Merge pull request #3759 from jessica-mitchell/fix-sli

Remove last mentions of SLI

Author: heplesser

cmake/ProcessOptions.cmake

@@ -173,9 +173,8 @@ function( NEST_PROCESS_STATIC_LIBRARIES )
 
     # Note: "$ORIGIN" (on Linux) and "@loader_path" (on MacOS) are not CMake variables, but special keywords for the
     # Linux resp. the macOS dynamic loader. They refer to the path in which the object is located, e.g.
-    # ``${CMAKE_INSTALL_PREFIX}/bin`` for the nest and sli executables, ``${CMAKE_INSTALL_PREFIX}/lib/nest`` for all
-    # dynamic libraries except PyNEST (libnestkernel.so, etc.), and  something like
-    # ``${CMAKE_INSTALL_PREFIX}/lib/python3.x/site-packages/nest`` for ``pynestkernel.so``. The RPATH is relative to
+    # ``${CMAKE_INSTALL_PREFIX}/bin`` for helper scripts and  something like
+# ``${CMAKE_INSTALL_PREFIX}/lib/python3.x/site-packages/nest`` for ``nestkernel_api.so``. The RPATH is relative to
     # this origin, so the binary ``bin/nest`` can find the files in the relative location ``../lib/nest``, and
     # similarly for PyNEST and the other libraries. For simplicity, we set all the possibilities on all generated
     # objects.

doc/fulldoc.conf.in

@@ -746,13 +746,11 @@ WARN_LOGFILE           = doxygen.log
 INPUT		=	@PROJECT_SOURCE_DIR@/README.md \
 			@PROJECT_SOURCE_DIR@/doc \
 			@PROJECT_SOURCE_DIR@/examples \
-			@PROJECT_SOURCE_DIR@/lib \
 			@PROJECT_SOURCE_DIR@/libnestutil \
 			@PROJECT_SOURCE_DIR@/models \
 			@PROJECT_SOURCE_DIR@/nest \
 			@PROJECT_SOURCE_DIR@/nestkernel \
 			@PROJECT_SOURCE_DIR@/pynest \
-			@PROJECT_SOURCE_DIR@/sli \
 			@PROJECT_SOURCE_DIR@/testsuite
 
 # This tag can be used to specify the character encoding of the source files

doc/htmldoc/tutorials/music_tutorial/music_tutorial_1.rst

@@ -29,14 +29,14 @@ A Quick Introduction to NEST and MUSIC
 --------------------------------------
 
 In this tutorial, we will show you how to use the MUSIC library together
-with NEST. We will cover how to use the library from PyNEST and from the
-SLI language interface. In addition, we'll introduce the use of MUSIC in
+with NEST. We will cover how to use the library from PyNEST. In addition,
+we'll introduce the use of MUSIC in
 a C++ application and how to connect such an application to a NEST
 simulation.
 
 Our aim is to show practical examples of how to use MUSIC, and
 highlight common pitfalls that can trip the unwary. Also, we assume only
-a minimal knowledge of Python, C++ and (especially) SLI, so the examples
+a minimal knowledge of Python and C++, so the examples
 will favour clarity and simplicity over elegance and idiomatic
 constructs.
 

libnestutil/README.md

@@ -1,3 +1,3 @@
 # `libnestutil` folder
 
-General purpose auxiliary library used by SLI and NEST. This library contains the memory allocator and helpers for handling threads, debugging, numerics and reference counted pointers. This directory basically contains all files that do not fit anywhere else.
+General-purpose auxiliary library used by NEST. This library provides the `Dictionary` class, the memory allocator and helpers for handling numerics, strings and debugging.

models/iaf_psc_alpha_ps.cpp

@@ -359,7 +359,7 @@ nest::iaf_psc_alpha_ps::update( Time const& origin, const long from, const long
       {
         // If we use S_.V_m_ * std::exp( -V_.h_ms_ / P_.tau_m_ ) instead of
         // V_.expm1_tau_m_ * S_.V_m_ + S_.V_m_ here, the accuracy decreases,
-        // see test_iaf_ps_dc_t_accuracy.sli for details.
+        // see test_iaf_ps_dc_t_accuracy.py for details.
         S_.V_m_ = V_.P30_ * ( P_.I_e_ + S_.y_input_ ) + V_.P31_ex_ * S_.dI_ex_ + V_.P32_ex_ * S_.I_ex_
           + V_.P31_in_ * S_.dI_in_ + V_.P32_in_ * S_.I_in_ + V_.expm1_tau_m_ * S_.V_m_ + S_.V_m_;
 

models/iaf_psc_exp_ps.cpp

@@ -328,7 +328,7 @@ nest::iaf_psc_exp_ps::update( const Time& origin, const long from, const long to
       {
         // If we use S_.y2_ * std::exp( -V_.h_ms_ / P_.tau_m_ ) instead of
         // V_.expm1_tau_m_ * S_.y2_ + S_.y2_ here, the accuracy decreases,
-        // see test_iaf_ps_dc_t_accuracy.sli for details.
+        // see test_iaf_ps_dc_t_accuracy.py for details.
         S_.y2_ = V_.P20_ * ( P_.I_e_ + S_.y0_ ) + V_.P21_ex_ * S_.y1_ex_ + V_.P21_in_ * S_.y1_in_
           + V_.expm1_tau_m_ * S_.y2_ + S_.y2_;
 

