "/bin/bash", "-c"]
 # Copy hfe requirements.txt and install requirements
-COPY ./requirements.txt .
-RUN pip install --no-cache-dir -r requirements.txt
+COPY ./requirements.text .
+RUN pip install --no-cache-dir -r requirements.text
 RUN pip install -U scikit-image
 RUN pip install imutils
 
 # Set GitHub username and personal access token
 ARG GITHUB_USERNAME
-ARG GITHUB_TOKEN
 ARG USER_UID=1000
 ARG USER_GID=1000
 
-# Install the meshing package # TODO: reactivate when github action is cloning from public repo
-RUN git clone https://${GITHUB_USERNAME}:${GITHUB_TOKEN}@github.com/artorg-unibe-ch/spline_mesher.git ./pyhexspline/spline_mesher
+# Install the meshing package
+RUN git clone https://${GITHUB_USERNAME}:@github.com/artorg-unibe-ch/spline_mesher.git ./pyhexspline/spline_mesher
 WORKDIR ./pyhexspline/spline_mesher
 RUN pip install -e .
 

02_CODE/docker_apptainer_hpc/Dockerfile.ubuntu24.04.ifort

@@ -37,19 +37,18 @@ ENV PATH="/opt/miniconda/bin:$PATH"
 RUN conda create -n hfe-essentials python=3.12
 SHELL ["conda", "run", "-n", "hfe-essentials", "/bin/bash", "-c"]
 # Copy hfe requirements.txt and install requirements
-COPY ./requirements.txt .
-RUN pip install --no-cache-dir -r requirements.txt
+COPY ./requirements.text .
+RUN pip install --no-cache-dir -r requirements.text
 RUN pip install -U scikit-image
 RUN pip install imutils
 
 # Set GitHub username and personal access token
 ARG GITHUB_USERNAME
-ARG GITHUB_TOKEN
 ARG USER_UID=1000
 ARG USER_GID=1000
 
 # Install the meshing package
-RUN git clone https://${GITHUB_USERNAME}:${GITHUB_TOKEN}@github.com/artorg-unibe-ch/spline_mesher.git ./pyhexspline/spline_mesher
+RUN git clone https://${GITHUB_USERNAME}:@github.com/artorg-unibe-ch/spline_mesher.git ./pyhexspline/spline_mesher
 WORKDIR ./pyhexspline/spline_mesher
 RUN pip install -e .
 

02_CODE/docker_apptainer_hpc/requirements.text

@@ -0,0 +1,16 @@
+coloredlogs==15.0.1
+Cython==3.0.9
+fast_simplification==0.1.7
+hydra-core==1.3.2
+matplotlib==3.8.3
+numba==0.59.1
+numpy==1.26.4
+omegaconf==2.3.0
+pandas==2.2.2
+psutil==5.9.8
+pyvista==0.43.4
+PyYAML==6.0.1
+scipy==1.13.0
+setuptools==70.3.0
+SimpleITK==2.3.1
+vtk==9.3.0

02_CODE/requirements.txt

@@ -8,11 +8,8 @@ numpy==1.26.4
 omegaconf==2.3.0
 pandas==2.2.2
 psutil==5.9.8
-# pyhexspline==0.1.0
-# pyhexspline.egg==info
 pyvista==0.43.4
 PyYAML==6.0.1
-PyYAML==6.0.1
 scipy==1.13.0
 setuptools==70.3.0
 SimpleITK==2.3.1

02_CODE/src/docs/.gitignore

@@ -0,0 +1,3 @@
+*.swp
+/_build
+/doctrees

02_CODE/src/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

02_CODE/src/docs/_build/html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: a565ca8934d45de2233f702231a97bae
+tags: 645f666f9bcd5a90fca523b33c5a78b7