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Release prep 1.4.0 (#1253)

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* Updated CHANGELOG for 1.4.0

* changing a word

* fixing formatting

* adding links (thanks mike)

* adding links

* adding description

* updating changelog
This commit is contained in:
Alyssa Travitz
2025-04-25 07:02:27 -07:00
committed by GitHub
parent b6c7f19c81
commit 9296aa7fb0
7 changed files with 31 additions and 151 deletions
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42
docs/CHANGELOG.rst
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@@ -4,6 +4,26 @@ Changelog
.. current developments
v1.4.0
====================
This release includes significant quality of life improvements for the CLI's ``openfe gather`` command.
**Added:**
* ``openfe gather`` now accepts any number of filepaths and/or directories containing results JSON files, instead of only accepting one results directory (`PR #1212 <https://github.com/OpenFreeEnergy/openfe/pull/1212>`_).
* When running ``openfe gather --report=dg`` and result edges have fewer than 2 replicates, an error will be thrown up-front instead of failing downstream with a ``numpy.linalg.LinAlgError: SVD did not converge`` error (`PR #1243 <https://github.com/OpenFreeEnergy/openfe/pull/1243>`_).
* ``openfe gather`` includes failed simulations in its output, with ``Error`` listed in place of a computed value, instead of simply omitting those results from the output table (`PR #1227 <https://github.com/OpenFreeEnergy/openfe/pull/1227>`_).
* ``openfe gather --report=dg`` (the default) checks for connectivity of the results network and throws an error if the network is disconnected or has fewer than 3 edges (`PR #1227 <https://github.com/OpenFreeEnergy/openfe/pull/1227>`_).
* ``openfe gather`` prints warnings for all results JSONs whose simulations have failed or are otherwise invalid (`PR #1227 <https://github.com/OpenFreeEnergy/openfe/pull/1227>`_ ).
* ``openfe gather`` now throws an error up-front if no valid results are provided, instead of returning an empty table (`PR #1245 <https://github.com/OpenFreeEnergy/openfe/pull/1245>`_).
**Changed:**
* Improved formatting of ``openfe gather`` output tables. Use ``--tsv`` to instead view the raw tsv formatted output (this was the default behavior as of v1.3.x) (`PR #1246 <https://github.com/OpenFreeEnergy/openfe/pull/1246>`_).
* Improved responsiveness of several CLI commands (`PR #1254 <https://github.com/OpenFreeEnergy/openfe/pull/1254>`_).
v1.3.1
====================
Bugfix release - Improved error handling and code cleanup.
@@ -13,21 +33,21 @@ Any platform-specific bugs will be addressed when possible, but as a low priorit
**Added:**
* ``openfe gather`` now detects failed simulations up-front and prints warnings to stdout (PR #1207).
* ``openfe gather`` now detects failed simulations up-front and prints warnings to stdout (`PR #1207 <https://github.com/OpenFreeEnergy/openfe/pull/1207>`_).
**Changed:**
* Temporarily disabled bootstrap uncertainties in forward/reverse analysis due to solver loop issues when dealing with too small a set of samples (PR #1174).
* Temporarily disabled bootstrap uncertainties in forward/reverse analysis due to solver loop issues when dealing with too small a set of samples (`PR #1174 <https://github.com/OpenFreeEnergy/openfe/pull/1174>`_).
**Removed:**
* Dropped official support for MacOSX-x86_64. Any platform-specific bugs will be addressed when possible, but as a low priority.
* Unused trajectory handling code was removed from ``openfe.utils``, please use ``openfe-analysis`` instead (PR #1182).
* Unused trajectory handling code was removed from ``openfe.utils``, please use ``openfe-analysis`` instead (`PR #1182 <https://github.com/OpenFreeEnergy/openfe/pull/1182>`_).
**Fixed:**
* Fixed issue #1178 -- The GPU system probe is now more robust to different ways the ``nvidia-smi`` command can fail (PR #1186)
* Fixed bug where openmm protocols using default settings would re-load from JSON as a different gufe key due to unit name string representation discrepancies (PR #1210)
* Fixed `issue #1178 <https://github.com/OpenFreeEnergy/openfe/issues/1178>`_ -- The GPU system probe is now more robust to different ways the ``nvidia-smi`` command can fail (`PR #1186 <https://github.com/OpenFreeEnergy/openfe/pull/1186>`_)
* Fixed bug where openmm protocols using default settings would re-load from JSON as a different gufe key due to unit name string representation discrepancies (`PR #1210 <https://github.com/OpenFreeEnergy/openfe/pull/1210>`_)
v1.3.0
@@ -93,23 +113,23 @@ v1.1.0
* The `PersesAtomMapper` now uses openff.units inline with the rest of the package.
* Structural analysis data is no longer written to `structural_analysis.json`
but rather a 32bit numpy compressed file named `structural_analysis.npz`
(PR #937).
(`PR #937 <https://github.com/OpenFreeEnergy/openfe/pull/937>`_).
* Structural analysis array data is no longer directly returned in the
RelativeHybridTopologyProtocol result dictionary. Instead it should
be accessed from the serialized NPZ file `structural_analysis.npz`.
The `structural_analysis` key now contains a path to the NPZ file,
if the structural analysis did not fail (the `structural_analysis_error`
key will instead be present on failure) (PR #937).
key will instead be present on failure) (`PR #937 <https://github.com/OpenFreeEnergy/openfe/pull/937>`_).
* Add duecredit citations for pymbar when calling
`openfe.protocols.openmm_utils.multistate_analysis`.
**Fixed:**
* 2D RMSD plotting now allows for fewer than 5 states (PR #896).
* 2D RMSD plotting now allows for fewer than 5 states (`PR #896 <https://github.com/OpenFreeEnergy/openfe/pull/896>`_).
* 2D RMSD plotting no longer draws empty axes when
the number of states - 1 is not divisible by 4 (PR #896).
the number of states - 1 is not divisible by 4 (`PR #896 <https://github.com/OpenFreeEnergy/openfe/pull/896>`_).
* The RelativeHybridTopologyProtocol result unit is now much smaller,
due to the removal of structural analysis data (PR #937).
due to the removal of structural analysis data (`PR #937 <https://github.com/OpenFreeEnergy/openfe/pull/937>`_).
@@ -131,6 +151,6 @@ v1.0.1
* Calling `get_forward_and_reverse_energy_analysis` in the RFE and AFE protocols now results a warning if any results are ``None`` due to MBAR convergence issues.
* Checkpoint interval default value has been set to 250 ps instead of 1 ps.
This better matches the previous default for openfe versions < 1.0rc
(See issue #772).
(See `issue #772 <https://github.com/OpenFreeEnergy/openfe/issues/772>`_ ).

