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A conda-smithy repository for cdo.

License: BSD 3-Clause "New" or "Revised" License

Shell 100.00%

cdo-feedstock's Introduction

About cdo-feedstock

Feedstock license: BSD-3-Clause

Home: https://code.mpimet.mpg.de/projects/cdo

Package license: BSD-3-Clause

Summary: CLI tools to manipulate and analyse Climate and NWP model Data

Current build status

Azure

Variant	Status
linux_64
osx_64
osx_arm64

Current release info

Name	Downloads	Version	Platforms

Installing cdo

Installing cdo from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, cdo can be installed with conda:

conda install cdo

or with mamba:

mamba install cdo

It is possible to list all of the versions of cdo available on your platform with conda:

conda search cdo --channel conda-forge

or with mamba:

mamba search cdo --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search cdo --channel conda-forge

# List packages depending on `cdo`:
mamba repoquery whoneeds cdo --channel conda-forge

# List dependencies of `cdo`:
mamba repoquery depends cdo --channel conda-forge

About conda-forge

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge anaconda.org channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating cdo-feedstock

If you would like to improve the cdo recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/cdo-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

If the version of a package is not being increased, please add or increase the build/number.
If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

cdo-feedstock's People

Contributors

Stargazers

Watchers

Forkers

ocefpaf conda-forge-admin lexual ucyo regro-cf-autotick-bot akrherz wachsylon conda-forge-linter zklaus

cdo-feedstock's Issues

Build cdo on Windows

There are no Windows builds at the moment

cannot load libjpeg.so.9

I installed cdo with Python 2.7.12, anaconda 64-bit, Redhat Linux 7. The installation went OK. But as soon as I run cdo, it reports the following error

cdo: error while loading shared libraries: libjpeg.so.9: cannot open shared object file: No such file or directory

I checked the lib directory in anaconda installation and only found libjpeg.so.8 not 9. Do I need to install the library separately or is there any easy fix? Thanks!

netcdf support does not work

I am currently unable to install cdo with netcdf support, and when using the cdo installed via conda install cdo, I obtain errors such as:

cdo seltimestep: Open failed on >/Volumes/Research_HD/cosmos-aso-wiso/Eem130-S2/post/mpiom/Eem130-S2_mpiom_main_THO_levels_6-100_vertmean_months_678_yearmean.nc<
Unsupported file type (library support not compiled in)
To create a CDO application with NetCDF support use: ./configure --with-netcdf=<NetCDF root directory> ...

I suspect that the recipie must be changed to enable netcdf, but I am unsure how to do this,

Update SPDX License Identifier

Comment:

Currently, the license is still listed as GPL-2.0. This should be updated to the applicable GPL-2.0-or-later or GPL-2.0-only.

New cdo=1.9.7.1 that is mpi-agnostic depends on proj4>=6.1.1 that is causing massive conflicts

Issue: proj4>6.1.1 as dependency for cdo=1.9.7.1 (mpi agnostic, =h7d1db5e_1) is causing a lot of conflicts since a lot of packages from conda-forge are limiting proj4 versions to <6.1.1

Environment (conda list):

$ conda list
(base)

No point adding the conda list output since I am using the (base) from conda=4.7.11 and trying to create a TEST environment like this:

---
name: cdoenv
channels:
  - conda-forge

dependencies:
  - libgdal
  - cdo=1.9.7.1=h7d1db5e_1

That fails since

Package proj4 conflicts for:
libgdal -> proj4[version='5.2.0.*|>=5.2.0,<5.2.1.0a0|>=6.1.0,<6.1.1.0a0']
cdo==1.9.7.1=h7d1db5e_1 -> proj4[version='>=6.1.1,<6.1.2.0a0']
Note that strict channel priority may have removed packages required for satisfiability.

Is the new cdo not compatible with older proj4 versions like 5.2.0?

Incorrect HDF5 Version

Issue:
When install cdo with Conda on MacOS, the hdf5 library is downgraded to 1.10.4, but cdo wants 1.10.5.

conda install -c conda-forge cdo                                     ✔  INSERT  (LIG)      10150  09:30:16  
Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Initial quick solve with frozen env failed.  Unfreezing env and trying again.
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
Initial quick solve with frozen env failed.  Unfreezing env and trying again.
Solving environment: done

