Merge branch 'devel'

Author: chryswoods

README.rst

@@ -37,23 +37,23 @@ Installation
 The easiest way to install Sire is using our `conda channel <https://anaconda.org/openbiosim/repo>`__.
 Sire is built using dependencies from `conda-forge <https://conda-forge.org/>`__,
 so please ensure that the channel takes strict priority. We recommend using
-`mambaforge <https://github.com/conda-forge/miniforge#mambaforge>`__.
+`miniforge3 <https://github.com/conda-forge/miniforge#miniforge3>`__.
 
 To create a new environment:
 
 .. code-block:: bash
 
-    mamba create -n openbiosim "python<3.11"
-    mamba activate openbiosim
-    mamba install -c conda-forge -c openbiosim sire
+    conda create -n openbiosim "python<3.12"
+    conda activate openbiosim
+    conda install -c conda-forge -c openbiosim sire
 
 To install the latest development version you can use:
 
 .. code-block:: bash
 
-    mamba create -n openbiosim-dev "python<3.11"
-    mamba activate openbiosim-dev
-    mamba install -c conda-forge -c openbiosim/label/dev sire
+    conda create -n openbiosim-dev "python<3.12"
+    conda activate openbiosim-dev
+    conda install -c conda-forge -c openbiosim/label/dev sire
 
 However, as you are here, it is likely you want to download the latest,
 greatest version of the code, which you will need to compile. To compile
@@ -65,32 +65,32 @@ First, you need to create and activate a conda environment, e.g.
 
 .. code-block:: bash
 
-    mamba create -n openbiosim-dev "python<3.11"
-    mamba activate openbiosim-dev
+    conda create -n openbiosim-dev "python<3.12"
+    conda activate openbiosim-dev
 
 Next, you need to install the Sire build dependencies.
 
 .. code-block:: bash
 
-    mamba install cmake pip-requirements-parser
+    conda install cmake pip-requirements-parser
 
 You will also need to install compilers, e.g. on Linux use
 
 .. code-block:: bash
 
-    mamba install gcc gxx
+    conda install gcc gxx
 
 on MacOS use
 
 .. code-block:: bash
 
-    mamba install clang clangxx
+    conda install clang clangxx
 
 and on Windows use
 
 .. code-block:: bash
 
-    mamba install conda-build
+    conda install conda-build
 
 Next, you can clone the sire source code and compile and install sire::
 

SECURITY.md

@@ -4,13 +4,13 @@
 
 As we have limited resource, we only support the latest major release
 of sire with security updates. For example, if the current version
-is 2023.1.0, then only versions 2023.1.0 to 2023.1.X wil have updates,
-which will be released as 2023.1.X+1.
+is 2023.5.0, then only versions 2023.5.0 to 2023.5.X wil have updates,
+which will be released as 2023.5.X+1.
 
 | Version | Supported          |
 | ------- | ------------------ |
-| 2023.1.x | :white_check_mark: |
-| < 2023.1.x| :x:                |
+| 2023.5.x | :white_check_mark: |
+| < 2023.5.x| :x:                |
 
 ## Reporting a Vulnerability
 

corelib/src/libs/SireCAS/lambdaschedule.cpp

@@ -56,6 +56,13 @@ QDataStream &operator<<(QDataStream &ds, const LambdaSchedule &schedule)
     return ds;
 }
 
+Symbol LambdaSchedule::lambda_symbol("λ");
+Symbol LambdaSchedule::initial_symbol("initial");
+Symbol LambdaSchedule::final_symbol("final");
+
+Expression LambdaSchedule::default_morph_equation = (1.0 - LambdaSchedule::lam()) * LambdaSchedule::initial() +
+                                                    LambdaSchedule::lam() * LambdaSchedule::final();
+
 QDataStream &operator>>(QDataStream &ds, LambdaSchedule &schedule)
 {
     VersionID v = readHeader(ds, r_schedule);
@@ -68,6 +75,21 @@ QDataStream &operator>>(QDataStream &ds, LambdaSchedule &schedule)
             schedule.lever_names >> schedule.stage_names >>
             schedule.default_equations >> schedule.stage_equations >>
             static_cast<Property &>(schedule);
+
+        for (auto &expression : schedule.default_equations)
+        {
+            if (expression == LambdaSchedule::default_morph_equation)
+                expression = LambdaSchedule::default_morph_equation;
+        }
+
+        for (auto &stage_equations : schedule.stage_equations)
+        {
+            for (auto &expression : stage_equations)
+            {
+                if (expression == LambdaSchedule::default_morph_equation)
+                    expression = LambdaSchedule::default_morph_equation;
+            }
+        }
     }
     else
         throw version_error(v, "1", r_schedule, CODELOC);
@@ -203,10 +225,6 @@ LambdaSchedule LambdaSchedule::charge_scaled_morph(double scale)
     return l;
 }
 
