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Upgraded to version 5.20.2.
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‎.github/workflows/brief.yml‎

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@@ -15,14 +15,14 @@ jobs:
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strategy:
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fail-fast: false
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matrix:
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platform: [windows-latest, macos-latest, ubuntu-18.04]
18+
platform: [windows-latest, macos-latest, ubuntu-latest]
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xml_parser_option: ["-DWITH_EXPAT"]
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with_namespace: ["True"]
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strict: ["True"]
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with_examples: ["True"]
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package_option: ["-DWITH_ALL_PACKAGES=ON"]
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language_bindings:
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[ "-DWITH_JAVA=True -DWITH_CSHARP=True -DWITH_PYTHON=True"]
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[ "-DWITH_JAVA=True -DWITH_CSHARP=True"]
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cpp_standard: [98, 20]
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runs-on: ${{ matrix.platform }}
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@@ -72,14 +72,17 @@ jobs:
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shell: bash
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run: |
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echo RUNTIME_LINKING_OPTION="-DWITH_STATIC_RUNTIME=ON" >> "${GITHUB_ENV}"
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echo PYTHON_LINKING_OPTION="-DWITH_PYTHON=ON" >> "${GITHUB_ENV}"
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- name: Install Ubuntu dependencies
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# ubuntu already has SWIG and libxml2 by default
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if: matrix.platform == 'ubuntu-18.04'
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if: matrix.platform == 'ubuntu-latest'
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shell: bash
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run: |
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sudo apt-get update
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sudo apt-get install -y check ccache
82-
echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
85+
echo PYTHON_LINKING_OPTION="-DWITH_PYTHON=ON -DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
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echo R_BINDINGS="-DWITH_R=True" >> "${GITHUB_ENV}"
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git clone https://github.com/libexpat/libexpat
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cmake -G Ninja -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=./dependencies -B libexpat -S libexpat/expat

‎.github/workflows/doxygen.yml‎

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name: Documentation generation
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on:
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workflow_dispatch:
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pull_request:
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types: [opened, synchronize, ready_for_review, reopened] # defaults + ready_to_review
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branches:
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- development
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v3
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- uses: seanmiddleditch/gha-setup-ninja@master
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- name: Install Ubuntu dependencies
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shell: bash
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run: |
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sudo apt-get update
23+
sudo apt-get install --no-install-recommends -y check ccache doxygen graphviz
24+
git clone https://github.com/libexpat/libexpat
25+
cmake -G Ninja -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=./dependencies -B libexpat -S libexpat/expat
26+
cmake --build libexpat
27+
cmake --install libexpat
28+
29+
- name: Create Build Environment
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run: cmake -E make_directory ${{runner.workspace}}/build
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32+
# - name: Setup tmate session
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# uses: mxschmitt/action-tmate@v3
34+
35+
- name: Configure
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shell: bash
37+
working-directory: ${{runner.workspace}}/build
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run: |
39+
cmake $GITHUB_WORKSPACE \
40+
-G "Ninja" \
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-DCMAKE_BUILD_TYPE=Debug \
42+
-DWITH_CHECK=OFF \
43+
-DWITH_LIBXML=OFF \
44+
-DWITH_EXPAT=ON \
45+
-DWITH_STABLE_PACKAGES=ON \
46+
-DWITH_DOXYGEN=ON
47+
48+
- name: Build
49+
working-directory: ${{runner.workspace}}/build
50+
shell: bash
51+
run: |
52+
cmake --build . --config Release --target api_docs_cpp
53+
54+
- name: Deploy
55+
uses: peaceiris/actions-gh-pages@v3
56+
with:
57+
github_token: ${{ secrets.GITHUB_TOKEN }}
58+
publish_dir: ./docs/formatted/cpp-api

