q-rai
commented
6 years ago First attempt!
conda create -n hydro python=3.6 numpy matplotlib shapely
source activate hydro
conda install matplotlib
conda install -c conda-forge fiona
conda install -c conda-forge rasterio
conda install shapely
pip install MeshPy
conda install scipy
conda install vtk
conda install ipykernelTo add the environment to jupyter notebooks, run python -m ipykernel install --user --name hydro --display-name "Python 3 (Hydro)"
So far, so good. But gdal refused to install.
The solution is supposedly this, according to one of many search results I went through:
conda install -c conda-forge fiona "libgdal<2.0"But this would uninstall rasterio. When trying anyway, I got “An unexpected error has occurred.”
Issues along the way
-
Code couldn’t find the workflow library
- tried adding the
ideal_octo_waffleto PYTHONPATH before calling jupyter notebook — no luck - tried the
.pthsolution here: https://stackoverflow.com/a/37008663 — no luck - would like to try the
setup.pysolution, that seems cleanest — later
- tried adding the
-
Error at
from rasterio._base import get_windowinworkflow/clip.py:ImportError: cannot import name 'get_window'- Solution: removed that line and prepended
rasterio._basein front ofget_window-- seems to work, no more error
-
Error at
from fiona.ogrext import Iterator, ItemsIterator, KeysIteratorinworkflow/hilev.pyImportError: dlopen(/Users/vib/anaconda/envs/hydro/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libpoppler.76.dylib Referenced from: /Users/vib/anaconda/envs/hydro/lib/libgdal.20.dylib Reason: image not found- Tried:
conda install -c conda-forge fiona "libgdal<2.0"https://github.com/conda-forge/fiona-feedstock/issues/13#issuecomment-220841908 - this would uninstall rasterio
- tried anyway — no luck (see error below)
- I don’t even understand why it’s using python 2.7! My prompt says I’m in the
hydroenv:(hydro) vibmbpro:site-packages vib$ conda install -c conda-forge fiona "libgdal<2.0"
Result:
Preparing transaction: done
Verifying transaction: failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):```
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/exceptions.py", line 819, in __call__
return func(*args, **kwargs)
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 78, in _main
exit_code = do_call(args, p)
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/cli/conda_argparse.py", line 77, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/cli/main_install.py", line 11, in execute
install(args, parser, 'install')
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/cli/install.py", line 253, in install
handle_txn(unlink_link_transaction, prefix, args, newenv)
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/cli/install.py", line 282, in handle_txn
unlink_link_transaction.execute()
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/core/link.py", line 223, in execute
self.verify()
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/common/io.py", line 46, in decorated
return f(*args, **kwds)
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/core/link.py", line 210, in verify
exceptions = self._verify(self.prefix_setups, self.prefix_action_groups)
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/core/link.py", line 481, in _verify
cls._verify_transaction_level(prefix_setups),
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/core/link.py", line 476, in <genexpr>
exceptions = tuple(exc for exc in concatv(
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/core/link.py", line 334, in _verify_individual_level
error_result = axn.verify()
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/core/path_actions.py", line 292, in verify
source_sha256 = compute_sha256sum(self.source_full_path)
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/gateways/disk/read.py", line 75, in compute_sha256sum
return _digest_path('sha256', file_full_path)
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/gateways/disk/read.py", line 64, in _digest_path
with open(path, "rb") as fh:
File "/Users/vib/anaconda/lib/python2.7/site-packages/conda/common/compat.py", line 121, in open
errors=errors, newline=newline, closefd=closefd)
IOError: [Errno 13] Permission denied: '/Users/vib/anaconda/pkgs/vtk-6.3.0-py27_1/bin/vtkHashSource-6.3'
ecoon
The tutorial is for complete installs. To keep things nicely separated, I'm trying to build a conda environment for the project.
It's been a couple of attempts and I figure it makes more sense to track the progress in an issue right with the code, rather than completely separately. I'll document my progress here, starting by pasting the documentation I have of my attempts so far.