The pull request for the part of gravity anomaly from SUSTech #12

MetaronWang · 2019-02-08T12:30:42Z

This is Southern University of Science and Technology. We design and write a new part for this project about the gravity anomaly. We write the python file by the structure like the file in the project before, and the folder structure is also like the project structure.

lheagy · 2019-02-09T17:57:30Z

👋 Hi @thast would you be willing to review the notebook added by @wwzzyyzzrr?

thast · 2019-02-10T02:45:15Z

on my to-do list.

lheagy · 2019-02-10T02:52:25Z

many thanks @thast :) Please let me know if you need anything from me

thast · 2019-02-11T01:57:51Z

Hi @wwzzyyzzrr,

Thanks a lot for your first-time contribution to this repository, that's awesome! Gravity is a really key feature and many people will have use for it.

I want first to highlight a couple of points here before doing any in-depth review. This will help get things right from the start and the long-term use of the work you have developed:

SimPEG.PF have been fixed. Your PR is failing on the style test (see the contributing page for more details). Having consistent formatting help the readability. I will start the review once Travis passed. If you experience difficulties with it, please feel free to contact us and we will help.
I notice there is no comment at all in your code. Please add some documentation to your functions and code. This will help both the review and the maintenance, as this is likely to be used, improved and built upon in the future.
Once the PR is merged, we also usually release PR notes, basically a description of what have been added, fixed or improved upon (like names of the new notebooks, what do they do and how etc.). If you could provide it, that will also help both the review and the users.
As this is a new section, we most likely need to add a travis test for it test_grav.py (see the files in geosci-labs/tests )

For all those points, please take a look at the contributing page for more details (like on PEP8, Black, Flake8 for formatting, PR description etc.)

Please feel free to contact us and ask any question you might have.

@lheagy : let us know if you have any additional comment or thought about it.

MetaronWang · 2019-02-11T02:50:16Z

Hi, @Thibaut Astic: Thankyou for your work. We will finsh it in time and pull request again. And for the comments, we had found that the codes in the folder geoscilabs have no comment, so we delete all of them, what should we do for it next step? Add comments in the python file or write in document? 2019年2月11日 09:57，"Thibaut Astic" <notifications@github.com>写道： Hi @wwzzyyzzrr <https://github.com/wwzzyyzzrr>, Thanks a lot for your first-time contribution to this repository, that's awesome! Gravity is a really key feature and many people will have use for it. I want first to highlight a couple of points here before doing any in-depth review. This will help get things right from the start and the long-term use of the work you have developed: - SimPEG.PF have been fixed. Your PR is failing on the style test (see the contributing page <https://github.com/geoscixyz/geosci-labs/blob/master/CONTRIBUTING.md> for more details). Having consistent formatting help the readability. I will start the review once Travis passed. If you experience difficulties with it, please feel free to contact us and we will help. - I notice there is no comment at all in your code. Please add some documentation to your functions and code. This will help both the review and the maintenance, as this is likely to be used, improved and built upon in the future. - Once the PR is merged, we also usually release PR notes, basically a description of what have been added, fixed or improved upon (like names of the new notebooks, what do they do and how etc.). If you could provide it, that will also help both the review and the users. For all those points, please take a look at the contributing page <https://github.com/geoscixyz/geosci-labs/blob/master/CONTRIBUTING.md> for more details (like on PEP8, Black, Flake8 for formatting, PR description etc.) Please feel free to contact us and ask any question you might have. @lheagy <https://github.com/lheagy> : let us know if you have any additional comment or thought about it. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#12 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AWez5qzVoCjKgeVpRMfGW0_VnWGD2EjSks5vMM4ggaJpZM4avZlL> .

thast · 2019-02-11T03:38:56Z

@wwzzyyzzrr : Ah I see! Sorry for the confusion. Documentation and comments in the python file is better in my opinion, makes it easier to understand, review, debug and improve. I do not know how easy it is for you to "put it back" but that would be really valuable. Also from a long-term perspective, we would likely build the API documentation for the code comments itself.