models/iaf_psc_exp_ps_lossless.cpp

@@ -365,7 +365,7 @@ nest::iaf_psc_exp_ps_lossless::update( const Time& origin, const long from, cons
       {
         // If we use S_.y2_ * std::exp( -V_.h_ms_ / P_.tau_m_ ) instead of
         // V_.expm1_tau_m_ * S_.y2_ + S_.y2_ here, the accuracy decreases,
-        // see test_iaf_ps_dc_t_accuracy.sli for details.
+        // see test_iaf_ps_dc_t_accuracy.py for details.
         S_.y2_ = V_.P20_ * ( P_.I_e_ + S_.y0_ ) + V_.P21_ex_ * S_.I_syn_ex_ + V_.P21_in_ * S_.I_syn_in_
           + V_.expm1_tau_m_ * S_.y2_ + S_.y2_;
 

nestkernel/node.h

@@ -80,23 +80,19 @@ class WeightOptimizer;
  * @ingroup user_interface
  */
 
-/** @BeginDocumentation
-
-   Name: Node - General properties of all nodes.
-
-   Parameters:
-   frozen     booltype    - Whether the node is updated during simulation
-   global_id  integertype - The node ID of the node (cf. local_id)
-   local      booltype    - Whether the node is available on the local process
-   model      literaltype - The model type the node was created from
-   state      integertype - The state of the node (see the help on elementstates
-                            for details)
-   thread     integertype - The id of the thread the node is assigned to (valid
-                            locally)
-   vp         integertype - The id of the virtual process the node is assigned
-                            to (valid globally)
-
-   SeeAlso: GetStatus, SetStatus, elementstates
+/**
+ * General properties of all nodes.
+ *
+ * Parameters:
+ * - frozen     (bool)   - Whether the node is updated during simulation
+ * - global_id  (int)    - The node ID of the node (cf. local_id)
+ * - local      (bool)   - Whether the node is available on the local process
+ * - model      (string) - The model type the node was created from
+ * - state      (int)    - The state of the node (see elementstates for details)
+ * - thread     (int)    - The id of the thread the node is assigned to (valid locally)
+ * - vp         (int)    - The id of the virtual process the node is assigned to (valid globally)
+ *
+ * @see GetStatus, SetStatus
  */
 
 class Node
@@ -172,7 +168,7 @@ class Node
    *
    * Returns name of node model (e.g. "iaf_psc_alpha") as string.
    * This name is identical to the name that is used to identify
-   * the model in the interpreter's model dictionary.
+   * the model in the NEST model registry.
    */
   std::string get_name() const;
 
@@ -319,14 +315,13 @@ class Node
    * @defgroup status_interface Configuration interface.
    *
    * Functions and infrastructure, responsible for the configuration
-   * of Nodes from the SLI Interpreter level.
-   *
-   * Each node can be configured from the SLI level through a named
-   * parameter interface. In order to change parameters, the user
-   * can specify name value pairs for each parameter. These pairs
-   * are stored in a data structure which is called Dictionary.
-   * Likewise, the user can query the configuration of any node by
-   * requesting a dictionary with name value pairs.
+   * of Nodes via the PyNEST API.
+   *
+   * Each node can be configured through a named parameter interface.
+   * In order to change parameters, the user can specify name-value pairs
+   * for each parameter. These pairs are stored in a data structure which
+   * is called Dictionary. Likewise, the user can query the configuration
+   * of any node by requesting a dictionary with name-value pairs.
    *
    * The configuration interface consists of four functions which
    * implement storage and retrieval of named parameter sets.

pynest/nest/lib/README.md

@@ -3,24 +3,14 @@
 Definition of high-level API of PyNEST.
 
 This file defines the user-level functions of NEST's Python interface
-by mapping NEST/SLI commands to Python. Please try to follow these
+by mapping NEST commands to Python. Please try to follow these
 rules:
 
-1. SLI commands have the same name in Python. This means that most
-   function names are written in camel case, although the Python
-   guidelines suggest to use lower case for function names. However,
-   this way, it is easier for users to migrate from SLI to Python.
+1. Nodes are identified by their global IDs (node ID) by default.
 
-2. Nodes are identified by their global IDs (node ID) by default.
-
-3. node IDs are always represented by a NodeCollection, e.g.
+2. node IDs are always represented by a NodeCollection, e.g.
    NodeCollection(metadata=None, model=iaf_psc_alpha, size=10, first=1, last=10)
 
-4. Commands that return a node ID must return it as NodeCollection.
-
-5. When possible, loops over nodes should be propagated down to the
-   SLI level. This minimizes the number of Python<->SLI conversions
-   and increases performance. Loops in SLI are also faster than in
-   Python.
+3. Commands that return a node ID must return it as NodeCollection.
 
-6. If you have a *very* good reason, you may deviate from these guidelines.
+4. If you have a *very* good reason, you may deviate from these guidelines.

pynest/nest/lib/hl_api_connection_helpers.py

@@ -141,7 +141,7 @@ def _process_syn_spec(syn_spec, conn_spec, prelength, postlength, use_connect_ar
 def _process_spatial_projections(conn_spec, syn_spec):
     """
     Processes the connection and synapse specifications to a single dictionary
-    for the SLI function `ConnectLayers`.
+    for the spatial ``connect_layers`` C++ function.
     """
     allowed_conn_spec_keys = [
         "mask",
@@ -212,7 +212,7 @@ def _process_spatial_projections(conn_spec, syn_spec):
 
 
 def _connect_layers_needed(conn_spec, syn_spec):
-    """Determins if connection has to be made with the SLI function `ConnectLayers`."""
+    """Determines if the connection must use the spatial ``connect_layers`` path."""
     if isinstance(conn_spec, dict):
         # If a conn_spec entry is based on spatial properties, we must use ConnectLayers.
         for key, item in conn_spec.items():