SCM-NV · mhellstr · Feb 13, 2026 · Feb 13, 2026 · Feb 13, 2026 · Feb 20, 2026
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -59,7 +59,8 @@ uv pip install $AMSHOME/scripting/scm/amspipe
 ```
 or:
 ```bash
-uv pip install $AMSHOME/scripting/wheels/amspipe-0.1-py3-none-any.whl
+uv pip install --index-url "https://<scm-username>:<pwd>@downloads.scm.com/Downloads/packages/uv/channels/2026.1/simple/" \
+  scm-amspipe scm-external-engines plams
 ```
 To run tests use:
 ```bash

diff --git a/doc/source/components/functions.rst b/doc/source/components/functions.rst
@@ -9,6 +9,7 @@ This chapter gathers information about public functions that can be used in PLAM
 
 .. autofunction:: init
 .. autofunction:: finish
+.. autofunction:: jobs_in_directory
 .. autofunction:: load
 .. autofunction:: load_all
 .. autofunction:: read_molecules

diff --git a/doc/source/components/settings.rst b/doc/source/components/settings.rst
@@ -15,7 +15,7 @@ Any derived settings class is interchangeable with the base |Settings| class of
 Tree-like structure
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The |Settings| class is based on the regular Python dictionary (built-in class :class:`dict`, tutorial can be found :ref:`here<tut-dictionaries>`) and in many aspects works just like it::
+The |Settings| class is based on the regular Python dictionary (built-in class :class:`dict`, tutorial can be found `here <https://docs.python.org/3/tutorial/datastructures.html#tut-dictionaries>`__) and in many aspects works just like it::
 
     >>> s = Settings()
     >>> s['abc'] = 283
@@ -190,7 +190,16 @@ For example:
     config.job.pickle = False
     config.default_jobrunner = JobRunner(parallel=True, maxjobs=8)
 
-The structure for the defined options on the nested settings objects is defined below.
+A context manager ``config_context`` is provided to override the global ``config`` within a specific scope:
+
+.. autofunction:: scm.plams.core.functions.config_context
+
+This can be useful for temporarily disabling or changing global settings.
+If you use this context manager, obtain ``config`` with the ``get_config`` function:
+
+.. autofunction:: scm.plams.core.functions.get_config
+
+The structure for all the defined options on the nested settings objects is defined below.
 
 .. autoclass:: ConfigSettings
 

diff --git a/doc/source/components/utils.rst b/doc/source/components/utils.rst
@@ -57,6 +57,8 @@ the :ref:`BalanceReactionEquationsExample` example.
 
 .. autofunction:: scm.plams.tools.reaction.balance
 
+.. autoclass:: scm.plams.tools.reaction.ReactionEquation
+
 
 Older functions:
 

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -191,7 +191,6 @@ def setup(app):
 
 extensions += [
     "sphinx.ext.autodoc",
-    "sphinx.ext.intersphinx",
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
     "sphinx_copybutton",
@@ -206,9 +205,6 @@ def setup(app):
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"
 
-# configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {"python3": ("http://docs.python.org/3.8", None)}
-
 autodoc_default_options = {"members": True, "private-members": True, "special-members": True}
 autodoc_member_order = "bysource"
 autodoc_typehints = "description"

diff --git a/doc/source/examples/ADFFrag/ADFFrag.rst b/doc/source/examples/ADFFrag/ADFFrag.rst
@@ -21,6 +21,7 @@ It simply redirects the usual |AMSResults| methods to the results of the full sy
 
 
 .. literalinclude:: ../../../../src/scm/plams/recipes/adffragment.py
+   :language: python
 
 .. include:: ADFFrag.common_header.rst
 .. include:: adffrag.ipynb.rst

diff --git a/doc/source/examples/ADFNBO/ADFNBO.rst b/doc/source/examples/ADFNBO/ADFNBO.rst
@@ -18,7 +18,8 @@ No specialized |Results| subclass is defined for ``ADFNBOJob``.
 The source code of the whole module:
 
 .. literalinclude:: ../../../../src/scm/plams/recipes/adfnbo.py
+   :language: python
 
 .. include:: ADFNBO.common_header.rst
 .. include:: ADFNBO.ipynb.rst
-.. include:: ADFNBO.common_footer.rst
+.. include:: ADFNBO.common_footer.rst
diff --git a/doc/source/examples/BAND_NiO_HubbardU.rst b/doc/source/examples/BAND_NiO_HubbardU.rst
@@ -5,16 +5,22 @@ BAND: NiO with DFT+U
 
 The hubbard method is a way to calculate band gaps for metal oxides for which a normal GGA fails to predict a band gap.
 