## Package Plan ##

  environment location: /Users/pgierz/anaconda3/envs/LIG

  added / updated specs:
    - cdo


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-h01d97ff_0
  cdo                conda-forge/osx-64::cdo-1.9.7.1-h561daef_0
  curl               conda-forge/osx-64::curl-7.63.0-heae2a1f_1000
  eccodes            conda-forge/osx-64::eccodes-2.12.3-hac8aea4_1
  fftw               conda-forge/osx-64::fftw-3.3.8-mpi_openmpi_h2385e66_1006
  hdf4               conda-forge/osx-64::hdf4-4.2.13-hf3c6af0_1002
  jasper             conda-forge/osx-64::jasper-1.900.1-h636a363_1006
  krb5               conda-forge/osx-64::krb5-1.16.2-h24a3359_1000
  libaec             conda-forge/osx-64::libaec-1.0.4-h0a44026_0
  libcurl            conda-forge/osx-64::libcurl-7.63.0-h76de61e_1000
  libnetcdf          conda-forge/osx-64::libnetcdf-4.6.2-h6b88ef6_1001
  libssh2            conda-forge/osx-64::libssh2-1.8.0-hf30b1f0_1003
  libxml2            conda-forge/osx-64::libxml2-2.9.9-hd80cff7_2
  llvm-openmp        conda-forge/osx-64::llvm-openmp-8.0.0-h770b8ee_0
  mpi                conda-forge/osx-64::mpi-1.0-openmpi
  openmpi            conda-forge/osx-64::openmpi-4.0.1-ha90c164_1
  ossuuid            conda-forge/osx-64::ossuuid-1.6.2-h0a44026_1000
  udunits2           conda-forge/osx-64::udunits2-2.2.27.6-h776b7f1_1001

The following packages will be DOWNGRADED:

  hdf5                           1.10.5-nompi_h0cbb7df_1100 --> 1.10.4-nompi_h0cbb7df_1106

Although the install works normally, when trying to use cdo, the following error is produced:

$ cdo --version
dyld: Library not loaded: @rpath/libhdf5.103.dylib
  Referenced from: /Users/pgierz/anaconda3/envs/LIG/bin/cdo
  Reason: Incompatible library version: cdo requires version 105.0.0 or later, but libhdf5.103.dylib provides version 104.0.0
[2]    3472 abort      cdo --version

I guess this is connected to an incorrect dependency being pinned, but I don't know where to change that...

Environment (conda list):

