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pmlmodelling / nctoolkit

A Python package for netCDF analysis and post-processing
https://nctoolkit.readthedocs.io/en/latest/
GNU General Public License v3.0
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installation testing mac #8

Closed fipoucat closed 3 years ago

fipoucat commented 3 years ago

I installed the toolkit but have many errors at plot stage.

ds = nc.open_data("/Users/sarr/Downloads/test.nc") ds.plot() Traceback (most recent call last): File "", line 1, in File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/nctoolkit/plot.py", line 2, in plot from ncplot import view File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ncplot/init.py", line 1, in from ncplot.plot import view File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ncplot/plot.py", line 4, in from cartopy import crs File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cartopy/init.py", line 104, in import cartopy.crs File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cartopy/crs.py", line 19, in import shapely.geometry as sgeom File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/shapely/geometry/init.py", line 4, in from .base import CAP_STYLE, JOIN_STYLE File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/shapely/geometry/base.py", line 18, in from shapely.coords import CoordinateSequence File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/shapely/coords.py", line 8, in from shapely.geos import lgeos File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/shapely/geos.py", line 112, in _lgeos = CDLL(os.path.join(sys.prefix, 'lib', 'libgeos_c.dylib')) File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/ctypes/init.py", line 373, in init self._handle = _dlopen(self._name, mode) OSError: dlopen(/Library/Frameworks/Python.framework/Versions/3.8/lib/libgeos_c.dylib, 6): image not found

What could be causing this? and what to do?

Thanks

robertjwilson commented 3 years ago

This appears to be an issue with the cartopy installation, not nctoolkit per se.

The smoothest way to nctoolkit is using conda, as that will sort out system dependencies. But if you are using pip, you should probably install cartopy's system dependencies here: https://scitools.org.uk/cartopy/docs/latest/installing.html. It looks like GEOS is the problem.

fipoucat commented 3 years ago

I am trying to reinstall using conda and will update you.

On Tue, Aug 31, 2021 at 11:47 AM Robert Wilson @.***> wrote:

This appears to be an issue with the cartopy installation, not nctoolkit per se.

The smoothest way to nctoolkit is using conda, as that will sort out system dependencies. But if you are using pip, you should probably install cartopy's system dependencies here: https://scitools.org.uk/cartopy/docs/latest/installing.html. It looks like GEOS is the problem.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/pmlmodelling/nctoolkit/issues/8#issuecomment-909161701, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXY6LLBC7QZ4BNCN32E3FDT7S6OJANCNFSM5DD5MCRQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

fipoucat commented 3 years ago

Stil having the same errors after install using conda instead of pip?

On Tue, Aug 31, 2021 at 12:38 PM Abdoulaye Sarr @.***> wrote:

I am trying to reinstall using conda and will update you.

On Tue, Aug 31, 2021 at 11:47 AM Robert Wilson @.***> wrote:

This appears to be an issue with the cartopy installation, not nctoolkit per se.

The smoothest way to nctoolkit is using conda, as that will sort out system dependencies. But if you are using pip, you should probably install cartopy's system dependencies here: https://scitools.org.uk/cartopy/docs/latest/installing.html. It looks like GEOS is the problem.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/pmlmodelling/nctoolkit/issues/8#issuecomment-909161701, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXY6LLBC7QZ4BNCN32E3FDT7S6OJANCNFSM5DD5MCRQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

robertjwilson commented 3 years ago

What is the error message when using conda?

What do you get if you simply import cartopy and nothing else?

fipoucat commented 3 years ago

(/Applications/anaconda3) macasarr:~ sarr$ python Python 3.8.2 (v3.8.2:7b3ab5921f, Feb 24 2020, 17:52:18) [Clang 6.0 (clang-600.0.57)] on darwin Type "help", "copyright", "credits" or "license" for more information.

import nctoolkit as nc nctoolkit is using Climate Data Operators version 1.9.10 ds = nc.open_data("/Users/sarr/Downloads/test.nc") ds.plot() Traceback (most recent call last): File "", line 1, in File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/nctoolkit/plot.py", line 2, in plot from ncplot import view File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ncplot/init.py", line 1, in from ncplot.plot import view File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ncplot/plot.py", line 4, in from cartopy import crs File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cartopy/init.py", line 104, in import cartopy.crs File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cartopy/crs.py", line 19, in import shapely.geometry as sgeom File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/shapely/geometry/init.py", line 4, in from .base import CAP_STYLE, JOIN_STYLE File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/shapely/geometry/base.py", line 18, in from shapely.coords import CoordinateSequence File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/shapely/coords.py", line 8, in from shapely.geos import lgeos File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/shapely/geos.py", line 112, in _lgeos = CDLL(os.path.join(sys.prefix, 'lib', 'libgeos_c.dylib')) File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/ctypes/init.py", line 373, in init self._handle = _dlopen(self._name, mode) OSError: dlopen(/Library/Frameworks/Python.framework/Versions/3.8/lib/libgeos_c.dylib, 6): image not found

On Tue, Aug 31, 2021 at 6:00 PM Robert Wilson @.***> wrote:

What is the error message when using conda?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/pmlmodelling/nctoolkit/issues/8#issuecomment-909463671, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXY6LJKARPHAFDWLWQFLJLT7UKCLANCNFSM5DD5MCRQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

robertjwilson commented 3 years ago

I'm not a Mac user. But is that actually the conda version of Python?

fipoucat commented 3 years ago

I'll check this more closely, because I am having the same error message when I try to import cartopy

On Tue, Aug 31, 2021 at 7:23 PM Robert Wilson @.***> wrote:

I'm not a Mac user. But is that actually the conda version of Python?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/pmlmodelling/nctoolkit/issues/8#issuecomment-909535848, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXY6LPF65TYZJ26Z3ISMHDT7UTZJANCNFSM5DD5MCRQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

robertjwilson commented 3 years ago

I'm closing the issue, as it relates purely to cartopy.