-**Example usage:** (:download:`Download BAND_NiO_HubbardU.py <../../../examples/BAND_NiO_HubbardU.py>`)
+**Example usage:**
+
+* Download :download:`BAND_NiO_HubbardU.py <../../../examples/BAND_NiO_HubbardU.py>` (run as ``$AMSBIN/amspython BAND_NiO_HubbardU.py``).
 
 .. literalinclude:: ../../../examples/BAND_NiO_HubbardU.py
 	:language: python
 
 Results
 -------
 
+The following results appear upon execution.
+
 .. parsed-literal::
 
    Top of valence band:       -6.67 eV
    Bottom of conduction band: -5.41 eV
    Band gap:                  1.25 eV
+
+A folder called ``NiO`` is also created containing other files.
diff --git a/doc/source/examples/BandFrag/BandFrag.rst b/doc/source/examples/BandFrag/BandFrag.rst
@@ -20,6 +20,7 @@ It simply redirects the usual |AMSResults| methods to the results of the full sy
 A derived subclass |NOCVBandFragmentJob| is also provided. It can be usefull for generating NOCV plots after the PEDA-NOCV calculation.
 
 .. literalinclude:: ../../../../src/scm/plams/recipes/bandfragment.py
+   :language: python
 
 .. include:: BandFrag.common_header.rst
 .. include:: bandfrag.ipynb.rst

diff --git a/doc/source/examples/COSMORSCompound/COSMORSCompound.rst b/doc/source/examples/COSMORSCompound/COSMORSCompound.rst
@@ -15,10 +15,11 @@ Source code for ``ADFCOSMORSCompound``
 .. dropdown::
 
     .. literalinclude:: ../../../../src/scm/plams/recipes/adfcosmorscompound.py
+       :language: python
 
 Brief API Documentation
 -----------------------
 
 .. automodule:: scm.plams.recipes.adfcosmorscompound
     :no-special-members:
-    :exclude-members: _result_type, __init__, new_children, postrun, _get_radii, adf_settings
+    :exclude-members: _result_type, __init__, new_children, postrun, _get_radii, adf_settings
diff --git a/...xamples/ChargeTransferIntegralsADF/ChargeTransferIntegralsADF.common_header.rst b/...xamples/ChargeTransferIntegralsADF/ChargeTransferIntegralsADF.common_header.rst
@@ -1,4 +1,8 @@
-To follow along, either
+To follow along
 
-* Download :download:`ChargeTransferIntegralsADF.py <../../../../examples/ChargeTransferIntegralsADF/ChargeTransferIntegralsADF.py>` (run as ``$AMSBIN/amspython ChargeTransferIntegralsADF.py``).
+* Download :download:`BenzeneDimer.xyz <../../../../examples/ChargeTransferIntegralsADF/BenzeneDimer.xyz>`
+
+then, either
+
+* Download :download:`ChargeTransferIntegralsADF.py <../../../../examples/ChargeTransferIntegralsADF/ChargeTransferIntegralsADF.py>` (run as ``$AMSBIN/amspython ChargeTransferIntegralsADF.py``)
 * Download :download:`ChargeTransferIntegralsADF.ipynb <../../../../examples/ChargeTransferIntegralsADF/ChargeTransferIntegralsADF.ipynb>` (see also: how to install `Jupyterlab <../../../Scripting/Python_Stack/Python_Stack.html#install-and-run-jupyter-lab-jupyter-notebooks>`__ in AMS)
diff --git a/doc/source/examples/ConformersGeneration/ConformersGeneration.rst b/doc/source/examples/ConformersGeneration/ConformersGeneration.rst
@@ -15,8 +15,6 @@ Conformers Generation
 
 Example illustrating how to generate conformers with AMS.
 