$ conda list
# packages in environment at /Users/pgierz/anaconda3/envs/LIG:
#
# Name                    Version                   Build  Channel
appnope                   0.1.0                    py37_0    conda-forge
asn1crypto                0.24.0                py37_1003    conda-forge
attrs                     19.1.0                   py37_1  
backcall                  0.1.0                    py37_0  
bcrypt                    3.1.6            py37h01d97ff_1    conda-forge
bleach                    3.1.0                    py37_0  
bzip2                     1.0.8                h01d97ff_0    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
cartopy                   0.17.0          py37hdb866aa_1005    conda-forge
cdo                       1.5.3                    pypi_0    pypi
certifi                   2019.6.16                py37_1    conda-forge
cffi                      1.12.3           py37hccf1714_0    conda-forge
chardet                   3.0.4                 py37_1003    conda-forge
cryptography              2.5              py37hdbc3d79_1    conda-forge
curl                      7.63.0            heae2a1f_1000    conda-forge
cycler                    0.10.0                     py_1    conda-forge
dbus                      1.13.6               h90a0687_0  
decorator                 4.4.0                    py37_1  
defusedxml                0.6.0                      py_0  
eccodes                   2.12.3               hac8aea4_1    conda-forge
entrypoints               0.3                      py37_0  
expat                     2.2.6                h0a44026_0  
fftw                      3.3.8           mpi_openmpi_h2385e66_1006    conda-forge
freetype                  2.10.0               h24853df_0    conda-forge
geos                      3.7.2                h6de7cb9_1    conda-forge
gettext                   0.19.8.1             h15daf44_3  
glib                      2.56.2               hd9629dc_0  
hdf4                      4.2.13            hf3c6af0_1002    conda-forge
hdf5                      1.10.4          nompi_h0cbb7df_1106    conda-forge
icu                       58.2                 h4b95b61_1  
idna                      2.8                   py37_1000    conda-forge
ipykernel                 5.1.1            py37h39e3cac_0  
ipython                   7.6.1            py37h39e3cac_0  
ipython_genutils          0.2.0                    py37_0  
ipywidgets                7.4.2                    py37_0  
jasper                    1.900.1           h636a363_1006    conda-forge
jedi                      0.13.3                   py37_0    conda-forge
jinja2                    2.10.1                   py37_0  
jpeg                      9c                h1de35cc_1001    conda-forge
json5                     0.8.5                      py_0    conda-forge
jsonschema                3.0.1                    py37_0    conda-forge
jupyter                   1.0.0                    py37_7  
jupyter_client            5.2.4                    py37_0  
jupyter_console           6.0.0                    py37_0  
jupyter_core              4.5.0                      py_0  
jupyterlab                1.0.2                    py37_0    conda-forge
jupyterlab_server         1.0.0                      py_1    conda-forge
kiwisolver                1.1.0            py37h770b8ee_0    conda-forge
krb5                      1.16.2            h24a3359_1000    conda-forge
libaec                    1.0.4                h0a44026_0    conda-forge
libblas                   3.8.0               10_openblas    conda-forge
libcblas                  3.8.0               10_openblas    conda-forge
libcurl                   7.63.0            h76de61e_1000    conda-forge
libcxx                    4.0.1                hcfea43d_1  
libcxxabi                 4.0.1                hcfea43d_1  
libedit                   3.1.20181209         hb402a30_0  
libffi                    3.2.1                h475c297_4  
libgfortran               3.0.1                         0    conda-forge
libiconv                  1.15                 hdd342a3_7  
liblapack                 3.8.0               10_openblas    conda-forge
libnetcdf                 4.6.2             h6b88ef6_1001    conda-forge
libopenblas               0.3.6                hd44dcd8_4    conda-forge
libpng                    1.6.37               h2573ce8_0    conda-forge
libsodium                 1.0.16               h3efe00b_0  
libssh2                   1.8.0             hf30b1f0_1003    conda-forge
libtiff                   4.0.10            hd08fb8f_1003    conda-forge
libxml2                   2.9.9                hd80cff7_2    conda-forge
llvm-openmp               8.0.0                h770b8ee_0    conda-forge
lz4-c                     1.8.3             h6de7cb9_1001    conda-forge
markupsafe                1.1.1            py37h1de35cc_0    conda-forge
matplotlib                3.1.1                    py37_0    conda-forge
matplotlib-base           3.1.1            py37h3a684a6_0    conda-forge
mistune                   0.8.4            py37h1de35cc_0  
mpi                       1.0                     openmpi    conda-forge
nbconvert                 5.5.0                      py_0    conda-forge
nbformat                  4.4.0                    py37_0  
ncurses                   6.1                  h0a44026_1  
notebook                  5.7.8                    py37_0    conda-forge
numpy                     1.16.4           py37h6b0580a_0    conda-forge
olefile                   0.46                       py_0    conda-forge
openblas                  0.3.6                hd44dcd8_4    conda-forge
openmpi                   4.0.1                ha90c164_1    conda-forge
openssl                   1.0.2r               h1de35cc_0    conda-forge
ossuuid                   1.6.2             h0a44026_1000    conda-forge
owslib                    0.18.0                     py_0    conda-forge
pandas                    0.24.2           py37h86efe34_0    conda-forge
pandoc                    2.2.3.2                       0  
pandocfilters             1.4.2                    py37_1  
paramiko                  2.6.0                    py37_0    conda-forge
parso                     0.5.0                      py_0    conda-forge
pcre                      8.43                 h0a44026_0  
pexpect                   4.7.0                    py37_0    conda-forge
pickleshare               0.7.5                    py37_0  
pillow                    5.3.0           py37hbddbef0_1000    conda-forge
pip                       19.1.1                   py37_0    conda-forge
proj4                     6.1.0                h2cc77ee_2    conda-forge
prometheus_client         0.7.1                      py_0    conda-forge
prompt_toolkit            2.0.9                    py37_0  
ptyprocess                0.6.0                    py37_0    conda-forge
pycparser                 2.19                     py37_1    conda-forge
pyepsg                    0.4.0                      py_0    conda-forge
pygments                  2.4.2                      py_0    conda-forge
pykdtree                  1.3.1           py37h917ab60_1002    conda-forge
pynacl                    1.3.0           py37h1de35cc_1000    conda-forge
pyopenssl                 19.0.0                   py37_0    conda-forge
pyparsing                 2.4.0                      py_0    conda-forge
pyproj                    2.2.1            py37h804dea5_0    conda-forge
pyqt                      5.9.2            py37h655552a_2  
pyrsistent                0.14.11          py37h1de35cc_0    conda-forge
pyshp                     2.1.0                      py_0    conda-forge
pysocks                   1.7.0                    py37_0    conda-forge
python                    3.7.0                hc167b69_0  
python-dateutil           2.8.0                      py_0    conda-forge
pytz                      2019.1                     py_0    conda-forge
pyzmq                     18.0.0           py37h0a44026_0  
qt                        5.9.7                h468cd18_1  
qtconsole                 4.5.1                      py_0    conda-forge
readline                  7.0                  h1de35cc_5  
requests                  2.22.0                   py37_0    conda-forge
scipy                     1.3.0            py37hab3da7d_0    conda-forge
send2trash                1.5.0                    py37_0  
setuptools                41.0.1                   py37_0    conda-forge
shapely                   1.6.4           py37h0567c5e_1006    conda-forge
sip                       4.19.8           py37h0a44026_0  
six                       1.12.0                py37_1000    conda-forge
sqlite                    3.28.0               ha441bb4_0  
terminado                 0.8.2                    py37_0    conda-forge
testpath                  0.4.2                    py37_0  
tk                        8.6.8                ha441bb4_0    conda-forge
tornado                   6.0.3            py37h01d97ff_0    conda-forge
tqdm                      4.32.2                     py_0    conda-forge
traitlets                 4.3.2                    py37_0    conda-forge
udunits2                  2.2.27.6          h776b7f1_1001    conda-forge
urllib3                   1.24.3                   py37_0    conda-forge
wcwidth                   0.1.7                    py37_0  
webencodings              0.5.1                    py37_1  
wheel                     0.33.4                   py37_0    conda-forge
widgetsnbextension        3.4.2                    py37_0  
xarray                    0.12.3                     py_0    conda-forge
xlrd                      1.2.0                      py_0    conda-forge
xz                        5.2.4                h1de35cc_4  
zeromq                    4.3.1                h0a44026_3  
zlib                      1.2.11               h1de35cc_3  
zstd                      1.4.0                ha9f0a20_0    conda-forge

