Installation via Anaconda - obspy/obspy GitHub Wiki
Anaconda (you can also use Miniconda for a smaller footprint) is a scientific Python installation shipping with essentially all needed packages. Install it according to the instructions on their homepage. You can use any Anaconda Python version. An Anaconda Python installation is completely separate from any existing system wide or user space Python installation, so Anaconda can be tested without the fear of breaking an existing installation.
Anaconda works on most systems without root access!
-
Add the
conda-forgechannel to your Anaconda configuration (see conda docs regarding channels):
$ conda config --add channels conda-forge
- We strongly recommend to work with separate Anaconda environments, and especially not use the special
baseenvironment (formerly namedrooton conda versions <4.4; this environment is used for allcondacommands and environment manipulations, package installations etc.) for anything besides updating thecondapackage itself (if necessary). All needed packages can be installed simultaneously while creating the new environment. The conda package by default does not install a mapping package. ObsPy, as of early 2022, is compatible withcartopywhich can be installed alongside ObsPy. We also recommend to installpytestandpytest-json-reportpackages which are needed to run the tests.
$ conda create -n obspy python=3.10 obspy cartopy pytest pytest-json # or other supported Python version
$ conda activate obspy # activate the obspy environment
(obspy) $
- If some packages were missed when creating the environment they can be installed after activation with:
(obspy) $ conda install obspy
Updating
(obspy) $ conda update obspy
or (if you did not add the conda-forge channel to your default channels):
(obspy) $ conda update -c conda-forge obspy
Try to stick to only using conda package manager to install packages whenever possible! Other tools like pip (or even its outdated easy_install predecessor) should really only be used for Python packages that are not packaged by Anaconda (search for available pre-packaged versions first doing conda search <package_name> -- or if it's not available in the default channel doing anaconda search -t conda <package_name>). And even when needing to install a package from source using pip it is a good idea to at least install the package's dependencies via conda beforehand.
Troubleshooting:
- If you have problems, be sure to check out the Troubleshooting page of Anaconda
- Especially beware of mixing in Python packages from outside the environment, not handled/installed by the
condapackage manager. This is usually unwanted and coming from older (and way more sloppy) Python installations and bound to bring forth very unexpected and hard to debug behavior and errors. This can happen outside of anaconda's control by..- having
PYTHONPATHandPYTHONHOMEenvironment variables set, or (less common) by.. - having Python modules in specific user space locations which Python looks for
- having
Tip:
Versions of packages can be fixed by pinning in Anaconda (e.g. so that certain packages stay on same version even when updating packages that depend on them). It can be a good idea to pin the installed numpy version as many packages are compiled against a certain numpy version and only update numpy deliberately. Also, ObsPy major version can be fixed in the same way to keep an Anaconda environment on the a fixed version, e.g.:
(Note: Recent conda version >=4.0 has significant improvements and properly takes numpy dependent packages into account when trying to update numpy, so pinning numpy is not as important anymore with an updated conda package)
numpy 1.10.*
matplotlib 1.5.*
basemap 1.0.*
obspy 1.0.*
Example:
This example shows how to set up a separate anaconda environment (after anaconda installation) for the old ObsPy version 0.10.2 (assuming a Python2 installation):
- add our obspy Anaconda channel (only needs to be done once after Anaconda installation)
$ conda config --add channels obspy
- create separate, bare environment with name "obspy0.10"
$ conda create -n obspy0.10 python=2.7
Fetching package metadata: ........
Solving package specifications: ...........
Package plan for installation in environment /home/megies/anaconda/envs/obspy0.10:
The following NEW packages will be INSTALLED:
openssl: 1.0.2g-0
pip: 8.1.1-py27_0
python: 2.7.11-0
readline: 6.2-2
setuptools: 20.3-py27_0
sqlite: 3.9.2-0
tk: 8.5.18-0
wheel: 0.29.0-py27_0
zlib: 1.2.8-0
Proceed ([y]/n)? y
Extracting packages ...
