Merge pull request #6 from cantinilab/dev

Update main to version 0.3.4

.github/workflows/codecov.yaml

@@ -19,6 +19,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install flake8 pytest pre-commit
+          pip install circe-py
           pip install .[full]
       - name: Run tests and collect coverage
         run: |

.github/workflows/wheels.yml

@@ -20,8 +20,9 @@ jobs:
         if: runner.os == 'Linux'
         run: sudo apt-get update && sudo apt-get install -y liblapack-dev
       - name: Build SDist
-        run: python -m build
-
+        run: |
+          pip install build twine
+          python -m build
       - name: Check metadata
         run: python -m twine check dist/*
 
@@ -40,7 +41,13 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-
+      - name: Install LAPACK (Linux only)
+        if: matrix.os == 'ubuntu-latest'
+        run: sudo apt-get update && sudo apt-get install -y liblapack-dev
+      - name: Build SDist
+        run: |
+          pip install build
+          python -m build
       - uses: pypa/cibuildwheel@v2.21
         env:
           CIBW_ARCHS_MACOS: auto universal2

MANIFEST.in

@@ -0,0 +1,4 @@
+include pyquic_ext/*.pyx
+include pyquic_ext/*.C
+include pyquic_ext/*.h
+include setup.py

circe/__init__.py

@@ -1,9 +1,9 @@
-from .circe import extract_atac_links, \
+from circe.circe import extract_atac_links, \
     compute_atac_network, \
     add_region_infos, \
     sliding_graphical_lasso, \
     subset_region
 
-from .draw import plot_connections
-from .ccan_module import find_ccans, add_ccans
-from . import metacells
+from circe.draw import plot_connections
+from circe.ccan_module import find_ccans, add_ccans
+from circe import metacells