diff --git a/.github/workflows/check_format.yml b/.github/workflows/check_format.yml index 2a42042..63b266f 100644 --- a/.github/workflows/check_format.yml +++ b/.github/workflows/check_format.yml @@ -13,7 +13,7 @@ jobs: strategy: matrix: os: [ubuntu-latest] - python-version: [3.8] + python-version: ['3.10'] requires: ['latest'] steps: diff --git a/.github/workflows/issue_title_labeler.yml b/.github/workflows/issue_title_labeler.yml index 83b0262..dbe469d 100644 --- a/.github/workflows/issue_title_labeler.yml +++ b/.github/workflows/issue_title_labeler.yml @@ -13,7 +13,7 @@ jobs: - uses: actions/checkout@v3 - uses: actions/setup-python@v4 with: - python-version: '3.8' + python-version: '3.10' - name: Install packages run: | python -m pip install --upgrade --user pip diff --git a/.github/workflows/pr_title_labeler.yml b/.github/workflows/pr_title_labeler.yml index 755fe9d..7ce17e2 100644 --- a/.github/workflows/pr_title_labeler.yml +++ b/.github/workflows/pr_title_labeler.yml @@ -12,7 +12,7 @@ jobs: - uses: actions/checkout@v3 - uses: actions/setup-python@v4 with: - python-version: '3.8' + python-version: '3.10' - name: Install packages run: | python -m pip install --upgrade --user pip diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml index e083aee..7ec83c4 100644 --- a/.github/workflows/test_package.yml +++ b/.github/workflows/test_package.yml @@ -15,7 +15,7 @@ jobs: # max-parallel: 6 matrix: os: [ubuntu-latest] - python-version: [3.8] + python-version: ['3.10'] requires: ['minimal', 'latest'] steps: @@ -53,16 +53,6 @@ jobs: python -m pip install --upgrade --user pip pip install setuptools tox pip install -e .[test] - # Force upgrading packages to workaround the `scilpy` requested versions - pip install --upgrade matplotlib==3.1.0 - pip install --upgrade numpy==1.23.0 - # Force upgrading packages to avoid numpy-related built-in type deprecation warnings - pip install --upgrade dipy==1.4.1 - pip install --upgrade fury==0.7.1 - pip install --upgrade h5py==3.0.0 - pip install --upgrade nibabel==3.2.1 - pip install --upgrade scikit-learn==0.24.0 - pip install --upgrade scipy==1.7.0 python --version pip --version pip list diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 09788fd..0624e8f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,5 @@ default_language_version: - python: python3.8 + python: python3.10 repos: - repo: https://github.com/pre-commit/pre-commit-hooks diff --git a/README.md b/README.md index 88fc1a1..61014a8 100644 --- a/README.md +++ b/README.md @@ -17,11 +17,11 @@ Tractography learning. ## Installation To use tractolearn, it is recommended to create a virtual environment using -python 3.8 that will host the necessary dependencies. Torch tested with an +python 3.10 that will host the necessary dependencies. Torch tested with an NVIDIA RTX 3090 with: ```sh - virtualenv tractolearn_env --python=python3.8 + virtualenv tractolearn_env --python=python3.10 source tractolearn_env/bin/activate ``` diff --git a/pyproject.toml b/pyproject.toml index 28cb812..1f387d9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,25 +20,25 @@ dependencies = [ # common dependencies "importlib-metadata", "comet-ml == 3.0.0", - "h5py == 2.10.0", - "matplotlib >= 2.2.0", - "numpy >= 1.20.0", + "h5py == 3.7.0", + "matplotlib == 3.6.0", + "numpy == 1.23.0", "pandas", "pathos", "pyyaml", "seaborn == 0.11.0", - "scikit-learn == 0.22.0", - "scipy == 1.4.0", - "torch == 1.8.1", + "scikit-learn == 1.2.0", + "scipy == 1.9.0", + "torch == 1.13.0", "torchsummary == 1.5.1", "tqdm", "umap-learn", # DWI dependencies - "dipy == 1.3.0", - "fury == 0.7.1", - "nibabel == 3.0.0", + "dipy == 1.7.0", + "fury == 0.8.0", + "nibabel == 4.0.0", # Git dependencies - "scilpy @ git+https://github.com/scilus/scilpy@1.2.2", + "scilpy @ git+https://github.com/scilus/scilpy@eb5d3fbe3cb2697a1ea90fe8ea88512e9686802b", ] description = "Tractography learning" dynamic = ["version"] @@ -48,16 +48,16 @@ maintainers = [ ] name = "tractolearn" readme = "README.md" -requires-python = ">=3.8" +requires-python = ">=3.10" [project.optional-dependencies] test = [ "hypothesis >= 6.8.0", - "pytest == 5.3", + "pytest == 7.2.0", "pytest-cov", "pytest-pep8", "pytest-xdist", - "pytest_console_scripts", + "pytest_console_scripts == 1.3.0", ] dev = [ "black == 22.12", @@ -86,7 +86,7 @@ repository = "https://github.com/scil-vital/tractolearn" [tool.black] line-length = 79 -target-version = ["py38"] +target-version = ["py310"] exclude =''' ( /( diff --git a/tox.ini b/tox.ini index 4a6e1ac..eeaa96f 100644 --- a/tox.ini +++ b/tox.ini @@ -1,5 +1,5 @@ [tox] -envlist = py38 +envlist = py310 isolated_build = True [testenv]