No current publication of pygbif on conda-forge #83

pjgoodall · 2021-05-31T22:08:04Z

The current publication of pygbif on the conda platform is nearly 5 years old. Can I encourage pygbif to be published on conda-forge please? Recently python-dwca-reader was given an automated build onto conda-forge after a 7-year hiatus (many thanks to Jordan Cook).

Please see:

The text was updated successfully, but these errors were encountered:

sckott · 2021-06-01T23:11:22Z

thanks for the ping @pjgoodall

I set up a recipe but it didn't work when I ran it locally. Perhaps I need to include something about requirements.txt in the recipe

CONFIG=osx64 ./.scripts/run_docker_build.sh

Client:
 Context:    default
 Debug Mode: false
 Plugins:
  app: Docker App (Docker Inc., v0.9.1-beta3)
  buildx: Build with BuildKit (Docker Inc., v0.5.1-docker)
  compose: Docker Compose (Docker Inc., 2.0.0-beta.1)
  scan: Docker Scan (Docker Inc., v0.8.0)

Server:
 Containers: 1
  Running: 0
  Paused: 0
  Stopped: 1
 Images: 174
 Server Version: 20.10.6
 Storage Driver: overlay2
  Backing Filesystem: extfs
  Supports d_type: true
  Native Overlay Diff: true
  userxattr: false
 Logging Driver: json-file
 Cgroup Driver: cgroupfs
 Cgroup Version: 1
 Plugins:
  Volume: local
  Network: bridge host ipvlan macvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
 Swarm: inactive
 Runtimes: io.containerd.runc.v2 io.containerd.runtime.v1.linux runc
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 05f951a3781f4f2c1911b05e61c160e9c30eaa8e
 runc version: 12644e614e25b05da6fd08a38ffa0cfe1903fdec
 init version: de40ad0
 Security Options:
  seccomp
   Profile: default
 Kernel Version: 5.10.25-linuxkit
 Operating System: Docker Desktop
 OSType: linux
 Architecture: x86_64
 CPUs: 2
 Total Memory: 1.942GiB
 Name: docker-desktop
 ID: 5ZSH:XI6P:ITWO:NJ4Q:HJ24:XDL6:EXII:PCPP:V6DI:ARFE:SWTA:42AO
 Docker Root Dir: /var/lib/docker
 Debug Mode: true
  File Descriptors: 42
  Goroutines: 46
  System Time: 2021-06-01T22:46:15.748640314Z
  EventsListeners: 3
 HTTP Proxy: http.docker.internal:3128
 HTTPS Proxy: http.docker.internal:3128
 Registry: https://index.docker.io/v1/
 Labels:
 Experimental: true
 Insecure Registries:
  127.0.0.0/8
 Live Restore Enabled: false

./.scripts/run_docker_build.sh: line 24: shyaml: command not found
WARNING: DOCKER_IMAGE variable not set and shyaml not installed. Falling back to quay.io/condaforge/linux-anvil-comp7
useradd: warning: the home directory already exists.
Not copying any file from skel directory into it.
+ export PYTHONUNBUFFERED=1
+ PYTHONUNBUFFERED=1
+ cat
+ cp -r /home/conda/staged-recipes /home/conda/staged-recipes-copy
+ find /home/conda/staged-recipes-copy/recipes -maxdepth 1 -name .DS_Store -delete
+ echo 'Pending recipes.'
Pending recipes.
+ ls -la /home/conda/staged-recipes-copy/recipes
total 32
drwxr-xr-x  8 conda conda 4096 Jun  1 22:46 .
drwxr-xr-x 10 conda conda 4096 Jun  1 22:46 ..
drwxr-xr-x  2 conda conda 4096 Jun  1 22:46 example
drwxr-xr-x  2 conda conda 4096 Jun  1 22:46 fcmaes
drwxr-xr-x  2 conda conda 4096 Jun  1 22:46 koncept
drwxr-xr-x  2 conda conda 4096 Jun  1 22:46 pygbif
drwxr-xr-x  2 conda conda 4096 Jun  1 22:46 r-available
drwxr-xr-x  2 conda conda 4096 Jun  1 22:46 r-freqprof
+ echo 'Finding recipes merged in master and removing them from the build.'
Finding recipes merged in master and removing them from the build.
+ pushd /home/conda/staged-recipes/recipes
+ '[' False == True ']'
+ git ls-tree --name-only master -- .
+ xargs -I '{}' sh -c 'rm -rf ~/staged-recipes-copy/recipes/{} && echo Removing recipe: {}'
Removing recipe: example
Removing recipe: fcmaes
Removing recipe: koncept
Removing recipe: r-available
Removing recipe: r-freqprof
+ popd
+ conda index /home/conda/staged-recipes/build_artifacts
+ conda install --yes --quiet 'conda>4.7.12' 'conda-forge-ci-setup=3.*' conda-forge-pinning networkx=2.4 'conda-build>=3.16'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:
    - conda-build[version='>=3.16']
    - conda-forge-ci-setup=3
    - conda-forge-pinning
    - conda[version='>4.7.12']
    - networkx=2.4


