clean up repo for minor release v0.6.6

csyhuang · Apr 9, 2023 · 77daecb · 77daecb
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diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -76,9 +76,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.6.5'
+version = u'0.6.6'
 # The full version, including alpha/beta/rc tags.
-release = u'0.6.5'
+release = u'0.6.6'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -97,7 +97,7 @@ Issues Reporting
 
 Please make inquiries about / report issues / with the package and suggest feature extensions on the `Issues page <https://github.com/csyhuang/hn2016_falwa/issues>`_. 
 
-If you need help analyzing output from particular model/analysis with our techniques, feel free to email me *csyhuang@protonmail.com* with sample datasets and I can configure the code for you.
+If you need help analyzing output from particular model/analysis with our techniques, feel free to email me *csyhuang@uchicago.edu* with sample datasets and I can configure the code for you.
 
 
 Indices and tables

diff --git a/hn2016_falwa/__init__.py b/hn2016_falwa/__init__.py
@@ -4,7 +4,7 @@
 Author: Clare Huang, Christopher Polster
 """
 
-__version__ = "0.6.5"
+__version__ = "0.6.6"
 from .interpolate_fields import interpolate_fields
 from .interpolate_fields_direct_inv import interpolate_fields_direct_inv
 from .compute_qref_and_fawa_first import compute_qref_and_fawa_first

diff --git a/readme.md b/readme.md
@@ -1,4 +1,4 @@
-## Python Library: hn2016_falwa (v0.6.5)
+## Python Library: hn2016_falwa (v0.6.6)
 
 [![Build Status](https://github.com/csyhuang/hn2016_falwa/actions/workflows/workflow.yml/badge.svg)](https://github.com/csyhuang/hn2016_falwa/actions/workflows/workflow.yml)[![codecov.io](https://codecov.io/gh/csyhuang/hn2016_falwa/branch/master/graph/badge.svg)](https://codecov.io/gh/csyhuang/hn2016_falwa)[![Documentation Status](https://readthedocs.org/projects/hn2016-falwa/badge/?version=latest)](http://hn2016-falwa.readthedocs.io/en/latest/?badge=latest)[![DOI](https://zenodo.org/badge/63908662.svg)](https://zenodo.org/badge/latestdoi/63908662)
 
@@ -79,6 +79,6 @@ are added upon users' request on new functionalities to test hypotheses (also se
 
 ## Inquiries / Issues reporting
 
-- If you are interested in using the package, please leave your contact [here](https://goo.gl/forms/5L8fv0mUordugq6v2) or email me(csyhuang@protonmail.com) such that I can keep you updated of any changes made.
+- If you are interested in using the package, please leave your contact [here](https://goo.gl/forms/5L8fv0mUordugq6v2) or email me(csyhuang@uchicago.edu) such that I can keep you updated of any changes made.
 - If you encounter *coding issues/bugs* when using the package, please create an [Issue ticket](https://github.com/csyhuang/hn2016_falwa/issues).
-- If you have scientific questions, please contact Clare S. Y. Huang via email(csyhuang@protonmail.com).
+- If you have scientific questions, please contact Clare S. Y. Huang via email(csyhuang@uchicago.edu).
diff --git a/scripts/nhn_grl2022/env_nhn_grl2022.yml b/scripts/nhn_grl2022/env_nhn_grl2022.yml
@@ -0,0 +1,18 @@
+name: env_nhn_grl2022
+
+dependencies:
+- intel::numpy=1.22.3
+- intel::scipy=1.7.3
+- pytest=7.1.2
+- matplotlib=3.6.2
+- cartopy=0.21.1
+- conda-forge::netCDF4=1.6.0
+
+# 1. To create the environment, run:
+# $ conda env create -f scripts/nhn_grl2022/env_nhn_grl2022.yml
+# 2. Activate the environment
+# $ conda activate env_nhn_grl2022
+# 3. Remove any existing compiled fortran modules by:
+# $ rm hn2016_falwa/*.so
+# 4. Install hn2016_falwa by running in command line:
+# $ python setup.py develop
diff --git a/scripts/nhn_grl2022/readme.md b/scripts/nhn_grl2022/readme.md
@@ -1,9 +1,11 @@
-## Demo script for the analyses done in Neal et al. (submitted to GRL)
+# Demo script for the analyses done in Neal et al. (submitted to GRL)
 