Details about conda and system ( conda info ):

$ conda info
     active environment : LIG
    active env location : /Users/pgierz/anaconda3/envs/LIG
            shell level : 2
       user config file : /Users/pgierz/.condarc
 populated config files : /Users/pgierz/.condarc
          conda version : 4.7.10
    conda-build version : 3.18.5
         python version : 3.7.3.final.0
       virtual packages : 
       base environment : /Users/pgierz/anaconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/pgierz/anaconda3/pkgs
                          /Users/pgierz/.conda/pkgs
       envs directories : /Users/pgierz/anaconda3/envs
                          /Users/pgierz/.conda/envs
               platform : osx-64
             user-agent : conda/4.7.10 requests/2.21.0 CPython/3.7.3 Darwin/18.2.0 OSX/10.14.2
                UID:GID : 952471260:355342394
             netrc file : None
           offline mode : False

Failure linking on OS X

cdo 1.7.2 fails when adding any extra dependency on OS X. See #8 (comment)

netCDF root directory not set on macOS

Hi,

when doing a conda install cdo on mac, I get the following error when trying to use cdo and netcdf files:

Unsupported file type (library support not compiled in)
To create a CDO application with NetCDF support use: ./configure --with-netcdf=<NetCDF root directory>

Likely, the configure recipie isn't correct for mac, since it is missing some parts that appear to be set in the uname check. I haven't been using conda very long; and while I would try to fix this on my own, I'm not sure where exactly to start.

Switch from ossuuid to libuuid?

This package depends on ossuuid, which cannot be installed at the same time as libuuid, used by many other packages such as matplotlib (see e.g. conda-forge/libcf-feedstock#20, conda-forge/cmor-feedstock#9, PCMDI/cmor#458). Would it be possible to switch to libuuid?

It looks like you might also encounter this issue when adding cmor as a dependency again in #79, since that package has now switched.

ClobberWarning: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000, conda-forge/linux-64::ossuuid-1.6.2-hf484d3e_1000
  path: 'lib/libuuid.a'


ClobberWarning: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000, conda-forge/linux-64::ossuuid-1.6.2-hf484d3e_1000
  path: 'lib/libuuid.la'


ClobberWarning: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000, conda-forge/linux-64::ossuuid-1.6.2-hf484d3e_1000
  path: 'lib/libuuid.so'


ClobberWarning: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000, conda-forge/linux-64::ossuuid-1.6.2-hf484d3e_1000
  path: 'lib/pkgconfig/uuid.pc'

HDF5 is not thread-safe

cdo needs to be rebuild on conda-forge/hdf5-feedstock#48 is merged. See #8 (comment)

latest cdo=1.7.2=1 is missing netcdf support on linux

For reasons i don't know is the latest build of cdo missing netcdf support on Linux.

$  conda create -n cdo python=2 cdo
$ source activate cdo
$ cdo sinfo pr_Amon_MPI-ESM-LR_historical_r1i1p1_185001-200512.nc 

cdo sinfo: Open failed on >pr_Amon_MPI-ESM-LR_historical_r1i1p1_185001-200512.nc<
Unsupported file type (library support not compiled in)
To create a CDO application with NetCDF support use: ./configure --with-netcdf=<NetCDF root directory> ...

Missing dependency on hdf5

Issue:

The CDO package is missing a dependency on hdf5. Installing it in a clean environment installs hdf5=1.10.6, when CDO wants hdf5=1.10.5

Running the command

$ cdo genycon,tgt.nc src.nc wgt.nc

gives the error

Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.10.5, library is 1.10.6

Environment (conda list):

$ conda list
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       0_gnu    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2020.4.5.1           hecc5488_0    conda-forge
cdo                       1.9.8                h6e5f144_8    conda-forge
curl                      7.69.1               h33f0ec9_0    conda-forge
eccodes                   2.17.0               hf05d9b7_2    conda-forge
expat                     2.2.9                he1b5a44_2    conda-forge
fftw                      3.3.8           nompi_h7f3a6c3_1110    conda-forge
hdf4                      4.2.13            hf30be14_1003    conda-forge
hdf5                      1.10.6          nompi_h3c11f04_100    conda-forge
icu                       67.1                 he1b5a44_0    conda-forge
jasper                    1.900.1           h07fcdf6_1006    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
krb5                      1.17.1               h2fd8d38_0    conda-forge
libaec                    1.0.4                he1b5a44_1    conda-forge
libcurl                   7.69.1               hf7181ac_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgfortran-ng            7.5.0                hdf63c60_6    conda-forge
libgomp                   9.2.0                h24d8f2e_2    conda-forge
libiconv                  1.15              h516909a_1006    conda-forge
libnetcdf                 4.7.4           nompi_h84807e1_104    conda-forge
libpng                    1.6.37               hed695b0_1    conda-forge
libssh2                   1.9.0                hab1572f_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libtiff                   4.1.0                hc7e4089_6    conda-forge
libwebp-base              1.1.0                h516909a_3    conda-forge
libxml2                   2.9.10               h72b56ed_1    conda-forge
lz4-c                     1.9.2                he1b5a44_1    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
openssl                   1.1.1g               h516909a_0    conda-forge
ossuuid                   1.6.2             hf484d3e_1000    conda-forge
proj                      7.0.0                h966b41f_4    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
udunits2                  2.2.27.6          h4e0c4b3_1001    conda-forge
xz                        5.2.5                h516909a_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.4                h6597ccf_3    conda-forge

