Merge branch 'master' into shallow_and_baro

Conflicts:
	.gitignore
	src/extra/python/isca/__init__.py

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,65 @@
+---
+name: Bug report
+about: Use this template for submitting bug reports.
+title: "[ISSUE TITLE]"
+labels: bug
+assignees:
+---
+
+<!--
+Thank you for taking the time to create an issue for your topic/question.
+This issue provides a permanent record for others with similar questions
+to gain insight at a later date - your contributions here are significant
+to the community and much appreciated!
+
+Please always remember to be courteous to others posting on this forum as
+we are all here voluntarily to help others use Isca.
+
+NOTE:
+Isca team members are all full-time research scientists, so while we are very happy to provide
+some support, response times may vary. If you need in-depth support, then we may suggest that one
+ of us becomes a co-author on your next paper by providing long-term support on the issue.
+-->
+
+<!--
+Please be sure to add an informative title to this issue
+-->
+
+## Description
+<!--
+Fill out a concise description of your topic/question in this section.
+Feel free to post your code here using Markdown formatting
+-->
+
+-----
+**Screenshots**
+<!--
+If applicable, add screenshots to help explain your problem.
+-->
+
+-----
+**Isca version**
+<!--
+Please provide here your recent commit ID and tell us if you are working off your own fork or just
+using the main Execlim verion.
+-->
+
+-----
+**System Information:**
+To help us track down bugs faster, please provide the details about the machine where you run Isca.
+
+To do this, run the following code in Python:
+```py
+import platform
+print(platform.uname())
+```
+and paste the output below.
+```txt
+# Paste system info here
+
+```
+-----
+## Minimal reproducible example
+<!--
+It greatly helps us address your question if you have example data or script for us to work with.
+-->

.github/ISSUE_TEMPLATE/docs_issue.md

@@ -0,0 +1,33 @@
+---
+name: Documentation issue
+about: Use this template for submitting documentation-related issues.
+title: "[ISSUE TITLE]"
+labels: docs
+assignees:
+---
+
+<!--
+Thank you for taking the time to create an issue for your topic/question.
+This issue provides a permanent record for others with similar questions
+to gain insight at a later date - your contributions here are significant
+to the community and much appreciated!
+
+Please always remember to be courteous to others posting on this forum as
+we are all here voluntarily to help others use Isca.
+
+NOTE:
+Isca team members are all full-time research scientists, so while we are very happy to provide
+some support, response times may vary. If you need in-depth support, then we may suggest that one
+ of us becomes a co-author on your next paper by providing long-term support on the issue.
+-->
+
+<!--
+Please be sure to add an informative title to this issue
+-->
+
+## Description
+<!--
+Fill out a concise description of your topic/question in this section.
+Feel free to post your code here using Markdown formatting
+-->
+

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,23 @@
+---
+name: Feature Request
+about: Suggest an idea for something new to add
+labels: 
+---
+<!--
+Thank you for taking the time to create an issue for your topic/question.
+This issue provides a permanent record for others with similar questions
+to gain insight at a later date - your contributions here are significant
+to the community and much appreciated!
+
+Please always remember to be courteous to others posting on this forum as
+we are all here voluntarily to help others use Isca.
+
+NOTE:
+Isca team members are all full-time research scientists, so while we are very happy to provide
+some support, response times may vary. If you need in-depth support, then we may suggest that one
+ of us becomes a co-author on your next paper by providing long-term support on the issue.
+-->
+## Description
+<!--
+Include a clear description and an example or even a scholarly source of information about the feature.
+-->

