risk-network 0.0.3b2__py3-none-any.whl → 0.0.3b4__py3-none-any.whl

risk/__init__.py

@@ -10,4 +10,4 @@ RISK: RISK Infers Spatial Kinship
 
 from risk.risk import RISK
 
-__version__ = "0.0.3-beta.2"
+__version__ = "0.0.3-beta.4"

risk/log/params.py

@@ -147,14 +147,11 @@ class Params:
         params = self.load()
         # Open the file in write mode
         with open(filepath, "w") as txt_file:
-            for key, nested_dict in params.items():
-                # Write the key
-                txt_file.write(f"{key}:\n")
-                # Write the nested dictionary values, one per line
-                for nested_key, nested_value in nested_dict.items():
-                    txt_file.write(f"  {nested_key}: {nested_value}\n")
-                # Add a blank line between different keys
-                txt_file.write("\n")
+            for key, value in params.items():
+                # Write the key and its corresponding value
+                txt_file.write(f"{key}: {value}\n")
+            # Add a blank line after each entry
+            txt_file.write("\n")
 
     def load(self) -> Dict[str, Any]:
         """Load and process various parameters, converting any np.ndarray values to lists.

risk/stats/stats.py

@@ -153,9 +153,11 @@ def _run_permutation_test(
             results = pool.starmap_async(_permutation_process_subset, params_list)
 
             # Update progress bar based on progress_counter
+            # NOTE: Waiting for results to be ready while updating progress bar gives a big improvement
+            # in performance, especially for large number of permutations and workers
             while not results.ready():
                 progress.update(progress_counter.value - progress.n)
-                results.wait(0.1)
+                results.wait(1)  # Wait for 1 second
 
             # Ensure progress bar reaches 100%
             progress.update(total_progress - progress.n)

{risk_network-0.0.3b2.dist-info → risk_network-0.0.3b4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.3b2
+Version: 0.0.3b4
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.3b2.dist-info → risk_network-0.0.3b4.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=H7Oal2XxdwvgwfVdxjsgEpAPdyruGRh2shgYLfJXFCs,122
+risk/__init__.py,sha256=7JTz-sr7kIgP1-2x6p8-HirKCr90zZTsy-gIbKdeYMw,122
 risk/constants.py,sha256=AICk3x5qRQhls_ijTb4VdbdxU6mZ1aLGbAjLEdBwfJI,550
 risk/risk.py,sha256=cWpYogZ-vma4ZZjewVNRMzb2TqHv8YABuzP2brXpOqo,16399
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
@@ -6,7 +6,7 @@ risk/annotations/annotations.py,sha256=gZ9gihK_eTWaX3eByh08xr97FX4-XKe6MBwCCjasE
 risk/annotations/io.py,sha256=ozi7aFn3_geB6G0kt7Ya1qVhNOqP6rB0YISjriSZyNw,7989
 risk/log/__init__.py,sha256=xuLImfxFlKpnVhzi_gDYlr2_c9cLkrw2c_3iEsXb1as,107
 risk/log/console.py,sha256=im9DRExwf6wHlcn9fewoDcKIpo3vPcorZIaNAl-0csY,355
-risk/log/params.py,sha256=VI52p9zlHptm-m05QBO1cBVZKn6rZA_QKBgDuZQhXY0,6494
+risk/log/params.py,sha256=Tbb-sovFTptGBqPDKafUA8KOpby4zFObutAT_Iti1hE,6302
 risk/neighborhoods/__init__.py,sha256=tKKEg4lsbqFukpgYlUGxU_v_9FOqK7V0uvM9T2QzoL0,206
 risk/neighborhoods/community.py,sha256=eL2IGT-8sbiJIyfyb_FGngev7pEMxw7tZb8YzbzOYw8,6512
 risk/neighborhoods/domains.py,sha256=HwuChmZH0RGD9eQOvk2-ezQDJRUHHn93vhVgHb-kX6I,10192
@@ -18,9 +18,9 @@ risk/network/io.py,sha256=KmdrsDZe-ZT4O59NYZM_nQd8Ew9qpbzQcqWS_PaE7eA,12559
 risk/network/plot.py,sha256=fy21X677xqJPFkn564Jegxy05C9x0pJXovd5fm3NZ4Q,34554
 risk/stats/__init__.py,sha256=4s9gdJo5B1G_cQc0iMoeIBt5OrQNXkdtNXkAMFQkLxc,103
 risk/stats/permutation.py,sha256=xgaZbaxo57t_FzPlpcb2nsq8oCzc_wj-zAm-xj3P2dA,3404
-risk/stats/stats.py,sha256=_3Fj5H8Nml4cExvLg7Mt_i1HCLAJJcJSDiiSzr3uFlo,15798
-risk_network-0.0.3b2.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.3b2.dist-info/METADATA,sha256=y75hZFuUFJ99JoFX2koM3Xf_aI28MKXxiFKHV8iV4yw,43256
-risk_network-0.0.3b2.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-risk_network-0.0.3b2.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.3b2.dist-info/RECORD,,
+risk/stats/stats.py,sha256=Yu9LMSUtCRkg-h0ErJurb-rkajHgTvdzBcymHldJs5k,16007
+risk_network-0.0.3b4.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.3b4.dist-info/METADATA,sha256=_xhdIlmS0XAYJWRI1yjQppksLevhfTX_wFjKzX5hf9Q,43256
+risk_network-0.0.3b4.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+risk_network-0.0.3b4.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.3b4.dist-info/RECORD,,