Updates install procedure (#149)

See #149

CHANGELOG.md

@@ -0,0 +1,7 @@
+# SeisFlows Changelog
+
+## v2.1.1
+
+- Updates and simplifies install procedure using 'environment.yml' and 
+  'pyproject.toml' files. 
+- Docs: Adds contributor's guide message to main docs page

README.md

@@ -1,8 +1,9 @@
 SeisFlows 
 ==========
 
+[![Documentation Status](https://readthedocs.org/projects/seisflows/badge/?version=devel)](https://seisflows.readthedocs.io/en/devel/?badge=devel)
 [![SCOPED](https://img.shields.io/endpoint?url=https://runkit.io/wangyinz/scoped/branches/master/adjTomo)](https://github.com/SeisSCOPED/container/pkgs/container/adjtomo)
-[![Documentation Status](https://readthedocs.org/projects/seisflows/badge/?version=latest)](https://seisflows.readthedocs.io/en/latest/?badge=latest)
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 SeisFlows is an open-source, Python-based waveform inversion package that tackles the problems of full waveform inversion, seismic migration, and adjoint tomography. 
 
@@ -23,12 +24,11 @@ References
 ----------
 If you use this package in your own research, please cite the following papers:
 
-- Bryant Chow, Yoshihiro Kaneko, Carl Tape, Ryan Modrak, John Townend, An automated workflow for adjoint tomography     —waveform misfits and synthetic inversions for the North Island, New Zealand, Geophysical Journal International, Volume 223, Issue 3, December 2020, Pages 1461–1480, https://doi.org/10.1093/gji/ggaa381
+- Bryant Chow, Yoshihiro Kaneko, Carl Tape, Ryan Modrak, John Townend, *An automated workflow for adjoint tomography     —waveform misfits and synthetic inversions for the North Island, New Zealand*, Geophysical Journal International, Volume 223, Issue 3, December 2020, Pages 1461–1480, https://doi.org/10.1093/gji/ggaa381
 
-- Ryan Modrak, Dmitry Borisov, Matthieu Lefebvre, Jeroen Tromp; SeisFlows—Flexible waveform inversion software, Computers & Geosciences, Volume 115, June 2018, Pages 88-95, https://doi.org/10.1016/j.cageo.2018.02.004
+- Ryan Modrak, Dmitry Borisov, Matthieu Lefebvre, Jeroen Tromp; *SeisFlows—Flexible waveform inversion software*, Computers & Geosciences, Volume 115, June 2018, Pages 88-95, https://doi.org/10.1016/j.cageo.2018.02.004
 
 The following paper can also be cited relative to this software:
 
-- Ryan Modrak, Jeroen Tromp; Seismic waveform inversion best practices: regional, global and exploration test cases, Geophysical Journal International, Volume 206, Issue 3, 1 September 2016, Pages 1864–1889, https://doi.org/10.1093/gji/ggw202
-
+- Ryan Modrak, Jeroen Tromp; *Seismic waveform inversion best practices: regional, global and exploration test cases*, Geophysical Journal International, Volume 206, Issue 3, 1 September 2016, Pages 1864–1889, https://doi.org/10.1093/gji/ggw202
 

docs/index.rst

@@ -25,6 +25,9 @@ Quickstart
   `open a GitHub Issue! <https://github.com/adjtomo/seisflows/issues>`__
 - Want to talk about SeisFlows?
   `Check in on the discussions page. <https://github.com/orgs/adjtomo/discussions>`__
+- Contributions are encouranged and welcome! Have a look at the 
+  `adjTomo Contributor's Guide <https://pyatoa.readthedocs.io/en/latest/contributing.html>`__  to see how you can contribute (hosted on Pyatoa's docs).
+
 
 ---------------------------------
 
@@ -36,29 +39,17 @@ a Conda environment to not affect your root environment. The `devel` branch
 houses the most up-to-date codebase.
 
 .. note::
+
     SeisFlows is installed using the Pip ``-e`` which enables development
-    mode, where source code changes are immediately acccessible to Python.
+    mode, where source code changes are immediately acccessible to Python (i.e.,
+    you do **not** need to re-install SeisFlows when updating source code).
 
 .. code:: bash
 
-   conda create -n seisflows python=3.10
-   conda activate seisflows
    git clone --branch devel https://github.com/adjtomo/seisflows.git
    cd seisflows
-   conda install --file requirements.txt --channel conda-forge
-   pip install -e .
-
-SeisFlows requires the waveform measurement capabilities of 
-`Pyatoa <https://github.com/adjtomo/pyatoa>`__, which currently must be 
-installed manually to the same Conda environment.
-
-.. code:: bash
-
-   cd ..
-   git clone --branch devel https://github.com/adjtomo/pyatoa.git
-   cd pyatoa
-   conda install --file requirements.txt --channel conda-forge
-   pip install -e .
+   conda env create -f environment.yml
+   conda activate seisflows
 
 ---------------------------------
 

environment.yml

@@ -0,0 +1,18 @@
+name: seisflows
+channels:
+    - conda-forge
+    - defaults
+dependencies:
+    - pip
+    - obspy
+    - cartopy
+    - pyyaml
+    # Pyatoa requirements, ensure they are installed via Conda
+    - pyasdf 
+    - pillow
+    - pypdf2
+    # Install Pyatoa via Pip which will install adjTomo tools
+    - pip:
+      - git+https://github.com/adjtomo/pyatoa@devel
+      - -e .
+

pyproject.toml

@@ -0,0 +1,34 @@
+[build-system]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "seisflows"
+version = "2.1.1"
+description = "An automated workflow tool for full waveform inversion"
+readme = "README.md"
+requires-python = ">=3.7"
+license = {file = "LICENSE"}
+authors = [
+    {name = "adjTomo Dev Team"},
+    {email = "adjtomo@gmail.com"}
+]
+dependencies = [
+    "obspy",
+    "pyyaml",
+	"IPython",
+	"dill",
+	"pyatoa @ git+https://github.com/adjtomo/pyatoa@devel",
+]
+
+[project.optional-dependencies]
+test = ["pytest"]
+dev = ["pytest", "ipython", "ipdb"]
+
+[project.urls]
+homepage = "https://github.com/adjtomo/"
+documentation = "https://seisflows.readthedocs.io"
+repository = "https://github.com/adjtomo/seisflows"
+
+[project.scripts]
+seisflows = "seisflows.seisflows:main"