conda-forge / fitsio-feedstock

A conda-smithy repository for fitsio.

About fitsio-feedstock

Feedstock license: BSD-3-Clause

Home: https://github.com/esheldon/fitsio

Package license: GPL-2.0-only AND Zlib

Summary: A python library to read from and write to FITS files.

Development: https://github.com/esheldon/fitsio

Documentation: https://github.com/esheldon/fitsio

This is a python extension written in c and python. Data are read into numerical python arrays. A version of cfitsio is bundled with this package, there is no need to install your own, nor will this conflict with a version you have installed.

Current build status

Azure

Variant Status linux_64_numpy1.22python3.10.____cpython linux_64_numpy1.22python3.8.____cpython linux_64_numpy1.22python3.9.____cpython linux_64_numpy1.23python3.11.____cpython linux_64_numpy1.26python3.12.____cpython linux_aarch64_numpy1.22python3.10.____cpython linux_aarch64_numpy1.22python3.8.____cpython linux_aarch64_numpy1.22python3.9.____cpython linux_aarch64_numpy1.23python3.11.____cpython linux_aarch64_numpy1.26python3.12.____cpython osx_64_numpy1.22python3.10.____cpython osx_64_numpy1.22python3.8.____cpython osx_64_numpy1.22python3.9.____cpython osx_64_numpy1.23python3.11.____cpython osx_64_numpy1.26python3.12.____cpython osx_arm64_numpy1.22python3.10.____cpython osx_arm64_numpy1.22python3.8.____cpython osx_arm64_numpy1.22python3.9.____cpython osx_arm64_numpy1.23python3.11.____cpython osx_arm64_numpy1.26python3.12.____cpython

Current release info

Name	Downloads	Version	Platforms

Installing fitsio

Installing fitsio 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, fitsio can be installed with conda:

conda install fitsio

or with mamba:

mamba install fitsio

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

conda search fitsio --channel conda-forge

or with mamba:

mamba search fitsio --channel conda-forge

Alternatively, mamba repoquery may provide more information:

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

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

# List dependencies of `fitsio`:
mamba repoquery depends fitsio --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-Cloud 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 fitsio-feedstock

If you would like to improve the fitsio 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/fitsio-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

• @beckermr

fitsio-feedstock's Issues

@conda-forge-admin add bot automerge

Issue:

Environment (conda list):

$ conda list

Details about conda and system ( conda info ):

$ conda info

Getting conflicts trying to update fitsio >= 1.0

I don't know if this still ought to be an issue, since @beckermr already found a solution for me, but in case this is pointing at some problem somewhere, here is the problem I had and the solution Matt found for me.

Issue:

At Nersc, I had a conda environment with fitsio 0.9.11 installed. Trying to update to 1.1.0 (or >=1.0), I got the following error:

$ conda install fitsio==1.1.0
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: - 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.

<snip>

UnsatisfiableError: The following specifications were found to be incompatible with each other:     
Package readline conflicts for:
fitsio==1.1.0 -> python[version='>=3.8,<3.9.0a0'] -> readline[version='>=7.0,<8.0a0|>=8.0,<9.0a0']
python==3.6 -> readline[version='6.2|6.2.*']
Package python conflicts for:
python==3.6
Package sqlite conflicts for:
python==3.6 -> sqlite=3.13
fitsio==1.1.0 -> python[version='>=3.8,<3.9.0a0'] -> sqlite[version='>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.27.2,<4.0a0|>=3.28.0,<4.0a0|>=3.29.0,<4.0a0|>=3.30.0,<4.0a0|>=3.30.1,<4.0a0']
Package openssl conflicts for:
python==3.6 -> openssl[version='1.0.*|1.0.2.*']
fitsio==1.1.0 -> libcurl[version='>=7.64.1,<8.0a0'] -> openssl[version='>=1.1.1,<1.1.2.0a0|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a']
Package tk conflicts for:
python==3.6 -> tk[version='8.5.*|8.5.18']
fitsio==1.1.0 -> python[version='>=3.8,<3.9.0a0'] -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.9,<8.7.0a0']

This looked like it was thinking that fitsio needed python 3.8, which I didn't really want. So I tried installing the 3.6 version explicitly:

$ conda install fitsio==1.1.0=py36h0c87ef4_0 
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.

