Remove python (SimVascular#34)

* Remove python folder * Delete python test * Make simulate function return a pandas dataframe * Cleanup tests and dependencies * Remove coverage settings for pytest * Remove python doc * Move cpp docs one level up * Update doxyfile * Update Readme * Update github actions * Remove unnecessary entries from gitignore * Fix bug * Add stub file * Fix tests * Test cases for shared library interface (SimVascular#33) * added test case and included in github/workflows/test.yml * modified test * included dylib extension for macos * clean up * added test2 * updated library path * add cmake build to github workflows * updated docs * more docs updates * added svzerdcalibrator to features in doc * cmake build for interface tests * tests use common LPNSolverInterface * added to github workflows --------- Co-authored-by: Karthik Menon <[email protected]> Co-authored-by: Karthik Menon <[email protected]> Co-authored-by: Karthik Menon <[email protected]> * Remove python folder * Delete python test * Make simulate function return a pandas dataframe * Cleanup tests and dependencies * Remove coverage settings for pytest * Remove python doc * Move cpp docs one level up * Update doxyfile * Update Readme * Update github actions * Remove unnecessary entries from gitignore * Fix bug * Add stub file * Fix tests * Fix bug * Update documentation * Fix bug --------- Co-authored-by: Jakob Richter <[email protected]> Co-authored-by: Karthik Menon <[email protected]> Co-authored-by: Karthik Menon <[email protected]> Co-authored-by: Karthik Menon <[email protected]> Co-authored-by: Karthik Menon <[email protected]> Co-authored-by: Martin R. Pfaller <[email protected]>
menon-karthik · Sep 20, 2023 · 7d8afbf · 7d8afbf
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diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -1,4 +1,4 @@
-# This workflow builds and deploys the html documentation for svZeroDSolver.
+# This workflow builds and deploys the html documentation for svZeroDPlus.
 name: Documentation
 on: [push, pull_request]
 permissions:
@@ -8,32 +8,23 @@ jobs:
  runs-on: ubuntu-latest
  steps:
  - uses: actions/checkout@v2
- - name: Make html directory
- run: mkdir docs/html
+ - name: Make build directory
+ run: mkdir docs/build
  - name: Build doxygen documentation
  continue-on-error: true
  uses: mattnotmitt/[email protected]
  with:
  working-directory: '.'
- doxyfile-path: 'docs/cpp/Doxyfile'
+ doxyfile-path: 'docs/Doxyfile'
  enable-latex: true
- - name: Install sphinx dependencies
- run: |
- conda create -n zerod python=3.9
- conda run -n zerod pip install -e .[dev]
- - name: Build sphinx documentation
- continue-on-error: true
- run: |
- conda run -n zerod sphinx-apidoc -o docs/python/source svzerodsolver
- conda run -n zerod sphinx-build -b html -d docs/python/build/doctrees docs/python/source docs/html/python
  - name: Save documentation
  uses: actions/upload-artifact@v3
  with:
  name: documentation
- path: ./docs/html
+ path: ./docs/build/html
  - name: Deploy documentation
  if: github.ref == 'refs/heads/master'
  uses: peaceiris/actions-gh-pages@v3
  with:
  github_token: ${{ secrets.GITHUB_TOKEN }}
- publish_dir: ./docs/html
+ publish_dir: ./docs/build/html
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,10 +1,9 @@
-# This workflow builds and tests svZeroDSolver. The Python version is tested on
-# ubuntu and the C++ version is built and tested on different versions of
-# ubuntu and macOS.
+# This workflow builds and tests svZeroDPlus. It is built and tested on
+# different versions of ubuntu and macOS.
 name: Build and test
 on: [push, pull_request]
 jobs:
- cpp:
+ test:
  runs-on: ${{ matrix.os }}
  strategy:
  matrix:
@@ -18,11 +17,11 @@ jobs:
  - name: Install svZeroDPlus
  run: |
  conda create -n zerod python=3.9
- conda run -n zerod pip install pytest pytest-cov pytest-mock
- conda run -n zerod pip install -e .
+ conda run -n zerod pip install -e ".[dev]"
  - name: Test the build
  run: |
- conda run -n zerod pytest tests/test_integration_cpp.py
+ cd tests
+ conda run -n zerod pytest
  - name: Build using CMake
  run: |
  mkdir Release
@@ -39,26 +38,4 @@ jobs:
  cd test_01
  ./svZeroD_interface_test01 ../../../../Release ../../test_01/svzerod_3Dcoupling.json
  cd ../test_02
- ./svZeroD_interface_test02 ../../../../Release ../../test_02/svzerod_tuned.json
- python:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Set up environment
- uses: actions/setup-python@v2
- with:
- python-version: 3.9
- - name: Install dependencies
- run: |
- conda create -n zerod python=3.9
- conda run -n zerod pip install pytest pytest-cov pytest-mock
- conda run -n zerod pip install -e .
- - name: Run pytest
- run: |
- conda run -n zerod pytest tests/test_integration.py
- - name: Save coverage report
- uses: actions/upload-artifact@v3
- with:
- name: coverage_report
- path: htmlcov
-
+ ./svZeroD_interface_test02 ../../../../Release ../../test_02/svzerod_tuned.json
diff --git a/.gitignore b/.gitignore
@@ -18,11 +18,7 @@ __pycache__
 public
 
