Merge pull request #134 from saezlab/arange-numba-fix

Transition to `poetry` + address `numpy 2.0` and `numba 0.60` related issues

.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<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
 serialize = {major}.{minor}.{patch}

.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}

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

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)
 

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])

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 = p.argsort()[::-1]
     by_orig = by_descend.argsort()
     steps = float(len(p)) / np.arange(len(p), 0, -1)