zmap-tools 0.2.2__tar.gz → 0.2.2.2__tar.gz

{zmap_tools-0.2.2 → zmap_tools-0.2.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: zmap-tools
-Version: 0.2.2
+Version: 0.2.2.2
 Summary: API for working with ZMAP (Zebrafish Multi-Atlas Project)
 Author-email: Daniel Wagner <Daniel.Wagner@ucsf.edu>
 License: BSD 3-Clause License
@@ -47,19 +47,23 @@ Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: anndata>=0.10
-Requires-Dist: scanpy>=1.9
-Requires-Dist: numpy>=1.24
+Requires-Dist: anndata==0.12.18
+Requires-Dist: scanpy==1.12.1
+Requires-Dist: numpy==2.0.2
+Requires-Dist: numba==0.60.0
+Requires-Dist: llvmlite==0.43.0
 Requires-Dist: pandas<3.0,>=2.0
-Requires-Dist: matplotlib>=3.7
+Requires-Dist: matplotlib<4.0,>=3.7
 Requires-Dist: requests>=2.31
-Requires-Dist: scipy>=1.10
-Requires-Dist: scikit-learn>=1.3
-Requires-Dist: faiss-cpu>=1.8
-Requires-Dist: seaborn>=0.12
+Requires-Dist: scipy==1.16.3
+Requires-Dist: scikit-learn==1.6.1
+Requires-Dist: faiss-cpu==1.14.3
+Requires-Dist: seaborn==0.13.2
 Requires-Dist: tqdm>=4.66
 Requires-Dist: adjustText>=0.8
-Requires-Dist: symphonypy>=0.2
+Requires-Dist: symphonypy==0.2.4
+Requires-Dist: igraph==1.0.0
+Requires-Dist: leidenalg==0.12.0
 Dynamic: license-file
 
 # zmap-tools

{zmap_tools-0.2.2 → zmap_tools-0.2.2.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "zmap-tools"
-version = "0.2.2"
+version = "0.2.2.2"
 description = "API for working with ZMAP (Zebrafish Multi-Atlas Project)"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -27,19 +27,25 @@ classifiers = [
 ]
 
 dependencies = [
-  "anndata>=0.10",
-  "scanpy>=1.9",
-  "numpy>=1.24",
+  "anndata==0.12.18",
+  "scanpy==1.12.1",
+
+  "numpy==2.0.2",
+  "numba==0.60.0",
+  "llvmlite==0.43.0",
+
   "pandas>=2.0,<3.0",
-  "matplotlib>=3.7",
+  "matplotlib>=3.7,<4.0",
   "requests>=2.31",
-  "scipy>=1.10",
-  "scikit-learn>=1.3",
-  "faiss-cpu>=1.8",
-  "seaborn>=0.12",
+  "scipy==1.16.3",
+  "scikit-learn==1.6.1",
+  "faiss-cpu==1.14.3",
+  "seaborn==0.13.2",
   "tqdm>=4.66",
   "adjustText>=0.8",
-  "symphonypy>=0.2",
+  "symphonypy==0.2.4",
+  "igraph==1.0.0",
+  "leidenalg==0.12.0",
 ]
 
 [project.urls]

{zmap_tools-0.2.2 → zmap_tools-0.2.2.2}/src/zmap/predict/predict.py

@@ -232,6 +232,7 @@ def preprocess_adata_query(
         adata.X = np.log1p(X_tpm)
 
     # ---- 5. bookkeeping ----
+    adata.uns["log1p"] = {"base": None}
     adata.uns.setdefault("ZMAP_preprocessing", {})
     adata.uns["ZMAP_preprocessing"]["query"] = {
         "counts_source": counts_source,
@@ -3266,7 +3267,7 @@ def annotate_with_zmap(
     predict_kwargs: Mapping[str, Any] | None = None,
 
     # --- output controls ---
-    verbosity: int = 2,               # 0=silent, 1=progress, 2=summary+UMAP+QC, 3=full
+    verbosity: int = 3,               # 0=silent, 1=progress, 2=summary+UMAP+QC, 3=full
     debug: bool = False,              # if True, re-raise exceptions instead of catching
     print_summary: bool | None = None,   # deprecated → use verbosity
     show_plots: bool | None = None,      # deprecated → use verbosity
@@ -3362,7 +3363,7 @@ def annotate_with_zmap(
         Extra keyword arguments forwarded to ``predict_labels_kNN``.
         For common options, prefer the top-level ``tissue_aware`` and
         ``evaluate`` parameters instead of passing dicts manually.
-    verbosity : int, default ``2``
+    verbosity : int, default ``3``
         Controls how much output is printed and displayed inline:
 