‎.github/workflows/extensive.yml‎

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@@ -21,7 +21,7 @@ jobs:
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fail-fast: false
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matrix:
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xml_parser_option: ["-DWITH_LIBXML"]
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platform: [windows-latest, macos-latest, ubuntu-18.04]
24+
platform: [windows-latest, macos-latest, ubuntu-latest]
2525
with_namespace: ["True", "False"]
2626
strict: ["True"]
2727
with_examples: ["True"]
@@ -64,14 +64,14 @@ jobs:
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language_bindings: ""
6565
# extra Ubuntu runs
6666
- xml_parser_option: "-DWITH_EXPAT"
67-
platform: ubuntu-18.04
67+
platform: ubuntu-latest
6868
with_namespace: "True"
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strict: "True"
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with_examples: "True"
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package_option: "-DWITH_ALL_PACKAGES=ON"
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language_bindings: ""
7373
- xml_parser_option: "-DWITH_XERCES"
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platform: ubuntu-18.04
74+
platform: ubuntu-latest
7575
with_namespace: "True"
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strict: "True"
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with_examples: "True"
@@ -135,9 +135,10 @@ jobs:
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- name: Install Ubuntu dependencies
137137
# ubuntu already has SWIG and libxml2 by default
138-
if: matrix.platform == 'ubuntu-18.04'
138+
if: matrix.platform == 'ubuntu-latest'
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shell: bash
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run: |
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sudo apt-get update
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sudo apt-get install -y check libxerces-c-dev expat ccache
142143
echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
143144
git clone https://github.com/libexpat/libexpat

‎.github/workflows/matlab.yml‎

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name: Matlab (ubuntu) build and test
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on: [push]
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env:
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MATLAB_VERSION: R2021a
7+
CC: gcc-9
8+
CXX: g++-9
9+
10+
jobs:
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build:
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runs-on: ubuntu-latest
13+
steps:
14+
- name: Checkout code
15+
uses: actions/checkout@v3
16+
17+
- uses: seanmiddleditch/gha-setup-ninja@master
18+
19+
- name: Set up MATLAB
20+
uses: matlab-actions/setup-matlab@v1
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# with:
22+
# release: ${{ env.MATLAB_VERSION }}
23+
24+
- name: Install Ubuntu dependencies
25+
shell: bash
26+
run: |
27+
sudo apt-get update
28+
sudo apt-get install -y check ccache
29+
git clone https://github.com/libexpat/libexpat
30+
cmake -G Ninja -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=./dependencies -B libexpat -S libexpat/expat
31+
cmake --build libexpat
32+
cmake --install libexpat
33+
34+
- name: Create Build Environment
35+
run: cmake -E make_directory ${{runner.workspace}}/build
36+
37+
# - name: Setup tmate session
38+
# uses: mxschmitt/action-tmate@v3
39+
40+
- name: Configure
41+
shell: bash
42+
working-directory: ${{runner.workspace}}/build
43+
run: |
44+
cmake $GITHUB_WORKSPACE \
45+
-G "Ninja" \
46+
-DCMAKE_BUILD_TYPE=Debug \
47+
-DWITH_CHECK=ON \
48+
-DWITH_LIBXML=OFF \
49+
-DWITH_EXPAT=ON \
50+
-DWITH_MATLAB=ON \
51+
-DWITH_STABLE_PACKAGES=ON
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53+
- name: Build
54+
working-directory: ${{runner.workspace}}/build
55+
shell: bash
56+
run: |
57+
cmake --build . --config Debug --target matlab_binding_TranslateSBML
58+
cmake --build . --config Debug --target matlab_binding_OutputSBML
59+
60+
- name: Run Test
61+
uses: matlab-actions/run-command@v1
62+
with:
63+
command: cd('../build/src/bindings/matlab/test'); runTests

‎.github/workflows/octave.yml‎

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working-directory: ${{runner.workspace}}/build
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shell: bash
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run: |
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cmake -DCMAKE_INSTALL_PREFIX=${{runner.workspace}}/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DWITH_BZIP2=ON -DWITH_CHECK=OFF -DWITH_EXPAT=ON -DWITH_LIBXML=OFF -DWITH_OCTAVE=ON $GITHUB_WORKSPACE
45+
cmake -DCMAKE_INSTALL_PREFIX=${{runner.workspace}}/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DWITH_BZIP2=ON -DWITH_CHECK=OFF -DWITH_EXPAT=ON -DWITH_LIBXML=OFF -DWITH_OCTAVE=ON -DWITH_STABLE_PACKAGES=ON $GITHUB_WORKSPACE
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- name: Build
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working-directory: ${{runner.workspace}}/build