-Symbol LambdaSchedule::lambda_symbol("λ");
-Symbol LambdaSchedule::initial_symbol("initial");
-Symbol LambdaSchedule::final_symbol("final");
-
 /** Return the symbol used to represent the :lambda: coordinate.
  *  This symbol is used to represent the per-stage :lambda:
  *  variable that goes from 0.0-1.0 within that stage.
@@ -438,8 +456,7 @@ void LambdaSchedule::clear()
  */
 void LambdaSchedule::addMorphStage(const QString &name)
 {
-    this->addStage(name, (this->lam() * this->final()) +
-                             ((1 - this->lam()) * this->initial()));
+    this->addStage(name, default_morph_equation);
 }
 
 /** Append a morph stage onto this schedule. The morph stage is a
@@ -501,9 +518,14 @@ void LambdaSchedule::addChargeScaleStages(double scale)
 void LambdaSchedule::prependStage(const QString &name,
                                   const SireCAS::Expression &equation)
 {
+    auto e = equation;
+
+    if (e == default_morph_equation)
+        e = default_morph_equation;
+
     if (this->nStages() == 0)
     {
-        this->appendStage(name, equation);
+        this->appendStage(name, e);
         return;
     }
 
@@ -514,7 +536,7 @@ void LambdaSchedule::prependStage(const QString &name,
                                      CODELOC);
 
     this->stage_names.prepend(name);
-    this->default_equations.prepend(equation);
+    this->default_equations.prepend(e);
     this->stage_equations.prepend(QHash<QString, Expression>());
 }
 
@@ -532,8 +554,13 @@ void LambdaSchedule::appendStage(const QString &name,
                                          .arg(name),
                                      CODELOC);
 
+    auto e = equation;
+
+    if (e == default_morph_equation)
+        e = default_morph_equation;
+
     this->stage_names.append(name);
-    this->default_equations.append(equation);
+    this->default_equations.append(e);
     this->stage_equations.append(QHash<QString, Expression>());
 }
 
@@ -546,14 +573,19 @@ void LambdaSchedule::insertStage(int i,
                                  const QString &name,
                                  const SireCAS::Expression &equation)
 {
+    auto e = equation;
+
+    if (e == default_morph_equation)
+        e = default_morph_equation;
+
     if (i == 0)
     {
-        this->prependStage(name, equation);
+        this->prependStage(name, e);
         return;
     }
     else if (i >= this->nStages())
     {
-        this->appendStage(name, equation);
+        this->appendStage(name, e);
         return;
     }
 
@@ -564,7 +596,7 @@ void LambdaSchedule::insertStage(int i,
                                      CODELOC);
 
     this->stage_names.insert(i, name);
-    this->default_equations.insert(i, equation);
+    this->default_equations.insert(i, e);
     this->stage_equations.insert(i, QHash<QString, Expression>());
 }
 
@@ -605,7 +637,12 @@ int LambdaSchedule::find_stage(const QString &stage) const
 void LambdaSchedule::setDefaultEquation(const QString &stage,
                                         const Expression &equation)
 {
-    this->default_equations[this->find_stage(stage)] = equation;
+    auto e = equation;
+
+    if (e == default_morph_equation)
+        e = default_morph_equation;
+
+    this->default_equations[this->find_stage(stage)] = e;
 }
 
 /** Set the custom equation used to control the specified
@@ -617,12 +654,17 @@ void LambdaSchedule::setEquation(const QString &stage,
                                  const QString &lever,
                                  const Expression &equation)
 {
+    auto e = equation;
+
+    if (e == default_morph_equation)
+        e = default_morph_equation;
+
     auto &lever_expressions = this->stage_equations[this->find_stage(stage)];
 
     if (not this->lever_names.contains(lever))
         this->addLever(lever);
 
-    lever_expressions[lever] = equation;
+    lever_expressions[lever] = e;
 }
 
 /** Remove the custom equation for the specified `lever` at the
@@ -875,21 +917,31 @@ QVector<double> LambdaSchedule::morph(const QString &lever_name,
     const auto equation = this->stage_equations[stage].value(
         lever_name, this->default_equations[stage]);
 
-    Values input_values = this->constant_values;
-    input_values.set(this->lam(), std::get<1>(resolved));
-
     QVector<double> morphed(nparams);
-
     auto morphed_data = morphed.data();
     const auto initial_data = initial.constData();
     const auto final_data = final.constData();
 
-    for (int i = 0; i < nparams; ++i)
+    if (equation == default_morph_equation)
     {
-        input_values.set(this->initial(), initial_data[i]);
-        input_values.set(this->final(), final_data[i]);
+        for (int i = 0; i < nparams; ++i)
+        {
+            morphed_data[i] = (1.0 - lambda_value) * initial_data[i] +
+                              lambda_value * final_data[i];
+        }
+    }
+    else
+    {
+        Values input_values = this->constant_values;
+        input_values.set(this->lam(), std::get<1>(resolved));
+
+        for (int i = 0; i < nparams; ++i)
+        {
+            input_values.set(this->initial(), initial_data[i]);
+            input_values.set(this->final(), final_data[i]);
 
