Make arbor-build-catalogue part of pyarb.

CMakeLists.txt

@@ -269,9 +269,7 @@ add_library(arborio-public-deps INTERFACE)
 install(TARGETS arborio-public-deps EXPORT arborio-targets)
 
 # Add scripts and supporting CMake for setting up external catalogues
-
 install(PROGRAMS scripts/arbor-build-catalogue DESTINATION ${CMAKE_INSTALL_BINDIR})
-install(FILES mechanisms/BuildModules.cmake DESTINATION ${ARB_INSTALL_DATADIR})
 
 # Add all dependencies.
 

arbor/include/arbor/util/expected.hpp

@@ -484,13 +484,9 @@ struct expected<void, E> {
     // No emplace ops.
 
     // Swap ops.
-
-    void swap(expected& other) {
-        data_.swap(other.data);
-    }
+    void swap(expected& other) { data_.swap(other.data_); }
 
     // Accessors.
-
     bool has_value() const noexcept { return !data_; }
     explicit operator bool() const noexcept { return has_value(); }
 

arbor/profile/profiler.cpp

@@ -144,23 +144,16 @@ const std::vector<profile_accumulator>& recorder::accumulators() const {
 }
 
 void recorder::enter(region_id_type index) {
-    if (index_!=npos) {
-        throw std::runtime_error("recorder::enter without matching recorder::leave");
-    }
-    if (index>=accumulators_.size()) {
-        accumulators_.resize(index+1);
-    }
+    if (index_!=npos) throw std::runtime_error("recorder::enter without matching recorder::leave.");
+    if (index>=accumulators_.size()) accumulators_.resize(index+1);
     index_ = index;
     start_time_ = timer::tic();
 }
 
 void recorder::leave() {
     // calculate the elapsed time before any other steps, to increase accuracy.
     auto delta = timer::toc(start_time_);
-
-    if (index_==npos) {
-        throw std::runtime_error("recorder::leave without matching recorder::enter");
-    }
+    if (index_==npos) throw std::runtime_error("recorder::leave without matching recorder::enter.");
     accumulators_[index_].count++;
     accumulators_[index_].time += delta;
     index_ = npos;

doc/contrib/test.rst

@@ -4,8 +4,65 @@ Tests
 =====
 
 C++ tests are located in ``/tests`` and Python (binding) tests in
-``/python/test``. See the documentation on :ref:`building <building>` for the
-C++ tests and ``/python/test/readme.md`` for the latter.
+``/python/test``. See also the documentation on :ref:`building <building>` for
+the C++ tests and ``/python/test/readme.md`` for the latter.
+
+Building and Running Tests
+--------------------------
+
+The C++ tests need to be built using the usual proecdure via CMake + Ninja.
+It is usually advisable to enable assertions for debugging.
+
+.. code-block:: sh
+
+    # more arguments omitted
+    cmake .. -DCMAKE_BUILD_TYPE=debug -DARB_WITH_ASSERTIONS=ON [..]
+    ninja tests
+
+This will produce three binaries
+
+- ``bin/unit`` basic unit tests for Arbor.
+- ``bin/unit-modcc`` unit tests for Arbor's NMODL compiler
+- ``bin/unit-mpi`` unit tests for Arbor's MPI funcionality. Only produced if MPI
+  enabled.
+- ``bin/unit-local`` local (i.e. without MPI) version of ``unit-mpi``.
+
+All accept some arguments determined by the testing framework, among others
+filters to include/exclude tests, try ``bin/unit --help`` for more information.
+Some tests might be skipped if GPU-support is not enabled. Building with GPU and
+failing to locate a GPU will register as failures. Except ``unit-mpi`` each
+testsuite can be run like a normal executable; for MPI tests use
+
+.. code-block:: sh
+
+    mpirun -n 2 bin/unit-mpi
+
+If you are working on the MPI parts of Arbor, don't forget to try different
+process counts.
+
+There also is a collection of micro benchmarks; build these with ``ninja
+ubenches``. Each benchmark will result in a separate executable which measures
+the performance of a critical building block of Arbor.
+
+For Python, two more testsuites are provided in ``python/test``. During
+development these can be run like this
+
+.. code-block:: sh
+
+  # Assuming we have built Arbor in ~/src/arbor/build
+  # and Arbor was cloned into ~/src/arbor
+  PYTHONPATH=$HOME/src/arbor/build/python python3 -munittest discover -v -s $HOME/src/arbor/python/
+
+This will use Arbor's Python module without installing. If you did install Arbor
+beforehand
+
+.. code-block:: sh
+
+  # Assuming Arbor was cloned into ~/src/arbor
+  python3 -munittest discover -v -s $HOME/src/arbor/python/
+
+is sufficient. However, this requires an install step after each change in
+Arbor.
 