-**This example is only compatible with AMS2023**.
-
 .. include:: ConformersGeneration.common_header.rst
 .. include:: conformers.ipynb.rst
-.. include:: ConformersGeneration.common_footer.rst
+.. include:: ConformersGeneration.common_footer.rst
diff --git a/doc/source/examples/HydrogenBondsFromMD.rst b/doc/source/examples/HydrogenBondsFromMD.rst
@@ -12,7 +12,7 @@ The script ``get_hbonds.py`` accepts the name of an MD trajectory RKF file, and
 
 .. code-block:: bash
 
-   amspython get_hbonds.py path/to/ams.rkf path/to/indices.txt
+   $AMSBIN/amspython get_hbonds.py path/to/ams.rkf path/to/indices.txt
 
 In its simplest form, the input file indices.txt will contain only one or more element names.
 
@@ -29,10 +29,19 @@ The script ``get_hbonds.py``.
 .. literalinclude:: ../../../examples/get_hbonds.py
 	:language: python
 
+**Example usage:** 
 (:download:`Download get_water_indices.py <../../../examples/get_water_indices.py>`)
 
-The script ``get_water_indices`` can create the file ``indices.txt`` that is required by the ``get_hbonds.py`` script, for the specific case where the indices of all water oxygen atoms are required. The script accepts the name of the MD trajectory RKF file.
+The script ``get_water_indices`` can create the file ``indices.txt`` that is required by the ``get_hbonds.py`` script, for the specific case where the indices of all water oxygen atoms are required. The script accepts the name of the MD trajectory RKF file and can be called from the command line as follows.
+
+.. code-block:: bash
+
+   $AMSBIN/amspython get_water_indices.py path/to/ams.rkf
+
+The script ``get_water_indices.py``.
 
 .. literalinclude:: ../../../examples/get_water_indices.py
 	:language: python
 
+
+
diff --git a/doc/source/examples/IonicConductivityFromMD.rst b/doc/source/examples/IonicConductivityFromMD.rst
@@ -5,16 +5,38 @@ Ionic conductivity from ams.rkf trajectory
 
 First, an ams.rkf trajectory with ions in the system needs to be calculated, as is done, for example, in the
 `Ionic Conductivity Tutorial <../../Tutorials/MolecularDynamicsAndMonteCarlo/IonicConductivity.html>`__.
-Next, the ionic conductivity for the ions in the solution can be computed. The below script first identifies the ions in the molecular system, and guesses their charges (in the case of metals it uses a simple charge equilibration scheme). It then runs the AMS trajectory analysis tool to compute the ionic conductivity for these ions.
+Next, the ionic conductivity for the ions in the solution can be computed. The script below first identifies the ions in the molecular system and guesses their charges (for metals, it uses a simple charge equilibration scheme). It then runs the AMS trajectory analysis tool to compute the ionic conductivity for these ions.
 
 **Example usage:** (:download:`Download get_ionic_conductivity.py <../../../examples/IonicConductivity/get_ionic_conductivity.py>`)
 
-.. code-block:: none
+.. code-block:: bash
 
    $AMSBIN/amspython get_ionic_conductivity.py /path/to/ams.rkf
 
-To create an example ams.rkf file, a PLAMS script can be found here (:download:`Download NaClwater.py <../../../examples/IonicConductivity/NaClwater.py>`). This script is designed for efficiency. For a more reliable setup, follow the `Ionic Conductivity Tutorial <../../Tutorials/MolecularDynamicsAndMonteCarlo/IonicConductivity.html>`__.
+To create an example ``ams.rkf`` file, you can use this PLAMS script (:download:`Download NaClwater.py <../../../examples/IonicConductivity/NaClwater.py>`). This script is designed for efficiency. For a more reliable setup, follow the `Ionic Conductivity Tutorial <../../Tutorials/MolecularDynamicsAndMonteCarlo/IonicConductivity.html>`__.
 
