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Commit ec82d64b authored by Hu Zhao's avatar Hu Zhao
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docs: elaborate on installation and add info about tests

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...@@ -11,13 +11,15 @@ efficiently inverstigating uncertainties associated with physics-based models ...@@ -11,13 +11,15 @@ efficiently inverstigating uncertainties associated with physics-based models
Python-related dependencies are automatically taken care of. It should be noted Python-related dependencies are automatically taken care of. It should be noted
that some modules of `PSimPy` rely on / take advantage of non-Python package and that some modules of `PSimPy` rely on / take advantage of non-Python package and
software. More specifically, the emulator module `robustgasp.py` relies on the R software. More specifically, the emulator module `robustgasp.py` relies on the R
package `RobustGaSP`; the simulator module `ravaflow.py` relies on the open package `RobustGaSP`; the simulator module `ravaflow24.py` relies on the open
source software `r.avaflow 2.4`. If you want to use these modules or any other source software `r.avaflow 2.4`. If you want to use these modules or any other
modules relying on these modules, corresponding non-Python dependencies need to modules relying on these modules, corresponding non-Python dependencies need to
be installed. be installed.
You can find how to install `r.avaflow 2.4` following its official documentation If the simulator module `ravaflow.py` is desired, you may follow the official
under https://www.landslidemodels.org/r.avaflow/. documentation of `r.avaflow 2.4` under https://www.landslidemodels.org/r.avaflow/
to install it. The installation of the R package `RobustGaSP` is covered in
following steps.
We recommond you to install `PSimPy` in a virtual environment such as a `conda` We recommond you to install `PSimPy` in a virtual environment such as a `conda`
environment. You may want to first install `Anaconda` or `Miniconda` if you environment. You may want to first install `Anaconda` or `Miniconda` if you
...@@ -29,9 +31,9 @@ haven't. The steps afterwards are as follows: ...@@ -29,9 +31,9 @@ haven't. The steps afterwards are as follows:
conda create --name your_env_name python=3.9 conda create --name your_env_name python=3.9
``` ```
2. Install `R` if you don't have it on your machine 2. Install `R` if you don't have it on your machine (if you have `R`, you can
(if you have `R`, you can skip this step; alternatively, you can follow this step skip this step; alternatively, you can still follow this step to install `R` in
to install `R` in the conda environment): the conda environment):
```bash ```bash
conda activate your_env_name conda activate your_env_name
conda install -c conda-forge r-base=3.6 conda install -c conda-forge r-base=3.6
...@@ -41,22 +43,33 @@ conda install -c conda-forge r-base=3.6 ...@@ -41,22 +43,33 @@ conda install -c conda-forge r-base=3.6
```bash ```bash
R R
install.packages("RobustGaSP",repos="https://cran.r-project.org",version="0.6.4") install.packages("RobustGaSP",repos="https://cran.r-project.org",version="0.6.4")
q() ```
Try if it is successfully installed by
```bash
library("RobustGaSP")
``` ```
4. Configure the environment variable `R_HOME` so that `rpy2` knows where to find 4. Configure the environment variable `R_HOME` so that `rpy2` knows where to find
`R` packages. You can find the value of your `R_HOME` by typing the following `R` packages. You can find your `R_HOME` by typing the following command in the
command in the R terminal: R terminal:
```bash ```bash
R.home() R.home()
q()
``` ```
Then set `R_HOME` in your conda environment by It is a path like ".../lib/R". Set the environment variable `R_HOME` in your
conda environment by
```bash ```bash
conda env config vars set R_HOME=your_R_HOME_value conda env config vars set R_HOME=your_R_HOME
```
Afterwards reactivate your conda environment to make the change take effect by
```bash
conda deactivate
conda activate your_env_name
``` ```
5. Install `PSimPy` using `pip` in your conda environment by 5. Install `PSimPy` using `pip` in your conda environment by
```bash ```bash
conda install -c conda-forge pip
pip install psimpy pip install psimpy
``` ```
...@@ -66,10 +79,34 @@ Now you should have `PSimPy` and its dependencies successfully installed. ...@@ -66,10 +79,34 @@ Now you should have `PSimPy` and its dependencies successfully installed.
Examples are currently in preparation and will be available soon in coming Examples are currently in preparation and will be available soon in coming
versions. You may want to have a look at the tests which are currently available versions. You may want to have a look at the tests which are currently available
at https://git-ce.rwth-aachen.de/mbd/psimpy. They give a glimpse of how `PSimpy` at https://git-ce.rwth-aachen.de/mbd/psimpy. They give a glimpse of how `PSimpy`
can be used. can be used. You may download the `tests` folder onto your local machine, and run
any test using `pytest`.
First install `pytest` by
```bash
conda activate your_env_name
conda install pytest
```
Then navigate to the folder where `tests` folder is located on your machine.
You may run all the tests by
```bash
pytest tests/
```
or a specific test like `test_active_learning` by
```bash
pytest tests/test_active_learning.py
```
Some tests save results including plots into temporary folders. The temporary
folders will be deleted automatically if `test_clear_temp_file` is called. If
you want to exclude a specific test such as `test_clear_temp_file`, you may run
```bash
pytest tests/ --ignore=tests/test_clear_temp_file.py
```
## Documentation ## Documentation
Documentation is currently in preparation and will be available soon. The source codes of `PSimPy` contains detailed docstrings which explain how it
can be used. More documentation about the theories is currently in preparation
and will be available soon.
## License ## License
......
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