I think that the codes that are still in geosci-labs were developed years ago, before it became a shared resources, thus a lack of time dedicated to document it. The most advanced programs got moved to SimPEG and documented, but the ones really more specific to the original teaching material stayed poorly documented.

lheagy · 2019-02-12T02:36:16Z

Many thanks @thast for leading the review! Just one minor thing I will jump in with, the test that is failing is the "style" test, meaning that the code is not formatted. From the main directory (geosci-labs) you can run:

make format

to format the code (or have a look at the Makefile and copy the command into your terminal). This runs black so that the code if formatted consistently. You can then commit and push any changes it suggests.

After this, try running

make check

and this will check that the code has been formatted and will also check that the code style (loosley) follows the pep8 guidelines for naming and a few other best-practices. If make check runs cleanly, then the test should pass on travis.

MetaronWang · 2019-02-13T06:05:11Z

I have modified the files that I think need to be changed. And the test of the flake8 is also pass, so could you review the commits of us again? Thank you.

thast · 2019-02-13T18:05:36Z

Good job @wwzzyyzzrr on the style repair :)
It seems the gravity notebooks are not tested in Travis (one travis test per module, and I do not see gravity in the list). Could you add the test? Let us know if you need help.

MetaronWang · 2019-02-16T07:24:17Z

Thanks, @thast :
We have added the test file for the gravity and add it into the .travis.yml, all the tests have been passed.

lheagy

Hi @wwzzyyzzrr, thanks for all of your work - this is looking good! I have a few minor comments in the code and a couple notes about the notebooks. Please let me know if you have any questions:

In the notebooks, we prefer not to import * as it can make debugging challenging
```
from geoscilabs.gravity.gravitySphere import *
```
instead, could you please explicitly import the names of the functions / classes that you need e.g.:
```
from geoscilabs.gravity.gravitySphere import interact_gravity_sphere, printResults
```
I really like the images showing the setup! Rather than embedding them as binary-blobs, could you please add them to the images directory? This makes it easier to maintain the notebooks and makes it easier to maintain them down the road. You can reference them locally right now, e.g.
```
![gravity-setup](../images/gravity/setup)
```

lheagy · 2019-02-18T20:37:11Z

environment.yml

@@ -17,4 +17,4 @@ dependencies:
    - deepdish
    - SimPEG
    - empymod
-    - git+https://github.com/geoscixyz/geosci-labs
+    - git+https://github.com/wwzzyyzzrr/geosci-labs


could you please revert this change? the environment.yml should point to the main repository.

In the future, you can just create a branch on this repo rather than using a fork and that should simplify things a bit. You should now have the ability to push to this repo since you are a geoscixyz team member 🎉

lheagy · 2019-02-18T20:39:19Z

geoscilabs/gravity/gravityDike.py

+        )
+
+
+if __name__ == "__main__":


this doesn't need to be here. It is really only necessary if you expect people to try and run this file as a python script, but users will be interacting with it by importing the package.

lheagy · 2019-02-18T20:40:07Z

requirements.txt

@@ -9,4 +9,4 @@ ipywidgets
 deepdish
 Pillow
 requests
-git+https://github.com/geoscixyz/geoscilabs
+git+https://github.com/wwzzyyzzrr/geosci-labs


same comment here, please use the geoscixyz version, not the fork

lheagy · 2019-02-18T20:40:45Z

setup.py

@@ -51,7 +51,7 @@
    long_description=LONG_DESCRIPTION,
    keywords="geophysics, electromagnetics",
    url="https://geosci.xyz",
-    download_url="https://github.com/geoscixyz/geoscilabs",
+    download_url="https://github.com/wwzzyyzzrr/geosci-labs",


and again here. Please stick with the geoscixyz version

MetaronWang · 2019-02-19T01:29:29Z

Hi, @lheagy :
Thanks for your suggestions, I have revised the problems mentioned above.

thast · 2019-02-19T17:28:13Z

geoscilabs/gravity/gravityDike.py

+
+# get the value of the delta gravity
+def calculategravity(delta_rho, z1, z2, b, beta, x) -> float:
+    G = 6.67259e-8