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news/add_filepaths_support.rst
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@@ -1,23 +0,0 @@
**Added:**
* ``openfe gather`` now accepts any number of filepaths and/or directories containing results JSON files, instead of only accepting one results directory.
**Changed:**
* <news item>
**Deprecated:**
* <news item>
**Removed:**
* <news item>
**Fixed:**
* <news item>
**Security:**
* <news item>

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news/cli_responsiveness.rst
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@@ -1,23 +0,0 @@
**Added:**
* <news item>
**Changed:**
* Improved responsiveness of several CLI commands (`PR #1254 <https://github.com/OpenFreeEnergy/openfe/pull/1254>`_).
**Deprecated:**
* <news item>
**Removed:**
* <news item>
**Fixed:**
* <news item>
**Security:**
* <news item>

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news/error_handling_for_single_repeat_dgs.rst
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@@ -1,23 +0,0 @@
**Added:**
* When running ``openfe gather`` with ``--report=dg`` and result edges have fewer than 2 replicates, an error will be thrown up-front instead of failing downstream with a ```numpy.linalg.LinAlgError: SVD did not converge`` error.
**Changed:**
* <news item>
**Deprecated:**
* <news item>
**Removed:**
* <news item>
**Fixed:**
* <news item>
**Security:**
* <news item>

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news/failed_sims_passthrough.rst
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@@ -1,25 +0,0 @@
**Added:**
* ``openfe gather`` includes failed simulations in its output, with ``Error`` listed instead of a computed value, instead of simply omitting those results from the output table.
* ``openfe gather --report=dg`` (the default) checks for connectivity of the results network and throws an error if the network is disconnected or has fewer than 3 edges.
* `openfe gather` prints warnings for all results JSONs whose simulations have failed or are otherwise invalid.
**Changed:**
<news item>
*
**Deprecated:**
* <news item>
**Removed:**
* <news item>
**Fixed:**
* <news item>
**Security:**
* <news item>

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news/no_results_error.rst
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@@ -1,23 +0,0 @@
**Added:**
* `openfe gather` now throws an error up-front if no valid results are provided, instead of returning an empty table (PR #1245).
**Changed:**
* <news item>
**Deprecated:**
* <news item>
**Removed:**
* <news item>
**Fixed:**
* <news item>
**Security:**
* <news item>

23
news/pretty_print.rst
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@@ -1,23 +0,0 @@
**Added:**
* <news item>
**Changed:**
* Improved formatting of ``openfe gather`` output tables. Use ``--tsv`` to instead view the raw tsv formatted output (this was the default behavior as of v1.3.x)
**Deprecated:**
* <news item>
**Removed:**
* <news item>
**Fixed:**
* <news item>
**Security:**
* <news item>