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Remove deprecated get method calls #238

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merged 18 commits into from
Mar 18, 2023

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@t-young31 t-young31 commented Jan 22, 2023

Resolves #217


Checklist

  • Rebase onto master when v1.3.5 is merged
  • The changes include an associated explanation of how/why
  • Test pass
  • Documentation has been updated

t-young31 and others added 3 commits January 15, 2023 11:46
…ing (duartegroup#202)

* make autode compatible with windows: replace multiprocessing with joblib and loky

* remove comment autode/utils.py

* check total memory in utils

* use loky for parallel processing

* loky context is used for better handling of parallelisation

* fixes for timeout wrapper in POSIX

* use class instances instead of class attributes for Config

* pass parent Config state into child processes

* keep default timeout wrapper, also add new wrapper

* separate parallelisation scheme for windows, restore default for linux/mac

* fix test_config_in_worker_proc for posix

* codecov on windows

* add tests for config copy

* change config implementation for updating in worker process

* add context manager for temporary config, minor fix in experimental timeout for windows

* add tests for context manager

* use bash for installing xtb in CI runner

* add tests for cleanup after timeout

* exclude setup.py from codecov

* make config picklable and easily readable

* add test and minor fixes

* move xtb install script to .github/scripts

* use temporary_config for test_utils.py

* update changelog and contributor list

* resolve conflicts with v1.4.0

Co-authored-by: Tom Young <39765193+t-young31@users.noreply.github.com>
@t-young31 t-young31 changed the base branch from master to v1.4.0 January 22, 2023 17:42
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codecov bot commented Jan 31, 2023

Codecov Report

Merging #238 (6c4156c) into v1.4.0 (1f42142) will increase coverage by 0.36%.
The diff coverage is 97.18%.

@@            Coverage Diff             @@
##           v1.4.0     #238      +/-   ##
==========================================
+ Coverage   96.86%   97.22%   +0.36%     
==========================================
  Files         195      195              
  Lines       20403    20392      -11     
==========================================
+ Hits        19763    19827      +64     
+ Misses        640      565      -75     
Flag Coverage Δ
unittests 97.22% <97.18%> (+0.36%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
autode/calculations/calculation.py 99.11% <ø> (-0.21%) ⬇️
autode/transition_states/transition_state.py 70.12% <22.22%> (-4.55%) ⬇️
autode/neb/original.py 95.97% <96.96%> (-1.73%) ⬇️
autode/__init__.py 100.00% <100.00%> (ø)
autode/constraints.py 98.78% <100.00%> (+0.07%) ⬆️
autode/neb/ci.py 82.60% <100.00%> (-1.84%) ⬇️
autode/neb/idpp.py 100.00% <100.00%> (ø)
autode/neb/neb.py 100.00% <100.00%> (ø)
autode/opt/optimisers/dimer.py 98.03% <100.00%> (-0.02%) ⬇️
autode/path/__init__.py 100.00% <100.00%> (ø)
... and 19 more

... and 8 files with indirect coverage changes

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@t-young31 t-young31 marked this pull request as ready for review February 26, 2023 20:52
autode/neb/original.py Outdated Show resolved Hide resolved
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@shoubhikraj shoubhikraj left a comment

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I haven't found any other issue/suggestion from two revisions, so I am approving. But I may have missed something as there were lots of changes made.

@t-young31 t-young31 enabled auto-merge (squash) March 18, 2023 13:44
@t-young31 t-young31 disabled auto-merge March 18, 2023 13:44
@t-young31 t-young31 merged commit 784b579 into duartegroup:v1.4.0 Mar 18, 2023
@t-young31 t-young31 deleted the remove_calc_get_method_calls branch March 18, 2023 13:46
shoubhikraj added a commit to shoubhikraj/autodE that referenced this pull request Mar 23, 2023
* Removal of deprecated functions [skip actions]

* Add force constant [skip actions]

* NEB refactoring

* Fix units for div mul

* Update changelog

* PR suggestions

---------

Co-authored-by: Shoubhik Maiti <17470159+shoubhikraj@users.noreply.github.com>
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Remove ade.Calculation.get_<X>
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