 # Documentation
-docs/html
-docs/python/source/*.rst
-!docs/python/source/index.rst
-!docs/python/source/modules.rst
-docs/python/build
+docs/build
 
 # C++ build and externals directories
 Release*/

diff --git a/README.md b/README.md
@@ -9,14 +9,11 @@
 </div>
 
 svZeroDPlus is a fast simulation tool for modeling the hemodynamics of
-vascular networks using zero-dimensional (0D) lumped parameter models. There
-are two different implementations of the solver, a high performance C++
-version and an easy to use Python version. You can find more information about
-both under the following links:
+vascular networks using zero-dimensional (0D) lumped parameter models.
+You can find more information about svZeroDPlus under the following links:
 
-* [**C++ Documentation**](https://StanfordCBCL.github.io/svZeroDPlus/cpp)
-* [**C++ Developer Guide**](https://StanfordCBCL.github.io/svZeroDPlus/cpp/md_developer_guide.html)
-* [**Python Documentation**](https://StanfordCBCL.github.io/svZeroDPlus/python)
+* [**Documentation**](https://StanfordCBCL.github.io/svZeroDPlus)
+* [**Developer Guide**](https://StanfordCBCL.github.io/svZeroDPlus/md_developer_guide.html)
 * [**Wiki**](https://github.com/StanfordCBCL/svZeroDPlus/wiki)
 * [**Bug Reports**](https://github.com/StanfordCBCL/svZeroDPlus/issues)
 * [**Forum**](https://github.com/StanfordCBCL/svZeroDPlus/discussions)

diff --git a/applications/svzerodplus.cpp b/applications/svzerodplus.cpp
@@ -44,7 +44,6 @@ namespace py = pybind11;
 
 PYBIND11_MODULE(svzerodplus, m) {
  using Solver = SOLVE::Solver<double>;
- m.doc() = "svZeroDSolver";
  py::class_<Solver>(m, "Solver")
  .def(py::init([](py::dict& config) {
  const nlohmann::json& config_json = config;
@@ -55,17 +54,32 @@ PYBIND11_MODULE(svzerodplus, m) {
  const auto& config_json = nlohmann::json::parse(ifs);
  return Solver(config_json);
  }))
- .def("copy", [](Solver& solver) { return Solver(solver); })
  .def("run", &Solver::run)
  .def("get_single_result", &Solver::get_single_result)
  .def("get_single_result_avg", &Solver::get_single_result_avg)
- .def("update_block_params", &Solver::update_block_params);
+ .def("get_full_result", [](Solver& solver) {
+ py::module_ pd = py::module_::import("pandas");
+ py::module_ io = py::module_::import("io");
+ auto result = solver.get_full_result();
+ return pd.attr("read_csv")(io.attr("StringIO")(result));
+ });
 
  m.def("simulate", [](py::dict& config) {
+ py::module_ pd = py::module_::import("pandas");
+ py::module_ io = py::module_::import("io");
  const nlohmann::json& config_json = config;
  auto solver = Solver(config_json);
  solver.run();
- return solver.get_full_result();
+ return pd.attr("read_csv")(io.attr("StringIO")(solver.get_full_result()));
+ });
+ m.def("simulate", [](std::string config_file) {
+ py::module_ pd = py::module_::import("pandas");
+ py::module_ io = py::module_::import("io");
+ std::ifstream ifs(config_file);
+ const auto& config_json = nlohmann::json::parse(ifs);
+ auto solver = Solver(config_json);
+ solver.run();
+ return pd.attr("read_csv")(io.attr("StringIO")(solver.get_full_result()));
  });
  m.def("calibrate", [](py::dict& config) {
  const nlohmann::json& config_json = config;