<snip>       

UnsatisfiableError: The following specifications were found to be incompatible with each other:     
Package sqlite conflicts for:
python==3.6 -> sqlite=3.13
fitsio==1.1.0=py36h0c87ef4_0 -> python[version='>=3.6,<3.7.0a0'] -> sqlite[version='>=3.25.2,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.29.0,<4.0a0|>=3.30.1,<4.0a0']
Package ncurses conflicts for:
fitsio==1.1.0=py36h0c87ef4_0 -> python[version='>=3.6,<3.7.0a0'] -> readline[version='>=7.0,<8.0a0'] -> ncurses[version='>=6.0,<7.0a0']
fitsio==1.1.0=py36h0c87ef4_0 -> python[version='>=3.6,<3.7.0a0'] -> ncurses[version='>=6.1,<6.2.0a0|>=6.1,<7.0a0']
python==3.6 -> ncurses=5.9
Package openssl conflicts for:
python==3.6 -> openssl[version='1.0.*|1.0.2.*']
fitsio==1.1.0=py36h0c87ef4_0 -> libcurl[version='>=7.64.1,<8.0a0'] -> openssl[version='>=1.1.1,<1.1.2.0a0|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a']
Package python conflicts for:
python==3.6
Package tk conflicts for:
fitsio==1.1.0=py36h0c87ef4_0 -> libcurl[version='>=7.64.1,<8.0a0'] -> krb5[version='>=1.17.1,<1.18.0a0'] -> tk[version='>=8.6.10,<8.7.0a0']
fitsio==1.1.0=py36h0c87ef4_0 -> python[version='>=3.6,<3.7.0a0'] -> tk[version='>=8.6.8,<8.7.0a0|>=8.6.9,<8.7.0a0']
python==3.6 -> tk[version='8.5.*|8.5.18']
Package readline conflicts for:
fitsio==1.1.0=py36h0c87ef4_0 -> python[version='>=3.6,<3.7.0a0'] -> readline[version='>=7.0,<8.0a0|>=8.0,<9.0a0']
python==3.6 -> readline[version='6.2|6.2.*']

Matt suggested trying to update everything, which did work straight away with no conflicts:

$ conda update --all
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
  current version: 4.7.12
  latest version: 4.8.2
Please update conda by running
    $ conda update -n base -c defaults conda
## Package Plan ##
  environment location: /global/homes/m/mjarvis/.conda/envs/piff
The following packages will be downloaded:
    package                    |            build
    ---------------------------|-----------------
    fitsio-1.1.0               |   py36h0c87ef4_0         669 KB  conda-forge
    pybind11-2.4.3             |   py36hc9558a2_1         119 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         788 KB
The following NEW packages will be INSTALLED:
  krb5               conda-forge/linux-64::krb5-1.16.4-h2fd8d38_0
  libcurl            conda-forge/linux-64::libcurl-7.68.0-hda55be3_0
  libedit            conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001
  libssh2            conda-forge/linux-64::libssh2-1.8.2-h22169c7_2
The following packages will be UPDATED:
  fitsio                           0.9.11-py36h53b300e_1001 --> 1.1.0-py36h0c87ef4_0
  galsim                               2.2.2-py36hb745460_1 --> 2.2.3-py36hb745460_0
  ncurses                                            5.9-10 --> 6.1-hf484d3e_1002
  numpy                               1.17.3-py36h95a1406_0 --> 1.18.1-py36h95a1406_0
  openssl                                 1.0.2u-h516909a_0 --> 1.1.1d-h516909a_0
  pybind11                                     2.2.2-py36_0 --> 2.4.3-py36hc9558a2_1
  python                                            3.6.0-2 --> 3.6.7-h357f687_1006
  readline                                            6.2-0 --> 8.0-hf8c457e_0
  sqlite                                           3.13.0-1 --> 3.30.1-hcee41ef_0
  tk                                               8.5.19-2 --> 8.6.10-hed695b0_0
Proceed ([y]/n)? 
Downloading and Extracting Packages
pybind11-2.4.3       | 119 KB    | ######################################################### | 100% 
fitsio-1.1.0         | 669 KB    | ######################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

So, not sure whether this is pointing to someone having a problematic dependency specification somewhere or what. I would have thought that conda could have found the eventual solution when I just asked for fitsio to be updated.

Environment (conda list):

After the update, here is my full environment. (Sorry - I didn't do this before the successful update.)