Details about conda and system ( conda info ):

$ conda info
     active environment : testcdo
    active env location : /***/testcdo
            shell level : 3
       user config file : /***/.condarc
 populated config files : /***/.condarc
          conda version : 4.8.0
    conda-build version : 3.18.11
         python version : 3.7.6.final.0
       virtual packages : __glibc=2.23
       base environment : /local/opt/miniconda  (writable)
           channel URLs : https://conda.anaconda.org/ScottWales/linux-64
                          https://conda.anaconda.org/ScottWales/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /***/conda/pkgs
       envs directories : /l***/conda
                          /local/opt/miniconda/envs
                          /home/***/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.0 requests/2.22.0 CPython/3.7.6 Linux/4.15.0-88-generic ubuntu/16.04.6 glibc/2.23
                UID:GID : 1389014447:1389014447
             netrc file : None
           offline mode : False

Jasper is not working on Linux

See #19 (comment)

Request to update cdo feedstock to v1.9.7.1

Please can you update the cdo feedstock to v1.9.7.1. We have users requesting this on the JASMIN environment. Thanks :-)

NetCDF currently not supported

Issue: NetCDF currently not supported

The NetCDF format is widely used in the climate modelling community. Integrating NetCDF support in conda-forge cdo would allow an easy installation of cdo for many users. Currently, those who need NetCDF support have to compile cdo on their system.

Current conda-forge cdo (cdo -V):

Libraries:
Filetypes: srv ext ieg grb1
     CDI library version : 1.9.5
 CGRIBEX library version : 1.9.1
    EXSE library version : 1.4.0
    FILE library version : 1.8.3

Suggested library support cdo -V:

Libraries: HDF5/1.10.4 proj/5.2 curl/7.64.0
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5
     CDI library version : 1.9.5
GRIB_API library version : 2.9.0
  NetCDF library version : 4.6.1 of Dec 10 2018 12:31:57 $
    HDF5 library version : 1.10.4
    EXSE library version : 1.4.0
    FILE library version : 1.8.3

CDO with CMOR

@ocefpaf
Hi Filipe,
I finally managed to do a pull request with changes required to run cdo with cmor (I hope you have received it). The conda-build and some tests worked on my machine. Beginning with the current cdo-1.9.4.rc2, the installation should work.

I would like to have a dev-release subchannel for the cmor branch so I will have an independent statistic about the usage rate of this feature. This is coordinated with the developers of cdo (Ralf and Uwe).
Thank you for your help and best regards,
Fabi

cdo -z szip gives: Warning (cdfDefVarSzip): Szip compression failed, NetCDF4/szlib not available!

[X ] I read the conda-forge documentation and could not find the solution for my problem there.

Issue: szip internal compression for netcdf4 files does not work

Environment (conda list):

$ conda list
# packages in environment at /opt/conda.io/miniconda3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
blosc                     1.21.0               h9c3ff4c_0    conda-forge
blosc-hdf5-plugin         1.0.0                h646ab9b_2    conda-forge
brotlipy                  0.7.0           py39h3811e60_1001    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h7f98852_1    conda-forge
ca-certificates           2020.12.5            ha878542_0    conda-forge
cdo                       1.9.9               had776b3_14    conda-forge
certifi                   2020.12.5        py39hf3d152e_1    conda-forge
cffi                      1.14.5           py39he32792d_0    conda-forge
chardet                   4.0.0            py39hf3d152e_1    conda-forge
conda                     4.10.1           py39hf3d152e_0    conda-forge
conda-package-handling    1.7.3            py39h3811e60_0    conda-forge
cryptography              3.4.7            py39hbca0aa6_0    conda-forge
curl                      7.76.1               h979ede3_1    conda-forge
eccodes                   2.21.0               ha0e6eb6_0    conda-forge
expat                     2.3.0                h9c3ff4c_0    conda-forge
fftw                      3.3.9           nompi_h74d3f13_101    conda-forge
hdf4                      4.2.13            h10796ff_1005    conda-forge
hdf5                      1.10.6          nompi_h6a2412b_1114    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
jasper                    1.900.1           h07fcdf6_1006    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
krb5                      1.17.2               h926e7f8_0    conda-forge
ld_impl_linux-64          2.35.1               hea4e1c9_2    conda-forge
libaec                    1.0.4                h9c3ff4c_1    conda-forge
libcurl                   7.76.1               hc4aaa36_1    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc-ng                 9.3.0               h2828fa1_19    conda-forge
libgfortran-ng            9.3.0               hff62375_19    conda-forge
libgfortran5              9.3.0               hff62375_19    conda-forge
libgomp                   9.3.0               h2828fa1_19    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libnetcdf                 4.7.4           nompi_h56d31a8_107    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libssh2                   1.9.0                ha56f1ee_6    conda-forge
libstdcxx-ng              9.3.0               h6de172a_19    conda-forge
libtiff                   4.2.0                hdc55705_1    conda-forge
libwebp-base              1.2.0                h7f98852_2    conda-forge
libxml2                   2.9.10               h72842e0_4    conda-forge
lz4-c                     1.9.3                h9c3ff4c_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
openssl                   1.1.1k               h7f98852_0    conda-forge
ossuuid                   1.6.2             hf484d3e_1000    conda-forge
pip                       21.1.1             pyhd8ed1ab_0    conda-forge
proj                      7.2.0                h277dcde_2    conda-forge
pycosat                   0.6.3           py39h3811e60_1006    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pyopenssl                 20.0.1             pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py39hf3d152e_3    conda-forge
python                    3.9.2           hffdb5ce_0_cpython    conda-forge
python_abi                3.9                      1_cp39    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.25.1             pyhd3deb0d_0    conda-forge
ruamel_yaml               0.15.80         py39h3811e60_1004    conda-forge
setuptools                49.6.0           py39hf3d152e_3    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.35.5               h74cdb3f_0    conda-forge
tk                        8.6.10               h21135ba_1    conda-forge
tqdm                      4.60.0             pyhd8ed1ab_0    conda-forge
tzdata                    2021a                he74cb21_0    conda-forge
udunits2                  2.2.27.27            h975c496_1    conda-forge
urllib3                   1.26.4             pyhd8ed1ab_0    conda-forge
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h516909a_0    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.4.9                ha95c52a_0    conda-forge`

