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Some countries borders not showing up in map #566
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Hi @guidocioni! Which OS, Python version and basemap version are you using? |
CentOs 7 |
Sorry to bother again, can you share the value of your |
No worries, and you're right I haven't attached them 😛 [6.0, 19.0, 36.0, 47.7] |
Hello @molinav , do you have any update on this? Thanks |
Hi @guidocioni! Sorry for being so late with this. For the moment, I can confirm you the bug using the following code snippet: import sys
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.basemap import __version__ as basemap_version
from mpl_toolkits.basemap import Basemap
print("Python version: ", sys.version)
print("Basemap version:", basemap_version)
plt.clf()
ax = plt.gca()
extents = [6.0, 19.0, 36.0, 47.7]
bmap = Basemap(projection="merc",
llcrnrlat=extents[2],
urcrnrlat=extents[3],
llcrnrlon=extents[0],
urcrnrlon=extents[1],
lat_ts=20,
resolution="h")
bmap.drawcountries(linewidth=1, color="blue")
bmap.drawcoastlines(linewidth=1, color="red") This returns the following in my console:
And the following image is obtained, with Switzerland borders missing, as in your original message: I would need to check the internals of |
Yes from my previous experience there is some "sweet spot" while setting the projection extents that causes the Switzerland borders to be exlcuded. |
I have found the code block that is causing the issue: basemap/packages/basemap/src/mpl_toolkits/basemap/__init__.py Lines 1371 to 1373 in c20c146
When the Switzerland border is picked in your example, In the next lines, So there is clearly a bug here to be inspected more, because it cannot be that we identify the polygon and the boundary box as not disjoint, but when asking for the concrete polygon coordinates inside the boundary box we get none. I am still not sure where the bug comes from, but it is either GEOS itself (I would be surprised) or the Cython interface to GEOS. I will try to test this with a newer GEOS (since the |
Bingo, the issue is in the Cython interface: basemap/packages/basemap/src/_geoslib.pyx Lines 275 to 316 in c20c146
After the call to
So your problem is coming from the incapability of the Cython interface to process One fast workaround below would be to check if basemap/packages/basemap/src/mpl_toolkits/basemap/__init__.py Lines 1371 to 1373 in c20c146
Of course the Cython interface still would need the real fix, but then I might not make it for |
In the end, I fixed the source of the problem in |
I have just released |
@molinav thank you so much for this! I have to admit I haven't followed everything here but I'm glad you were able to find a solution for a long standing bug that I randomly discovered 😄 |
Hey @molinav , I'm trying to deploy this in production but having troubles updating basemap with conda. I tried to update it but it wouldn't let me, then I tried to install the specific version and I'm getting these incompatibilities. However, it seems that there is always a good candidate so I'm not sure where the incompatibility is coming from.