[ COMPLETE ]|######################################| 100%
Linking packages ...
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#
# To activate this environment, use:
# $ source activate obspy0.10
#
# To deactivate this environment, use:
# $ source deactivate
#
- activate environment for use in this terminal
$ source activate obspy0.10
discarding /path/to/anaconda/bin from PATH
prepending /path/to/anaconda/envs/obspy0.10/bin to PATH
(obspy0.10)$ which python # just to illustrate which python is in use now
/path/to/anaconda/envs/obspy0.10/bin/python
- set desired version numbers by pinning in environment (create new text file "pinned" in correct folder, see above)
# contents of /path/to/anaconda/envs/obspy0.10/conda-meta/pinned:
python 2.7.*
numpy 1.10.*
matplotlib 1.5.*
basemap 1.0.*
obspy 0.10.*
- now install obspy and dependencies
(obspy0.10)$ conda install obspy
Fetching package metadata: ........
Solving package specifications: ...........
Package plan for installation in environment /home/megies/anaconda/envs/obspy0.10:
The following packages will be downloaded:
package | build
---------------------------|-----------------
libgfortran-3.0 | 0 261 KB
future-0.15.2 | py27_0 616 KB
numpy-1.9.3 | py27_2 5.7 MB
pytz-2016.2 | py27_0 176 KB
lxml-3.6.0 | py27_0 2.8 MB
python-dateutil-2.5.1 | py27_0 235 KB
scipy-0.17.0 | np19py27_2 29.9 MB
------------------------------------------------------------
Total: 39.7 MB
The following NEW packages will be INSTALLED:
basemap: 1.0.7-np19py27_0
cairo: 1.12.18-6
flake8: 2.5.1-py27_0
fontconfig: 2.11.1-5
freetype: 2.5.5-0
funcsigs: 0.4-py27_0
future: 0.15.2-py27_0
geos: 3.3.3-0
libgfortran: 3.0-0
libpng: 1.6.17-0
libxml2: 2.9.2-0
libxslt: 1.1.28-0
lxml: 3.6.0-py27_0
matplotlib: 1.4.3-np19py27_2
mccabe: 0.3.1-py27_0
mkl: 11.3.1-0
mock: 1.3.0-py27_0
numpy: 1.9.3-py27_2
obspy: 0.10.2-np19py27_0
pbr: 1.3.0-py27_0
pep8: 1.7.0-py27_0
pixman: 0.32.6-0
py2cairo: 1.10.0-py27_2
pyflakes: 1.1.0-py27_0
pyparsing: 2.0.3-py27_0
pyqt: 4.11.4-py27_1
python-dateutil: 2.5.1-py27_0
pytz: 2016.2-py27_0
qt: 4.8.7-1
scipy: 0.17.0-np19py27_2
sip: 4.16.9-py27_0
six: 1.10.0-py27_0
sqlalchemy: 1.0.12-py27_0
Proceed ([y]/n)?
Fetching packages ...
libgfortran-3. 100% |######################################| Time: 0:00:00 442.02 kB/s
future-0.15.2- 100% |######################################| Time: 0:00:00 756.18 kB/s
numpy-1.9.3-py 100% |######################################| Time: 0:00:04 1.40 MB/s
pytz-2016.2-py 100% |######################################| Time: 0:00:00 356.89 kB/s
lxml-3.6.0-py2 100% |######################################| Time: 0:00:03 793.42 kB/s
python-dateuti 100% |######################################| Time: 0:00:00 473.91 kB/s
scipy-0.17.0-n 100% |######################################| Time: 0:00:20 1.54 MB/s
Extracting packages ...
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Linking packages ...
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- done!
Test your Installation
Run the test suite to assure everything works correctly.
$ obspy-runtests
Offline installation
For installation of Anaconda including ObsPy in an offline environment, see https://discourse.obspy.org/t/obspy-update-failure-following-anaconda-failure-and-subsequent-re-install/607/3