Example using the internal temp data set:

(base) CDO/conda % cdo -f nc4 temp temp.nc4 
cdo    temp:  [0.01s 26MB].
(base) CDO/conda % cdo -z szip copy temp.nc4 temp_szip.nc4
Warning (cdfDefVarSzip): Szip compression failed, NetCDF4/szlib not available!
cdo    copy: Processed 259200 values from 1 variable over 1 timestep [0.01s 26MB].
(base) CDO/conda % ls -l *.nc4
-rw-r--r--. 1 gwhite bod 1056084 May  6 20:56 temp.nc4
-rw-r--r--. 1 gwhite bod 1056150 May  6 20:57 temp_szip.nc4

Details about conda and system ( conda info ):

% conda info                                 

     active environment : base
    active env location : /opt/conda.io/miniconda3
            shell level : 1
       user config file : /home/gwhite/.condarc
 populated config files : /home/gwhite/.condarc
          conda version : 4.10.1
    conda-build version : not installed
         python version : 3.9.2.final.0
       virtual packages : __linux=5.11.17=0
                          __glibc=2.32=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /opt/conda.io/miniconda3  (writable)
      conda av data dir : /opt/conda.io/miniconda3/etc/conda
  conda av metadata url : https://repo.anaconda.com/pkgs/main
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/conda.io/miniconda3/pkgs
                          /home/gwhite/.conda/pkgs
       envs directories : /opt/conda.io/miniconda3/envs
                          /home/gwhite/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.1 requests/2.25.1 CPython/3.9.2 Linux/5.11.17-200.fc33.x86_64 fedora/33 glibc/2.32
                UID:GID : 5137:2063
             netrc file : /home/gwhite/.netrc
           offline mode : False

Arch migration

I read the conda-forge documentation and could not find the solution for my problem there.

Issue: i would like to run cdo and python-cdo on arm64. Currently only built for linux64 and osx64. as in conda-forge/esmf-feedstock#74

Environment (conda list):

$ conda list

Details about conda and system ( conda info ):

$ conda info

cdo: error while loading shared libraries: libicui18n.so.58: ... No such file or directory

Attempting to use conda-forge python3.6 cdo 1.8.2 on RHEL6 and the following is noted