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2021.5.30  |       ha878542_0         136 KB  conda-forge
    certifi-2021.5.30          |   py38h578d9bd_0         141 KB  conda-forge
    click-8.0.1                |   py38h578d9bd_0         146 KB  conda-forge
    conda-env-2.6.0            |                1           2 KB  conda-forge
    conda-forge-ci-setup-3.9.4 |   py38hcd7a344_0          36 KB  conda-forge
    conda-forge-pinning-2021.06.01.05.21.06|       hd8ed1ab_0          16 KB  conda-forge
    decorator-5.0.9            |     pyhd8ed1ab_0          11 KB  conda-forge
    jq-1.6                     |    h36c2ea0_1000         346 KB  conda-forge
    networkx-2.4               |             py_1         1.2 MB  conda-forge
    oniguruma-6.9.7.1          |       h7f98852_0         409 KB  conda-forge
    shyaml-0.6.2               |     pyhd3deb0d_0          21 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         2.4 MB

The following NEW packages will be INSTALLED:

  click              conda-forge/linux-64::click-8.0.1-py38h578d9bd_0
  conda-env          conda-forge/noarch::conda-env-2.6.0-1
  conda-forge-ci-se~ conda-forge/linux-64::conda-forge-ci-setup-3.9.4-py38hcd7a344_0
  conda-forge-pinni~ conda-forge/noarch::conda-forge-pinning-2021.06.01.05.21.06-hd8ed1ab_0
  decorator          conda-forge/noarch::decorator-5.0.9-pyhd8ed1ab_0
  jq                 conda-forge/linux-64::jq-1.6-h36c2ea0_1000
  networkx           conda-forge/noarch::networkx-2.4-py_1
  oniguruma          conda-forge/linux-64::oniguruma-6.9.7.1-h7f98852_0
  shyaml             conda-forge/noarch::shyaml-0.6.2-pyhd3deb0d_0

The following packages will be UPDATED:

  ca-certificates                      2020.12.5-ha878542_0 --> 2021.5.30-ha878542_0
  certifi                          2020.12.5-py38h578d9bd_1 --> 2021.5.30-py38h578d9bd_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ export FEEDSTOCK_ROOT=/home/conda/staged-recipes
+ FEEDSTOCK_ROOT=/home/conda/staged-recipes
+ export CI_SUPPORT=/home/conda/staged-recipes-copy/.ci_support
+ CI_SUPPORT=/home/conda/staged-recipes-copy/.ci_support
+ setup_conda_rc /home/conda/staged-recipes /home/conda/staged-recipes-copy/recipes /home/conda/staged-recipes-copy/.ci_support/osx64.yaml
Warning: 'conda-forge' already in 'channels' list, moving to the top
+ source run_conda_forge_build_setup
++ export PYTHONUNBUFFERED=1
++ PYTHONUNBUFFERED=1
++ conda config --set show_channel_urls true
++ conda config --set auto_update_conda false
++ conda config --set add_pip_as_python_dependency false
++ export CONDA_BLD_PATH=/home/conda/staged-recipes/build_artifacts
++ CONDA_BLD_PATH=/home/conda/staged-recipes/build_artifacts
++ set +u
++ '[' '' = drone ']'
++ export CPU_COUNT=2
++ CPU_COUNT=2
+++ cat /home/conda/staged-recipes/conda-forge.yml
+++ shyaml get-value channel_priority strict
++ conda config --set channel_priority strict
++ [[ ! -z '' ]]
++ '[' '!' -z osx64 ']'
++ '[' '!' -z '' ']'
++ cat /home/conda/staged-recipes-copy/.ci_support/osx64.yaml
c_compiler:
  - clang
cxx_compiler:
  - clangxx
fortran_compiler:
  - gfortran
channel_sources:
  - conda-forge,defaults
target_platform:
  - osx-64
++ set -u
++ mkdir -p /opt/conda/etc/conda/activate.d
++ echo 'export CONDA_BLD_PATH='\''/home/conda/staged-recipes/build_artifacts'\'''
++ '[' -n 2 ']'
++ echo 'export CPU_COUNT='\''2'\'''
++ echo 'export PYTHONUNBUFFERED='\''1'\'''
+++ cat /home/conda/staged-recipes-copy/.ci_support/osx64.yaml
+++ shyaml get-value cuda_compiler_version.0 None
++ CUDA_VERSION=None
++ [[ None != \N\o\n\e ]]
++++ dirname /opt/conda/bin/run_conda_forge_build_setup
+++ cd /opt/conda/bin
+++ pwd
++ SCRIPT_DIR=/opt/conda/bin
++ source /opt/conda/bin/cross_compile_support.sh
++++ jq -r .platform
++++ conda info --json
+++ BUILD_PLATFORM=linux-64
+++ '[' -f /home/conda/staged-recipes-copy/.ci_support/osx64.yaml ']'
++++ cat /home/conda/staged-recipes-copy/.ci_support/osx64.yaml
++++ shyaml get-value target_platform.0 linux-64
+++ HOST_PLATFORM=osx-64
+++ HOST_PLATFORM=osx-64
+++ [[ osx-64 != \l\i\n\u\x\-\6\4 ]]
+++ echo 'export CONDA_BUILD_CROSS_COMPILATION=1'
+++ export CONDA_BUILD_CROSS_COMPILATION=1
+++ CONDA_BUILD_CROSS_COMPILATION=1
+++ '[' -f /home/conda/staged-recipes-copy/.ci_support/osx64.yaml ']'
+++ echo build_platform:
+++ echo '- linux-64'
+++ [[ linux-64 == \l\i\n\u\x\-\6\4 ]]
+++ [[ osx-64 == linux-* ]]
++ '[' -f /home/conda/staged-recipes-copy/.ci_support/osx64.yaml ']'
+++ shyaml get-value MACOSX_DEPLOYMENT_TARGET.0 0
+++ cat /home/conda/staged-recipes-copy/.ci_support/osx64.yaml
++ need_osx_sdk=0
++ [[ 0 != \0 ]]
++ conda info