         - ``0`` — silent (no print, no inline plots).
@@ -3737,6 +3738,7 @@ def annotate_with_zmap(
 
     # ------------------------------------------------------------------
     # 8. Copy colormap dict from reference → query (order-independent)
+    # Also copy reference color palettes and order lists
     # ------------------------------------------------------------------
     cmap_src_key = _COLORMAP_UNS_KEY.get(ref_label_col)
     if cmap_src_key and cmap_src_key in adata_ref.uns:
@@ -3756,6 +3758,13 @@ def annotate_with_zmap(
             "arrays — palette may be incorrect if query categories differ from reference.",
             stacklevel=2,
         )
+    
+    # Standard palettes
+    keys = ["ZMAP_CellType_order","ZMAP_Tissue_order","ZMAP_colormap_C12","ZMAP_colormap_C79",
+        "ZMAP_colormap_G7","ZMAP_colormap_T28","ZMAP_colormap_T7"]
+    for k in keys:
+        if k in adata_ref.uns:
+            adata_query.uns[k] = adata_ref.uns[k]
 
     # ------------------------------------------------------------------
     # 9. UMAP overlay figure (v >= 2)

{zmap_tools-0.2.2 → zmap_tools-0.2.2.2}/src/zmap_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: zmap-tools
-Version: 0.2.2
+Version: 0.2.2.2
 Summary: API for working with ZMAP (Zebrafish Multi-Atlas Project)
 Author-email: Daniel Wagner <Daniel.Wagner@ucsf.edu>
 License: BSD 3-Clause License
@@ -47,19 +47,23 @@ Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: anndata>=0.10
-Requires-Dist: scanpy>=1.9
-Requires-Dist: numpy>=1.24
+Requires-Dist: anndata==0.12.18
+Requires-Dist: scanpy==1.12.1
+Requires-Dist: numpy==2.0.2
+Requires-Dist: numba==0.60.0
+Requires-Dist: llvmlite==0.43.0
 Requires-Dist: pandas<3.0,>=2.0
-Requires-Dist: matplotlib>=3.7
+Requires-Dist: matplotlib<4.0,>=3.7
 Requires-Dist: requests>=2.31
-Requires-Dist: scipy>=1.10
-Requires-Dist: scikit-learn>=1.3
-Requires-Dist: faiss-cpu>=1.8
-Requires-Dist: seaborn>=0.12
+Requires-Dist: scipy==1.16.3
+Requires-Dist: scikit-learn==1.6.1
+Requires-Dist: faiss-cpu==1.14.3
+Requires-Dist: seaborn==0.13.2
 Requires-Dist: tqdm>=4.66
 Requires-Dist: adjustText>=0.8
-Requires-Dist: symphonypy>=0.2
+Requires-Dist: symphonypy==0.2.4
+Requires-Dist: igraph==1.0.0
+Requires-Dist: leidenalg==0.12.0
 Dynamic: license-file
 
 # zmap-tools

zmap_tools-0.2.2.2/src/zmap_tools.egg-info/requires.txt

@@ -0,0 +1,17 @@
+anndata==0.12.18
+scanpy==1.12.1
+numpy==2.0.2
+numba==0.60.0
+llvmlite==0.43.0
+pandas<3.0,>=2.0
+matplotlib<4.0,>=3.7
+requests>=2.31
+scipy==1.16.3
+scikit-learn==1.6.1
+faiss-cpu==1.14.3
+seaborn==0.13.2
+tqdm>=4.66
+adjustText>=0.8
+symphonypy==0.2.4
+igraph==1.0.0
+leidenalg==0.12.0

zmap_tools-0.2.2/src/zmap_tools.egg-info/requires.txt

@@ -1,13 +0,0 @@
-anndata>=0.10
-scanpy>=1.9
-numpy>=1.24
-pandas<3.0,>=2.0
-matplotlib>=3.7
-requests>=2.31
-scipy>=1.10
-scikit-learn>=1.3
-faiss-cpu>=1.8
-seaborn>=0.12
-tqdm>=4.66
-adjustText>=0.8
-symphonypy>=0.2