 .. literalinclude:: ../../../examples/IonicConductivity/get_ionic_conductivity.py
-	:language: python
-
+   :language: python
+
+**Results**
+
+If you have used the ``ams.rkf`` generated from running ``$AMSBIN/amspython NaClwater.py``,
+the output from ``get_ionic_conductivity.py`` should look something like:
+
+.. parsed-literal::
+     Average temperature 298.166533 K
+     Ion        N     Charge
+     Na        5    1.00000
+     Cl        5   -1.00000
+     [20.02|15:06:43] JOB plamsjob STARTED
+     [20.02|15:06:43] JOB plamsjob RUNNING
+     [20.02|15:06:43] JOB plamsjob FINISHED
+     [20.02|15:06:43] JOB plamsjob SUCCESSFUL
+     Na 2.4739268145933062e-09 m2/s
+     [20.02|15:06:43] JOB plamsjob STARTED
+     [20.02|15:06:43] Renaming job plamsjob to plamsjob.002
+     [20.02|15:06:43] JOB plamsjob.002 RUNNING
+     [20.02|15:06:43] JOB plamsjob.002 FINISHED
+     [20.02|15:06:43] JOB plamsjob.002 SUCCESSFUL
+     Cl 3.2624546292849828e-09 m2/s
+     Ionic conductivity:     2.6075090545e+01 Siemens/m
diff --git a/doc/source/examples/NumGrad/NumGrad.rst b/doc/source/examples/NumGrad/NumGrad.rst
@@ -18,7 +18,8 @@ Any function that takes results of a single point job and returns a single numbe
 The source code of the whole module with both abovementioned classes:
 
 .. literalinclude:: ../../../../src/scm/plams/recipes/numgrad.py
+   :language: python
 
 .. include:: NumGrad.common_header.rst
 .. include:: NumGrad.ipynb.rst
-.. include:: NumGrad.common_footer.rst
+.. include:: NumGrad.common_footer.rst
diff --git a/doc/source/examples/NumHess/NumHess.rst b/doc/source/examples/NumHess/NumHess.rst
@@ -18,7 +18,8 @@ The returned Hessian can optionally be mass weighted.
 The source code of the whole module with both aforementioned classes:
 
 .. literalinclude:: ../../../../src/scm/plams/recipes/numhess.py
+   :language: python
 
 .. include:: NumHess.common_header.rst
 .. include:: NumHess.ipynb.rst
-.. include:: NumHess.common_footer.rst
+.. include:: NumHess.common_footer.rst
diff --git a/doc/source/examples/ReorganizationEnergy/ReorganizationEnergy.rst b/doc/source/examples/ReorganizationEnergy/ReorganizationEnergy.rst
@@ -18,6 +18,7 @@ In this recipe we build a job class ``ReorganizationEnergyJob`` by extending |Mu
 In ``ReorganizationEnergyResults``, the reorganization energy is computed by fetching and combining the results from the children jobs.
 
 .. literalinclude:: ../../../../src/scm/plams/recipes/reorganization_energy.py
+   :language: python
 
 
 .. include:: ReorganizationEnergy.common_header.rst

diff --git a/doc/source/examples/pyAHFCDOS.rst b/doc/source/examples/pyAHFCDOS.rst
@@ -8,5 +8,6 @@ The ``FCFDOS`` class allows one to easily calculate the density of states for an
 For an example, see :ref:`Vibronic Density of States with ADF<fcf_dos>`.
 
 .. literalinclude:: ../../../src/scm/plams/recipes/fcf_dos.py
+   :language: python
 
 
diff --git a/doc/source/general.rst b/doc/source/general.rst
@@ -109,6 +109,47 @@ The latest (unreleased) development version can be downloaded from the `trunk br
 Once the downloaded zip file has been extracted, navigate to its location and run ``pip install .`` to install into your Python environment.
 