# ldd /opt/miniconda3/bin/cdo
	libicui18n.so.58 => not found
	libicuuc.so.58 => not found
	libicudata.so.58 => not found
# ll /opt/miniconda3/lib/libicui18n.so.54
lrwxrwxrwx 1 root root 18 Aug 23 12:26 /opt/miniconda3/lib/libicui18n.so.54 -> libicui18n.so.54.1
# conda list
# packages in environment at /opt/miniconda3:
#
asn1crypto                0.22.0                   py36_0  
cdo                       1.8.2                         0    conda-forge
cffi                      1.10.0                   py36_0  
conda                     4.3.23                   py36_0    conda-forge
conda-env                 2.6.0                         0    conda-forge
cryptography              1.8.1                    py36_0  
curl                      7.54.1                        0    conda-forge
cycler                    0.10.0                   py36_0  
dbus                      1.10.20                       0  
ecmwf_grib                1.19.0                        0    conda-forge
esmf                      7.0.0                         6    conda-forge
expat                     2.1.0                         0  
fftw                      3.3.6                         3    conda-forge
fontconfig                2.12.1                        3  
freetype                  2.5.5                         2  
glib                      2.50.2                        1  
gsl                       2.1                           2    conda-forge
gst-plugins-base          1.8.0                         0  
gstreamer                 1.8.0                         0  
hdf4                      4.2.12                        0    conda-forge
hdf5                      1.8.18                        1    conda-forge
icu                       54.1                          0  
idna                      2.5                      py36_0  
jasper                    1.900.1                       4    conda-forge
jpeg                      9b                            0  
krb5                      1.14.2                        0    conda-forge
libffi                    3.2.1                         1  
libgcc                    5.2.0                         0  
libgfortran               3.0.0                         1  
libiconv                  1.14                          0  
libnetcdf                 4.4.1.1                       6    conda-forge
libpng                    1.6.27                        0  
libssh2                   1.8.0                         1    conda-forge
libxcb                    1.12                          1  
libxml2                   2.9.4                         0  
matplotlib                2.0.2               np113py36_0  
mkl                       2017.0.3                      0  
mpich                     3.2                           4    conda-forge
nco                       4.6.7                         2    conda-forge
netcdf-fortran            4.4.4                         3    conda-forge
numpy                     1.13.1                   py36_0  
openblas                  0.2.19                        2    conda-forge
openssl                   1.0.2l                        0  
packaging                 16.8                     py36_0  
pcre                      8.39                          1  
pip                       9.0.1                    py36_1  
proj4                     4.9.3                         4    conda-forge
pycosat                   0.6.2                    py36_0  
pycparser                 2.17                     py36_0  
pyopenssl                 17.0.0                   py36_0  
pyparsing                 2.1.4                    py36_0  
pyqt                      5.6.0                    py36_2  
python                    3.6.1                         2  
python-dateutil           2.6.1                    py36_0  
pytz                      2017.2                   py36_0  
qt                        5.6.2                         5  
readline                  6.2                           2  
requests                  2.14.2                   py36_0  
ruamel_yaml               0.11.14                  py36_1  
setuptools                27.2.0                   py36_0  
sip                       4.18                     py36_0  
six                       1.10.0                   py36_0  
sqlite                    3.13.0                        0  
tk                        8.5.18                        0  
udunits2                  2.2.23                        0    conda-forge
util-linux                2.21                          0  
wheel                     0.29.0                   py36_0  
xz                        5.2.2                         1  
yaml                      0.1.6                         0  
zlib                      1.2.8                         3  
# cdo
cdo: error while loading shared libraries: libicui18n.so.58: cannot open shared object file: No such file or directory

Thanks for your efforts on CDO :)

error in

My system is a CentOS 6.9 machine with Anaconda2 4.2.0
I created a conda environment for CDO with the latest version which installs ecCodes instead of GRIB-API,
All of the package dependencies load:

$ conda list --name CDO
# packages in environment at /opt/HEF/anaconda2/envs/CDO:
#
cdo                       1.9.2                         0    file://opt/HEF/CondaForge_bz2
certifi                   2017.1.23                py27_0    file:///opt/HEF/CondaForge_bz2
curl                      7.52.1                        0    file://opt/HEF/CondaForge_bz2
eccodes                   2.5.0                         0    file://opt/HEF/CondaForge_bz2
expat                     2.1.0                         2    file://opt/HEF/CondaForge_bz2
fftw                      3.3.7                         0    file://opt/HEF/CondaForge_bz2
hdf4                      4.2.12                        0    file://opt/HEF/CondaForge_bz2
hdf5                      1.8.17                       10    file://opt/HEF/CondaForge_bz2
icu                       58.1                          1    file://opt/HEF/CondaForge_bz2
jasper                    1.900.1                       4    file://opt/HEF/CondaForge_bz2
jpeg                      9b                            0    file://opt/HEF/CondaForge_bz2
libgcc                    4.8.5                         2    file://opt/HEF/CondaForge_bz2
libgfortran               3.0.0                         1    file://opt/HEF/CondaForge_bz2
libiconv                  1.14                          4    file://opt/HEF/CondaForge_bz2
libnetcdf                 4.4.1.1                       2    file://opt/HEF/CondaForge_bz2
libpng                    1.6.28                        0    file://opt/HEF/CondaForge_bz2
libxml2                   2.9.4                         4    file://opt/HEF/CondaForge_bz2
ncurses                   5.9                          10    file:///opt/HEF/CondaForge_bz2
openssl                   1.0.2j                        0    file:///opt/HEF/CondaForge_bz2
pip                       9.0.1                    py27_0    file:///opt/HEF/CondaForge_bz2
proj4                     4.9.3                         3    file://opt/HEF/CondaForge_bz2
python                    2.7.12                        2    file:///opt/HEF/CondaForge_bz2
readline                  6.2                           2    file:///opt/HEF/CondaForge_bz2
setuptools                27.3.1                   py27_0    file:///opt/HEF/CondaForge_bz2
sqlite                    3.13.0                        1    file:///opt/HEF/CondaForge_bz2
tk                        8.5.19                        1    file:///opt/HEF/CondaForge_bz2
udunits2                  2.2.25                        1    file://opt/HEF/CondaForge_bz2
util-linux                2.21                          0    file://opt/HEF/CondaForge_bz2
wheel                     0.29.0                   py27_0    file:///opt/HEF/CondaForge_bz2
xz                        5.2.2                         0    file://opt/HEF/CondaForge_bz2
zlib                      1.2.11                        0    file:///opt/HEF/CondaForge_bz2