-        morphed_data[i] = equation(input_values);
+            morphed_data[i] = equation(input_values);
+        }
     }
 
     return morphed;

corelib/src/libs/SireCAS/lambdaschedule.h

@@ -204,6 +204,9 @@ namespace SireCAS
 
         /** The symbol used to represent the final value */
         static SireCAS::Symbol final_symbol;
+
+        /** The default morph equation */
+        static SireCAS::Expression default_morph_equation;
     };
 
 }

corelib/src/libs/SireIO/pdbx.cpp

@@ -149,7 +149,7 @@ PDBx::PDBx(const SireSystem::System &system, const PropertyMap &map) : ConcreteP
         throw SireError::unsupported(
             "No PDBx writer function has been registered. You need to "
             "install a library to write PDBx/mmCIF files, e.g. gemmi. "
-            "Do this by running 'mamba install -c conda-forge gemmi' "
+            "Do this by running 'conda install -c conda-forge gemmi' "
             "and then re-running this script.",
             CODELOC);
 
@@ -274,7 +274,7 @@ QVector<QString> PDBx::toLines() const
         throw SireError::unsupported(
             "No PDBx writer function has been registered. You need to "
             "install a library to write PDBx/mmCIF files, e.g. gemmi. "
-            "Do this by running 'mamba install -c conda-forge gemmi' "
+            "Do this by running 'conda install -c conda-forge gemmi' "
             "and then re-running this script.",
             CODELOC);
 
@@ -321,7 +321,7 @@ void PDBx::parseLines(const PropertyMap &map)
         throw SireError::unsupported(
             "No PDBx reader function has been registered. You need to "
             "install a library to read PDBx/mmCIF files, e.g. gemmi. "
-            "Do this by running 'mamba install -c conda-forge gemmi' "
+            "Do this by running 'conda install -c conda-forge gemmi' "
             "and then re-running this script.",
             CODELOC);
 

doc/source/acknowledgements.rst

@@ -119,11 +119,11 @@ does not affect :mod:`sire`. CMake is excellent. You can read more about it
 Anaconda
 ---------
 
-:mod:`sire` uses Anaconda Python (specifically mambaforge and conda-forge) to
+:mod:`sire` uses Anaconda Python (specifically miniforge and conda-forge) to
 simplify the management and installation of Python and the various
 modules on which :mod:`sire` depends.
 
-Anaconda (and miniconda) are distributed as
+Anaconda (and miniforge) are distributed as
 `open source projects <https://www.continuum.io/open-source-core-modern-software>`__.
 As :mod:`sire` does not explicitly link with them, the license is not an issue.
 You can find out more about Anaconda `from here <https://www.continuum.io/>`__.

doc/source/changelog.rst

@@ -12,6 +12,20 @@ Development was migrated into the
 `OpenBioSim <https://github.com/openbiosim>`__
 organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 
+`2023.5.1 <https://github.com/openbiosim/sire/compare/2023.5.0...2023.5.1>`__ - January 2024
+--------------------------------------------------------------------------------------------
+
+* Added a ``.dynamics().step(num_steps)`` function to make it easier to quickly run
+  steps of OpenMM dynamics with minimal overhead (this directly called ``Integrator.step()``)
+
+* Some optimisations to the OpenMM layer that make full use of the
+  experimental "updateSomeParametersInContext" functions.
+
+* Updated gemmi to 0.6.4, so that it can be default-enabled on all supported platforms.
+  As part of this, had to change the version of the compilers used on Windows and Linux
+  to make the conda packages. Windows now uses Visual Studio 2022 instead of 2017,
+  and Linux now uses GCC 12.3.0 instead of GCC 13.
+
 `2023.5.0 <https://github.com/openbiosim/sire/compare/2023.4.2...2023.5.0>`__ - December 2023
 ---------------------------------------------------------------------------------------------
 
@@ -918,14 +932,14 @@ Here is the changelog for this stage of development.
                only pythonize the C++ layer, and avoid the circular dependencies
                that were causing random import errors (particularly on Windows).
 
-    [2023.0.2] December 2023: Fix multiple distance restraint bug in SOMD
+    [2023.0.2] December 2022: Fix multiple distance restraint bug in SOMD
                (@fjclark). Add support for PME FEP with SOMD and fix
                associated bugs (@halx, @jmichel80). Fix CI issues so that
                PRs use the correct URL when triggered by external forks.
                Exclude dummy atoms when repartitioning hydrogen masses.
                Deprecate py37.
 
-    [2023.0.1] November 2023: Improve handling of HETATM and TER records in
+    [2023.0.1] November 2022: Improve handling of HETATM and TER records in
                PDB files. Fix SOMD selection issues following update to the
                2023 API. Fix writing of steps to SOMD simfile.dat (@fjclark).
                Throw exception when CHAMBER format AMBER topology files are
@@ -940,7 +954,7 @@ Here is the changelog for this stage of development.
                order. Ensure Sire is built against packages with the "dev"
                label.
 
-    [2023.0.0] July 2023 - Updated Sire's API to a more pythonic style.
+    [2023.0.0] July 2022 - Updated Sire's API to a more pythonic style.
                Module names are in lower case, e.g. `import Sire` becomes
                `import sire`, or `import sire as sr`. Functions are in
                underscore_case. This change is not backwards compatible. To