|
Hi @guidocioni, can you provide the details of your environment (OS, Python version, anaconda or miniforge, steps to create the environment? Then I can try to reproduce your issue. |
I believe you can try to reproduce with a dump of the environment alone. I'm updating the YAML. name: stations
channels:
- conda-forge
- default
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- _py-xgboost-mutex=2.0=cpu_0
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- openssl=3.1.4=hd590300_0
- opt_einsum=3.3.0=pyhd8ed1ab_1
- orc=1.8.2=hfdbbad2_2
- ossuuid=1.6.2=hf484d3e_1000
- owslib=0.29.1=pyhd8ed1ab_0
- p11-kit=0.24.1=hc5aa10d_0
- packaging=23.1=pyhd8ed1ab_0
- pandas=2.0.0=py310h9b08913_0
- pandoc=2.19.2=h32600fe_2
- pandocfilters=1.5.0=pyhd8ed1ab_0
- panel=1.3.1=pyhd8ed1ab_0
- pango=1.50.14=hd33c08f_0
- parallel=20230322=ha770c72_0
- param=2.0.0=pyhca7485f_0
- parquet-cpp=1.5.1=2
- parso=0.8.3=pyhd8ed1ab_0
- partd=1.4.0=pyhd8ed1ab_0
- patsy=0.5.3=pyhd8ed1ab_0
- pcre=8.45=h9c3ff4c_0
- pcre2=10.40=hc3806b6_0
- perl=5.32.1=2_h7f98852_perl5
- pexpect=4.8.0=pyh1a96a4e_2
- pickleshare=0.7.5=py_1003
- pillow=9.4.0=py310h023d228_1
- pint=0.20.1=pyhd8ed1ab_0
- pip=23.1=pyhd8ed1ab_0
- pixman=0.40.0=h36c2ea0_0
- pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0
- platformdirs=3.2.0=pyhd8ed1ab_0
- plotly=5.14.1=pyhd8ed1ab_0
- ply=3.11=py_1
- pooch=1.7.0=pyha770c72_3
- poppler=23.03.0=h091648b_0
- poppler-data=0.4.12=hd8ed1ab_0
- portaudio=19.6.0=h583fa2b_7
- postgresql=15.2=h3248436_0
- proj=9.1.1=h8ffa02c_2
- prometheus_client=0.16.0=pyhd8ed1ab_0
- prompt-toolkit=3.0.38=pyha770c72_0
- prompt_toolkit=3.0.38=hd8ed1ab_0
- prophet=1.1.4=py310h56eac3b_0
- protobuf=4.21.12=py310heca2aa9_0
- psutil=5.9.5=py310h1fa729e_0
- psycopg2=2.9.3=py310h416cc33_2
- pthread-stubs=0.4=h36c2ea0_1001
- ptyprocess=0.7.0=pyhd3deb0d_0
- pulseaudio=16.1=hcb278e6_3
- pulseaudio-client=16.1=h5195f5e_3
- pulseaudio-daemon=16.1=ha8d29e2_3
- pure_eval=0.2.2=pyhd8ed1ab_0
- py-xgboost=1.7.4=cpu_py310hd1aba9c_0
- pyarrow=11.0.0=py310h633f555_5_cpu
- pyasn1=0.4.8=py_0
- pyasn1-modules=0.2.7=py_0
- pycodestyle=2.10.0=pyhd8ed1ab_0
- pycparser=2.21=pyhd8ed1ab_0
- pyct=0.4.6=py_0
- pyct-core=0.4.6=py_0
- pyflakes=3.0.1=pyhd8ed1ab_0
- pygments=2.15.1=pyhd8ed1ab_0
- pyjwt=2.8.0=pyhd8ed1ab_0
- pykdtree=1.3.7.post0=py310h0a54255_0
- pykrige=1.7.0=py310h278f3c1_1
- pymeeus=0.5.12=pyhd8ed1ab_0
- pyopenssl=23.1.1=pyhd8ed1ab_0
- pyorbital=1.7.3=pyhd8ed1ab_0
- pyparsing=3.0.9=pyhd8ed1ab_0
- pyproj=3.4.1=py310h15e2413_1
- pyqt=5.15.7=py310hab646b1_3
- pyqt5-sip=12.11.0=py310heca2aa9_3
- pyresample=1.26.1=py310h9b08913_0
- pyrsistent=0.19.3=py310h1fa729e_0
- pyshp=2.3.1=pyhd8ed1ab_0
- pysocks=1.7.1=pyha2e5f31_6
- pyspectral=0.12.3=pyhd8ed1ab_0
- python=3.10.10=he550d4f_0_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python-eccodes=1.6.0=py310h278f3c1_0
- python-fastjsonschema=2.16.3=pyhd8ed1ab_0
- python-flatbuffers=23.5.26=pyhd8ed1ab_0
- python-geotiepoints=1.6.0=py310h0a54255_0
- python-kaleido=0.2.1=pyhd8ed1ab_0