$ conda list
# packages in environment at /global/homes/m/mjarvis/.conda/envs/piff:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
asteval                   0.9.17                   pypi_0    pypi
astropy                   4.0              py36h516909a_1    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2019.11.28           hecc5488_0    conda-forge
certifi                   2019.11.28               py36_0    conda-forge
cffi                      1.13.2           py36h8022711_0    conda-forge
cycler                    0.10.0                   pypi_0    pypi
eigen                     3.3.7             hc9558a2_1001    conda-forge
fftw                      3.3.8           nompi_h7f3a6c3_1110    conda-forge
fitsio                    1.1.0            py36h0c87ef4_0    conda-forge
future                    0.18.2                   py36_0    conda-forge
galsim                    2.2.2                    pypi_0    pypi
joblib                    0.14.0                   pypi_0    pypi
kiwisolver                1.1.0                    pypi_0    pypi
krb5                      1.16.4               h2fd8d38_0    conda-forge
libblas                   3.8.0               15_openblas    conda-forge
libcblas                  3.8.0               15_openblas    conda-forge
libcurl                   7.68.0               hda55be3_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgfortran-ng            7.3.0                hdf63c60_5    conda-forge
liblapack                 3.8.0               15_openblas    conda-forge
libopenblas               0.3.8                h5ec1e0e_0    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
llvm-openmp               9.0.1                hc9558a2_2    conda-forge
lmfit                     0.9.14                   pypi_0    pypi
lsstdesc.coord            1.2.0            py36hc9558a2_0    conda-forge
matplotlib                3.1.1                    pypi_0    pypi
ncurses                   6.1               hf484d3e_1002    conda-forge
numpy                     1.18.1           py36h95a1406_0    conda-forge
openssl                   1.1.1d               h516909a_0    conda-forge
pip                       20.0.2                     py_2    conda-forge
pybind11                  2.4.3                    pypi_0    pypi
pycparser                 2.19                       py_2    conda-forge
python                    3.6.7             h357f687_1006    conda-forge
python-dateutil           2.8.1                    pypi_0    pypi
pyyaml                    5.1.2                    pypi_0    pypi
readline                  8.0                  hf8c457e_0    conda-forge
scikit-learn              0.21.3                   pypi_0    pypi
scipy                     1.3.2                    pypi_0    pypi
setuptools                45.2.0                   py36_0    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
treecorr                  4.0.10                   pypi_0    pypi
uncertainties             3.1.2                    pypi_0    pypi
wheel                     0.34.2                     py_1    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge

Details about conda and system ( conda info ):

$ conda info

     active environment : piff
    active env location : /global/homes/m/mjarvis/.conda/envs/piff
            shell level : 1
       user config file : /global/homes/m/mjarvis/.condarc
 populated config files : /global/homes/m/mjarvis/.condarc
          conda version : 4.7.12
    conda-build version : 3.18.8
         python version : 2.7.16.final.0
       virtual packages : 
       base environment : /usr/common/software/python/2.7-anaconda-2019.07  (read only)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/astropy/linux-64
                          https://conda.anaconda.org/astropy/noarch
                          https://conda.anaconda.org/anaconda/linux-64
                          https://conda.anaconda.org/anaconda/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 : /usr/common/software/python/2.7-anaconda-2019.07/pkgs
                          /global/homes/m/mjarvis/.conda/pkgs
       envs directories : /global/homes/m/mjarvis/.conda/envs
                          /usr/common/software/python/2.7-anaconda-2019.07/envs
               platform : linux-64
             user-agent : conda/4.7.12 requests/2.22.0 CPython/2.7.16 Linux/4.12.14-150.47-default sles/15 glibc/2.26
                UID:GID : 34001:1034001
             netrc file : None
           offline mode : False

@conda-forge-admin, please update circle

@conda-forge-admin, please update circle

@conda-forge-admin rerender

Issue:

Environment (conda list):

$ conda list

Details about conda and system ( conda info ):

$ conda info

linking to bzip2 outside of conda

Issue: It appears that fitsio is linking to bzip2 outside of conda.

Environment (conda list):

