diff --git a/ChangeLog.md b/ChangeLog.md
index c9bd1844..5112e7ee 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -1,6 +1,11 @@
 Change Log {#changelog}
 ==========
 
+# 1.4.1 - 2022-11-21 # {#changelog_1_4_1}
+- Build fixes to work with SWIG 4.1.
+- Various internal build scripts now use 'python3' rather than
+  unversioned 'python'.
+
 # 1.4 - 2022-03-10 # {#changelog_1_4}
 - RMF now requires a C++11 compiler and SWIG 3 (or later) to build. Most
   recent compilers should support C++11, such as gcc, clang
diff --git a/config.h.in b/config.h.in
index dda2d498..69e3e080 100644
--- a/config.h.in
+++ b/config.h.in
@@ -11,6 +11,11 @@
 #ifndef RMF_CONFIG_H
 #define RMF_CONFIG_H
 
+/* Protect against RMFEXPORT being defined already */
+#ifdef RMFEXPORT
+#undef RMFEXPORT
+#endif
+
 #ifdef _MSC_VER
 
 #ifdef RMF_EXPORTS
diff --git a/rmf.sublime-project b/rmf.sublime-project
deleted file mode 100644
index 7762a624..00000000
--- a/rmf.sublime-project
+++ /dev/null
@@ -1,8 +0,0 @@
-{
-	"folders":
-	[
-		{
-			"path": "../rmf"
-		}
-	]
-}
diff --git a/rmf.sublime-workspace b/rmf.sublime-workspace
deleted file mode 100644
index 14801987..00000000
--- a/rmf.sublime-workspace
+++ /dev/null
@@ -1,470 +0,0 @@
-{
-	"auto_complete":
-	{
-		"selected_items":
-		[
-			[
-				"lib",
-				"lib"
-			]
-		]
-	},
-	"buffers":
-	[
-		{
-			"file": "scripts/make-decorators.py",
-			"settings":
-			{
-				"buffer_size": 11609,
-				"line_ending": "Unix"
-			}
-		},
-		{
-			"file": "CMakeLists.txt",
-			"settings":
-			{
-				"buffer_size": 2453,
-				"line_ending": "Unix"
-			}
-		},
-		{
-			"file": "src/backend/avro/avro_schemas.h",
-			"settings":
-			{
-				"buffer_size": 3725,
-				"line_ending": "Unix"
-			}
-		},
-		{
-			"file": "src/CMakeLists.txt",
-			"settings":
-			{
-				"buffer_size": 477,
-				"line_ending": "Unix"
-			}
-		},
-		{
-			"file": "test/CMakeLists.txt",
-			"settings":
-			{
-				"buffer_size": 1101,
-				"line_ending": "Unix"
-			}
-		}
-	],
-	"build_system": "Packages/User/scons_all.sublime-build",
-	"command_palette":
-	{
-		"height": 47.0,
-		"selected_items":
-		[
-			[
-				"IMP.rmf",
-				"Build: IMP.rmf"
-			]
-		],
-		"width": 392.0
-	},
-	"console":
-	{
-		"height": 0.0
-	},
-	"distraction_free":
-	{
-		"menu_visible": true,
-		"show_minimap": false,
-		"show_open_files": false,
-		"show_tabs": false,
-		"side_bar_visible": false,
-		"status_bar_visible": false
-	},
-	"file_history":
-	[
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/CMakeLists.txt",
-		"/Users/drussel/src/rmf/rmf/AvroCpp/CMakeLists.txt",
-		"/Users/drussel/src/rmf/rmf/include/RMF/internal/hash.h",
-		"/Users/drussel/src/rmf/rmf/scripts/make-decorators.py",
-		"/Users/drussel/src/rmf/rmf/swig/RMF_HDF5.i",
-		"/Users/drussel/src/rmf/rmf/bin/rmf_pdb.cpp",
-		"/Users/drussel/src/rmf/rmf/include/RMF/compiler_macros.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/internal/swig_helpers.h",
-		"/Users/drussel/src/rmf/rmf/swig/RMF.i",
-		"/Users/drussel/src/rmf/rmf/bin/rmf_slice.cpp",
-		"/Users/drussel/src/rmf/rmf/swig/CMakeLists.txt",
-		"/Users/drussel/src/dotfiles/Library/Application Support/Sublime Text 2/Packages/Rails/form_for-submit.sublime-snippet",
-		"/Users/drussel/src/rmf/rmf/include/RMF/infrastructure_macros.h",
-		"/Users/drussel/src/rmf/rmf/AvroCpp/impl/FileStream.cc",
-		"/Users/drussel/src/rmf/rmf/doc/mapping.dox",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/MultipleAvroFileBase.cpp",
-		"/Users/drussel/src/rmf/rmf/include/RMF/Category.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/constants.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/CoordinateTransformer.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/decorator_utility.h",
-		"/Users/drussel/src/rmf/rmf/bin/rmf_interpolate.cpp",