diff --git a/docs/cpp/Doxyfile → docs/Doxyfile b/docs/cpp/Doxyfile → docs/Doxyfile
@@ -8,7 +8,7 @@ PROJECT_NAME = svZeroDPlus
 PROJECT_NUMBER = 
 PROJECT_BRIEF = 
 PROJECT_LOGO =
-OUTPUT_DIRECTORY = docs/html
+OUTPUT_DIRECTORY = docs/build
 CREATE_SUBDIRS = NO
 OUTPUT_LANGUAGE = English
 BRIEF_MEMBER_DESC = YES
@@ -27,7 +27,7 @@ ABBREVIATE_BRIEF = "The $name class" \
 ALWAYS_DETAILED_SEC = YES
 INLINE_INHERITED_MEMB = NO
 FULL_PATH_NAMES = YES
-STRIP_FROM_PATH = "src" "docs/cpp/pages"
+STRIP_FROM_PATH = "src" "docs/pages"
 STRIP_FROM_INC_PATH = 
 SHORT_NAMES = NO
 JAVADOC_AUTOBRIEF = NO
@@ -90,8 +90,8 @@ SHOW_USED_FILES = YES
 SHOW_FILES = YES
 SHOW_NAMESPACES = YES
 FILE_VERSION_FILTER =
-LAYOUT_FILE = ./docs/cpp/DoxygenLayout.xml
-CITE_BIB_FILES = ./docs/cpp/references.bib
+LAYOUT_FILE = ./docs/DoxygenLayout.xml
+CITE_BIB_FILES = ./docs/references.bib
 #---------------------------------------------------------------------------
 # Configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
@@ -106,7 +106,7 @@ WARN_LOGFILE =
 # Configuration options related to the input files
 #---------------------------------------------------------------------------
 INPUT = "src" \
- "docs/cpp/pages"
+ "docs/pages"
 INPUT_ENCODING = UTF-8
 FILE_PATTERNS = *.cpp \
  *.hpp \
@@ -122,7 +122,7 @@ EXCLUDE_SYMBOLS =
 EXAMPLE_PATH = 
 EXAMPLE_PATTERNS = *
 EXAMPLE_RECURSIVE = NO
-IMAGE_PATH = docs/cpp
+IMAGE_PATH = images
 INPUT_FILTER =
 FILTER_PATTERNS =
 FILTER_SOURCE_FILES = NO
@@ -149,12 +149,12 @@ IGNORE_PREFIX =
 # Configuration options related to the HTML output
 #---------------------------------------------------------------------------
 GENERATE_HTML = YES
-HTML_OUTPUT = cpp
+HTML_OUTPUT = html
 HTML_FILE_EXTENSION = .html
 HTML_HEADER =
 HTML_FOOTER =
 HTML_STYLESHEET =
-HTML_EXTRA_STYLESHEET = ./docs/cpp/doxygen-awesome.css
+HTML_EXTRA_STYLESHEET = ./docs/doxygen-awesome.css
 HTML_EXTRA_FILES =
 HTML_COLORSTYLE_HUE = 220
 HTML_COLORSTYLE_SAT = 100

diff --git a/docs/cpp/DoxygenLayout.xml → docs/DoxygenLayout.xml b/docs/cpp/DoxygenLayout.xml → docs/DoxygenLayout.xml
diff --git a/docs/cpp/doxygen-awesome.css → docs/doxygen-awesome.css b/docs/cpp/doxygen-awesome.css → docs/doxygen-awesome.css
diff --git a/docs/cpp/pages/developer_guide.md → docs/pages/developer_guide.md b/docs/cpp/pages/developer_guide.md → docs/pages/developer_guide.md
@@ -95,7 +95,7 @@ The documentation is automatically build in the GitHub CI/CD and published
 on GitHub pages. If you want to build the documentation locally, you can use:
 
 ```
-doxygen docs/cpp/Doxyfile
+doxygen docs/Doxyfile
 ```
 
