poetry 1.8.3

.devcontainer/devcontainer.json

@@ -6,7 +6,10 @@
 		// Sets the run context to one level up instead of the .devcontainer folder.
 		"context": "..",
 		// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
-		"dockerfile": "../docker/development.Dockerfile"
+		"dockerfile": "../docker/development.Dockerfile",
+		"args": {
+			"POETRY_VERSION": "1.8.3"
+		}
 	},
 
 	// Features to add to the dev container. More info: https://containers.dev/features.
@@ -16,13 +19,13 @@
 	// "forwardPorts": [],
 
 	// Uncomment the next line to run commands after the container is created.
-	"postCreateCommand": "poetry install",
+	"postCreateCommand": "poetry shell",
 
 	// Configure tool-specific properties.
 	// "customizations": {},
 
 	// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
 	"mounts": [
-		"source=${localWorkspaceFolder},target=/project,type=bind,consistency=cached"
+		"source=${localWorkspaceFolder},target=/src,type=bind,consistency=cached"
 	]
 }

.github/workflows/CI.yaml

@@ -47,7 +47,7 @@ jobs:
       - uses: abatilo/[email protected]
         with:
           poetry-version: ${{ env.POETRY_VERSION }}
-      - run: poetry install --no-interaction
+      - run: poetry install --no-interaction --only=docs,main
       - name: Build docs
         run: poetry run mkdocs build
 

.readthedocs.yaml

@@ -11,10 +11,10 @@ build:
     python: "3.8"
   jobs:
     post_create_environment:
-      - pip install poetry==1.1.11
+      - pip install poetry==1.8.3
     post_install:
       # TODO: Change to docs group after poetry upgrade
-      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install 
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --only=docs,main
 
 
 mkdocs:

Contributing.md

@@ -17,7 +17,7 @@
 1. Install pipx - instructions are available [here](https://github.com/pypa/pipx?tab=readme-ov-file#install-pipx)
 2. Install poetry via pipx 
    ```
-   pipx install --suffix=@1.1.11 poetry==1.1.11
+   pipx install --suffix=@1.8.3 poetry==1.8.3
    ```
 
 ### Install project
@@ -29,13 +29,13 @@
    ```
 2. Configure poetry to use python 3.8.13
    ```
-   poetry@1.1.11 env use 3.8.13
+   poetry@1.8.3 env use 3.8.13
    ```
 3. Install project dependencies 
    ```
-   poetry@1.1.11 install
+   poetry@1.8.3 install
    ```
 4. Validate installation
    ```
-   poetry@1.1.11 run pd-dwi --help
+   poetry@1.8.3 run pd-dwi --help
    ```

Dockerfile

@@ -4,7 +4,7 @@ ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update --yes && \
     apt-get install -y python3-pip
 
-ENV POETRY_VERSION=1.1.11
+ENV POETRY_VERSION=1.8.3
 RUN pip3 install --upgrade pip && pip3 install "poetry==$POETRY_VERSION"
 
 

docker/development.Dockerfile

@@ -2,19 +2,19 @@ FROM ubuntu:20.04
 
 ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update --yes && \
-    apt-get install -y python3-pip
+    apt-get install -y python3-pip git
 
-ENV POETRY_VERSION=1.1.11
+ENV POETRY_VERSION=1.8.3
 RUN pip3 install --upgrade pip && pip3 install "poetry==$POETRY_VERSION"
 
 
 RUN mkdir /src
 WORKDIR /src
 
-RUN poetry config virtualenvs.create false
+RUN poetry config virtualenvs.create true
 
 # Install dependencies (cached)
-COPY pyproject.toml poetry.lock ./
+COPY pyproject.toml poetry.lock README.md ./
 RUN poetry install
 
 CMD ["/bin/bash"]

docs/installation/install_package.md

@@ -22,7 +22,7 @@ PD-DWI can also be installed from source code.
 
     * git
     * python 3.8
-    * poetry 1.1.11
+    * poetry 1.8.3
 
 1. Clone the repository
 ```console

github.env

@@ -1,2 +1,2 @@
 PYTHON_VERSION=3.8.18
-POETRY_VERSION=1.1.11
+POETRY_VERSION=1.8.3

mkdocs.yml

@@ -3,9 +3,9 @@ site_name: PD-DWI
 repo_url: https://github.com/technionComputationalMRILab/PD-DWI/
 
 theme:
-  name: readthedocs
-  highlightjs: true
-  include_homepage_in_sidebar: true
+  name: material
+  # highlightjs: true
+  # include_homepage_in_sidebar: true
 
 nav:
   - Home: index.md

pyproject.toml

@@ -25,14 +25,13 @@ documentation = "https://pd-dwi.readthedocs.io/en/stable/"
 pd-dwi = "pd_dwi.scripts.cli:pd_dwi_cli"
 pd-dwi-preprocessing = "pd_dwi.scripts.cli:preprocessing_cli"
 
-
 [tool.poetry.dependencies]
 python = ">=3.8.1,<3.9"
-Cython = "^0.29.30"
+cython = "^0.29.30"
 jsonschema = "^4.6.0"
 numpy = "^1.22.0"
 pyradiomics = "^3.0.1"
-PyYAML = "^6.0"
+pyyaml = "^6.0"
 scikit-learn = "^1.0.2"
 xgboost = "^1.6.1"
 pandas = "^1.4.3"
@@ -41,13 +40,15 @@ pydantic-yaml = "^1.2.1"
 StrEnum = {version = "^0.4.15", python = "<3.11"}
 pydicom = "^2.4.4"
 
-[tool.poetry.dev-dependencies]
+[tool.poetry.group.dev.dependencies]
 pytest = "7.1.2"
 pytest-cov = "^4.1.0"
 pytest-mock = "^3.12.0"
 pytest-subtests = "^0.12.1"
 mypy = "^1.9.0"
 types-PyYAML = "^6.0.12"
+
+[tool.poetry.group.docs.dependencies]
 mkdocs = "^1.6.0"
 mkdocs-plotly-plugin = "^0.1.3"
 pymdown-extensions = "^10.8.1"
@@ -67,7 +68,6 @@ disallow_untyped_defs = true
 module = "pd_dwi.scripts.*"
 disallow_untyped_defs = false
 
-
 [build-system]
-requires = ["poetry-core>=1.0.0"]
+requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"