gsMap3D 0.1.0a1__py3-none-any.whl → 0.1.0a3__py3-none-any.whl

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Files changed (7) hide show
  1. gsMap/config/utils.py +4 -0
  2. gsMap/pipeline/__init__.py +9 -0
  3. {gsmap3d-0.1.0a1.dist-info → gsmap3d-0.1.0a3.dist-info}/METADATA +5 -3
  4. {gsmap3d-0.1.0a1.dist-info → gsmap3d-0.1.0a3.dist-info}/RECORD +7 -6
  5. {gsmap3d-0.1.0a1.dist-info → gsmap3d-0.1.0a3.dist-info}/WHEEL +0 -0
  6. {gsmap3d-0.1.0a1.dist-info → gsmap3d-0.1.0a3.dist-info}/entry_points.txt +0 -0
  7. {gsmap3d-0.1.0a1.dist-info → gsmap3d-0.1.0a3.dist-info}/licenses/LICENSE +0 -0
gsMap/config/utils.py CHANGED
@@ -234,6 +234,10 @@ def process_h5ad_inputs(config, input_options):
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  sample_h5ad_dict[sample_name] = h5ad_path
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  elif processing_type == 'list':
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+ # Handle single string or Path input by wrapping in a list
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+ if isinstance(field_value, (str, Path)):
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+ field_value = [field_value]
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+
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  logger.info(f"Using {option_name} with {len(field_value)} files")
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  for h5ad_path in field_value:
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  h5ad_path = Path(h5ad_path)
gsMap/pipeline/__init__.py ADDED
@@ -0,0 +1,9 @@
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+ """
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+ gsMap pipeline module.
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+
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+ This module provides high-level pipeline functions for running gsMap analyses.
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+ """
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+
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+ from gsMap.pipeline.quick_mode import run_quick_mode
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+
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+ __all__ = ["run_quick_mode"]
{gsmap3d-0.1.0a1.dist-info → gsmap3d-0.1.0a3.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: gsMap3D
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- Version: 0.1.0a1
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+ Version: 0.1.0a3
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  Summary: Genetically informed spatial mapping of cells for complex traits
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  Project-URL: Home, https://github.com/Ganten-Hornby/gsMap3D
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  Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap3d/docs
@@ -40,7 +40,7 @@ Requires-Dist: bitarray<3.0.0,>=2.9.2
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  Requires-Dist: distinctipy>=1.3.4
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  Requires-Dist: einops
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  Requires-Dist: h5py>=3.0.0
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- Requires-Dist: jax~=0.9.0
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+ Requires-Dist: jax<1.0.0,>=0.7.2
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  Requires-Dist: jinja2
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  Requires-Dist: kaleido
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  Requires-Dist: matplotlib
@@ -66,7 +66,7 @@ Requires-Dist: tqdm
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  Requires-Dist: typer~=0.20.0
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  Requires-Dist: zarr>=2.18.0
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  Provides-Extra: cuda
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- Requires-Dist: jax[cuda12]>=0.8.1; extra == 'cuda'
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+ Requires-Dist: jax[cuda13]<1.0.0,>=0.7.2; extra == 'cuda'
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  Provides-Extra: doc
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  Requires-Dist: furo; extra == 'doc'
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  Requires-Dist: myst-parser; extra == 'doc'
@@ -93,6 +93,8 @@ Provides-Extra: tests
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  Requires-Dist: coverage; extra == 'tests'
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  Requires-Dist: pytest-cov>=4.0.0; extra == 'tests'