-		"/Users/drussel/src/rmf/rmf/include/RMF/Decorator.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/types.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/Object.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/MutableAttributes.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/handle.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/Group.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/File.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/DataSetIndexD.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/DataSetD.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/DataSetCreationPropertiesD.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/DataSetAccessPropertiesD.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/ConstGroup.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/ConstFile.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/ConstDataSetD.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/ConstAttributes.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/HDF5/internal/types.h",
-		"/Users/drussel/src/rmf/rmf/src/Validator.cpp",
-		"/Users/drussel/src/rmf/rmf/src/utility.cpp",
-		"/Users/drussel/src/rmf/rmf/src/SetCurrentFrame.cpp",
-		"/Users/drussel/src/rmf/rmf/src/profile.cpp",
-		"/Users/drussel/src/rmf/rmf/src/NodeHandle.cpp",
-		"/Users/drussel/src/rmf/rmf/src/NodeConstHandle.cpp",
-		"/Users/drussel/src/rmf/rmf/src/names.cpp",
-		"/Users/drussel/src/rmf/rmf/src/log.cpp",
-		"/Users/drussel/src/rmf/rmf/src/Key.cpp",
-		"/Users/drussel/src/rmf/rmf/src/hdf5_wrapper.cpp",
-		"/Users/drussel/src/rmf/rmf/src/FrameID.cpp",
-		"/Users/drussel/src/rmf/rmf/src/FrameHandle.cpp",
-		"/Users/drussel/src/rmf/rmf/src/FrameConstHandle.cpp",
-		"/Users/drussel/src/rmf/rmf/src/FileHandle.cpp",
-		"/Users/drussel/src/rmf/rmf/src/FileConstHandle.cpp",
-		"/Users/drussel/src/rmf/rmf/src/exceptions.cpp",
-		"/Users/drussel/src/rmf/rmf/src/decorator_utility.cpp",
-		"/Users/drussel/src/rmf/rmf/src/CoordinateTransformer.cpp",
-		"/Users/drussel/src/rmf/rmf/src/internal/SharedData.cpp",
-		"/Users/drussel/src/rmf/rmf/src/internal/paths.cpp",
-		"/Users/drussel/src/rmf/rmf/src/internal/errors.cpp",
-		"/Users/drussel/src/rmf/rmf/src/internal/Transform.cpp",
-		"/Users/drussel/src/rmf/rmf/src/internal/utility.cpp",
-		"/Users/drussel/src/rmf/rmf/src/backend/hdf5/names.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/hdf5/HDF5SharedData.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/hdf5/HDF5SharedData.cpp",
-		"/Users/drussel/src/rmf/rmf/src/backend/hdf5/HDF5DataSetCacheD.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/hdf5/HDF5DataSetCache3D.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/hdf5/HDF5DataSetCache2D.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/hdf5/HDF5DataSetCache1D.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/hdf5/create.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/hdf5/create.cpp",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/SingleAvroFile.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/SingleAvroFile.cpp",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/MultipleAvroFileWriter.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/MultipleAvroFileWriter.cpp",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/MultipleAvroFileReader.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/MultipleAvroFileReader.cpp",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/MultipleAvroFileBase.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/create.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/create.cpp",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/AvroSharedData.types.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/AvroSharedData.impl.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/AvroSharedData.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/AvroKeysAndCategories.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/avro_schemas.h",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/avro_schemas.cpp",