 
+What's new in PLAMS for AMS2026?
+--------------------------------------
+
+Added
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Improved molecular visualization. The :func:`~scm.plams.tools.view.view` function allows visualization of molecules and chemical systems using AMSView, which can be easily rendered in a Jupyter notebook or saved as images.
+* Improvements to the |JobAnalysis| tool for collecting and analyzing job results, with additional methods:
+    * :meth:`~scm.plams.tools.job_analysis.JobAnalysis.add_rkf_field` to simplify adding values from an RKF file to the analysis
+    * :meth:`~scm.plams.tools.job_analysis.JobAnalysis.get_settings_field_key` and :meth:`~scm.plams.tools.job_analysis.JobAnalysis.get_rkf_field_key` methods to simplify getting the keys for analysis fields
+* Additional functionality to assist with workflows:
+    * :func:`~scm.plams.core.functions.jobs_in_directory` context manager to allow jobs to run in a subdirectory of the PLAMS working directory
+    * :meth:`~scm.plams.core.basejob.Job.delete` and :meth:`~scm.plams.core.basejob.Job.rename` methods for deleting/renaming job files and directories
+    * :meth:`~scm.plams.core.settings.JobSettings.on_status_change` callback, available on global ``config``, which fires any time a job status is updated and allows notifications when jobs finish or error
+    * :func:`~scm.plams.core.functions.config_context` context manager and :func:`~scm.plams.core.functions.get_config` function allow context-based override of global ``config`` settings
+* Additional methods to get results from AMS calculations:
+    * :meth:`~scm.plams.interfaces.adfsuite.ams.AMSResults.get_pvdos` method to get partial vibrational spectra
+    * :meth:`~scm.plams.interfaces.adfsuite.ams.AMSResults.get_main_engine_name`
+    * :meth:`~scm.plams.interfaces.adfsuite.ams.AMSResults.get_reduced_masses`
+* Dedicated job for Energy Decomposition Analysis in BAND |BANDFragmentJob|
+* Method :meth:`~scm.plams.tools.reaction.balance` to find a balanced :class:`~scm.plams.tools.reaction.ReactionEquation`
+* Many type hints added across the code to aid scripting through an IDE
+
+Changed
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* :class:`~scm.plams.interfaces.adfsuite.amsanalysis.AMSAnalysisJob` has PISA support, accepts multiple |AMSJob| instances as input, and no longer overwrites user-supplied input settings
+* :meth:`~scm.plams.interfaces.adfsuite.ams.AMSResults.get_normal_modes` explicitly gives the option to return mass-weighted Hessian eigenvectors
+* |JobAnalysis| returns an updated copy on modification instead of performing operations in-place
+* :func:`~scm.plams.interfaces.molecule.packmol.packmol` function made more flexible, now accepting a single ``None`` value for ``n_molecules`` if two of ``n_atoms``, ``density`` and ``box_bounds`` are specified (the missing value is then auto-calculated)
+
+Fixed
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Method to guess density in :func:`~scm.plams.interfaces.molecule.packmol.packmol_around` changed to resolve large underestimations in molecular volumes
+
+Deprecated
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* :func:`~scm.plams.core.functions.add_to_class` decorator is deprecated in favor of using standalone functions or subclasses
+
 What's new in PLAMS for AMS2025?
 --------------------------------------
 

diff --git a/src/scm/plams/core/functions.py b/src/scm/plams/core/functions.py
@@ -40,25 +40,27 @@
 @contextmanager
 def config_context() -> Generator[ConfigSettings, None, None]:
     """
-    Enter a context with a |config| specific only to the current context.
+    Enter a context with a ``config`` specific only to the current context.
 
-    The global |config| will be copied into a new |ConfigSettings|, which can then be modified independently of the global instance.
+    The global ``config`` will be copied into a new |ConfigSettings|, which can then be modified independently of the global instance.
 