     active environment : base
    active env location : /opt/conda
            shell level : 1
       user config file : /home/conda/.condarc
 populated config files : /home/conda/.condarc
          conda version : 4.10.1
    conda-build version : 3.21.4
         python version : 3.8.10.final.0
       virtual packages : __linux=5.10.25=0
                          __glibc=2.12=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /opt/conda  (writable)
      conda av data dir : /opt/conda/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/pkgs
                          /home/conda/.conda/pkgs
       envs directories : /opt/conda/envs
                          /home/conda/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.1 requests/2.25.1 CPython/3.8.10 Linux/5.10.25-linuxkit centos/6.10 glibc/2.12
                UID:GID : 501:501
             netrc file : None
           offline mode : False

++ conda config --show-sources
==> /home/conda/.condarc <==
add_pip_as_python_dependency: False
auto_update_conda: False
channel_priority: strict
channels:
  - conda-forge
  - defaults
show_channel_urls: True
conda-build:
  root-dir: /home/conda/staged-recipes/build_artifacts

==> envvars <==
bld_path: /home/conda/staged-recipes/build_artifacts

++ conda list --show-channel-urls
# packages in environment at /opt/conda:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
anaconda-client           1.7.2              pyhd8ed1ab_1    conda-forge
attrs                     21.2.0             pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.9.3              pyhb0f4dca_0    conda-forge
brotlipy                  0.7.0           py38h497a2fe_1001    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h7f98852_1    conda-forge
ca-certificates           2021.5.30            ha878542_0    conda-forge
certifi                   2021.5.30        py38h578d9bd_0    conda-forge
cffi                      1.14.5           py38ha65f79e_0    conda-forge
chardet                   4.0.0            py38h578d9bd_1    conda-forge
click                     8.0.1            py38h578d9bd_0    conda-forge
clyent                    1.2.2                      py_1    conda-forge
conda                     4.10.1           py38h578d9bd_0    conda-forge
conda-build               3.21.4           py38h578d9bd_0    conda-forge
conda-env                 2.6.0                         1    conda-forge
conda-forge-ci-setup      3.9.4            py38hcd7a344_0    conda-forge
conda-forge-pinning       2021.06.01.05.21.06      hd8ed1ab_0    conda-forge
conda-package-handling    1.7.3            py38h497a2fe_0    conda-forge
cryptography              3.4.7            py38ha5dfef3_0    conda-forge
curl                      7.76.1               hea6ffbf_2    conda-forge
decorator                 5.0.9              pyhd8ed1ab_0    conda-forge
expat                     2.3.0                h9c3ff4c_0    conda-forge
filelock                  3.0.12             pyh9f0ad1d_0    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
git                       2.30.2          pl5320h24fefe6_1    conda-forge
glob2                     0.7                        py_0    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
importlib-metadata        4.0.1            py38h578d9bd_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jinja2                    3.0.0              pyhd8ed1ab_0    conda-forge
jq                        1.6               h36c2ea0_1000    conda-forge
jsonschema                3.2.0              pyhd8ed1ab_3    conda-forge
jupyter_core              4.7.1            py38h578d9bd_0    conda-forge
krb5                      1.19.1               hcc1bbae_0    conda-forge
ld_impl_linux-64          2.35.1               hea4e1c9_2    conda-forge
libarchive                3.5.1                h3f442fb_1    conda-forge
libcurl                   7.76.1               h2574ce0_2    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
libgomp                   9.3.0               h2828fa1_19    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblief                   0.10.1               he1b5a44_2    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libssh2                   1.9.0                ha56f1ee_6    conda-forge
libstdcxx-ng              9.3.0               h6de172a_19    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markupsafe                2.0.0            py38h497a2fe_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
networkx                  2.4                        py_1    conda-forge