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  Requires-Dist: pytest>=7.0.0; extra == 'tests'
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+ Provides-Extra: tpu
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+ Requires-Dist: jax[tpu]<1.0.0,>=0.7.2; extra == 'tpu'
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  Description-Content-Type: text/markdown
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  # gsMap3D
{gsmap3d-0.1.0a1.dist-info → gsmap3d-0.1.0a3.dist-info}/RECORD RENAMED
@@ -17,7 +17,7 @@ gsMap/config/ldscore_config.py,sha256=yntZPspjcPbvrwhYNZ6WkAGJiQifOULKJBZtqVSlh-
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  gsMap/config/quick_mode_config.py,sha256=JkUjb0p-SqkxyPTbKebvJhHrTzFFud8MRwkJZUkctzY,9001
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  gsMap/config/report_config.py,sha256=9N-JiGFfJ3Lly8J9a1PpmCRUyBfFFijIp_X6iODkUdU,2730
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  gsMap/config/spatial_ldsc_config.py,sha256=5idEw6IyL52ANC8SrPR29lC65xySjPV0-H8x-t1PTwE,13012
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- gsMap/config/utils.py,sha256=LuZsVQFj7gPRD-KByBmncR6HzCqfJP7_w7kwS1fLjTU,12070
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+ gsMap/config/utils.py,sha256=wWuqm-7Kfy5cW-S53cGHr-vfY5c388A4Pm0x2EzmPK0,12239
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  gsMap/find_latent/__init__.py,sha256=bgXUn8hd9RAZwR4tA8JJQ9b751dDlLC4K-9GuEr11Q4,117
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  gsMap/find_latent/find_latent_representation.py,sha256=zzMLKDWTpE1zKZ1jPUNfS3atTf7RhTDrdeuLHC0hRn8,11566
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  gsMap/find_latent/st_process.py,sha256=C5Cpa5Q1gvl4iZ0BUd1OS58z6AHhEak_Y-hE39oom8c,29706
@@ -43,6 +43,7 @@ gsMap/ldscore/constants.py,sha256=I8jiwmS64V0HvfwMPPZjSvdFr5Ruqox_F6jolYGgqvs,21
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  gsMap/ldscore/io.py,sha256=ufrJd39NAZ1nGVhkYpfPZ7Ne_JYzhO6F9muk4_5fHnM,9119
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  gsMap/ldscore/mapping.py,sha256=6UgZ3HpYnLDTVJTuy4uZAik1Ifmwc2_tZlJxNUrJbsw,11374
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  gsMap/ldscore/pipeline.py,sha256=YQf6RJlVe1rjWl6o1ADGSLbQsFfizzzx-Jsc_4onIuM,24217
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+ gsMap/pipeline/__init__.py,sha256=FY6wJBV5Pj-Rb_EJV7lkvDwlQGeiibKLZ7sSf5mqu8U,195
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  gsMap/pipeline/quick_mode.py,sha256=sPutxA94jYvWpg_zjtuDkZryDXGJlKITeuzGcId_oys,5174
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  gsMap/report/__init__.py,sha256=Bo80Y_4o6w4Ag1ZA5NQAE2NJ6MNmsiw7FWp1tB80GCQ,74
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  gsMap/report/diagnosis.py,sha256=RYCRM0-nrR0olYQKHwpH8ygN0df9WXUEyE2wYWbPtl0,13931
@@ -67,8 +68,8 @@ gsMap/utils/jackknife.py,sha256=w_qMj9GlqViouHuOw1U80N6doWuCTXuPoAVU4P-5mm8,1767
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  gsMap/utils/manhattan_plot.py,sha256=fi-ee9pyXuJOu9VYsAJCNDGQSc86ZLDBIwNotUVdxhc,26509
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  gsMap/utils/regression_read.py,sha256=aHU44SdQyzMR7OcbxrmS8aNbv8jKT0rmjaf11joox34,5697
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  gsMap/utils/torch_utils.py,sha256=baHIoAlBcfEvoGOM2sH-oQLKVo5V0M5ZqzObgjm2I40,580
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- gsmap3d-0.1.0a1.dist-info/METADATA,sha256=nkrU-7t_sRzpciNpB3t-8oz6DfdL0PNKYvSQ5aPPCrg,7493
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- gsmap3d-0.1.0a1.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
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- gsmap3d-0.1.0a1.dist-info/entry_points.txt,sha256=EQ0WSo2RzyouAf3_mtECypKTd4TIrIMUZM1iRsDRPd0,40
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- gsmap3d-0.1.0a1.dist-info/licenses/LICENSE,sha256=F9Vd0M0bhtsefCFMCTzsR1n-sy6UhBa8OWk41HT_Rf8,1069
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- gsmap3d-0.1.0a1.dist-info/RECORD,,
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+ gsmap3d-0.1.0a3.dist-info/METADATA,sha256=5BTJEwuz7KXgxbJMII-17vbz-netNEf-K-jEPTCnnLM,7581
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+ gsmap3d-0.1.0a3.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
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+ gsmap3d-0.1.0a3.dist-info/entry_points.txt,sha256=EQ0WSo2RzyouAf3_mtECypKTd4TIrIMUZM1iRsDRPd0,40
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+ gsmap3d-0.1.0a3.dist-info/licenses/LICENSE,sha256=F9Vd0M0bhtsefCFMCTzsR1n-sy6UhBa8OWk41HT_Rf8,1069
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+ gsmap3d-0.1.0a3.dist-info/RECORD,,