-    The |config| for this context can be retrieved using the function :func:`get_config`.
+    The ``config`` for this context can be retrieved using the function :func:`get_config`.
+
+    .. note::
 
-     .. note::
         Starting a new thread creates a new context, so the context configuration will not automatically be used in the new thread.
         To copy over the parent thread context to the new thread, instead use :class:`~scm.plams.core.threading_utils.ContextAwareThread`
 
-     .. code:: python
-         >>> with config_context() as cfg:
-         >>>     cfg.log.stdout = 0
-         >>>     print(f"Stdout logging inside context disabled: {get_config().log.stdout == 0}")
-         >>> print(f"Stdout logging outside context disabled: {get_config().log.stdout == 0}")
-             Stdout logging inside context disabled: True
-             Stdout logging outside context disabled: False
+    .. code:: python
+
+        >>> with config_context() as cfg:
+        >>>     cfg.log.stdout = 0
+        >>>     print(f"Stdout logging inside context disabled: {get_config().log.stdout == 0}")
+        >>> print(f"Stdout logging outside context disabled: {get_config().log.stdout == 0}")
+            Stdout logging inside context disabled: True
+            Stdout logging outside context disabled: False
 
-    :return: copy of the global |config| instance in a new |ConfigSettings|
+    :return: copy of the global ``config`` instance in a new |ConfigSettings|
     """
     cfg: ConfigSettings = get_config().copy()
     token = _config.set(cfg)
@@ -72,7 +74,7 @@ def get_config() -> ConfigSettings:
     """
     Get the |ConfigSettings| for the current code context.
 
-    This will be the configuration used within a :func:`config_context` context, or otherwise the global |config|.
+    This will be the configuration used within a :func:`config_context` context, or otherwise the global ``config``.
 
     :return: |ConfigSettings| that should be used in the current code context
     """
@@ -658,6 +660,7 @@ def jobs_in_directory(path: Union[str, os.PathLike]) -> Generator[Path, None, No
         * The absolute path of the directory is returned on entering the context, which assumes the default |JobManager| is used. If another job manager is used within the context, the actual directory will be relative to its ``workdir``.
 
     .. code:: python
+
          >>> with jobs_in_directory("GeometryOptimization") as go_dir:
          >>>     with jobs_in_directory("DFTB"):
          >>>        job1.run()
@@ -671,6 +674,7 @@ def jobs_in_directory(path: Union[str, os.PathLike]) -> Generator[Path, None, No
             path/plams_workdir/GeometryOptimization/ML/M3GNet/job2
 
     .. note::
+
         Starting a new thread creates a new context, so the context configuration will not automatically be used in the new thread.
         To copy over the parent thread context to the new thread, instead use :class:`~scm.plams.core.threading_utils.ContextAwareThread`
 

diff --git a/src/scm/plams/core/jobrunner.py b/src/scm/plams/core/jobrunner.py
@@ -64,7 +64,7 @@ def wrapper(self: SelfT, /, *args: P.args, **kwargs: P.kwargs) -> None:
 
 
 def _limit(func: Callable[Concatenate[SelfT, P], None]) -> Callable[Concatenate[SelfT, P], None]:
-    """Decorator for an instance method. If ``_job_limit`` attribute of given instance is not ``None``, use this attribute to wrap decorated method via :ref:`with<with-locks>` statement."""
+    """Decorator for an instance method. If ``_job_limit`` attribute of given instance is not ``None``, use this attribute to wrap decorated method via `with <https://docs.python.org/3/library/threading.html#using-locks-conditions-and-semaphores-in-the-with-statement>`__ statement."""
 
     @functools.wraps(func)
     def wrapper(self: SelfT, /, *args: P.args, **kwargs: P.kwargs) -> None:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -57,6 +57,8 @@ the :ref:`BalanceReactionEquationsExample` example.

		.. autofunction:: scm.plams.tools.reaction.balance

		.. autoclass:: scm.plams.tools.reaction.ReactionEquation


		Older functions:

Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -8,5 +8,6 @@ The ``FCFDOS`` class allows one to easily calculate the density of states for an
		For an example, see :ref:`Vibronic Density of States with ADF<fcf_dos>`.

		.. literalinclude:: ../../../src/scm/plams/recipes/fcf_dos.py
		:language: python