Testing ci 2 (#12)

* add files for prerelease and test_pypi_nomcr

.github/workflows/build_on_prerelease.yml

@@ -0,0 +1,137 @@
+name: (Prerelease) Build Pipy, Dockerhub image and test
+
+on:
+  release:
+    types: [prereleased]
+
+jobs:
+
+  build-n-publish-testpypi:
+    name: Build and publish Python to Test PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Python 3.10.5
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.10.5
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+
+    - name: Publish distribution to Test PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository_url: https://test.pypi.org/legacy/
+
+  docker-build:
+    name: Build Docker image and Push to Docker Hub
+    needs: build-n-publish-testpypi
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v2
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: macatools/skullTo3d
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          file: Dockerfile_testpypi_nomcr
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+  run-pretest-spm-macaque:
+    name: Running all existing pipelines in skullTo3d_CI.zip (SPM_native macaque)
+    needs:  docker-build
+    runs-on: ubuntu-latest
+    timeout-minutes: 1440
+
+    steps:
+      - name: Pull latest docker image
+        run:
+            docker pull macatools/skullTo3d:latest
+
+      - name: Download dataset
+        run: |
+
+            wget --no-check-certificate --content-disposition  "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O skullTo3d_CI.zip
+            unzip -o skullTo3d_CI.zip -d skullTo3d_CI
+
+            pwd
+            echo ""
+
+            ls skullTo3d_CI
+            echo ""
+
+            ls skullTo3d_CI/cenir-macaque-petra
+
+            ls skullTo3d_CI/cenir-macaque-petra/sub-Magneto/anat
+
+            echo ""
+
+            ls skullTo3d_CI/cerimed-macaque-ct
+
+            ls skullTo3d_CI/cerimed-macaque-ct/sub-Marvin/sub-01/anat
+
+            echo ""
+
+            ls skullTo3d_CI/cerimed-marmo-petra
+
+            ls skullTo3d_CI/cerimed-marmo-petra/sub-Paolina/sub-01/anat
+
+            echo ""
+
+      - name: Running all test pipelines (ANTS deriv pad)
+        run: |
+            python segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results -soft ANTS_prep_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad
+
+            ls skullTo3d_CI/cenir-macaque-petra/results
+
+            ls skullTo3d_CI/cenir-macaque-petra/results/derivatives
+
+            ls skullTo3d_CI/cenir-macaque-petra/results/derivatives/macapype_crop_aladin_ants_skull_t1_petra_brain_t1_t2/sub-Magneto/anat
+
+            python segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results -soft ANTS_prep_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT -deriv -pad
+
+            ls skullTo3d_CI/cerimed-macaque-ct/results
+
+            ls skullTo3d_CI/cerimed-macaque-ct/results/derivatives
+
+            ls skullTo3d_CI/cerimed-macaque-ct/results/derivatives/macapype_crop_aladin_ants_skull_t1_CT_brain_t1_t2/sub-Marvin/-ses-01/anat
+
+
+            python segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results -soft ANTS_noseg_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad
+
+
+            ls skullTo3d_CI/cerimed-marmo-petra/results
+
+            ls skullTo3d_CI/cerimed-marmo-petra/results/derivatives
+
+            ls skullTo3d_CI/cerimed-marmo-petra/results/derivatives/macapype_crop_aladin_ants_skull_t1_petra_brain_t1_t2/sub-Paolina/-ses-01/anat
+
+

Dockerfile_testpypi_nomcr

@@ -0,0 +1,37 @@
+# Generated by: Neurodocker version 0.7.0+15.ga4940e3.dirty
+# Latest release: Neurodocker version 0.7.0
+#
+# Thank you for using Neurodocker. If you discover any issues
+# or ways to improve this software, please submit an issue or
+# pull request on our GitHub repository:
+#
+#     https://github.com/ReproNim/neurodocker
+#
+# Timestamp: 2020/12/02 18:33:44 UTC
+
+FROM macatools/macapype:v0.3.5-nomcr
+
+USER root
+
+ARG DEBIAN_FRONTEND="noninteractive"
+
+MAINTAINER David Meunier "david.meunier@univ-amu.fr"
+
+############################################# install skullTo3d
+
+RUN echo $(which python) && \
+    echo $(which python3) && \
+    ln -s /usr/bin/python3 /usr/bin/python && \
+    ln -s /usr/bin/pip3 /usr/bin/pip
+
+RUN pip install --no-deps --index-url https://test.pypi.org/simple/ --pre skullTo3d && python -c "import skullTo3d; print(skullTo3d.__version__)"
+
+################################################## Finishing
+RUN apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN rm -rf \
+     /tmp/hsperfdata* \
+     /var/*/apt/*/partial \
+     /var/log/apt/term*
+

setup.py

@@ -13,7 +13,8 @@
 try:
     verstrline = open('skullTo3d/_version.py', "rt").read()
 except EnvironmentError:
-    pass # Okay, there is no version file.
+    pass  # Okay, there is no version file.
+
 else:
     VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
     mo = re.search(VSRE, verstrline, re.M)
@@ -37,7 +38,7 @@
     long_description=open('README.md').read(),
     long_description_content_type='text/markdown',
     license='BSD 3',
-    entry_points = {
+    entry_points={
         'console_scripts': ['segment_skull = segment_skull:main']},
     install_requires=required_packages,
     include_package_data=True)