-		"/Users/drussel/src/rmf/rmf/config.h.in",
-		"/Users/drussel/src/rmf/rmf/bin/rmf_transform.cpp",
-		"/Users/drussel/src/rmf/rmf/src/backend/avro/Data.json",
-		"/Users/drussel/src/rmf/rmf/scripts/make-all-header.py",
-		"/Users/drussel/src/rmf/rmf/bin/rmf_cat.cpp",
-		"/Users/drussel/src/rmf/rmf/bin/common.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/internal/compiler_warnings.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/internal/compiler_macros.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/internal/SharedData.h",
-		"/Users/drussel/src/rmf/rmf/include/RMF/utility.h",
-		"/Users/drussel/src/rmf/rmf/pyext/RMF.i",
-		"/Users/drussel/src/rmf/rmf/AvroCpp/test/AvrogencppTests.cc",
-		"/Users/drussel/src/rmf/rmf/include/RMF/exceptions.h",
-		"/Users/drussel/src/rmf/rmf/pyext/CMakeLists.txt",
-		"/Users/drussel/src/imp/imp/modules/base/include/exception.h",
-		"/Users/drussel/src/imp/imp/modules/base/include/open_mp.h",
-		"/Users/drussel/src/imp/imp/modules/rmf/src/frames.cpp",
-		"/Users/drussel/src/imp/imp/modules/rmf/dependency/RMF/include/RMF/FileHandle.h",
-		"/Users/drussel/src/imp/imp/modules/kernel/include/container_base.h",
-		"/Users/drussel/src/imp/imp/modules/kernel/src/Container.cpp",
-		"/Users/drussel/src/imp/imp/modules/kernel/test/test_model.py",
-		"/Users/drussel/src/imp/imp/modules/kernel/include/internal/attribute_tables.h",
-		"/Users/drussel/src/imp/imp/modules/kernel/include/declare_Model.h",
-		"/Users/drussel/src/imp/imp/modules/kernel/include/Model.h",
-		"/Users/drussel/src/imp/imp/tools/maintenance/container_templates/container/PredicateNAMEsRestraint.cc",
-		"/Users/drussel/src/imp/imp/modules/isd/test/test_GaussianProcessInterpolationRestraint.py",
-		"/Users/drussel/src/imp/imp/modules/rmf/dependency/RMF/include/RMF/FileConstHandle.h",
-		"/Users/drussel/src/imp/imp/modules/rmf/dependency/RMF/src/backend/hdf5/HDF5DataSetCache1D.h",
-		"/Users/drussel/src/imp/imp/modules/rmf/dependency/RMF/src/backend/hdf5/HDF5SharedData.cpp",
-		"/Users/drussel/src/imp/imp/modules/rmf/dependency/RMF/src/backend/hdf5/HDF5DataSetCache3D.h",
-		"/Users/drussel/src/imp/imp/modules/atom/src/BrownianDynamics.cpp",
-		"/Users/drussel/src/imp/imp/modules/kernel/src/Restraint.cpp",
-		"/Users/drussel/src/imp/imp/modules/kernel/src/Model_evaluate.cpp",
-		"/Users/drussel/src/imp/imp/modules/kernel/include/ScoreAccumulator.h",
-		"/Users/drussel/src/imp/imp/modules/kernel/include/Key.h",
-		"/Users/drussel/src/imp/imp/modules/container/include/ClosePairContainer.h",
-		"/Users/drussel/src/imp/imp/modules/core/include/ExcludedVolumeRestraint.h",
-		"/Users/drussel/Library/Application Support/Sublime Text 2/Packages/User/Preferences.sublime-settings",
-		"/Users/drussel/src/imp/imp/modules/rmf/dependency/RMF/CMakeLists.txt",
-		"/Users/drussel/src/imp/imp/modules/core/benchmark/benchmark_omp_evaluate.cpp"
-	],
-	"find":
-	{
-		"height": 35.0
-	},
-	"find_in_files":
-	{
-		"height": 0.0,
-		"where_history":
-		[
-			"/Users/drussel/src/imp/imp",
-			""
-		]
-	},
-	"find_state":
-	{
-		"case_sensitive": false,
-		"find_history":
-		[
-			"_s",
-			"Python",
-			"FileBufferCopyIn",
-			"IMP",
-			"get_all_values_impl",
-			"get_all_values_helper",
-			"test",
-			"*this",
-			"char",
-			"input_outpu",
-			"inputoutput",
-			"exception",
-			" >=",
-			"flush",
-			"frame",
-			"add_frame",
-			"+=",
-			"slack",
-			"slack estimate"
-		],
-		"highlight": true,
-		"in_selection": false,
-		"preserve_case": false,
-		"regex": false,
-		"replace_history":