.github/ISSUE_TEMPLATE/installation_issue.md

@@ -0,0 +1,60 @@
+---
+name: Installation issue
+about: Use this template if you have an issue related to installing Isca.
+title: "[YOUR QUESTION]"
+labels: infrastructure
+assignees:
+---
+
+<!--
+Thank you for taking the time to create an issue for your topic/question.
+This issue provides a permanent record for others with similar questions
+to gain insight at a later date - your contributions here are significant
+to the community and much appreciated!
+
+Please always remember to be courteous to others posting on this forum as
+we are all here voluntarily to help others use Isca.
+
+NOTE:
+Isca team members are all full-time research scientists, so while we are very happy to provide
+some support, response times may vary. If you need in-depth support, then we may suggest that one
+ of us becomes a co-author on your next paper by providing long-term support on the issue.
+-->
+
+<!--
+Please be sure to add an informative title to this issue
+-->
+
+## Description
+<!--
+Fill out a concise description of your topic/question in this section.
+Feel free to post your code here using Markdown formatting
+-->
+
+-----
+**Screenshots**
+<!--
+If applicable, add screenshots to help explain your problem.
+-->
+
+-----
+**Isca version**
+<!--
+Please provide here your recent commit ID and tell us if you are working off your own fork or just
+using the main Execlim verion.
+-->
+
+-----
+**System Information:**
+To help us help you, provide the details about the machine where you are trying to install Isca.
+
+To do this, please run the following code in Python:
+```py
+import platform
+print(platform.uname())
+```
+and paste the output below.
+```txt
+# Paste system info here
+
+```

.github/ISSUE_TEMPLATE/science_issue.md

@@ -0,0 +1,42 @@
+---
+name: Science issue
+about: Use this template for submitting science-related issues.
+title: "[YOUR QUESTION]"
+labels:
+assignees:
+---
+
+<!--
+Thank you for taking the time to create an issue for your topic/question.
+This issue provides a permanent record for others with similar questions
+to gain insight at a later date - your contributions here are significant
+to the community and much appreciated!
+
+Please always remember to be courteous to others posting on this forum as
+we are all here voluntarily to help others use Isca.
+
+NOTE:
+Isca team members are all full-time research scientists, so while we are very happy to provide
+some support, response times may vary. If you need in-depth support, then we may suggest that one
+ of us becomes a co-author on your next paper by providing long-term support on the issue.
+-->
+
+<!--
+Please be sure to add an informative title to this issue
+-->
+
+## Description
+<!--
+Fill out a concise description of your topic/question in this section.
+Feel free to post your code here using Markdown formatting
+-->
+
+### Screenshots
+<!--
+If applicable, add screenshots to help explain your problem.
+-->
+
+## Minimal reproducible example
+<!--
+It greatly helps us address your question if you have example data or script for us to work with.
+-->

.gitignore

@@ -1,31 +1,114 @@
-exec.*/
+# Project-specific
 compilation*/
+docs/source/examples/index.rst
+exec.*/
+exp/st_test*
+exp/archived/*
+frierson_comparison_*old*
+*land_world_mountains.nc
+mima_pz.txt
+*output.txt
+old_exps
+opt_exps
+postprocessing/plevel_interpolation/scripts/*.nc
+postprocessing/plevel_interpolation/scripts/*.nml
+postprocessing/plevel_interpolation/scripts/archived/*
+spin_up_restart/
+src/extra/python/scripts/*.nc
+src/extra/python/scripts/archived/
+*.sh.*
+src/atmos_param/socrates/src/trunk*
+
+# Temporary files
 *.x
 *.o
 *~
 ~*
-spin_up_restart/
 nohup.out
 Makefile
-old_exps
-opt_exps
-frierson_comparison_*old*
-*.pyc
-exp/st_test*
-exp/archived/*
 *.DS_Store
-*.egg-info
 ._*
 *.mod
-postprocessing/plevel_interpolation/scripts/*.nc
-postprocessing/plevel_interpolation/scripts/*.nml
-postprocessing/plevel_interpolation/scripts/archived/*
-*land_world_mountains.nc
-*output.txt
-src/extra/python/scripts/*.nc
-src/extra/python/scripts/archived/
-mima_pz.txt
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+pip-wheel-metadata/
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
 test/.cache
 test/results.xml
 *.sh.e*
 *.sh.o*
+
+# Translations
+*.mo
+*.pot
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter
+Untitled*.ipynb
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# mkdocs documentation
+/site