pymbar4 #268
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pymbar4 #268
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Codecov Report
@@ Coverage Diff @@
## master #268 +/- ##
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+ Coverage 98.70% 98.74% +0.03%
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Files 26 26
Lines 1777 1747 -30
Branches 382 380 -2
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- Hits 1754 1725 -29
+ Misses 3 2 -1
Partials 20 20
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My suggestion: For right now, make a parallel branch. If there are any fixes for 1.0 that we want/need to make then I'd rather keep these in the standard master branch. Once we have a 1.0.x out, we'll make a 1.x legacy branch for any potential support pymbar3-alchemlyb and switch master to pymbar4. |
orbeckst
requested changes
Nov 7, 2022
| When a specific method is set, AutoMBAR will behave in the same way | ||
| as MBAR. | ||
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| .. versionadded:: 1.0.0 |
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create issue & a PR with deprecation of AutoMBAR
Closed
orbeckst
reviewed
Dec 9, 2022
devtools/conda-envs/test_env.yaml
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| @@ -5,7 +5,7 @@ dependencies: | |||
| - python | |||
| - numpy | |||
| - pandas | |||
| - pymbar >=3.0.5,<4 | |||
| - pymbar>4 | |||
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needs to be
Suggested change
| - pymbar>4 | |
| - pymbar >=4 |
orbeckst
reviewed
Dec 9, 2022
environment.yml
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| @@ -5,7 +5,7 @@ dependencies: | |||
| - python=3.8 | |||
| - numpy | |||
| - pandas | |||
| - pymbar >=3.0.5,<4 | |||
| - pymbar>4 | |||
orbeckst
reviewed
Dec 9, 2022
setup.py
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| @@ -44,6 +44,6 @@ | |||
| long_description_content_type='text/x-rst', | |||
| python_requires='>=3.8', | |||
| tests_require = ['pytest', 'alchemtest'], | |||
| install_requires=['numpy', 'pandas>=1.4', 'pymbar>=3.0.5,<4', | |||
| install_requires=['numpy', 'pandas>=1.4', 'pymbar>4', | |||
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Have to do >=4. Otherwise, I will be getting
Processing /home/docs/checkouts/readthedocs.org/user_builds/alchemlyb/checkouts/268
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: numpy in /home/docs/checkouts/readthedocs.org/user_builds/alchemlyb/conda/268/lib/python3.11/site-packages (from alchemlyb==1.0.1+13.g52762bf.dirty) (1.23.5)
Requirement already satisfied: pandas>=1.4 in /home/docs/checkouts/readthedocs.org/user_builds/alchemlyb/conda/268/lib/python3.11/site-packages (from alchemlyb==1.0.1+13.g52762bf.dirty) (1.5.2)
ERROR: Ignored the following versions that require a different python version: 1.21.2 Requires-Python >=3.7,<3.11; 1.21.3 Requires-Python >=3.7,<3.11; 1.21.4 Requires-Python >=3.7,<3.11; 1.21.5 Requires-Python >=3.7,<3.11; 1.21.6 Requires-Python >=3.7,<3.11
ERROR: Could not find a version that satisfies the requirement pymbar==4 (from alchemlyb) (from versions: 2.0.0b0, 2.0.1b0, 2.1.0b0, 3.0.dev3, 3.0.2, 3.0.3, 3.0.4, 3.0.5, 3.1.0, 4.0.1)
ERROR: No matching distribution found for pymbar==4
orbeckst
reviewed
Dec 9, 2022
| .. versionadded:: 0.6.0 | ||
| .. versionchanged:: 1.0.0 | ||
| The ``estimator`` accepts uppercase input. | ||
| The default for using ``estimator='MBAR'`` was changed from | ||
| :class:`~alchemlyb.estimators.MBAR` to :class:`~alchemlyb.estimators.AutoMBAR`. | ||
| .. versionchanged:: 2.0.0 | ||
| Use pymbar.MBAR instead of the AutoMBAR option. |
orbeckst
reviewed
Dec 9, 2022
src/alchemlyb/estimators/mbar_.py
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| @@ -158,7 +141,7 @@ def overlap_matrix(self): | |||
| --------- | |||
| pymbar.mbar.MBAR.computeOverlap | |||
| """ | |||
| return self._mbar.computeOverlap()["matrix"] | |||
| return self._mbar.compute_overlap()["matrix"] | |||
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| class AutoMBAR(MBAR): | |||
orbeckst
reviewed
Dec 9, 2022
src/alchemlyb/estimators/mbar_.py
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| @@ -1,4 +1,5 @@ | |||
| import logging | |||
| from warnings import warn | |||
orbeckst
approved these changes
Dec 12, 2022
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alchemlyb development is now officially 2.x |
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This PR allows the alchemlyb to use pymbar4. Fix #207
Should we make a dev branch for it or just merge to master?