Maybe fix history - result reconstruction mismatch (#902)

* tidy up .flake8

* tidy up tox.ini

* add none-ness and close-ness utility functions

* extend constants file

* simplify+doc test/base/test_store

* simplify pypest/optimize: suffixes, error types

* declare history error types

* add typehints to fun/res conversion functions

* minor edits pypest/objective/base

* fix history/optimizer result mismatch

* fixup

* python 3.8 does not conform

* Update pypesto/objective/util.py

Co-authored-by: Fabian Fröhlich <fabian_froehlich@hms.harvard.edu>

* Update pypesto/objective/util.py

Co-authored-by: Fabian Fröhlich <fabian_froehlich@hms.harvard.edu>

* apply suggestions from code review

* increase timeout

* flake8 seems to be tmp slow

Co-authored-by: Fabian Fröhlich <fabian_froehlich@hms.harvard.edu>

.flake8

@@ -9,6 +9,14 @@ extend-ignore =
   E203
   # Don't be crazy if line too long
   E501
+  # Missing docstring in public module
+  D100
+  # Missing docstring in public method
+  # D102
+  # Missing docstring in magic method
+  D105
+  # Missing docstring in __init__
+  D107
 
 per-file-ignores =
     # Imported but unused
@@ -20,7 +28,3 @@ per-file-ignores =
     pypesto/problem.py:D400,D205,D107
     pypesto/util.py:D400,D205,D107
     pypesto/C.py:D400,D205,D107
-    pypesto/version.py:D
-    # ignore D100='Missing docstring in public module',
-    # D105='Missing docstring in magic method' and D107='Missing docstring in __init__'.
-    *:D100,D105,D107

.github/workflows/ci.yml

@@ -37,7 +37,7 @@ jobs:
       run: .github/workflows/install_deps.sh amici
 
     - name: Run tests
-      timeout-minutes: 12
+      timeout-minutes: 15
       run: tox -e base
 
     - name: Coverage
@@ -176,7 +176,7 @@ jobs:
       run: tox -e size
 
     - name: Run quality checks
-      timeout-minutes: 1
+      timeout-minutes: 5
       run: tox -e project,flake8
 
     - name: Run pre-commit hooks

pypesto/C.py

@@ -34,8 +34,21 @@
 X0 = 'x0'
 ID = 'id'
 
-EXITFLAG = 'exitflag'
-MESSAGE = 'message'
+
+###############################################################################
+# HISTORY
+
+HISTORY = "history"
+TRACE = "trace"
+N_ITERATIONS = "n_iterations"
+MESSAGES = "messages"
+MESSAGE = "message"
+EXITFLAG = "exitflag"
+TRACE_SAVE_ITER = "trace_save_iter"
+
+SUFFIXES_CSV = ["csv"]
+SUFFIXES_HDF5 = ["hdf5", "h5"]
+SUFFIXES = SUFFIXES_CSV + SUFFIXES_HDF5
 
 
 ###############################################################################
@@ -166,7 +179,7 @@ class EnsembleType(Enum):
 
 
 ###############################################################################
-# Environment variables
+# ENVIRONMENT VARIABLES
 
 PYPESTO_MAX_N_STARTS: str = "PYPESTO_MAX_N_STARTS"
 PYPESTO_MAX_N_SAMPLES: str = "PYPESTO_MAX_N_SAMPLES"

pypesto/objective/__init__.py

@@ -11,10 +11,12 @@
 from .function import Objective
 from .history import (
     CsvHistory,
+    CsvHistoryTemplateError,
     Hdf5History,
     History,
     HistoryBase,
     HistoryOptions,
+    HistoryTypeError,
     MemoryHistory,
     OptimizerHistory,
 )

pypesto/objective/base.py

@@ -226,7 +226,6 @@ def call_unprocessed(
         result:
             A dict containing the results.
         """
-        raise NotImplementedError()
 
     def check_mode(self, mode: ModeType) -> bool:
         """
@@ -405,15 +404,13 @@ def update_from_problem(
             Vector of the same length as x_fixed_indices, containing the values
             of the fixed parameters.
         """
-        pre_post_processor = FixedParametersProcessor(
+        self.pre_post_processor = FixedParametersProcessor(
             dim_full=dim_full,
             x_free_indices=x_free_indices,
             x_fixed_indices=x_fixed_indices,
             x_fixed_vals=x_fixed_vals,
         )
 
-        self.pre_post_processor = pre_post_processor
-
     def check_grad_multi_eps(
         self,
         *args,