rename pydepsi to depsi

Author: rogerkuou

README.md

@@ -1,6 +1,5 @@
-# PyDePSI (Tentative name)
-
-This is repository is WIP, where we are developing a Python package for inteferometric SAR processing. The software will be inspired by the MATLAB software DePSI, but implemented in Python and include recent developments in the field.
+# DePSI 
+This is the WIP repository for the Python version of DePSI *(), a Python package for inteferometric SAR processing. The software is inspired by the MATLAB version DePSI. In this repository, we implement classic DePSI algorithms and new InSAR developments in Python.
 
 ## Installation for development
 
@@ -9,22 +8,22 @@ It is assumed that you have `mamba` installed. If not, you can find the installa
 Clone this repository and `cd` into it:
 
 ```bash
-git clone git@github.com:MotionbyLearning/PyDePSI.git
-cd PyDePSI
+git clone git@github.com:TUDelftGeodesy/DePSI.git
+cd DePSI
 ```
 
-Create a new conda environment (here we give an example name `pydepsi-dev`) with `mamba`.:
+Create a new conda environment (here we give an example name `depsi-dev`) with `mamba`.:
 
 ```bash
-mamba create -c conda-forge -n pydepsi-dev python=3.12
+mamba create -c conda-forge -n depsi-dev python=3.12
 ```
 
 Here we use Python 3.12 since we aim to support python 3.10 and above.
 
 Activate the environment:
 
 ```bash
-mamba activate pydepsi-dev
+mamba activate depsi-dev
 ```
 
 Install this package in development mode:

pydepsi/__init__.py depsi/__init__.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 
-from pydepsi.utils import _orbit_fit
+from depsi.utils import _orbit_fit
 
 # Define constants
 SC_N_PATTERN = r"\s+([-+]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?)"

pydepsi/io.py depsi/io.py

@@ -1,6 +1,6 @@
-# Example script for PyDePSI
+# Example script for DePSI
 
-This folder contains scripts to run PyDePSI on SLURM infrastructures. One needs to modify `exec_python.slurm` to specify 1) a conda environment with PyDePSI and 2) the desired Python script. The following command can be used to execute the specified script:
+This folder contains scripts to run DePSI on SLURM infrastructures. One needs to modify `exec_python.slurm` to specify 1) a conda environment with DePSI and 2) the desired Python script. The following command can be used to execute the specified script:
 
 ```bash
 sbatch exec_python.slurm
@@ -10,12 +10,12 @@ The submitted SLURM job will execute the Python script. A Dask cluster will be c
 
 ## Prerequisites
 
-It is assumed that the user has a working conda environment with PyDePSI installed. This conda environment is required in the `exec_python.slurm` script. 
+It is assumed that the user has a working conda environment with DePSI installed. This conda environment is required in the `exec_python.slurm` script. 
 
-Some HPC system (for example SURF Spider system, see [this documentation](https://doc.spider.surfsara.nl/en/latest/Pages/software_on_spider.html)) may require the user to execute the conda environment inside a container. One can for example use the [LUMI container wrapper](https://docs.lumi-supercomputer.eu/software/installing/container-wrapper/) as a solution. The [JupyterDaskOnSLURM](https://github.com/RS-DAT/JupyterDaskOnSLURM/tree/main) tool from RS-DAT platform provides the LUMI container wrapper together with Jupyter Lab interface and Dask-Slurm cluster, see the [Container wrapper for Spider system](https://github.com/RS-DAT/JupyterDaskOnSLURM/blob/main/user-guide.md#container-wrapper-for-spider-system) section. For more information on the RS-DAT platform, please refer to the following section "PyDePSI with RS-DAT".
+Some HPC system (for example SURF Spider system, see [this documentation](https://doc.spider.surfsara.nl/en/latest/Pages/software_on_spider.html)) may require the user to execute the conda environment inside a container. One can for example use the [LUMI container wrapper](https://docs.lumi-supercomputer.eu/software/installing/container-wrapper/) as a solution. The [JupyterDaskOnSLURM](https://github.com/RS-DAT/JupyterDaskOnSLURM/tree/main) tool from RS-DAT platform provides the LUMI container wrapper together with Jupyter Lab interface and Dask-Slurm cluster, see the [Container wrapper for Spider system](https://github.com/RS-DAT/JupyterDaskOnSLURM/blob/main/user-guide.md#container-wrapper-for-spider-system) section. For more information on the RS-DAT platform, please refer to the following section "DePSI with RS-DAT".
 
-## PyDePSI with RS-DAT
+## DePSI with RS-DAT
 
-The [RS-DAT platform](https://rs-dat.github.io/RS-DAT/) developed by Netherlands eScience Center can be used to start up a Jupyter environment with Dask cluster. RS-DAT can also be used to start a Dask cluster scheduler on a HPC system, to which other Python scripts/processes can connect by providing the scheduler address. In this way, the same Dask cluster can be re-used for multiple Python script executions. This can be useful for developing and testing PyDePSI scripts.
+The [RS-DAT platform](https://rs-dat.github.io/RS-DAT/) developed by Netherlands eScience Center can be used to start up a Jupyter environment with Dask cluster. RS-DAT can also be used to start a Dask cluster scheduler on a HPC system, to which other Python scripts/processes can connect by providing the scheduler address. In this way, the same Dask cluster can be re-used for multiple Python script executions. This can be useful for developing and testing DePSI scripts.
 
 Please refer to the [RS-DAT JupyterDaskOnSLURM user guide](https://github.com/RS-DAT/JupyterDaskOnSLURM/blob/main/user-guide.md) for this option.

pydepsi/slc.py depsi/slc.py

@@ -15,8 +15,8 @@
 from dask_jobqueue import SLURMCluster
 import sarxarray
 
-from pydepsi.slc import ifg_to_slc
-from pydepsi.io import read_metadata
+from depsi.slc import ifg_to_slc
+from depsi.io import read_metadata
 
 # Make a logger to log the stages of processing
 logger = logging.getLogger(__name__)

pydepsi/utils.py depsi/utils.py

@@ -3,7 +3,7 @@ requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "pydepsi"
+name = "depsi"
 version = "0.1.0"
 requires-python = ">=3.10"
 dependencies = [
@@ -48,7 +48,7 @@ demo = [
 ]
 
 [tool.setuptools]
-packages = ["pydepsi"]
+packages = ["depsi"]
 
 [tool.pytest.ini_options]
 minversion = "6.0"
@@ -59,7 +59,7 @@ testpaths = [
 
 [tool.coverage.run]
 branch = true
-source = ["pydepsi"]
+source = ["depsi"]
 
 [tool.ruff]
 lint.select = [

examples/notebooks/demo_pydepsi.ipynb

@@ -1,4 +1,4 @@
-from pydepsi.io import read_metadata
+from depsi.io import read_metadata
 
 
 def test_read_metadata_lines_pixels():

examples/scripts/README.md

@@ -3,7 +3,7 @@
 import numpy as np
 import xarray as xr
 
-from pydepsi.slc import _slc_complex_recontruct, ifg_to_slc
+from depsi.slc import _slc_complex_recontruct, ifg_to_slc
 
 
 def test__slc_complex_recontruct():