genericmappingtools / try-gmt Goto Github PK

1. Visit https://github.com/GenericMappingTools/try-gmt
2. In the upper right corner, click the link https://mybinder.org/v2/gh/GenericMappingTools/try-gmt/master?urlpath=lab/tree/landing-page.ipynb
3. We see "Starting repository: GenericMappingTools/try-gmt/master ", and underneath it a link "New to Binder? Check out the Binder Documentation for more information". But before we can read and comprehend and click the link, it has changed into something else! So frustrating!

Loading the GMT.jl package (using GMT) is very slow (~10 s) for the first time, because Julia needs to precompile the GMT.jl package. It would be better to precompile the package when building the docker image, so that the package is already precompiled when users run using GMT.

As I understand it, running julia -e "using GMT" may do the precompiling.

@joa-quim Is it correct? Is there a way to precompile all Julia packages?

Hello,

After the new update in Google Colab (March 2024), it's possible to run conda install() and conda gmt/pygmt. I've updated my script and I'm using it with my students. Feel free to integrate it into the try-gmt.

https://github.com/andrebelem/pythonverse/blob/main/Using_pygmt_in_COLAB_[version_2023].ipynb

The following example in the Julia demo notebook doesn't work:

basemap(region=:g, proj=(name=:Otho, center=(220,30)), figsize=8, frame=:g)
grdimage!("@earth_relief_20m", cmap=:geo, shade=true)
coast!(res=:crude, shore=true, area=1000)
plot!("@hotspots.txt", marker=:circle, size="0.2c", markerfacecolor=:red, show=true)

The error messages are:

┌ Warning: Very likely the projection name (Otho) is unknown to me. Expect troubles
└ @ GMT /srv/julia/pkg/packages/GMT/fZQQL/src/common_options.jl:436
psbasemap [WARNING]:  not a valid number and may not be decoded properly.
psbasemap [ERROR]: Your scale or width () resulted in a zero value.
psbasemap [ERROR]: Option -J parsing failure. Correct syntax:
	-Jo[a]<lon0>/<lat0>/<azimuth>/<scale> OR -JO[a]<lon0>/<lat0>/<azimuth>/<width>
	-Jo[b]<lon0>/<lat0>/<b_lon>/<b_lat>/<scale> OR -JO[b]<lon0>/<lat0>/<b_lon>/<b_lat>/<width>
	-Joc<lon0>/<lat0>/<lonp>/<latp>/<scale> OR -JOc<lon0>/<lat0>/<lonp>/<latp>/<width>
	  <scale> is <1:xxxx> or cm/oblique degree, or use <width> in cm
psbasemap [ERROR]: Offending option -JOt220/30/8
Something went wrong when calling the module. GMT error number = 71

Stacktrace:
 [1] error(::String, ::Int32) at ./error.jl:42
 [2] gmt(::String, ::Nothing) at /srv/julia/pkg/packages/GMT/fZQQL/src/gmt_main.jl:246
 [3] finish_PS_module(::Dict{Symbol,Any}, ::String, ::String, ::Bool, ::Bool, ::Bool, ::Nothing) at /srv/julia/pkg/packages/GMT/fZQQL/src/common_options.jl:2701
 [4] #basemap#213(::Bool, ::Base.Iterators.Pairs{Symbol,Any,NTuple{4,Symbol},NamedTuple{(:region, :proj, :figsize, :frame),Tuple{Symbol,NamedTuple{(:name, :center),Tuple{Symbol,Tuple{Int64,Int64}}},Int64,Symbol}}}, ::typeof(basemap), ::String, ::Nothing) at /srv/julia/pkg/packages/GMT/fZQQL/src/psbasemap.jl:64
 [5] (::GMT.var"#kw##basemap")(::NamedTuple{(:region, :proj, :figsize, :frame),Tuple{Symbol,NamedTuple{(:name, :center),Tuple{Symbol,Tuple{Int64,Int64}}},Int64,Symbol}}, ::typeof(basemap)) at ./none:0
 [6] top-level scope at In[7]:1

@joa-quim Anything wrong?

This repository sets up a single Jupyter lab environment, with the latest/stable GMT, PyGMT, and GMT.jl installed. The idea and some contents of this repository are from our older projects, gmt6demo, try-gmt-python, and foss4g2019oceania.

Anyone can run GMT commands (i.e., in bash), PyGMT, and GMT.jl in this online Jupyter lab, with no need to install anything locally.

I believe this Jupyter lab would be useful for both new and old GMT users who want to try GMT and its wrappers before spending some time setting up a local environment. It also provides a uniform environment for future GMT workshops and short courses, so that we don't have to spend hours solving the GMT installation problems (I'm not sure about its performance if dozens of peoples use it simultaneously).

The Jupyter lab is freely hosted by Pangeo Binder. You can try it by clicking the badge below:

it usually takes <30 s to launch the Jupyter lab, the you can try the three demos for bash, Python, and Julia, respectively.

