From 546f71fa1416582036ea78595fb5adba8b2f6c2a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Iv=C3=A1n=20Pulido?= Date: Tue, 2 Aug 2022 16:47:31 -0400 Subject: [PATCH 1/3] Release 0.21.5 - bugfix release candidate. Added entries in changelog. --- docs/releasehistory.rst | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst index 7a1b5a96..ceef34fd 100644 --- a/docs/releasehistory.rst +++ b/docs/releasehistory.rst @@ -6,7 +6,7 @@ Release History Changed behaviors ----------------- -- ``LangevinDynamicsMove`` now uses ``openmm.LangevinMiddleIntegrator`` (a BAOAB integrator) instead of `openmm.LangevinIntegrator`` (an OBABO integrator). +- ``LangevinDynamicsMove`` now uses ``openmm.LangevinMiddleIntegrator`` (a BAOAB integrator) instead of ``openmm.LangevinIntegrator`` (an OBABO integrator). (`Issue #599 `_) (`PR #600 `_) Bugfixes @@ -15,6 +15,13 @@ Bugfixes - Bug in equilibration detection #1: The user was allowed to specify ``statistical_inefficiency`` without specifying ``n_equilibration_iterations``, which doesn't make sense, as ``n_equilibration_iterations`` and ``n_effective_max`` cannot be computed from ``statistical_inefficiency`` alone. Fixed by preventing user from specifying ``statistical_inefficiency`` without ``n_equilibration_iterations``. Issue `#609 `_ (PR `#610 `_). - Bug in equilibration detection #2: If the user specified ``n_equilibration_iterations`` but not ``statistical_inefficiency``, the returned ``n_equilibration_iterations`` did not include number of equilibration iterations as computed from ``_get_equilibration_data_per_sample()``. Fixed by always including the ``_get_equilibration_data_per_sample()`` result in in the returned ``n_equilibration_iterations``. Issue `#609 `_ (PR `#610 `_). - Bug in equilibration detection #3: ``get_equilibration_data_per_sample`` returns 0 for ``n_equilibration_iterations``. Fixed by always discarding the first time origin returned by ``get_equilibration_data_per_sample``. To control the amount of data discarded by the first time origin, the user can now specify ``max_subset`` when initializing ``MultiStateSamplerAnalyzer``. Issue `#609 `_ (PR `#610 `_). +- Bug when restoring serialized files generated by ``openmmtools<0.21.3``. Fixed by catching the ``KeyError`` exception when deserializing. Issue `#612 `_, PR `#613 `_. +- Bug in generating real time analysis output when reporter is in the same working directory. Fixed by using ``os.path.join`` for creating the output path. Issue `#615 `_, PR `#616 `_. + +Enhancements +------------ +- ``LangevinDynamicsMove`` now allows ``constraint_tolerance`` parameter and public attribute, for specifying the fraction of the constrained distance within which constraints are maintained for the integrator (Refer to `Openmm's documentation `_ for more information). Issue `#608 `_, PR `#611 `_. +- Platform is now reported in the logs in DEBUG mode. Issue `#583 `_, PR `#605 `_. 0.21.4 - Bugfix release ======================= From c3bbbe38b697c31b1e60919df346812112c979d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Iv=C3=A1n=20Pulido?= Date: Tue, 2 Aug 2022 19:02:08 -0400 Subject: [PATCH 2/3] More informative changelog entries. Updated pull request template to ask for a changelog message. --- .github/PULL_REQUEST_TEMPLATE.md | 5 +++++ docs/releasehistory.rst | 6 +++--- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 00cfe9c7..30655c9b 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -9,3 +9,8 @@ Provide a brief description of the PR's purpose here. ## Status - [ ] Ready to go + +## Changelog message +``` + +``` \ No newline at end of file diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst index ceef34fd..43491909 100644 --- a/docs/releasehistory.rst +++ b/docs/releasehistory.rst @@ -11,12 +11,12 @@ Changed behaviors Bugfixes -------- -- Bug in returning velocities when propagating replicas. Fixed by using ``ignore_velocities=False`` in ``_propagate_replica``. Issue `#531 `_ (PR `#602 `_). +- Velocities were being incorrectly updated as zeros when resuming simulations or broadcasting from different mpi processes. Fixed by specifying ``ignore_velocities=False`` in ``_propagate_replica``. Issue `#531 `_ (PR `#602 `_). - Bug in equilibration detection #1: The user was allowed to specify ``statistical_inefficiency`` without specifying ``n_equilibration_iterations``, which doesn't make sense, as ``n_equilibration_iterations`` and ``n_effective_max`` cannot be computed from ``statistical_inefficiency`` alone. Fixed by preventing user from specifying ``statistical_inefficiency`` without ``n_equilibration_iterations``. Issue `#609 `_ (PR `#610 `_). - Bug in equilibration detection #2: If the user specified ``n_equilibration_iterations`` but not ``statistical_inefficiency``, the returned ``n_equilibration_iterations`` did not include number of equilibration iterations as computed from ``_get_equilibration_data_per_sample()``. Fixed by always including the ``_get_equilibration_data_per_sample()`` result in in the returned ``n_equilibration_iterations``. Issue `#609 `_ (PR `#610 `_). - Bug in equilibration detection #3: ``get_equilibration_data_per_sample`` returns 0 for ``n_equilibration_iterations``. Fixed by always discarding the first time origin returned by ``get_equilibration_data_per_sample``. To control the amount of data discarded by the first time origin, the user can now specify ``max_subset`` when initializing ``MultiStateSamplerAnalyzer``. Issue `#609 `_ (PR `#610 `_). -- Bug when restoring serialized files generated by ``openmmtools<0.21.3``. Fixed by catching the ``KeyError`` exception when deserializing. Issue `#612 `_, PR `#613 `_. -- Bug in generating real time analysis output when reporter is in the same working directory. Fixed by using ``os.path.join`` for creating the output path. Issue `#615 `_, PR `#616 `_. +- Deserializing simulations from ``openmmtools<0.21.3`` versions resulted in error. Fixed by catching the missing key, ``KeyError`` exception, when deserializing. Issue `#612 `_, PR `#613 `_. +- Not specifying a subdirectory for the reporter file resulted in ``PermissionError`` when writing the real time analysis file. Fixed by using ``os.path.join`` for creating the output paths. Issue `#615 `_, PR `#616 `_. Enhancements ------------ From ed0f37aca553700843937436dea4df061c3259a5 Mon Sep 17 00:00:00 2001 From: Ivy Zhang <35546250+zhang-ivy@users.noreply.github.com> Date: Tue, 2 Aug 2022 20:11:48 -0400 Subject: [PATCH 3/3] fix formatting --- docs/releasehistory.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst index 43491909..7813c4b8 100644 --- a/docs/releasehistory.rst +++ b/docs/releasehistory.rst @@ -6,8 +6,7 @@ Release History Changed behaviors ----------------- -- ``LangevinDynamicsMove`` now uses ``openmm.LangevinMiddleIntegrator`` (a BAOAB integrator) instead of ``openmm.LangevinIntegrator`` (an OBABO integrator). - (`Issue #599 `_) (`PR #600 `_) +- ``LangevinDynamicsMove`` now uses ``openmm.LangevinMiddleIntegrator`` (a BAOAB integrator) instead of ``openmm.LangevinIntegrator`` (an OBABO integrator). Issue `#599 `_ (PR `#600 `_). Bugfixes --------