From f78df71d711cf7ea4db3380485277bd0a9500bdb Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 9 Mar 2025 22:04:34 +0000 Subject: [PATCH 1/3] Finalize v2.9.0 release --- package/CHANGELOG | 17 +++++++++-------- package/MDAnalysis/version.py | 2 +- package/setup.py | 2 +- testsuite/MDAnalysisTests/__init__.py | 2 +- testsuite/setup.py | 2 +- 5 files changed, 13 insertions(+), 12 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index 2d274537769..ca492cc42eb 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -14,15 +14,17 @@ The rules for this file: ------------------------------------------------------------------------------- -??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy, +03/09/25 IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy, marinegor, hmacdope, jauy123 * 2.9.0 Fixes * Add support for TPR files produced by GROMACS 2024.4 - * Fixes invalid default unit from Angstrom to Angstrom^{-3} for convert_density() function. (Issue #4829) - * Fixes deprecation warning Array to scalar convertion. Replaced atan2() with np.arctan2() (Issue #4339) + * Fixes invalid default unit from Angstrom to Angstrom^{-3} for + convert_density() function. (Issue #4829) + * Fixes deprecation warning Array to scalar convertion. Replaced atan2() + with np.arctan2() (Issue #4339) * Replaced mutable defaults with None and initialized them within the function to prevent shared state. (Issue #4655) @@ -30,19 +32,18 @@ Enhancements * Improve distopia backend support in line with new functionality available in distopia >= 0.3.1 (PR #4734) * Addition of 'water' token for water selection (Issue #4839) - * Enables parallelization for analysis.density.DensityAnalysis (Issue #4677, PR #4729) + * Enables parallelization for analysis.density.DensityAnalysi + (Issue #4677, PR #4729) * Enables parallelization for analysis.contacts.Contacts (Issue #4660) * Enable parallelization for analysis.nucleicacids.NucPairDist (Issue #4670) - * Add check and warning for empty (all zero) coordinates in RDKit converter (PR #4824) + * Add check and warning for empty (all zero) coordinates in RDKit converter + (PR #4824) * Added `precision` for XYZWriter (Issue #4775, PR #4771) - Changes * Changed `fasteners` dependency to `filelock` (Issue #4797, PR #4800) * Codebase is now formatted with black (version `24`) (PR #4886) -Deprecations - 11/11/24 IAlibay, HeetVekariya, marinegor, lilyminium, RMeli, ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder, diff --git a/package/MDAnalysis/version.py b/package/MDAnalysis/version.py index e8384ed3470..ae1e08d7646 100644 --- a/package/MDAnalysis/version.py +++ b/package/MDAnalysis/version.py @@ -67,4 +67,4 @@ # e.g. with lib.log #: Release of MDAnalysis as a string, using `semantic versioning`_. -__version__ = "2.9.0-dev0" # NOTE: keep in sync with RELEASE in setup.py +__version__ = "2.9.0" # NOTE: keep in sync with RELEASE in setup.py diff --git a/package/setup.py b/package/setup.py index 1158330e7a7..ff78776cad9 100755 --- a/package/setup.py +++ b/package/setup.py @@ -58,7 +58,7 @@ from subprocess import getoutput # NOTE: keep in sync with MDAnalysis.__version__ in version.py -RELEASE = "2.9.0-dev0" +RELEASE = "2.9.0" is_release = "dev" not in RELEASE diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py index 75acebf06be..79dcfdee90f 100644 --- a/testsuite/MDAnalysisTests/__init__.py +++ b/testsuite/MDAnalysisTests/__init__.py @@ -97,7 +97,7 @@ logger = logging.getLogger("MDAnalysisTests.__init__") # keep in sync with RELEASE in setup.py -__version__ = "2.9.0-dev0" +__version__ = "2.9.0" # Do NOT import MDAnalysis at this level. Tests should do it themselves. diff --git a/testsuite/setup.py b/testsuite/setup.py index 63629d88791..fcefe474202 100755 --- a/testsuite/setup.py +++ b/testsuite/setup.py @@ -75,7 +75,7 @@ def run(self): if __name__ == "__main__": # this must be in-sync with MDAnalysis - RELEASE = "2.9.0-dev0" + RELEASE = "2.9.0" setup( version=RELEASE, From 0ad9c0a0cda70cd8093196054621750e1b2ac536 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 10 Mar 2025 12:47:58 +0000 Subject: [PATCH 2/3] Update package/CHANGELOG Co-authored-by: Rocco Meli --- package/CHANGELOG | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index e9361d6c007..c3de1b8b396 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -32,7 +32,7 @@ Enhancements * Improve distopia backend support in line with new functionality available in distopia >= 0.3.1 (PR #4734) * Addition of 'water' token for water selection (Issue #4839) - * Enables parallelization for analysis.density.DensityAnalysi + * Enables parallelization for analysis.density.DensityAnalysis (Issue #4677, PR #4729) * Enables parallelization for analysis.contacts.Contacts (Issue #4660) * Enable parallelization for analysis.nucleicacids.NucPairDist (Issue #4670) From 169502417cc645d9bdeb71127eb5de5eb7e15a26 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Tue, 11 Mar 2025 09:22:32 +0000 Subject: [PATCH 3/3] Update CHANGELOG --- package/CHANGELOG | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index c3de1b8b396..7432e97502a 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -14,7 +14,7 @@ The rules for this file: ------------------------------------------------------------------------------- -03/09/25 IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy, +03/11/25 IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy, marinegor, hmacdope, jauy123, al42and * 2.9.0