Future Plans

Here are some of my thoughts to improve it:

• Cache the low-resolution (>06m) earth relief data so that users don't have to wait for downloading them [Done in #4]
• Install a few extra Python packages (e.g., scipy, matplotlib) and Julia packages to make it more suitable for practical plots
• Create a dev branch and set up another Jupyter lab environment with the master/unstable/developing GMT, PyGMT, and GMT.jl installed.
• Host it on Google's colab servers (also free), which seem faster.
• Post it on the GMT forum to increase its visibility (https://forum.generic-mapping-tools.org/t/try-gmt-pygmt-gmt-jl-online-at-pangeo-binder/561)
• Add a "Try it online!" menu on the GMT homepage to increase its visibility (GenericMappingTools/website#71)
• Add "Try it online!" badges to the README file of GMT, PyGMT and GMT.jl repositories?

Any thoughts and suggestions? @GenericMappingTools/core @GenericMappingTools/gmt-contributors @GenericMappingTools/python @GenericMappingTools/python-contributors

After running the cell which installs conda etc. the import pygmt command fails with:

In Project.toml, we specify the Julia version using julia = "1.5", but the actual installed Julia version is still 1.3.

I must misunderstand how Project.toml works for Julia.

This post said the following syntax will work:

julia = "=1.0.4"

but PR #11 uses this syntax and still has Julia 1.3.

1. Visit https://github.com/GenericMappingTools/try-gmt
2. In the upper right corner, click the link https://mybinder.org/v2/gh/GenericMappingTools/try-gmt/master?urlpath=lab/tree/landing-page.ipynb
3. We end up on
   

where near the bottom it says run GMT command in bash.

A file gets downloaded to our computer with no instructions.

Should we install geopandas (an optional dependency of PyGMT) on try-gmt? Just asking because a new contributor trying to work on GenericMappingTools/pygmt#1374 is having trouble with setting up PyGMT and Geopandas locally, and it would be nice to have a virtual cloud environment with both these dependencies installed already.

Disadvantage is that the build and start-time for the Binder environment will take longer, because geopandas brings in some heavy dependencies like GEOS and PROJ (see https://geopandas.org/getting_started/install.html#dependencies).

Thoughts? Upvote 👍 to go for it, downvote 👎 for sticking to the status quo.

Hi,

Hope this message finds you well. I developed a teaching module using PyGMT back in February using Google Colab. I used this described solution to import PyGMT and things worked well. It sometimes took running the import cell another time -- some folks got an error upon first run -- but things worked successfully

I am currently preparing to teach this module again and just tried running through the code again. I am now getting the error appended. Do you know what may be causing this error? I didn't find any solutions on the forum and figured I may raise the issue here. Thanks in advance for any guidance.

Best,
Sarah

---------------------------------------------------------------------------
GMTCLibNotFoundError                      Traceback (most recent call last)
[<ipython-input-2-9b6890099622>](https://localhost:8080/#) in <cell line: 8>()
      6 condacolab.install()
      7 get_ipython().system('mamba install pygmt')
----> 8 import pygmt
      9 from matplotlib import pyplot as plt
     10 get_ipython().run_line_magic('matplotlib', 'inline')

4 frames
[/usr/local/lib/python3.10/site-packages/pygmt/clib/loading.py](https://localhost:8080/#) in load_libgmt(lib_fullnames)
     57 
     58     if error:
---> 59         raise GMTCLibNotFoundError("\n".join(error_msg))
     60 
     61     return libgmt

GMTCLibNotFoundError: Error loading GMT shared library at '/usr/local/lib/libgmt.so'.
/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /usr/local/lib/./libgdal.so.32)
Error loading GMT shared library at 'libgmt.so'.
libgmt.so: cannot open shared object file: No such file or directory

I've seen this error when building GMT on Ubuntu latest for CI. I'm guessing the usual dependencies shit between glib and GDAL. My solution wast to use a Ubuntu 2018

Description of the desired feature

A large part of the NASA proposal that we’re working on involves improving the GMT documentation, including tutorials. One goal is to make the tutorials reliably repeatable and fully reproducible. Remote files will be useful for this purpose, which are already used in the existing tutorial but not some other parts of the documentation. In addition, it would be great for people to be able to learn GMT, PyGMT, GMT.jl, and/or gmtmex without needing to go through the installation steps. My expectation is that Binder and JupyterLab environments would be an excellent way to ensure that the tutorials are reliably repeatable. The result would be similar to try-gmt. The binder-ready repos would complement static versions of the tutorials in the docs that users could follow in their local environments. Pinging @GenericMappingTools/core, @GenericMappingTools/gmt-contributors, @GenericMappingTools/python, and @GenericMappingTools/python-maintainers for opinions about whether this is worthwhile.

I am also to happy to chat in more detail about other documentation improvements included in the proposal, so please feel free to reach out. Slack is probably the easiest medium for a broader conversation about the proposal.

Are you willing to help implement and maintain this feature? Yes