guts-base 1.0.4__py3-none-any.whl → 1.0.5__py3-none-any.whl

guts_base/__init__.py

@@ -4,7 +4,7 @@ from . import data
 from . import prob
 from . import plot
 
-__version__ = "1.0.4"
+__version__ = "1.0.5"
 
 from .sim import (
     GutsBase,

guts_base/sim/base.py

@@ -812,17 +812,15 @@ class GutsBase(SimulationBase):
         still be some problems down the line.
         """
         with warnings.catch_warnings(action="ignore"):
-            # using the context manager here will not work, because it will prematurely
-            # remove the tempdir and its contents. This interacts badly with netcdf files.
-            # which are only transferred into memory when the contents are needed. 
-            tempdir = tempfile.TemporaryDirectory()
-            self.export(directory=tempdir.name)
-            print(os.listdir(tempdir.name))
-            sim_copy = type(self).from_directory(tempdir.name)
-
-            # set this attribute so that it can be cleaned up after the copied sim is
-            # no longer necessary.
-            sim_copy.tempdir = tempdir
+            # create the tempdir in the output path, because on the remote cluster
+            # the default temporary directory may not have enough space. Using the output
+            # path here resolves any path issues.
+            tmp_basedir = os.path.join(self.output_path, "tmp")
+            os.makedirs(tmp_basedir, exist_ok=True)
+            with tempfile.TemporaryDirectory(dir=tmp_basedir) as name:
+                self.export(directory=name)
+                print(f"Exported files ({name}):", os.listdir(name))
+                sim_copy = type(self).from_directory(name)
 
         return sim_copy
 

guts_base/sim/ecx.py

@@ -112,11 +112,6 @@ class ECxEstimator:
 
         self.condition_posterior_parameters(conditions=conditions_posterior)
 
-    def __del__(self):
-        if hasattr(self.sim, "tempdir"):
-            self.sim.tempdir.cleanup()
-
-
     def _assert_posterior(self):
         try:
             p = self.sim.inferer.idata.posterior

guts_base/sim/report.py

@@ -105,12 +105,6 @@ class GutsReport(Report):
 
             ecx.append(ecx_estimator.results.copy(deep=True))
             
-            # remove ecx_estimator to not blow up temp files.
-            # This triggers the __del__ method of ECxEstimator,
-            # which cleans up a temporary directory if it was
-            # created during init
-            del ecx_estimator
-
         results = pd.DataFrame(ecx)
         estimates[results.columns] = results
 

{guts_base-1.0.4.dist-info → guts_base-1.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: guts_base
-Version: 1.0.4
+Version: 1.0.5
 Summary: Basic GUTS model implementation in pymob
 Author-email: Florian Schunck <fluncki@protonmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{guts_base-1.0.4.dist-info → guts_base-1.0.5.dist-info}/RECORD

@@ -1,4 +1,4 @@
-guts_base/__init__.py,sha256=xW56Yo4_P0LRfBpKaMEOwnTnZsmTajA4breTU1mVad0,227
+guts_base/__init__.py,sha256=h51lqbwq425YF40jI1Cw6dT0CXtcO_WSrvxbmb1KA3U,227
 guts_base/mod.py,sha256=AzOCg1A8FP5EtVfp-66HT7G7h_wnHkenieaxTc9qCyk,5796
 guts_base/plot.py,sha256=Sr_d0sXHNajPLPelcGl72yCOEEqB7NGNWhViKYAiTng,6692
 guts_base/prob.py,sha256=ITwo5dAGMHr5xTldilHMbKU6AFsWo4_ZwbfaXh97Gew,5443
@@ -11,15 +11,15 @@ guts_base/data/survival.py,sha256=U-Ehloo8vnD81VeIglXLEUHX9lt7SjtEs2YEB0D9FHE,50
 guts_base/data/time_of_death.py,sha256=hwngUwfRP3u8WmD3dHyXrphuu5d8ZJTKyBovGRwAHNQ,21014
 guts_base/data/utils.py,sha256=u3gGDJK15MfRUP4iIxsS-I1oqxD2qH_ugsT7o_Eac18,236
 guts_base/sim/__init__.py,sha256=sbHmT1p2saN0MJ-iYnCDOHjkHtTcKgm7X-dHX5o0tYA,435
-guts_base/sim/base.py,sha256=XKW2_bFxb4oUdyb2Y8dfFLQ_mLmJhaHmqfhHyp97240,37788
+guts_base/sim/base.py,sha256=mYHRDS6KKOrTzgsTAy5IKcVn6zIhqJH9EY9dFrsY0So,37739
 guts_base/sim/constructors.py,sha256=Kz9FHIH3EHsSIKd9sQgHa3eveniFifFlk1Hf-QR69Pg,875
-guts_base/sim/ecx.py,sha256=QONOWuv2jvjq1UAwiojuvj_jJyxfz7haewASjj4oCbs,20913
+guts_base/sim/ecx.py,sha256=PeX8UVF1HMMNHaIU-jL6dml4JGezhWwiGSqPFJbOFM4,20808
 guts_base/sim/mempy.py,sha256=IHd87UrmdXpC7y7q0IjYQJH075frjbp2a-dMVBeqZ0U,10164
-guts_base/sim/report.py,sha256=__6BGnG6c3DJXNUO39R0WkMuf8A1PWAeTePThz7ydKo,7040
+guts_base/sim/report.py,sha256=Omm7czcnl3K-eWva_080uQi5RWzUrDxi7gYPjkNO_QM,6787
 guts_base/sim/utils.py,sha256=Qj_FPH6kywVxOwgCerS7w5CyuYR9HKmvBWFpmxwDFgk,256
-guts_base-1.0.4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-guts_base-1.0.4.dist-info/METADATA,sha256=fbcVvL249G1AjdaBQg8_ASjLhyKsnYqU1zv7rA20E4c,45426
-guts_base-1.0.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-guts_base-1.0.4.dist-info/entry_points.txt,sha256=icsHzG2jQ90ZS7XvLsI5Qj0-qGuPv2T0RBVN5daGCPU,183
-guts_base-1.0.4.dist-info/top_level.txt,sha256=PxhBgUd4r39W_VI4FyJjARwKbV5_glgCVnd6v_zAGdE,10
-guts_base-1.0.4.dist-info/RECORD,,
+guts_base-1.0.5.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+guts_base-1.0.5.dist-info/METADATA,sha256=TKQepymlj9INzwGyhPh3jZ37Zcm7BpULGR9L7FvhNR8,45426
+guts_base-1.0.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+guts_base-1.0.5.dist-info/entry_points.txt,sha256=icsHzG2jQ90ZS7XvLsI5Qj0-qGuPv2T0RBVN5daGCPU,183
+guts_base-1.0.5.dist-info/top_level.txt,sha256=PxhBgUd4r39W_VI4FyJjARwKbV5_glgCVnd6v_zAGdE,10
+guts_base-1.0.5.dist-info/RECORD,,