Merge pull request #62 from mirzaees/pip-install

Pip install
insarlab · Aug 22, 2023 · 25d896f · 25d896f
2 parents 65a4b29 + b305718
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diff --git a/conda_env.yml b/conda_env.yml
@@ -9,13 +9,14 @@ channels:
   - defaults
 dependencies:
   - c-compiler
-  - python>=3.6,<3.9
+  - python>=3.9
   - cartopy
   - cvxopt
+  - rasterio
   - dask>=1.0
   - dask-jobqueue>=0.3
   - defusedxml
-  - h5py<3
+  - h5py
   - lxml
   - matplotlib
   - numpy
@@ -24,6 +25,7 @@ dependencies:
   - scikit-image
   - scipy
   - gdal
+  - mintpy
   - isce2
   - cython
   - setuptools

diff --git a/docs/install b/docs/install
diff --git a/docs/installation.md b/docs/installation.md
@@ -1,78 +1,39 @@
 ## Install MiaplPy
 
-#### 1. Set the following environment variables in your source file. It could be ~/.bash_profile file for bash user or ~/.cshrc file for csh/tcsh user.
-
-```
-if [ -z ${PYTHONPATH+x} ]; then export PYTHONPATH=""; fi
-
-##--------- MintPy ------------------##
-export MINTPY_HOME=~/tools/MintPy
-export PYTHONPATH=${PYTHONPATH}:${MINTPY_HOME}
-export PATH=${PATH}:${MINTPY_HOME}/mintpy/cli
-
-#---------- MiaplPy ------------------##
-export MIAPLPY_HOME=~/tools/MiaplPy
-export PYTHONPATH=${PYTHONPATH}:${MIAPLPY_HOME}
-export PATH=${PATH}:${MIAPLPY_HOME}/miaplpy
-export PATH=${PATH}:${MIAPLPY_HOME}/snaphu/bin
-
-```
-#### 2. Download
-
+#### 1. Download source code
 ```
 cd ~/tools
 git clone https://github.com/insarlab/MiaplPy.git
-git clone https://github.com/insarlab/MintPy.git
+cd ~/tools/MiaplPy
 ```
 
-#### 3. install dependencies
-
-Install miniconda if you have not already done so. You may need to close and restart the shell for changes to take effect.
+#### 2. Install dependencies
 ```
-# download and install miniconda
-# use wget or curl to download in command line or click from the web brower
-# MacOS users: curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o Miniconda3-latest-MacOSX-x86_64.sh
-# Linux users: curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o Miniconda3-latest-Linux-x86_64.sh
-
-# Mac users:
-miniconda_version=Miniconda3-latest-MacOSX-x86_64.sh
-# Linux users:
-miniconda_version=Miniconda3-latest-Linux-x86_64.sh
-
-wget http://repo.continuum.io/miniconda/$miniconda_version --no-check-certificate -O $miniconda_version
-chmod +x $miniconda_version
-./$miniconda_version -b -p ~/tools/miniconda3
-~/tools/miniconda3/bin/conda init bash
+mamba env create --file conda-env.yml
 ```
-
-Run the following in your terminal to install the dependencies to a new environment miaplpy (recommended):
+or if you have an existing environment:
 
 ```
-conda env create -f $MIAPLPY_HOME/docs/conda_env.yml
-conda activate miaplpy
+mamba env update --name my-existing-env --file conda-env.yml
 ```
-Or run the following in your terminal to install the dependencies to your custom environment, the default is base:
 
+#### 3. Install MiaplPy via pip
 ```
-conda install --yes -c conda-forge --file ~/tools/MiaplPy/docs/requirements.txt
+conda activate dolphin-env
+python -m pip install .
 ```
 
-#### 4. Setup MiaplPy
-
-I. Compile
-```
-cd $MIAPLPY_HOME/miaplpy/lib;
-python setup.py
-```
-II. Install [SNAPHU](https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/) 
+#### 4. Install [SNAPHU](https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/) 
 ```
-cd $MIAPLPY_HOME;
+export TOOLS_DIR=~/tools
+cd ~/tools;
 wget --no-check-certificate  https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/snaphu-v2.0.5.tar.gz
 tar -xvf snaphu-v2.0.5.tar.gz
 mv snaphu-v2.0.5 snaphu;
 rm snaphu-v2.0.5.tar.gz;
-sed -i 's/\/usr\/local/$(MIAPLPY_HOME)\/snaphu/g' snaphu/src/Makefile
+sed -i 's/\/usr\/local/$(TOOLS_DIR)\/snaphu/g' snaphu/src/Makefile
 cd snaphu/src; make
+export PATH=${TOOLS_DIR}/snaphu/bin:${PATH}
 ```
 
 ### Notes

diff --git a/pyproject.toml b/pyproject.toml
@@ -15,15 +15,39 @@ license = { file = "LICENSE" }
 
 dynamic = ["version"] # , "dependencies"]
 
+# Entry points for the command line interface
+[project.scripts]
+miaplpyApp = "miaplpy.miaplpyApp:main"
+'check_ifgs.py' = "miaplpy.check_ifgs:main"
+'correct_geolocation.py' = "miaplpy.correct_geolocation:main"
+'cpxview.py' = "miaplpy.cpxview:main"
+'find_short_baselines.py' = "miaplpy.find_short_baselines:find_baselines"
+'generate_temporal_coherence.py' = "miaplpy.generate_temporal_coherence:main"
+'generate_unwrap_mask.py' = "miaplpy.generate_unwrap_mask:main"
+'load_ifgram.py' = "miaplpy.load_ifgram:main"
+'load_slc_geometry.py' = "miaplpy.load_slc_geometry:main"
+'network_inversion.py' = "miaplpy.network_inversion:main"
+'phase_linking.py' = "miaplpy.phase_linking:main"
+'prep_slc_isce.py' = "miaplpy.prep_slc_isce:main"
+'scatterview.py' = "miaplpy.scatterview:main"
+'simulation.py' = "miaplpy.simulation:simulate_and_calculate_different_method_rms"
+'tcoh_view.py' = "miaplpy.tcoh_view:main"
+'generate_ifgram.py' = "miaplpy.generate_ifgram:main"
+'unwrap_ifgram.py' = "miaplpy.unwrap_ifgram:main"
+
 
 [tool.setuptools.packages.find]
 where = ["src"]
+#include = ["defaults/*.cfg", "defaults/*.full"]
+
+[tool.setuptools.package-data]
+myModule = ["defaults/*.cfg", "defaults/*.full"]
 
 [tool.setuptools.dynamic]
-# dependencies = { file = ["requirements.txt"] }
+#dependencies = { file = ["requirements.txt"] }
 version = {attr = "miaplpy.__version__"}
 
 
 [project.urls]
 Homepage = "https://github.com/insarlab/MiaplPy/"
-"Bug Tracker" = "https://github.com/insarlab/MiaplPy/issues"
+"Bug Tracker" = "https://github.com/insarlab/MiaplPy/issues"
diff --git a/src/miaplpy/__main__.py b/src/miaplpy/__main__.py
@@ -0,0 +1,8 @@
+"""Main module to provide command line interface to the workflows."""
+import sys
+
+from .miaplpyApp import main
+
+# https://docs.python.org/3/library/__main__.html#packaging-considerations
+# allows `python -m miaplpyApp` to work
+sys.exit(main())