‎.github/workflows/store-artefact.yml‎

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strategy:
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fail-fast: false
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matrix:
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platform: [windows-latest, macos-latest, ubuntu-18.04]
22+
platform: [windows-latest, macos-latest, ubuntu-latest]
2323
xml_parser_option: ["-DWITH_EXPAT=ON"]
2424
with_namespace: ["True"]
2525
strict: ["True"]
@@ -88,9 +88,10 @@ jobs:
8888
8989
- name: Install Ubuntu dependencies
9090
# ubuntu already has SWIG but expat is too old
91-
if: matrix.platform == 'ubuntu-18.04'
91+
if: matrix.platform == 'ubuntu-latest'
9292
shell: bash
9393
run: |
94+
sudo apt-get update
9495
sudo apt-get install -y check ccache
9596
echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
9697
git clone https://github.com/libexpat/libexpat
@@ -245,7 +246,7 @@ jobs:
245246
if-no-files-found: error
246247

247248
- name: Upload Ubuntu binary archive
248-
if: matrix.platform == 'ubuntu-18.04'
249+
if: matrix.platform == 'ubuntu-latest'
249250
uses: actions/upload-artifact@v2
250251
with:
251252
name:

‎.gitignore‎

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# temporary files during testing
228228
src/sbml/test/test-data/tempOut.xml
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dev/packages/create_archives/*.zip
230+
231+
# temporary files during documentation generation
232+
docs/src/common-text/libsbml-group-spatial-intro.html
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docs/src/doxygen-config-common.txt
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docs/src/doxygen-config-c.1.txt
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docs/src/doxygen-config-c.2.txt
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docs/src/doxygen-config-cpp.1.txt
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docs/src/doxygen-config-cpp.2.txt
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docs/src/doxygen-config-python.1.txt
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docs/src/doxygen-config-python.2.txt

‎CMakeLists.txt‎

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@@ -175,6 +175,7 @@ set (LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindLIBSBML.
175175

176176
# Whether to compile examples
177177
option(WITH_EXAMPLES "Compile the libSBML example programs." OFF)
178+
option(WITH_CHECK "Enable testing of libSBML." OFF)
178179

179180
# Which language bindings should be built
180181
option(WITH_CSHARP "Generate the C# language interface for libSBML." OFF)
@@ -191,7 +192,7 @@ option(WITH_STABLE_PACKAGES "Compile libSBML with all stable packages." OFF)
191192
option(WITH_ALL_PACKAGES "Compile libSBML with all packages." OFF)
192193

193194
if (WITH_ALL_PACKAGES)
194-
set(_EXPERIMENTAL_PACKGES "arrays;dyn;spatial;REQUIREDELEMENTS")
195+
set(_EXPERIMENTAL_PACKGES "arrays;dyn;REQUIREDELEMENTS")
195196
foreach(package ${_EXPERIMENTAL_PACKGES})
196197
string(TOUPPER ${package} package_upper)
197198
string(CONCAT package_option "ENABLE_" ${package_upper})
@@ -201,7 +202,7 @@ if (WITH_ALL_PACKAGES)
201202
endif(WITH_ALL_PACKAGES)
202203

203204
if (WITH_STABLE_PACKAGES)
204-
set(_STABLE_PACKGES "comp;distrib;fbc;groups;layout;multi;qual;render")
205+
set(_STABLE_PACKGES "comp;distrib;fbc;groups;layout;multi;qual;render;spatial")
205206
foreach(package ${_STABLE_PACKGES})
206207
string(TOUPPER ${package} package_upper)
207208
string(CONCAT package_option "ENABLE_" ${package_upper})
@@ -1060,10 +1061,10 @@ libSBML version ${PACKAGE_VERSION}
10601061
----------------------------------------------------------------------
10611062
10621063
More information and the latest version are available online at
1063-
http://sbml.org/Software/libSBML
1064+
https://sbml.org/software/libsbml/
10641065
10651066
Please report problems using the issue tracker at
1066-
http://sbml.org/Software/libsbml/issue-tracker
1067+
https://github.com/sbmlteam/libsbml/issues
10671068
10681069
To contact the developers directly, email [email protected]
10691070

‎CMakeModules/FindBZ2.cmake‎

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include(CheckLibraryExists)
2+
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string(TOUPPER ${PROJECT_NAME} _UPPER_PROJECT_NAME)
24
set(_PROJECT_DEPENDENCY_DIR ${_UPPER_PROJECT_NAME}_DEPENDENCY_DIR)
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‎CMakeModules/FindLIBXML.cmake‎

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include(CheckLibraryExists)
2+
include(CheckCSourceCompiles)
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34
string(TOUPPER ${PROJECT_NAME} _UPPER_PROJECT_NAME)
45
set(_PROJECT_DEPENDENCY_DIR ${_UPPER_PROJECT_NAME}_DEPENDENCY_DIR)

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