Merge pull request #159 from pyplati/dockerfile-corrections

Dockerfile corrections

.github/workflows/package.yml

@@ -50,7 +50,7 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           context: .
-          file: service.Dockerfile
+          file: dev.Dockerfile
           platforms: linux/amd64
           push: true
           tags: |

.github/workflows/release.yml

@@ -1,4 +1,3 @@
-
 name: Release
 
 on:
@@ -10,49 +9,48 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.7'
-    - name: Install dependencies
-      run: |
-        curl -sSL https://install.python-poetry.org | python - --version 1.2.0rc1
-        poetry install --with dev,docs --all-extras
-        echo "PYTHONPATH=`pwd`" >> $GITHUB_ENV
-    - name: Autobump version
-      run: |
-        # from refs/tags/v1.2.3 get 1.2.3
-        VERSION=$(echo $GITHUB_REF | sed 's#.*/v##')
-        PLACEHOLDER='__version__ = "develop"'
-        VERSION_FILE='platipy/__init__.py'
-        grep "$PLACEHOLDER" "$VERSION_FILE"
-        sed -i "s/$PLACEHOLDER/__version__ = \"${VERSION}\"/g" "$VERSION_FILE"
-      shell: bash
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.7"
+      - name: Install dependencies
+        run: |
+          curl -sSL https://install.python-poetry.org | python - --version 1.2.1
+          poetry install --with dev,docs --all-extras
+          echo "PYTHONPATH=`pwd`" >> $GITHUB_ENV
+      - name: Autobump version
+        run: |
+          # from refs/tags/v1.2.3 get 1.2.3
+          VERSION=$(echo $GITHUB_REF | sed 's#.*/v##')
+          VERSION_PLACEHOLDER='__version__ = "0.0.0"'
+          VERSION_FILE='platipy/__init__.py'
+          grep "$VERSION_PLACEHOLDER" "$VERSION_FILE"
+          sed -i "s/$VERSION_PLACEHOLDER/__version__ = \"${VERSION}\"/g" 'platipy/__init__.py'
+          PYPROJECT_PLACEHOLDER='version = "0.0.0"'
+          PYPROJECT_FILE='pyproject.toml'
+          grep "$PYPROJECT_PLACEHOLDER" "$PYPROJECT_FILE"
+          sed -i "s/$PYPROJECT_PLACEHOLDER/version = \"${VERSION}\"/g" "$PYPROJECT_FILE"
+        shell: bash
 
-    - name: Build package
-      run: |
-        pip install setuptools wheel
-        python setup.py sdist bdist_wheel
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
-
-    - name: Build docs
-      run: |
-        sudo apt-get update -y && sudo apt-get install -y pandoc
-        poetry run sphinx-build -b html -a docs docs/site
-    - name: Deploy docs
-      uses: peaceiris/actions-gh-pages@v3
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./docs/site
+      - name: Build & publish package
+        run: |
+          poetry config pypi-token.pypi ${{ secrets.PYPI_API_TOKEN }}
+          poetry build
+          poetry publish
+      - name: Build docs
+        run: |
+          sudo apt-get update -y && sudo apt-get install -y pandoc
+          poetry run sphinx-build -b html -a docs docs/site
+      - name: Deploy docs
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/site
 
-    - name: Build docker
-      uses: peter-evans/repository-dispatch@v1
-      with:
-        token: ${{ secrets.REPO_ACCESS_TOKEN }}
-        repository: pyplati/platipy
-        event-type: docker
+      - name: Build docker
+        uses: peter-evans/repository-dispatch@v1
+        with:
+          token: ${{ secrets.REPO_ACCESS_TOKEN }}
+          repository: pyplati/platipy
+          event-type: docker

CONTRIBUTING.md

@@ -11,13 +11,21 @@ request](https://github.com/pyplati/platipy/compare) to merge your changes into
 (**master**). At this point the automated tests will run and maintainers will review your
 submission before merging.
 
-## Example Installation
+## Poetry
 
-To install a development environment run the following within a virtual environment:
+platipy uses poetry to manage dependencies. Instructions for installing poetry are available 
+[here](https://python-poetry.org/docs/#installation). Once installed, you can easily install the
+libraries required to develop for platipy using the following command:
 
 ```bash
-pip install -r requirements.txt -r requirements-dev.txt -r requirements-backend.txt
-pip install -e .
+poetry install --with dev --all-extras
+```
+
+This will automatically create a virtual environment managed by poetry. To run a script within this
+environment, use the `poetry run` followed by what to run. For example, to run a test.py script:
+
+```bash
+poetry run python test.py
 ```
 
 ## Style Guide

README.md

@@ -99,15 +99,22 @@ fig = vis.show()
 ![Figure 3](assets/figure_3.png)
 
 ## Getting started
-There aren't many requirements, just an installed Python interpreter (3.6 or greater). The list of
-required Python packages can be found in requirements.txt.
-
-PlatiPy can be installed with **pip**:
+There aren't many requirements, just an installed Python interpreter (3.7 or greater). PlatiPy can
+be installed with **pip**:
 
 ```bash
 pip install platipy
 ```
 
+The base installation of platipy does not include some large libraries needed for various
+components of platipy. The following extras are available to install to run specific platipy tools:
+
+```bash
+pip install platipy[cardiac]
+pip install platipy[nnunet]
+pip install platipy[backend]
+```
+
 ## Authors
 
 * **Phillip Chlap** - [[email protected]]([email protected])

docs/getting_started.rst

@@ -10,6 +10,13 @@ PlatiPy is available from the Python package repositories and can be installed w
 
 ``pip install platipy``
 
+The base installation of platipy does not include some large libraries needed for various
+components of platipy. The following extras are available to install to run specific platipy tools:
+
+``pip install platipy[cardiac]``
+``pip install platipy[nnunet]``
+``pip install platipy[backend]``
+
 If you have already installed the library, you can install the latest updates using:
 
 ``pip install --upgrade platipy``

pyproject.toml

@@ -78,9 +78,6 @@ nbsphinx = "^0.8.9"
 m2r2 = "^0.3.3"
 Jinja2 = "^3.1"
 
-[tool.poetry-dynamic-versioning]
-enable = true
-
 [build-system]
-requires = ["poetry-core>=1.1.0", "poetry-dynamic-versioning"]
-build-backend = "poetry_dynamic_versioning.backend"
+requires = ["poetry-core>=1.1.0"]
+build-backend = "poetry.core.masonry.api"

services/nnunet/Dockerfile

@@ -1,6 +1,6 @@
 FROM platipy/platipy:service
 
-RUN env -C /platipy /root/.local/bin/poetry install --E backend,nnunet
+RUN env -C /platipy /root/.local/bin/poetry install -E backend,nnunet
 
 COPY ./nnUNetTrainerHeart.py /usr/lib/python3.8/site-packages/nnunet/training/network_training/nnUNetTrainerHeart.py