- python-tzdata=2023.3=pyhd8ed1ab_0
- python_abi=3.10=3_cp310
- pytz=2023.3=pyhd8ed1ab_0
- pyu2f=0.1.5=pyhd8ed1ab_0
- pyviz_comms=2.3.2=pyhd8ed1ab_0
- pyyaml=6.0=py310h5764c6d_5
- pyzmq=25.0.2=py310h059b190_0
- qt-main=5.15.8=h5d23da1_6
- rasterio=1.3.6=py310h3e853a9_0
- rclone=1.63.1=h519d9b9_0
- re2=2023.02.01=hcb278e6_0
- readline=8.2=h8228510_1
- regionmask=0.9.0=pyhd8ed1ab_0
- requests=2.28.2=pyhd8ed1ab_1
- requests-oauthlib=1.3.1=pyhd8ed1ab_0
- rioxarray=0.14.1=pyhd8ed1ab_0
- rsa=4.9=pyhd8ed1ab_0
- rtree=1.0.1=py310hbdcdc62_1
- s2n=1.3.37=h3358134_0
- satpy=0.41.1=pyhd8ed1ab_0
- scikit-learn=1.2.2=py310h41b6a48_1
- scipy=1.10.1=py310h8deb116_0
- seaborn=0.12.2=hd8ed1ab_0
- seaborn-base=0.12.2=pyhd8ed1ab_0
- send2trash=1.8.0=pyhd8ed1ab_0
- setuptools=67.6.1=pyhd8ed1ab_0
- shapely=2.0.1=py310h8b84c32_0
- simplejson=3.19.1=py310h1fa729e_0
- sip=6.7.9=py310hc6cd4ac_0
- six=1.16.0=pyh6c4a22f_0
- snappy=1.1.10=h9fff704_0
- snuggs=1.4.7=py_0
- sortedcontainers=2.4.0=pyhd8ed1ab_0
- soupsieve=2.3.2.post1=pyhd8ed1ab_0
- sqlalchemy=2.0.9=py310h1fa729e_0
- sqlite=3.40.0=h4ff8645_0
- stack_data=0.6.2=pyhd8ed1ab_0
- stanio=0.3.0=pyhd8ed1ab_0
- statsmodels=0.13.5=py310hde88566_2
- svt-av1=1.4.1=hcb278e6_0
- sympy=1.11.1=pypyh9d50eac_103
- sysroot_linux-64=2.12=he073ed8_16
- tbb=2021.9.0=hf52228f_0
- tbb-devel=2021.9.0=hf52228f_0
- tblib=1.7.0=pyhd8ed1ab_0
- tenacity=8.2.2=pyhd8ed1ab_0
- tensorboard=2.11.2=pyhd8ed1ab_0
- tensorboard-data-server=0.6.1=py310h600f1e7_4
- tensorboard-plugin-wit=1.8.1=pyhd8ed1ab_0
- tensorflow=2.11.0=cpu_py310hd1aba9c_0
- tensorflow-base=2.11.0=cpu_py310hc9b7e7f_0
- tensorflow-estimator=2.11.0=cpu_py310hfed9998_0
- termcolor=2.3.0=pyhd8ed1ab_0
- terminado=0.17.1=pyh41d4057_0
- threadpoolctl=3.1.0=pyh8a188c0_0
- tiledb=2.13.2=hd532e3d_0
- tinycss2=1.2.1=pyhd8ed1ab_0
- tk=8.6.12=h27826a3_0
- toml=0.10.2=pyhd8ed1ab_0
- tomli=2.0.1=pyhd8ed1ab_0
- toolz=0.12.0=pyhd8ed1ab_0
- tornado=6.1=py310h5764c6d_3
- tqdm=4.65.0=pyhd8ed1ab_1
- traitlets=5.9.0=pyhd8ed1ab_0
- trollimage=1.20.1=pyhd8ed1ab_0
- trollsift=0.5.0=pyhd8ed1ab_0
- typing-extensions=4.5.0=hd8ed1ab_0
- typing_extensions=4.5.0=pyha770c72_0
- tzcode=2023c=h0b41bf4_0
- tzdata=2023c=h71feb2d_0
- uc-micro-py=1.0.1=pyhd8ed1ab_0
- ucx=1.14.0=h8c404fb_1
- udunits2=2.2.28=hc3e0081_0
- unicodedata2=15.0.0=py310h5764c6d_0
- urllib3=1.26.15=pyhd8ed1ab_0
- wcwidth=0.2.6=pyhd8ed1ab_0
- webencodings=0.5.1=py_1
- werkzeug=2.2.3=pyhd8ed1ab_0
- wheel=0.40.0=pyhd8ed1ab_0
- widgetsnbextension=4.0.7=pyhd8ed1ab_0
- wrapt=1.15.0=py310h1fa729e_0
- x264=1!164.3095=h166bdaf_2
- x265=3.5=h924138e_3
- xarray=2023.4.1=pyhd8ed1ab_0
- xcb-util=0.4.0=h166bdaf_0
- xcb-util-image=0.4.0=h166bdaf_0
- xcb-util-keysyms=0.4.0=h166bdaf_0
- xcb-util-renderutil=0.3.9=h166bdaf_0
- xcb-util-wm=0.4.1=h166bdaf_0
- xerces-c=3.2.4=h55805fa_0
- xgboost=1.7.4=cpu_py310hd1aba9c_0
- xkeyboard-config=2.38=h0b41bf4_0
- xlsxwriter=3.1.2=pyhd8ed1ab_0
- xorg-fixesproto=5.0=h7f98852_1002
- xorg-inputproto=2.3.2=h7f98852_1002
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h7f98852_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.8.4=h0b41bf4_0