I think it would be better here to add in the import:
from scipy.constants import G (be careful with the units)

thast · 2019-02-19T17:29:14Z

setup.py

@@ -51,7 +51,7 @@
    long_description=LONG_DESCRIPTION,
    keywords="geophysics, electromagnetics",
    url="https://geosci.xyz",
-    download_url="https://github.com/geoscixyz/geoscilabs",
+    download_url="https://github.com/geoscixyz/geosci-labs",


good catch!

thast · 2019-02-19T18:39:55Z

geoscilabs/gravity/gravityDike.py

+currentResult = []
+
+# The main function and draw the first table
+def drawfunction(delta_rho, z1, z2, b, beta, stationSpacing, B):


It would be good to have documentation such as:

def forward(nD,delta_rho):
"""
Parameters
----------
nD: int
number of data
delta_rho : numpy.array
model of density contrasts
Returns
-------
np.array
data, the forward data
"""

But maybe not required for this PR. What's your opinion on it @lheagy ?

It would be nice and very much appreciated, but I don't think we can ask that it be required for this PR. We haven't set that precedent within the codebase yet.

Sounds good!

thast · 2019-02-19T18:47:14Z

Hi @wwzzyyzzrr , thanks for your work. I have left a few comments above for you to review. If @lheagy also agree to let the documentation of the functions as it is, then switching the hard coded value of G for the import scipy.constants import G (with proper unit conversion) will do for the current PR. Please also provide releases notes: basically a description of what have been added, fixed or improved upon (like names of the new notebooks, what do they do and how etc.), to accompany the official release. It does not need to be long, just a few lines will do.
Good job!

lheagy

Thanks for leading the review @thast and for all of your work on this @wwzzyyzzrr! If you can address @thast's comments then it is good-to-go on my end.

@thast: are you willing to do the release?

merge to master
pull master, run coda minor (since there is new functionality), push
generate release notes and check that once travis has run, the new version of geoscilabs is on pypi (https://pypi.org/project/geoscilabs/)

wwzzyyzzrr and others added 7 commits January 25, 2019 23:56

Gravity Part

659e72e

gravity Part

62ed8d3

The Second version of the Gravity

5523e40

Clear the temp ipynb in the root folder

3dc55ac

gravity part

1a81e28

gravity part

7df3ab6

gravity module: add introduction

a89e9ab

yangdikun requested a review from lheagy February 8, 2019 12:35

Merge branch 'master' into master

14c79b8

Merge branch 'master' into master

41bb5bd

thast self-requested a review February 10, 2019 02:45

This was referenced Feb 12, 2019

Bring Gravity functions from geosci-labs to Geoana #14

Open

Checklist for reviewers #15

Open

wwzzyyzzrr added 2 commits February 13, 2019 13:37

The repair of the gravity part

c1bc1ef

Then repairs of the gravity part

0deaf75

MetaronWang closed this Feb 13, 2019

MetaronWang reopened this Feb 13, 2019

wwzzyyzzrr added 5 commits February 13, 2019 14:55

try to change environment.yml to deploy on the binder

f1a4079

Try to deploy on the binder

c02eaab

Try to deploy it on the binder

0362a79

Try to deploy on the binder

65d9156

try to deploy on the binder

36b984e

Create test_gravity.py

ad796ff

MetaronWang closed this Feb 16, 2019

MetaronWang reopened this Feb 16, 2019

Change .travis.yml

10d15ad

lheagy reviewed Feb 18, 2019

View reviewed changes

wwzzyyzzrr added 3 commits February 19, 2019 09:17

Change some problem for the commits before

18be6e1

Move the image to the folder image

dcb2b41

Move the image to the folder

71d70d5

thast reviewed Feb 19, 2019

View reviewed changes

lheagy approved these changes Feb 19, 2019

View reviewed changes

Change G from scipy.constants

83e4913

thast merged commit 9db1597 into geoscixyz:master Feb 20, 2019

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The pull request for the part of gravity anomaly from SUSTech #12

The pull request for the part of gravity anomaly from SUSTech #12

MetaronWang commented Feb 8, 2019

lheagy commented Feb 9, 2019

thast commented Feb 10, 2019

lheagy commented Feb 10, 2019

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The pull request for the part of gravity anomaly from SUSTech #12

The pull request for the part of gravity anomaly from SUSTech #12

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MetaronWang commented Feb 8, 2019

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