guts-base 1.0.2__tar.gz → 1.0.5__tar.gz

{guts_base-1.0.2 → guts_base-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: guts_base
-Version: 1.0.2
+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-1.0.2 → guts_base-1.0.5}/guts_base/__init__.py

@@ -4,7 +4,7 @@ from . import data
 from . import prob
 from . import plot
 
-__version__ = "1.0.2"
+__version__ = "1.0.5"
 
 from .sim import (
     GutsBase,

{guts_base-1.0.2 → guts_base-1.0.5}/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-1.0.2 → guts_base-1.0.5}/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-1.0.2 → guts_base-1.0.5}/guts_base/sim/report.py

@@ -14,6 +14,8 @@ from guts_base.sim.ecx import ECxEstimator
 class GutsReport(Report):
     ecx_estimates_times: List = [1, 2, 4, 10]
     ecx_estimates_x: List = [0.1, 0.25, 0.5, 0.75, 0.9]
+    ecx_draws: int = 250
+    ecx_force_draws: bool = False
     set_background_mortality_to_zero = True
 
     def additional_reports(self, sim: "SimulationBase"):
@@ -96,18 +98,13 @@ class GutsReport(Report):
             
             ecx_estimator.estimate(
                 mode=sim.ecx_mode,
-                draws=250,
+                draws=self.ecx_draws,
+                force_draws=self.ecx_force_draws,
                 show_plot=False
             )
 
             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-1.0.2 → guts_base-1.0.5}/guts_base.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: guts_base
-Version: 1.0.2
+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-1.0.2 → guts_base-1.0.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "guts_base"
-version = "1.0.2"
+version = "1.0.5"
 authors = [
   { name="Florian Schunck", email="fluncki@protonmail.com" },
 ]
@@ -49,7 +49,7 @@ import-openguts = "guts_base.data.openguts:create_database_and_import_data"
 convert-time-of-death-to-openguts = "guts_base.data.time_of_death:time_of_death_to_openguts"
 
 [tool.bumpver]
-current_version = "1.0.2"
+current_version = "1.0.5"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 tag_message = "{new_version}"