M3Drop 0.5.2__tar.gz → 0.5.4__tar.gz

{m3drop-0.5.2 → m3drop-0.5.4}/M3Drop/CoexpressionGPU.py

@@ -162,7 +162,9 @@ def NBumiCoexpressionGPU(
 
                     if nnz > 0:
 
-                        data_gpu    = cp.asarray(active_payload['data'],    dtype=cp.float64)
+                        data_gpu    = cp.empty(nnz, dtype=active_payload['data'].dtype)
+                        data_gpu.set(active_payload['data'], stream=cp.cuda.get_current_stream())
+                        data_gpu    = data_gpu.astype(cp.float64, copy=False)
                         indices_gpu = cp.asarray(active_payload['indices'])
                         indptr_gpu  = cp.asarray(active_payload['indptr'])
 

{m3drop-0.5.2 → m3drop-0.5.4}/M3Drop/FeatureSelectionGPU.py

@@ -203,7 +203,9 @@ def FitBasicModelGPU(
 
                 with streams[idx]:
                     start_events[idx].record(streams[idx])
-                    data_gpu = cp.asarray(payload['data'], dtype=cp.float64)
+                    data_gpu = cp.empty(nnz, dtype=payload['data'].dtype)
+                    data_gpu.set(payload['data'], stream=streams[idx])
+                    data_gpu = data_gpu.astype(cp.float64, copy=False)
                     indices_gpu = cp.asarray(payload['indices'])
                     indptr_gpu = cp.asarray(payload['indptr'])
                     end_events[idx].record(streams[idx])

{m3drop-0.5.2 → m3drop-0.5.4}/M3Drop/NormalizationGPU.py

@@ -271,7 +271,9 @@ def NBumiPearsonResidualsCombinedGPU(
 
                     with streams[idx]:
                         start_events[idx].record(streams[idx])
-                        data_gpu_raw    = cupy.asarray(payload['data'],    dtype=cupy.float64)
+                        data_gpu_raw    = cupy.empty(nnz, dtype=payload['data'].dtype)
+                        data_gpu_raw.set(payload['data'], stream=streams[idx])
+                        data_gpu_raw    = data_gpu_raw.astype(cupy.float64, copy=False)
                         indices_gpu_raw = cupy.asarray(payload['indices'])
                         indptr_gpu_raw  = cupy.asarray(payload['indptr'])
                         end_events[idx].record(streams[idx])

{m3drop-0.5.2 → m3drop-0.5.4}/M3Drop/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.5.0"
+__version__ = "0.5.4"
 
 try:
     from .ComputeBlockCPU import RunComputeBlockCPU

{m3drop-0.5.2 → m3drop-0.5.4/M3Drop.egg-info}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: M3Drop
-Version: 0.5.2
+Version: 0.5.4
 Summary: A Python implementation of the M3Drop single-cell RNA-seq analysis tool.
 Author-email: Tallulah Andrews <tandrew6@uwo.ca>
 License: MIT
-Project-URL: Homepage, https://github.com/PragalvhaSharma/m3DropNew
-Project-URL: Repository, https://github.com/PragalvhaSharma/m3DropNew
+Project-URL: Homepage, https://github.com/M3Drop/main
+Project-URL: Repository, https://github.com/M3Drop/main
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
@@ -30,7 +30,6 @@ Requires-Dist: statsmodels>=0.13.0
 Requires-Dist: numba>=0.57.0
 Requires-Dist: threadpoolctl>=3.0.0
 Requires-Dist: questionary>=2.0.0
-Requires-Dist: cupy-cuda12x; sys_platform != "darwin"
 Dynamic: license-file
 
 # M3Drop

{m3drop-0.5.2 → m3drop-0.5.4}/M3Drop.egg-info/requires.txt

@@ -9,6 +9,3 @@ statsmodels>=0.13.0
 numba>=0.57.0
 threadpoolctl>=3.0.0
 questionary>=2.0.0
-
-[:sys_platform != "darwin"]
-cupy-cuda12x

{m3drop-0.5.2/M3Drop.egg-info → m3drop-0.5.4}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: M3Drop
-Version: 0.5.2
+Version: 0.5.4
 Summary: A Python implementation of the M3Drop single-cell RNA-seq analysis tool.
 Author-email: Tallulah Andrews <tandrew6@uwo.ca>
 License: MIT
-Project-URL: Homepage, https://github.com/PragalvhaSharma/m3DropNew
-Project-URL: Repository, https://github.com/PragalvhaSharma/m3DropNew
+Project-URL: Homepage, https://github.com/M3Drop/main
+Project-URL: Repository, https://github.com/M3Drop/main
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
@@ -30,7 +30,6 @@ Requires-Dist: statsmodels>=0.13.0
 Requires-Dist: numba>=0.57.0
 Requires-Dist: threadpoolctl>=3.0.0
 Requires-Dist: questionary>=2.0.0
-Requires-Dist: cupy-cuda12x; sys_platform != "darwin"
 Dynamic: license-file
 
 # M3Drop

{m3drop-0.5.2 → m3drop-0.5.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "M3Drop"
-version = "0.5.2"
+version = "0.5.4"
 description = "A Python implementation of the M3Drop single-cell RNA-seq analysis tool."
 readme = "README.md"
 requires-python = ">=3.8"
@@ -24,6 +24,10 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
+# Note: cupy is NOT listed here. The GPU pipeline requires cupy at runtime,
+# but users must install it themselves (`pip install cupy` on HPC systems
+# after `module load cuda`, or `pip install cupy-cuda12x` on workstations).
+# This keeps `pip install M3Drop` working on login nodes and CPU-only machines.
 dependencies = [
     "anndata>=0.8.0",
     "h5py>=3.8.0",
@@ -36,12 +40,11 @@ dependencies = [
     "numba>=0.57.0",
     "threadpoolctl>=3.0.0",
     "questionary>=2.0.0",
-    "cupy-cuda12x; sys_platform != 'darwin'",
 ]
 
 [project.urls]
-Homepage = "https://github.com/PragalvhaSharma/m3DropNew"
-Repository = "https://github.com/PragalvhaSharma/m3DropNew"
+Homepage = "https://github.com/M3Drop/main"
+Repository = "https://github.com/M3Drop/main"
 
 [tool.setuptools.packages.find]
 include = ["M3Drop", "M3Drop.*"]