-		[
-			"RMF",
-			"e"
-		],
-		"reverse": false,
-		"show_context": true,
-		"use_buffer2": true,
-		"whole_word": false,
-		"wrap": true
-	},
-	"groups":
-	[
-		{
-			"selected": 4,
-			"sheets":
-			[
-				{
-					"buffer": 0,
-					"file": "scripts/make-decorators.py",
-					"settings":
-					{
-						"buffer_size": 11609,
-						"regions":
-						{
-						},
-						"selection":
-						[
-							[
-								0,
-								0
-							]
-						],
-						"settings":
-						{
-							"syntax": "Packages/Python/Python.tmLanguage",
-							"tab_size": 2,
-							"translate_tabs_to_spaces": true
-						},
-						"translation.x": 0.0,
-						"translation.y": 0.0,
-						"zoom_level": 1.0
-					},
-					"type": "text"
-				},
-				{
-					"buffer": 1,
-					"file": "CMakeLists.txt",
-					"settings":
-					{
-						"buffer_size": 2453,
-						"regions":
-						{
-						},
-						"selection":
-						[
-							[
-								787,
-								787
-							]
-						],
-						"settings":
-						{
-							"syntax": "Packages/User/CMake Listfile.tmLanguage",
-							"tab_size": 2,
-							"translate_tabs_to_spaces": true
-						},
-						"translation.x": 0.0,
-						"translation.y": 467.0,
-						"zoom_level": 1.0
-					},
-					"type": "text"
-				},
-				{
-					"buffer": 2,
-					"file": "src/backend/avro/avro_schemas.h",
-					"settings":
-					{
-						"buffer_size": 3725,
-						"regions":
-						{
-						},
-						"selection":
-						[
-							[
-								0,
-								0
-							]
-						],
-						"settings":
-						{
-							"syntax": "Packages/C++/C++.tmLanguage",
-							"tab_size": 2,
-							"translate_tabs_to_spaces": true
-						},
-						"translation.x": 0.0,
-						"translation.y": 65.0,
-						"zoom_level": 1.0
-					},
-					"type": "text"
-				},
-				{
-					"buffer": 3,
-					"file": "src/CMakeLists.txt",
-					"settings":
-					{
-						"buffer_size": 477,
-						"regions":
-						{
-						},
-						"selection":
-						[
-							[
-								294,
-								321
-							]
-						],
-						"settings":
-						{
-							"syntax": "Packages/User/CMake Listfile.tmLanguage"
-						},
-						"translation.x": 0.0,
-						"translation.y": 0.0,
-						"zoom_level": 1.0
-					},
-					"type": "text"
-				},
-				{
-					"buffer": 4,
-					"file": "test/CMakeLists.txt",
-					"settings":
-					{
-						"buffer_size": 1101,
-						"regions":
-						{
-						},
-						"selection":
-						[
-							[
-								390,
-								390
-							]
-						],
-						"settings":
-						{
-							"syntax": "Packages/User/CMake Listfile.tmLanguage",
-							"tab_size": 2,
-							"translate_tabs_to_spaces": true
-						},
-						"translation.x": 0.0,
-						"translation.y": 0.0,
-						"zoom_level": 1.0
-					},
-					"type": "text"
-				}
-			]
-		}
-	],
-	"incremental_find":
-	{
-		"height": 0.0
-	},
-	"input":
-	{
-		"height": 31.0
-	},
-	"layout":
-	{
-		"cells":
-		[
-			[
-				0,
-				0,
-				1,
-				1
-			]
-		],
-		"cols":
-		[
-			0.0,
-			1.0
-		],
-		"rows":
-		[
-			0.0,
-			1.0
-		]
-	},
-	"menu_visible": true,
-	"output.exec":
-	{
-		"height": 453.0
-	},
-	"replace":
-	{
-		"height": 64.0
-	},
-	"save_all_on_build": true,
-	"select_file":
-	{
-		"height": 0.0,
-		"selected_items":
-		[
-		],
-		"width": 0.0
-	},
-	"select_project":
-	{
-		"height": 0.0,
-		"selected_items":
-		[
-		],
-		"width": 0.0
-	},
-	"show_minimap": true,
-	"show_open_files": false,
-	"show_tabs": true,
-	"side_bar_visible": true,
-	"side_bar_width": 223.0,
-	"status_bar_visible": true
-}
diff --git a/setup_git.py b/setup_git.py
index 70704bc9..d2916745 100755
--- a/setup_git.py
+++ b/setup_git.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """Call the main setup_git.py. This should be
 copied to the main directory of your project and named setup_git.py."""