-This repo contains the sample script to reproduce the plots in Neal et al. "The 2021 Pacific Northwest heat wave and 
-associated blocking: Meteorology and the role of an upstream cyclone as a diabatic source of wave activity". 
+This directory contains the sample script to reproduce the plots in 
+Neal, et al. (2022). [The 2021 Pacific Northwest heat wave and associated blocking: meteorology and the role of an upstream cyclone as a diabatic source of wave activity](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021GL097699). *Geophysical Research Letters*, 49(8), e2021GL097699.
 
-To produce all the plots, required ERA5 data (6-hourly, 1° x 1° spatial resolution at all pressure levels 
+## Data required
+
+To produce all the plots, download ERA5 data files which contain (6-hourly, 1° x 1° spatial resolution at all pressure levels 
 (37 available levels), from June 1-30, 2021):
 
 - geopotential height (z)
@@ -16,20 +18,52 @@ To produce all the plots, required ERA5 data (6-hourly, 1° x 1° spatial resolu
 - total column water (tcw)
 - total column water vapor (tcwv)
 - sea level pressure (sp)
+
+## Scripts
 
 The run script `sample_run_script.py` called functions in `QGField` object (see `hn2016_falwa/oopinterface.py`) 
 to compute LWA and fluxes, while `scripts/graph_plot_module.py` contains the graph plotting functions to reproduce 
 all the figures in the paper.
 
-Note that there is a difference in computing reference state in this most recent manuscript. In the past, and also 
-the analysis in NH18 Science, we used equator as the latitudinal boundary. In this current version of the script 
+## Note on equatorward boundary condition used
+
+Note that there is a difference in computing reference state in this most recent manuscript. In the past (and also 
+the analysis in NH18 Science), we used equator as the latitudinal boundary. In this current version of the script 
 (release 0.6.0), we use absolute vorticity at 5°N as boundary condition such that the solution is no longer sensitive 
 to fields at the equator, which improves the quality of the analysis.
 
-We are in a hurry submitting the manuscript, so this version of code (v0.6.1) has not been properly refactored yet. 
+## How to create a virtual environment to run this script
+
+Create a conda environment by running:
+```bash
+conda env create -f scripts/nhn_grl2022/env_nhn_grl2022.yml
+```
+
+Activate the environment
+```bash
+conda activate env_nhn_grl2022
+```
+
+Remove any existing compiled fortran modules by:
+```bash
+rm hn2016_falwa/*.so
+```
+
+Install hn2016_falwa by running in command line:
+```bash
+python setup.py develop
+```
+
+You can then run the script to reproduce the graphs in the GRL paper:
+```bash
+python scripts/nhn_grl2022/sample_run_script.py
+```
+
+## Problem solving
+
 If you have any questions, please [submit an issue](https://github.com/csyhuang/hn2016_falwa/issues) or email me. 
 I'll get back ASAP.
 
 Thanks!
 
-Clare (csyhuang@protonmail.com)
+Clare S. Y. Huang (csyhuang@uchicago.edu)
diff --git a/setup.py b/setup.py
@@ -60,13 +60,13 @@
 
 setup(
     name='hn2016_falwa',
-    version='0.6.5',
+    version='0.6.6',
     description='python package to compute finite-amplitude local wave activity (Huang and Nakamura 2016, JAS)',
     long_description=LONG_DESCRIPTION,
     long_description_content_type='text/markdown',
     url='https://github.com/csyhuang/hn2016_falwa',
     author='Clare S. Y. Huang',
-    author_email='csyhuang@protonmail.com',
+    author_email='csyhuang@uchicago.edu',
     license='MIT',
     packages=find_packages(),
     install_requires=['numpy', 'scipy', 'xarray'],