 If you do not have Doxygen install you can do that with `brew install doxygen`

diff --git a/docs/cpp/pages/main.md → docs/pages/main.md b/docs/cpp/pages/main.md → docs/pages/main.md
@@ -125,35 +125,35 @@ you installed svZerodPlus via pip to enable this feature. We start by
 importing svzerodplus:
 
 ```python
-import svzerodplus
+>>> import svzerodplus
 ```
 
 Next, we create a solver from our configuration. The configuration can
 be specified by either a path to a JSON file:
 
 ```python
-solver = svzerodplus.Solver("tests/cases/steadyFlow_RLC_R.json")
+>>> solver = svzerodplus.Solver("tests/cases/steadyFlow_RLC_R.json")
 ```
 
 or as a Python dictionary:
 
 ```python
-my_config = {...}
-solver = svzerodplus.Solver(my_config)
+>>> my_config = {...}
+>>> solver = svzerodplus.Solver(my_config)
 ```
 
 To run the simulation we add:
 
 ```python
-solver.run()
+>>> solver.run()
 ```
 
 The simulation result is now saved in the solver instance. We can obtain
 results for individual degrees-of-freedom (DOFs) as
 ```python
-solver.get_single_result("flow:INFLOW:branch0_seg0")
+>>> solver.get_single_result("flow:INFLOW:branch0_seg0")
 
->>> array([5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5.,
+array([5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5.,
  5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5.,
  5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5.,
  5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5.,
@@ -164,11 +164,57 @@ The naming of the DOFs is similar to how results are written if the simulation
 option `output_variable_based` is activated (see below). We can also obtain
 the mean result for a DOF over time with:
 ```python
-solver.get_single_result_avg("flow:INFLOW:branch0_seg0")
+>>> solver.get_single_result_avg("flow:INFLOW:branch0_seg0")
+
+5.0
+```
+
+Or the result of the full simulation as a pandas data frame:
+
+```python
+>>> solver.get_full_result()
+
+ name time flow_in flow_out pressure_in pressure_out
+0 branch0_seg0 0.00 5.0 5.0 1100.0 600.0
+1 branch0_seg0 0.01 5.0 5.0 1100.0 600.0
+2 branch0_seg0 0.02 5.0 5.0 1100.0 600.0
+3 branch0_seg0 0.03 5.0 5.0 1100.0 600.0
+4 branch0_seg0 0.04 5.0 5.0 1100.0 600.0
+.. ... ... ... ... ... ...
+96 branch0_seg0 0.96 5.0 5.0 1100.0 600.0
+97 branch0_seg0 0.97 5.0 5.0 1100.0 600.0
+98 branch0_seg0 0.98 5.0 5.0 1100.0 600.0
+99 branch0_seg0 0.99 5.0 5.0 1100.0 600.0
+100 branch0_seg0 1.00 5.0 5.0 1100.0 600.0
+
+[101 rows x 6 columns]
+```
+
+There is also a function to retrieve the full result directly based on a given configuration:
+
+```python
+
+>>> my_config = {...}
+>>> svzerodplus.simulate(my_config)
+
+ name time flow_in flow_out pressure_in pressure_out
+0 branch0_seg0 0.00 5.0 5.0 1100.0 600.0
+1 branch0_seg0 0.01 5.0 5.0 1100.0 600.0
+2 branch0_seg0 0.02 5.0 5.0 1100.0 600.0
+3 branch0_seg0 0.03 5.0 5.0 1100.0 600.0
+4 branch0_seg0 0.04 5.0 5.0 1100.0 600.0
+.. ... ... ... ... ... ...
+96 branch0_seg0 0.96 5.0 5.0 1100.0 600.0
+97 branch0_seg0 0.97 5.0 5.0 1100.0 600.0
+98 branch0_seg0 0.98 5.0 5.0 1100.0 600.0
+99 branch0_seg0 0.99 5.0 5.0 1100.0 600.0
+100 branch0_seg0 1.00 5.0 5.0 1100.0 600.0
+
+[101 rows x 6 columns]
 
->>> 5.0
 ```
 
+
 ## Configuration
 
 svZeroDSolver is configured using either a JSON file or a Python

diff --git a/docs/python/source/conf.py b/docs/python/source/conf.py