diff --git a/.bumpversion.cfg b/.bumpversion.cfg index cd8ab5d..f2a83da 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,7 +1,7 @@ [bumpversion] -current_version = 1.6.2 +current_version = 1.6.3 commit = True tag = True -files = setup.py decoupler/__init__.py +files = pyproject.toml decoupler/__init__.py parse = (?P\d+)\.(?P\d+)\.(?P\d+) serialize = {major}.{minor}.{patch} diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..5276b8d --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,83 @@ +name: ci + +on: + push: + branches: [ main ] + pull_request: + types: [ opened, synchronize, reopened ] + +jobs: + build: + + runs-on: ${{ matrix.os }} + defaults: + run: + shell: bash -e {0} + + strategy: + fail-fast: false + matrix: + python: ['3.8', '3.9', '3.10', '3.11', '3.12'] + os: [ubuntu-latest, macos-latest] + + env: + OS: ${{ matrix.os }} + PYTHON: ${{ matrix.python }} + MODULE: decoupler + + steps: + - name: Check out main + uses: actions/checkout@v4 + - name: Setup Python ${{ matrix.python }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python }} + - name: System dependencies Linux + if: ${{ matrix.os == 'ubuntu-latest' }} + run: | + sudo apt-get update + sudo apt-get install -y libcurl4-openssl-dev + - name: System dependencies OSX + if: ${{ matrix.os == 'macos-latest' }} + run: | + brew install openssl + export LDFLAGS="-L/usr/local/opt/openssl@3/lib" + export CPPFLAGS="-I/usr/local/opt/openssl@3/include" + export PKG_CONFIG_PATH="/usr/local/opt/openssl@3/lib/pkgconfig" + - name: Install Poetry + uses: snok/install-poetry@v1 + with: + virtualenvs-create: true + virtualenvs-in-project: true + installer-parallel: true + - name: Load cached venv + id: cached-poetry-dependencies + uses: actions/cache@v4 + with: + path: .venv + key: venv-${{ runner.os }}-${{ matrix.python }}-${{ hashFiles('**/poetry.lock') }} + - name: Install dependencies + if: ${{ steps.cached-poetry-dependencies.outputs.cache-hit != 'true' }} + run: poetry install --no-interaction --no-root + - name: Install library + run: poetry install --no-interaction + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + poetry run flake8 $MODULE --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + poetry run flake8 $MODULE --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Tests and test coverage + if: ${{ github.event_name == 'push' }} + run: | + poetry run pytest --cov --disable-warnings + - name: Tests + if: ${{ github.event_name == 'pull_request' }} + run: | + poetry run pytest --disable-warnings + - name: Upload coverage reports to Codecov + if: ${{ github.event_name == 'push' }} + run: | + curl -Os https://uploader.codecov.io/latest/linux/codecov + chmod +x codecov + ./codecov -t ${CODECOV_TOKEN} diff --git a/.github/workflows/devel.yml b/.github/workflows/devel.yml deleted file mode 100644 index d9fab1d..0000000 --- a/.github/workflows/devel.yml +++ /dev/null @@ -1,64 +0,0 @@ -name: devel - -on: - push: - branches: [ devel ] - pull_request: - branches: [ main ] - -jobs: - build-linux: - - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v3 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: "3.11" - - name: Install dependencies - run: | - sudo apt-get update - sudo apt-get install -y libcurl4-openssl-dev - python -m pip install --upgrade pip - pip install wheel - pip install pytest flake8 scikit-learn skranger git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil igraph . - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test - run: | - pytest --disable-warnings . - - build-macOS: - - runs-on: macOS-latest - - steps: - - uses: actions/checkout@v3 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: "3.11" - - name: Install dependencies - run: | - brew install openssl - export LDFLAGS="-L/usr/local/opt/openssl@3/lib" - export CPPFLAGS="-I/usr/local/opt/openssl@3/include" - export PKG_CONFIG_PATH="/usr/local/opt/openssl@3/lib/pkgconfig" - python -m pip install --upgrade pip - pip install wheel - pip install pytest flake8 scikit-learn skranger git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil igraph . - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test - run: | - pytest --disable-warnings . diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml deleted file mode 100644 index 5e4787c..0000000 --- a/.github/workflows/main.yml +++ /dev/null @@ -1,67 +0,0 @@ -name: build - -on: - push: - branches: [ main ] - -jobs: - build-linux: - - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v3 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: "3.11" - - name: Install dependencies - run: | - sudo apt-get update - sudo apt-get install -y libcurl4-openssl-dev - python -m pip install --upgrade pip - pip install wheel - pip install pytest-cov flake8 scikit-learn git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil igraph . - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test and add coverage - run: | - pytest --cov --disable-warnings decoupler - - name: Upload coverage reports to Codecov - run: | - curl -Os https://uploader.codecov.io/latest/linux/codecov - chmod +x codecov - ./codecov -t ${CODECOV_TOKEN} - - build-macOS: - - runs-on: macOS-latest - - steps: - - uses: actions/checkout@v3 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: "3.11" - - name: Install dependencies - run: | - brew install openssl - export LDFLAGS="-L/usr/local/opt/openssl@3/lib" - export CPPFLAGS="-I/usr/local/opt/openssl@3/include" - export PKG_CONFIG_PATH="/usr/local/opt/openssl@3/lib/pkgconfig" - python -m pip install --upgrade pip - pip install wheel - pip install pytest flake8 scikit-learn git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil igraph . - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test - run: | - pytest --disable-warnings . diff --git a/decoupler/__init__.py b/decoupler/__init__.py index b81b031..894f1fc 100644 --- a/decoupler/__init__.py +++ b/decoupler/__init__.py @@ -1,4 +1,4 @@ -__version__ = '1.6.2' # noqa: F401 +__version__ = '1.6.3' # noqa: F401 __version_info__ = tuple([int(num) for num in __version__.split('.')]) # noqa: F401 from .pre import extract, match, rename_net, get_net_mat, filt_min_n, mask_features # noqa: F401 diff --git a/decoupler/method_aucell.py b/decoupler/method_aucell.py index b5d0969..b631440 100644 --- a/decoupler/method_aucell.py +++ b/decoupler/method_aucell.py @@ -34,7 +34,7 @@ def nb_aucell(row, net, starts, offsets, n_up, n_fsets): fset = net[srt:off] # Compute max AUC for fset - x_th = np.arange(start=1, stop=fset.shape[0]+1, dtype=nb.i8) + x_th = np.arange(1, stop=fset.shape[0]+1, dtype=nb.i8) x_th = x_th[x_th < n_up] max_auc = np.sum(np.diff(np.append(x_th, n_up)) * x_th) diff --git a/decoupler/method_gsva.py b/decoupler/method_gsva.py index 8d90973..ac3e975 100644 --- a/decoupler/method_gsva.py +++ b/decoupler/method_gsva.py @@ -83,7 +83,7 @@ def density(mat, kcdf=False): @nb.njit(nb.types.Tuple((nb.f4[:, :], nb.i8[:, :]))(nb.f4[:, :]), parallel=True, cache=True) def nb_get_D_I(mat): n = mat.shape[1] - rev_idx = np.abs(np.arange(start=n, stop=0, step=-1, dtype=nb.f4) - n / 2) + rev_idx = np.abs(np.arange(n, stop=0, step=-1, dtype=nb.f4) - n / 2) Idx = np.zeros(mat.shape, dtype=nb.i8) for i in nb.prange(mat.shape[0]): Idx[i] = np.argsort(-mat[i]) diff --git a/decoupler/utils.py b/decoupler/utils.py index a21461e..c3e4cd2 100644 --- a/decoupler/utils.py +++ b/decoupler/utils.py @@ -335,7 +335,7 @@ def p_adjust_fdr(p): """ # Code adapted from: https://stackoverflow.com/a/33532498/8395875 - p = np.asfarray(p) + p = np.asarray(p, dtype = 'float64') by_descend = 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Bio-Informatics" +] +keywords = [ + "systems biology", "molecular biology", "signaling network", + "transcriptomics", "modeling", "mechanistic modeling", + "activity inference", "molecular network", "omics", + "biomedicine", "molecular footprint", "molecular signature" +] +repository = "https://github.com/saezlab/decoupler-py" +homepage = "https://decoupler.readthedocs.io/" +documentation = "https://decoupler.readthedocs.io/" +readme = "README.md" + +[tool.poetry.urls] +"Bug Tracker" = "https://github.com/saezlab/decoupler-py/issues" + +[[tool.poetry.source]] +name = "pypi-public" +url = "https://pypi.org/simple/" + +[tool.poetry.dependencies] +python = "^3.9" +tqdm = "^4.66.4" +typing-extensions = "^4.12.2" +numba = "^0.60.0" +numpy = "^1" +pandas = "^2.2.2" + +[tool.poetry.group.dev.dependencies] +pytest = ">=6.0" +bump2version = "*" +pytest-cov = "^5.0.0" +scanpy = "^1.10.1" +psutil = "^5.9.8" +flake8-pyproject = {git = "https://github.com/john-hen/Flake8-pyproject.git"} +sphinx = 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