Package env (#255)

* Deleting stale setup instructions * Adding install scripts for Gadi, VDI and windows * Adding more packages to installation scripts * Adding more packages to install-scripts * Adding an install-script for linux * More updates to install-scripts * Minor changes to install-scripts * Minor changes to install scripts * Updating conda script for linux Conda env now includes geos and proj4 for compiling shapely and cartopy * Adding conda install script for osx * Upgrading to obspy 1.2.0 * Upgrading obspy and openmp versions * Upgrading obspy==1.2.2 for osx-conda * Upgrading obspy==1.2.2 for win-conda * Updating Install Scripts * Added gdal to linux env * Adding parallel h5py to vdi env * Adding remi to dependency list * Update README.rst * Adding a readme for setup scripts * Renaming readme * Update README.md * Updating readme with more details on windows setup instructions * Update README.md * Update README.rst * Update README.rst
GeoscienceAustralia · Sep 7, 2023 · a4ff15e · a4ff15e
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diff --git a/README.rst b/README.rst
@@ -25,11 +25,8 @@ Overview
 Current Contacts
 ================
 
-- Fei Zhang: fei.zhang@ga.gov.au
-
 - Rakib Hassan: rakib.hassan@ga.gov.au 
 
-
 - Alexei Gorbatov: alexei.gorbatov@ga.gov.au
 
 - Babak Hejrani: babak.hejrani@ga.gov.au
@@ -38,41 +35,27 @@ Current Contacts
 System Requirements
 ==========================
 
-- Linux OS, including Ubuntu and CentOS
-- Python 3.6 or higher (recommended)
-- Python 2.7 (deprecated, no longer supported)
-
-Third Party Library Dependencies
-================================
-
-Certain modules require specific third party (non-Python) libraries to be installed
-on the host system. For example, scripts that convert to sc3ml format also require Seiscomp3 to be
-installed and to be visible in the PATH. In most cases, Python libraries that depend on third party
-libraries will indicate their dependencies either during attempted installation, or when used at
-runtime. Note that the following list includes indirect dependencies, i.e. dependencies that come
-from Python libraries used by HiPerSeis.
-
-Current third party dependencies (actual requirements may vary by platform or Python distribution):
+- Python 3.6 (recommended)
 
-- `HDF5 <http://hdfgroup.org/>`_
-- MPI, for example `Open MPI <https://www.open-mpi.org/>`_
-- `PROJ <https://proj.org/>`_
-- `GEOS <https://trac.osgeo.org/geos>`_
-
-
-Installation Guide for Developers
+Setup Guide
 =================================
 
 1. First, obtain the source code from `Github repository <https://github.com/GeoscienceAustralia/hiperseis>`_
 
 -  ``git clone https://github.com/GeoscienceAustralia/hiperseis.git``
 - ``cd hiperseis``
-- ``git submodule init``
-- ``git submodule update``
+- ``git submodule update --init --recursive``
+
+2. HiPerSeis does not provide an installation script due to the number of dependencies involved, some of which require low-level libraries to be available on the host machine. Instead, shell scripts are provided in ``hiperseis/setup_scripts`` for Linux, OSX and Windows for installing dependencies through a combination of Conda and Pip. A shell script is provided for NCI GADI, tailored exclusively for the current list of low-level HPC libraries e.g. MPI, HDF5, etc. available on the system.
+
+3. To use HiPerSeis in the checked out location, you will need to add the root HiPerSeis folder to your PYTHONPATH variable. For example, if you checked out HiPerSeis to the folder `dev/hiperseis` relative to your home directory, then in a `bash` shell you need to execute the following shell command: ``export PYTHONPATH=$HOME/dev/hiperseis``.  This needs to be done for each command shell session, or added to ``.bashrc`` or its equivalent.
 
-2. Install Python environment and dependency packages. See `Wiki Pages <https://github.com/GeoscienceAustralia/hiperseis/wiki>`_
+Third Party Library Dependencies
+================================
 
-3. To use HiPerSeis in the checked out location, you will need to add the root HiPerSeis folder to your PYTHONPATH variable. For example, if you checked out HiPerSeis to the folder `dev/hiperseis` relative to your home directory, then in a `bash` shell you need to execute the following shell command: ``export PYTHONPATH=$HOME/dev/hiperseis``.  This needs to be done for each command shell session.
+Certain modules require specific third party (non-Python) libraries to be installed
+on the host system. For example, scripts that convert to sc3ml format also require Seiscomp3 to be
+installed and to be visible in the PATH.
 
 License
 ===============

diff --git a/seismic/traveltime/conda_env_setup.sh → legacy/hpc/conda_env_setup.sh b/seismic/traveltime/conda_env_setup.sh → legacy/hpc/conda_env_setup.sh
diff --git a/gadi_env.sh → legacy/hpc/gadi_env.sh b/gadi_env.sh → legacy/hpc/gadi_env.sh
diff --git a/vdi_env.sh → legacy/hpc/vdi_env.sh b/vdi_env.sh → legacy/hpc/vdi_env.sh
diff --git a/requirements.in b/requirements.in
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/setup_scripts/README.md b/setup_scripts/README.md
@@ -0,0 +1,40 @@
+# Anaconda-based Setups
+
+1. Setup scripts provided for Linux, OSX and Windows (conda_env_*.sh) are based on
+[Anaconda3-2021.11](https://repo.anaconda.com/archive/).
+Refer to Anaconda installation instructions [here](https://conda.io/projects/conda/en/latest/user-guide/install/index.html)
+
+2. Launch setup shell script for your OS:
+
+Note that the setup script for Windows is a whittled down version compared to the Linux and OSX versions. While most of the dependecies 
+are covered, some that require code compilation are excluded, specifically to cater to institutional Windows machines with strict security controlls in place. ``conda_env_windows.sh`` should be launched from Git BASH -- refer to its installation instructions [here](https://gitforwindows.org/).
+
+ Launch setup script, e.g. for Linux as follows:
+
+ ``source hiperseis/setup_scripts/conda_env_linux.sh env_name || true``
+
+ where, ``env_name`` is the name of the environment to be created (e.g. hiperseis_env) and
+ `` || true`` ensures the shell terminal the command is run from does not terminate
+ if errors are encountered.
+
+
+
+3. Activate the newly created environment:
+
+``conda activate env_name``
+
+Note that the environment must be activated for each new terminal session from which HiPerSeis scripts are to be run. Alternatively, it can be added to the ``.bashrc`` file.
+
+# GADI
+
+1. The setup script for GADI is launched as:
+
+``sh hiperseis/setup_scripts/setup_env_gadi.sh env_name``
+
+where, ``env_name`` is the name of the environment to be created (e.g. hiperseis_env).
+
+2. Activate the newly created environment:
+
+``source env_name/bin/activate``
+
+Note that the environment must be activated for each new terminal session from which HiPerSeis scripts are to be run. Alternatively, it can be added to the ``.bashrc`` file.