diff --git a/tools/dev_tools/.github/workflows/build.yml b/tools/dev_tools/.github/workflows/build.yml
index 8a286104..d7190075 100644
--- a/tools/dev_tools/.github/workflows/build.yml
+++ b/tools/dev_tools/.github/workflows/build.yml
@@ -20,7 +20,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        pip install pytest-flake8 pytest-cov
+        pip install 'pytest-flake8<1.1' pytest-cov
     - name: Test
       run: |
         py.test --cov=. --cov-branch --cov-report=xml -v --flake8 .
diff --git a/tools/dev_tools/check_standards.py b/tools/dev_tools/check_standards.py
index 0fb9fb1c..ddda6c0e 100755
--- a/tools/dev_tools/check_standards.py
+++ b/tools/dev_tools/check_standards.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """Print out any violations of IMP-specific standards."""
 
diff --git a/tools/dev_tools/cleanup_code.py b/tools/dev_tools/cleanup_code.py
index dd664d47..57098b8f 100755
--- a/tools/dev_tools/cleanup_code.py
+++ b/tools/dev_tools/cleanup_code.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """Use clang-format and autopep8 when available to clean up the listed source
    files."""
diff --git a/tools/dev_tools/cleanup_pycs.py b/tools/dev_tools/cleanup_pycs.py
index 4948fb9e..705b311c 100755
--- a/tools/dev_tools/cleanup_pycs.py
+++ b/tools/dev_tools/cleanup_pycs.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """Traverses the directory tree deleting any .pyc's who do not have a
    source .py. Helpful when switching between revisions with source control."""
diff --git a/tools/dev_tools/git/bootstrap_setup_git.py b/tools/dev_tools/git/bootstrap_setup_git.py
index 1f1a1fa9..cd553ebc 100755
--- a/tools/dev_tools/git/bootstrap_setup_git.py
+++ b/tools/dev_tools/git/bootstrap_setup_git.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """Update submodules and then call the main setup_git.py. This should be
 copied to the main directory of your project and named setup_git.py."""
diff --git a/tools/dev_tools/git/setup_git.py b/tools/dev_tools/git/setup_git.py
index 0fbbbea0..ec9451b7 100755
--- a/tools/dev_tools/git/setup_git.py
+++ b/tools/dev_tools/git/setup_git.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import sys
 import os.path
diff --git a/tools/dev_tools/make_all_header.py b/tools/dev_tools/make_all_header.py
index 288c9e1a..ec9af48a 100755
--- a/tools/dev_tools/make_all_header.py
+++ b/tools/dev_tools/make_all_header.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """Make a header that lists other headers.
 usage: make_all_header.py header_name.h include_prefix headers
diff --git a/tools/dev_tools/replace.py b/tools/dev_tools/replace.py
index b16d0173..d8f76dd6 100755
--- a/tools/dev_tools/replace.py
+++ b/tools/dev_tools/replace.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """Replace all instances of argv[1] with argv[2], only updating the file if
    changes were made. """
diff --git a/tools/dev_tools/setup_cmake.py b/tools/dev_tools/setup_cmake.py
index 7b0b2507..2e33bcac 100755
--- a/tools/dev_tools/setup_cmake.py
+++ b/tools/dev_tools/setup_cmake.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """Build Files.cmake listing source files for each src, test, examples,
    benchmark directory in the subtree."""