$ conda list
# packages in environment at /homes/mrbecker/miniconda3/envs/anl:
#
# Name                    Version                   Build  Channel
asn1crypto                0.24.0                py36_1003    conda-forge
astropy                   3.0.5            py36h470a237_0    conda-forge
atomicwrites              1.2.1                      py_0    conda-forge
attrs                     18.2.0                     py_0    conda-forge
blas                      1.1                    openblas    conda-forge
ca-certificates           2018.10.15           ha4d7672_0    conda-forge
certifi                   2018.10.15            py36_1000    conda-forge
cffi                      1.11.5           py36h5e8e0c9_1    conda-forge
chardet                   3.0.4                 py36_1003    conda-forge
click                     7.0                        py_0    conda-forge
configobj                 5.0.6                      py_0    conda-forge
cryptography              2.3.1            py36hdffb7b8_0    conda-forge
cryptography-vectors      2.3.1                 py36_1000    conda-forge
curl                      7.62.0               h74213dd_0    conda-forge
eigen                     3.3.5                h2d50403_1    conda-forge
esutil                    0.6.2.5                   <pip>
expat                     2.2.5                hfc679d8_2    conda-forge
fftw                      3.3.8                h470a237_0    conda-forge
fitsio                    0.9.11                    <pip>
future                    0.17.0                py36_1000    conda-forge
galsim                    2.0.7            py36h2d50403_0    conda-forge
gettext                   0.19.8.1             h5e8e0c9_1    conda-forge
git                       2.19.1          pl526hbb17d3c_1    conda-forge
globus-cli                1.8.0                     <pip>
globus-sdk                1.5.0                     <pip>
idna                      2.7                   py36_1002    conda-forge
jmespath                  0.9.3                      py_1    conda-forge
krb5                      1.16.2               hbb41f41_0    conda-forge
libcurl                   7.62.0               hbdb9355_0    conda-forge
libedit                   3.1.20170329         haf1bffa_1    conda-forge
libffi                    3.2.1                hfc679d8_5    conda-forge
libgcc-ng                 7.2.0                hdf63c60_3    conda-forge
libgfortran               3.0.0                         1    conda-forge
libiconv                  1.15                 h470a237_3    conda-forge
libssh2                   1.8.0                h5b517e9_2    conda-forge
libstdcxx-ng              7.2.0                hdf63c60_3    conda-forge
llvmlite                  0.25.0           py36hd28b015_1    conda-forge
lsstdesc.coord            1.0.5            py36h2d50403_0    conda-forge
meds                      0.9.5rc2                  <pip>
metadetect                0.1.0                     <pip>
more-itertools            4.3.0                 py36_1000    conda-forge
ncurses                   6.1                  hfc679d8_1    conda-forge
ngmix                     1.0.0                     <pip>
nomkl                     3.0                           0  
numba                     0.40.0           py36hf8a1672_0    conda-forge
numpy                     1.15.4          py36_blas_openblashb06ca3d_0  [blas_openblas]  conda-forge
openblas                  0.3.3                ha44fe06_1    conda-forge
openssl                   1.0.2p               h470a237_1    conda-forge
perl                      5.26.2               h470a237_0    conda-forge
pip                       18.1                  py36_1000    conda-forge
pizza-cutter              0.1.0                     <pip>
pluggy                    0.8.0                      py_0    conda-forge
psutil                    5.4.8            py36h470a237_0    conda-forge
py                        1.7.0                      py_0    conda-forge
pybind11                  2.2.4            py36h2d50403_1    conda-forge
pycparser                 2.19                       py_0    conda-forge
pyjwt                     1.6.4                      py_0    conda-forge
pyopenssl                 18.0.0                py36_1000    conda-forge
pysocks                   1.6.8                 py36_1002    conda-forge
pytest                    3.10.0                py36_1000    conda-forge
pytest-arraydiff          0.2                        py_0    conda-forge
pytest-astropy            0.4.0                      py_0    conda-forge
pytest-doctestplus        0.1.3                      py_0    conda-forge
pytest-openfiles          0.3.0                      py_0    conda-forge
pytest-remotedata         0.3.1                      py_0    conda-forge
python                    3.6.6                h5001a0f_3    conda-forge
pyyaml                    3.13             py36h470a237_1    conda-forge
readline                  7.0                  haf1bffa_1    conda-forge
requests                  2.20.0                py36_1000    conda-forge
scipy                     1.1.0           py36_blas_openblashb06ca3d_202  [blas_openblas]  conda-forge
sep                       1.0.3                     <pip>
setuptools                40.5.0                   py36_0    conda-forge
six                       1.11.0                py36_1001    conda-forge
sqlite                    3.25.2               hb1c47c0_0    conda-forge
tk                        8.6.8                ha92aebf_0    conda-forge
urllib3                   1.23                  py36_1001    conda-forge
wheel                     0.32.2                   py36_0    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
yaml                      0.1.7                h470a237_1    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

Details about conda and system ( conda info ):

$ conda info

     active environment : anl
    active env location : /homes/mrbecker/miniconda3/envs/anl
            shell level : 1
       user config file : /homes/mrbecker/.condarc
 populated config files : /homes/mrbecker/.condarc
          conda version : 4.5.11
    conda-build version : not installed
         python version : 3.7.0.final.0
       base environment : /homes/mrbecker/miniconda3  (writable)
           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/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /homes/mrbecker/miniconda3/pkgs
                          /homes/mrbecker/.conda/pkgs
       envs directories : /homes/mrbecker/miniconda3/envs
                          /homes/mrbecker/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.11 requests/2.20.0 CPython/3.7.0 Linux/3.10.0-327.36.3.el7.x86_64 rhel/7.2 glibc/2.17
                UID:GID : 9101:311
             netrc file : None
           offline mode : False