- xorg-libxau=1.0.9=h7f98852_0
- xorg-libxaw=1.0.14=h7f98852_1
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h0b41bf4_2
- xorg-libxfixes=5.0.3=h7f98852_1004
- xorg-libxi=1.7.10=h7f98852_0
- xorg-libxmu=1.1.3=h7f98852_0
- xorg-libxpm=3.5.13=h7f98852_0
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-libxt=1.2.1=h7f98852_2
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h0b41bf4_1003
- xorg-xproto=7.0.31=h7f98852_1007
- xyzservices=2023.2.0=pyhd8ed1ab_0
- xz=5.2.6=h166bdaf_0
- yaml=0.2.5=h7f98852_2
- yarl=1.9.2=py310h2372a71_0
- zarr=2.14.2=pyhd8ed1ab_0
- zeromq=4.3.4=h9c3ff4c_1
- zict=3.0.0=pyhd8ed1ab_0
- zipp=3.15.0=pyhd8ed1ab_0
- zlib=1.2.13=h166bdaf_4
- zstandard=0.19.0=py310h5764c6d_0
- zstd=1.5.2=h3eb15da_6
- pip:
- anyio==3.6.2
- bidict==0.22.1
- cdsapi==0.5.1
- eumdac==2.0.1
- fastapi==0.92.0
- fastapi-socketio==0.0.10
- h11==0.14.0
- httptools==0.5.0
- jdcal==1.4.1
- markdown2==2.4.8
- nicegui==1.1.11
- orjson==3.8.7
- pscript==0.7.7
- pydantic==1.10.6
- python-dotenv==1.0.0
- python-engineio==4.4.0
- python-multipart==0.0.6
- python-socketio==5.8.0
- pytz-deprecation-shim==0.1.0.post0
- rbf==2022.6.12+13.g53e6882
- skillmetrics==1.2.2
- sniffio==1.3.0
- starlette==0.25.0
- tzlocal==4.3
- uvicorn==0.20.0
- uvloop==0.17.0
- vbuild==0.8.1
- watchfiles==0.18.1
- websockets==10.4 I got to successfully update basemap into a different environment on the same machine, which means that one of the packages in this env is conflicting with basemap dependencies but I cannot understand which one. Re-creating the env for now it's not viable as it is production. |
At least the following block in your dump looks strange to me:
because from your environment dependencies I can see that you are using Python 3.10, but |
I think that log is just confusing because I can indeed find that version when searching with
|
I copied your environment definition into the file
|
Amazing...looks like I have to start back from scratch :( |
In the end it's only two pairs of incompatible packages, I guess if you find the appropriate pairs |
I'd like to believe that but I think conda/mamba are just shooting in the dark...if one of the packages is the source of the mess why they don't appear in the first incompatible reports? :( |
It was quite subtle, it seems your current
After this change, the environment is able to fetch all the
|
I think you can just remove the pip part altogether, those packages shouldn't be important. Anyway I decided to create a new environment from scratch with the dependencies I need, which successfully installed also the latest basemap version. I'll just need to move the production pipeline to this environment once I have some time. thank you anyway for the help @molinav !! |
I remember seeing this already a long time ago but I never managed to solve it.
I'm plotting a map using this
but some countries (like Switzerland) don't show up.
Weirdly enough when centering the projection over France Switzerland shows up
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