From b37326f562516fdbdcb2d4203b24b934b82fc0f7 Mon Sep 17 00:00:00 2001 From: Maya Date: Fri, 16 Aug 2024 18:12:08 +0300 Subject: [PATCH 1/4] poetry 1.8.3 --- .devcontainer/devcontainer.json | 9 +- .github/workflows/CI.yaml | 2 +- .readthedocs.yaml | 2 +- Contributing.md | 8 +- Dockerfile | 2 +- docker/development.Dockerfile | 8 +- docs/installation/install_package.md | 2 +- github.env | 2 +- poetry.lock | 1456 +++++++++++++++++++++----- pyproject.toml | 12 +- 10 files changed, 1224 insertions(+), 279 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index d8aead1..460aaad 100644 --- a/.devcontainer/devcontainer.json +++ b/.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" ] } diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 506cefd..34cd354 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -47,7 +47,7 @@ jobs: - uses: abatilo/actions-poetry@v2.0.0 with: poetry-version: ${{ env.POETRY_VERSION }} - - run: poetry install --no-interaction + - run: poetry install --no-interaction --only=docs - name: Build docs run: poetry run mkdocs build diff --git a/.readthedocs.yaml b/.readthedocs.yaml index c51d71b..6973575 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -11,7 +11,7 @@ build: python: "3.8" jobs: post_create_environment: - - pip install poetry==1.1.11 + - pip install poetry==1.8.3 post_install: # TODO: Change to docs group after poetry upgrade - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install diff --git a/Contributing.md b/Contributing.md index 57b0360..f8c3777 100644 --- a/Contributing.md +++ b/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 ``` \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index 9f89e82..a5969a6 100644 --- a/Dockerfile +++ b/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==$POETRY_VERSION" diff --git a/docker/development.Dockerfile b/docker/development.Dockerfile index 5ac1adc..94da7bd 100644 --- a/docker/development.Dockerfile +++ b/docker/development.Dockerfile @@ -2,19 +2,19 @@ FROM ubuntu:20.04 ENV DEBIAN_FRONTEND=noninteractive RUN apt-get update --yes && \ - apt-get install -y python3-pip + apt-get install -y python3-pip git -ENV POETRY_VERSION=1.1.11 +ENV POETRY_VERSION=1.8.3 RUN pip3 install --upgrade pip && pip3 install "poetry==$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"] diff --git a/docs/installation/install_package.md b/docs/installation/install_package.md index 40c587a..ad7bf76 100644 --- a/docs/installation/install_package.md +++ b/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 diff --git a/github.env b/github.env index 2c6851b..487f9d4 100644 --- a/github.env +++ b/github.env @@ -1,2 +1,2 @@ PYTHON_VERSION=3.8.18 -POETRY_VERSION=1.1.11 \ No newline at end of file +POETRY_VERSION=1.8.3 \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index 88ff4f4..13ee347 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,15 @@ +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + [[package]] name = "annotated-types" version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" -category = "main" optional = false python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, +] [package.dependencies] typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} @@ -13,47 +18,58 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} name = "atomicwrites" version = "1.4.1" description = "Atomic file writes." -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"}, +] [[package]] name = "attrs" -version = "23.2.0" +version = "24.2.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.7" +files = [ + {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, + {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, +] [package.extras] -cov = ["attrs", "coverage[toml] (>=5.3)"] -dev = ["attrs", "pre-commit"] -docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] -tests = ["attrs", "zope-interface"] -tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"] -tests-no-zope = ["attrs", "cloudpickle", "hypothesis", "pympler", "pytest-xdist", "pytest (>=4.3.0)"] +benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"] +tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] [[package]] name = "babel" -version = "2.15.0" +version = "2.16.0" description = "Internationalization utilities" -category = "dev" optional = false python-versions = ">=3.8" +files = [ + {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, + {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, +] [package.dependencies] pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} [package.extras] -dev = ["pytest (>=6.0)", "pytest-cov", "freezegun (>=1.0,<2.0)"] +dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "beautifulsoup4" version = "4.12.3" description = "Screen-scraping library" -category = "dev" optional = false python-versions = ">=3.6.0" +files = [ + {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"}, + {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"}, +] [package.dependencies] soupsieve = ">1.2" @@ -69,25 +85,122 @@ lxml = ["lxml"] name = "certifi" version = "2024.7.4" description = "Python package for providing Mozilla's CA Bundle." -category = "dev" optional = false python-versions = ">=3.6" +files = [ + {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"}, + {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"}, +] [[package]] name = "charset-normalizer" version = "3.3.2" description = "The Real First Universal Charset Detector. 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"^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" From 9835c4a5debb5860813b3b5013c1526e3b104c8a Mon Sep 17 00:00:00 2001 From: Maya Date: Fri, 16 Aug 2024 18:14:48 +0300 Subject: [PATCH 2/4] Missing requirements --- .github/workflows/CI.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 34cd354..19fa421 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -47,7 +47,7 @@ jobs: - uses: abatilo/actions-poetry@v2.0.0 with: poetry-version: ${{ env.POETRY_VERSION }} - - run: poetry install --no-interaction --only=docs + - run: poetry install --no-interaction --only=docs,main - name: Build docs run: poetry run mkdocs build From 1a047e0e42d08f6eca79dcef69b6751e23298282 Mon Sep 17 00:00:00 2001 From: Maya Date: Fri, 16 Aug 2024 18:25:25 +0300 Subject: [PATCH 3/4] only docs and main --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 6973575..3818181 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -14,7 +14,7 @@ build: - pip install poetry==1.8.3 post_install: # TODO: Change to docs group after poetry upgrade - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --only=docs,main mkdocs: From 185491859882da5bd3b9fe4253c345cfb45ac56c Mon Sep 17 00:00:00 2001 From: Maya Date: Fri, 16 Aug 2024 18:29:47 +0300 Subject: [PATCH 4/4] Try switching to material --- mkdocs.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index f883aba..15b15f2 100644 --- a/mkdocs.yml +++ b/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