It looks like there is an issue with hdf5. ecCodes uses hdf5 1.8.17 but when you use cdo to convert from netCDF to GRIB, I get an error with hdf5 as seen below:
$ cdo -f grb -copy 52.runoff.nc 52.runoff.grb
cdo: error while loading shared libraries: libhdf5_hl.so.100: cannot open shared object file: No such file or directory
lbihdf5_hl.so.100 is part of hdf5 1.10.1 and I can't load both versions in the conda environment.

I tried installing with just hdf5 1.10.1 but the conda installer won't install because of ecCodes wanting 1.8.17.

There is also a problem with libcom_err.so.3 being used - from what I read libcom_err.2.1 is actually the more recent and by putting in a symbolic link to libcom_err.2.1 in /lib64/ the error goes away - not sure if that's the right thing to do though:
ln -s /lib64/libcom_err.so.2.1 /lib64/libcom_err.so.3

Thanks!
Chris

self-define the parameters of configure?

Hi, thanks for this wonderful work.

Here, I has a question that how can i set the configure paramete like --enable-cgribex=no?

While if the file contain both grib1 and grib2, cdo would like to choose cgribex to handle grib1 and use grib_api for grib2. That's could be some mistake. So I want to set disable cgribex.

ps:
cdo1
cdo2

@conda-forge-admin, please add user @zklaus

Additional comment:

I'd like to try and help with the OSX arm migration

Can not install cdo on Linux ... dependency issue with hdf5

Usually the Linux installation works but since today I have a dependency issue and I couldn't figure out how to solve it. To reproduce it, I did the following on LinuxMint (Ubuntu) latest version:

$ conda create -n cdo -c conda-forge cdo
The following NEW packages will be INSTALLED:

    ca-certificates: 2017.7.27.1-0      conda-forge
    cdo:             1.9.0-0            conda-forge
    certifi:         2017.7.27.1-py27_0 conda-forge
    curl:            7.55.1-0           conda-forge
    ecmwf_grib:      1.23.1-1           conda-forge
    expat:           2.2.1-0            conda-forge
    fftw:            3.3.7-0            conda-forge
    hdf4:            4.2.13-0           conda-forge
    hdf5:            1.10.1-1           conda-forge
    icu:             58.2-0             conda-forge
    jasper:          1.900.1-4          conda-forge
    jpeg:            9b-2               conda-forge
    krb5:            1.14.2-0           conda-forge
    libgcc:          7.2.0-h69d50b8_2              
    libgcc-ng:       7.2.0-h7cc24e2_2              
    libgfortran:     3.0.0-1                       
    libiconv:        1.14-4             conda-forge
    libnetcdf:       4.4.1.1-10         conda-forge
    libpng:          1.6.28-2           conda-forge
    libssh2:         1.8.0-2            conda-forge
    libstdcxx-ng:    7.2.0-h7a57d05_2              
    libxml2:         2.9.5-1            conda-forge
    ncurses:         5.9-10             conda-forge
    openssl:         1.0.2l-0           conda-forge
    pip:             9.0.1-py27_0       conda-forge
    proj4:           4.9.3-5            conda-forge
    python:          2.7.14-1           conda-forge
    readline:        6.2-0              conda-forge
    setuptools:      36.6.0-py27_1      conda-forge
    sqlite:          3.13.0-1           conda-forge
    tk:              8.5.19-2           conda-forge
    udunits2:        2.2.25-1           conda-forge
    util-linux:      2.21-0                        
    wheel:           0.30.0-py_1        conda-forge
    xz:              5.2.3-0            conda-forge
    zlib:            1.2.11-0           conda-forge

$ source activate cdo
(cdo) $ cdo --version
cdo: error while loading shared libraries: libhdf5_hl.so.10: cannot open shared object file: No such file or directory

$ ldd .conda/envs/cdo/bin/cdo
libhdf5_hl.so.10 => not found
libhdf5.so.10 => not found

(cdo) $ cd .conda/envs/cdo/lib/
(cdo) $ ls libhdf5_hl.so*
libhdf5_hl.so  libhdf5_hl.so.100  libhdf5_hl.so.100.0.1
(cdo) $ ls libhdf5.so*
libhdf5.so  libhdf5.so.101  libhdf5.so.101.0.0

I tried it also with hdf5=1.8 and cdo=1.8 ... but I was always running in a hdf5 dependency issue.

It works on MacOS ;)

Check build status for binaries ready to be installed

Hi!

A user contacted me that the cdo binary for MacOS is still version 1.9.9 when searched/updated with conda. Is there any webpage where we can check which binaries are available?

conda-forge / cdo-feedstock Goto Github PK

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