 What to test?
 -------------

pyproject.toml

@@ -28,8 +28,8 @@ dependencies = [
 ]
 
 [project.scripts]
-modcc = "arbor:modcc"
-arbor-build-catalogue = "arbor:build_catalogue"
+modcc = "arbor.modcc:cli"
+arbor-build-catalogue = "arbor.build_catalogue:cli"
 
 [tool.scikit-build]
 cmake.args = [

python/CMakeLists.txt

@@ -82,6 +82,19 @@ set_target_properties(pyarb PROPERTIES LIBRARY_OUTPUT_DIRECTORY "${python_mod_pa
 file(COPY "${PROJECT_SOURCE_DIR}/python/__init__.py" DESTINATION "${python_mod_path}")
 file(COPY "${PROJECT_SOURCE_DIR}/VERSION" DESTINATION "${python_mod_path}")
 
+configure_file("${PROJECT_SOURCE_DIR}/scripts/arbor-build-catalogue"
+               "${CMAKE_BINARY_DIR}/bin/arbor-build-catalogue"
+               FILE_PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE WORLD_READ WORLD_EXECUTE GROUP_READ GROUP_EXECUTE
+               COPYONLY)
+configure_file("${PROJECT_SOURCE_DIR}/scripts/arbor-build-catalogue"
+               "${python_mod_path}/build_catalogue.py"
+               NO_SOURCE_PERMISSIONS
+               COPYONLY)
+configure_file("${PROJECT_SOURCE_DIR}/python/modcc.py"
+               "${python_mod_path}/modcc.py"
+               NO_SOURCE_PERMISSIONS
+               COPYONLY)
+
 # Set the installation path
 
 # Ask Python where it keeps its system (platform) packages.
@@ -106,7 +119,7 @@ mark_as_advanced(FORCE ARB_PYTHON_LIB_PATH)
 if(ARB_BUILD_PYTHON_STUBS)
   find_python_module(pybind11_stubgen REQUIRED)
 else()
-    find_python_module(pybind11_stubgen)
+  find_python_module(pybind11_stubgen)
 endif()
 if(HAVE_PYBIND11_STUBGEN)
   add_custom_command(TARGET pyarb POST_BUILD
@@ -117,7 +130,8 @@ if(HAVE_PYBIND11_STUBGEN)
                      COMMENT "Generating type stubs")
 endif()
 
-if(DEFINED SKBUILD_PROJECT_NAME)
+if(DEFINED
+    SKBUILD_PROJECT_NAME)
   # Building wheel through scikit-build-core
   set(_python_module_install_path .)
 else()
@@ -129,4 +143,8 @@ if(HAVE_PYBIND11_STUBGEN)
   install(DIRECTORY ${CMAKE_BINARY_DIR}/stubs/arbor/ DESTINATION ${_python_module_install_path})
 endif()
 install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/__init__.py DESTINATION ${_python_module_install_path})
+install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/modcc.py DESTINATION ${_python_module_install_path})
+install(FILES ${PROJECT_SOURCE_DIR}/scripts/arbor-build-catalogue
+        DESTINATION ${_python_module_install_path}
+        RENAME build_catalogue.py)
 install(FILES ${PROJECT_SOURCE_DIR}/VERSION ${PROJECT_SOURCE_DIR}/README.md ${PROJECT_SOURCE_DIR}/LICENSE DESTINATION ${_python_module_install_path})

python/__init__.py

@@ -16,33 +16,6 @@ def get_version():
         return version_file.read().strip()
 
 
-def modcc():
-    import os
-    import sys
-    import subprocess
-
-    sys.exit(
-        subprocess.call(
-            [os.path.join(os.path.dirname(__file__), "bin", "modcc"), *sys.argv[1:]]
-        )
-    )
-
-
-def build_catalogue():
-    import os
-    import sys
-    import subprocess
-
-    sys.exit(
-        subprocess.call(
-            [
-                os.path.join(os.path.dirname(__file__), "bin", "arbor-build-catalogue"),
-                *sys.argv[1:],
-            ]
-        )
-    )
-
-
 __version__ = get_version()
 __config__ = config()  # noqa:F405
 

python/modcc.py

@@ -0,0 +1,11 @@
+# NOTE this is a placeholder until we make pybind11 bindings for modcc
+def cli():
+    import os
+    import sys
+    import subprocess
+
+    sys.exit(
+        subprocess.call(
+            [os.path.join(os.path.dirname(__file__), "bin", "modcc"), *sys.argv[1:]]
+        )
+    )

python/strprintf.hpp

@@ -168,7 +168,7 @@ namespace impl {
             for (auto& x: s.seq_) {
                 if (!first) o << s.sep_;
                 first = false;
-                o << s.f(x);
+                o << s.f_(x);
             }
             return o;
         }

python/test/fixtures.py

@@ -6,6 +6,7 @@
 import subprocess
 import atexit
 import inspect
+from unittest import SkipTest
 
 _mpi_enabled = A.__config__["mpi"]
 _mpi4py_enabled = A.__config__["mpi4py"]
@@ -155,7 +156,6 @@ def _build_cat(name, path, context):
                 "Building catalogue in an MPI context, but `mpi4py` not found."
                 " Concurrent identical catalogue builds might occur."
             ) from None
-
         _build_cat_distributed(comm, name, path)
     else:
         _build_cat_local(name, path)
@@ -169,9 +169,15 @@ def dummy_catalogue(repo_path):
     Fixture that returns a dummy `A.catalogue`
     which contains the `dummy` mech.
     """
-    path = repo_path / "test" / "unit" / "dummy"
-    cat_path = _build_cat("dummy", path)
-    return A.load_catalogue(str(cat_path))
+    try:
+        path = repo_path / "test" / "unit" / "dummy"
+        cat_path = _build_cat("dummy", path)
+        cat = A.load_catalogue(str(cat_path))
+    except Exception:
+        raise SkipTest(
+            "Couldn't build catalogue, maybe need to install Arbor first?"
+        ) from None
+    return cat
 
 
 @_fixture