oniguruma                 6.9.7.1              h7f98852_0    conda-forge
openssl                   1.1.1k               h7f98852_0    conda-forge
patch                     2.7.6             h7f98852_1002    conda-forge
patchelf                  0.11                 he1b5a44_0    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
perl                      5.32.0               h36c2ea0_0    conda-forge
pip                       21.1.1             pyhd8ed1ab_0    conda-forge
pkginfo                   1.7.0              pyhd8ed1ab_0    conda-forge
psutil                    5.8.0            py38h497a2fe_1    conda-forge
py-lief                   0.10.1           py38h348cfbe_2    conda-forge
pycosat                   0.6.3           py38h497a2fe_1006    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pyopenssl                 20.0.1             pyhd8ed1ab_0    conda-forge
pyrsistent                0.17.3           py38h497a2fe_2    conda-forge
pysocks                   1.7.1            py38h578d9bd_3    conda-forge
python                    3.8.10          h49503c6_1_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python-libarchive-c       2.9              py38h578d9bd_2    conda-forge
python_abi                3.8                      1_cp38    conda-forge
pytz                      2021.1             pyhd8ed1ab_0    conda-forge
pyyaml                    5.4.1            py38h497a2fe_0    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.25.1             pyhd3deb0d_0    conda-forge
ripgrep                   12.1.1               h516909a_1    conda-forge
ruamel_yaml               0.15.80         py38h497a2fe_1004    conda-forge
setuptools                49.6.0           py38h578d9bd_3    conda-forge
shyaml                    0.6.2              pyhd3deb0d_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
soupsieve                 2.0.1                      py_1    conda-forge
sqlite                    3.35.5               h74cdb3f_0    conda-forge
su-exec                   0.2               h516909a_1002    conda-forge
tini                      0.18.0            h14c3975_1001    conda-forge
tk                        8.6.10               h21135ba_1    conda-forge
tqdm                      4.60.0             pyhd8ed1ab_0    conda-forge
traitlets                 5.0.5                      py_0    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
zipp                      3.4.1              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.4.9                ha95c52a_0    conda-forge
+ find /home/conda/staged-recipes-copy/recipes -mindepth 2 -maxdepth 2 -type f -name yum_requirements.txt
+ xargs -r /usr/bin/sudo -n yum install -y
+ grep -v -e '^#' -e '^$'
+ xargs -n1 cat
+ test 1 == 1
+ python /home/conda/staged-recipes-copy/.ci_support/build_all.py
Building pygbif with conda-forge/label/main
Setting build arch. This is only useful when pretending to be on another arch, such as for rendering necessary dependencies on a non-native arch. I trust that you know what you're doing.
WARNING conda_build.config:arch(318): Setting build arch. This is only useful when pretending to be on another arch, such as for rendering necessary dependencies on a non-native arch. I trust that you know what you're doing.
rendering /home/conda/staged-recipes-copy/recipes/pygbif for linux-64
Setting build platform. This is only useful when pretending to be on another platform, such as for rendering necessary dependencies on a non-native platform. I trust that you know what you're doing.
WARNING conda_build.config:platform(332): Setting build platform. This is only useful when pretending to be on another platform, such as for rendering necessary dependencies on a non-native platform. I trust that you know what you're doing.
Computed that there are 1 distributions to build from 1 recipes
Resolved dependencies, will be built in the following order:
    pygbif-0.5.0-on-linux-64
No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.16
WARNING conda_build.metadata:ns_cfg(118): No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.16
Adding in variants from internal_defaults
INFO conda_build.variants:_combine_spec_dictionaries(234): Adding in variants from internal_defaults
Adding in variants from /opt/conda/conda_build_config.yaml
INFO conda_build.variants:_combine_spec_dictionaries(234): Adding in variants from /opt/conda/conda_build_config.yaml
Adding in variants from /home/conda/staged-recipes-copy/.ci_support/linux64.yaml
INFO conda_build.variants:_combine_spec_dictionaries(234): Adding in variants from /home/conda/staged-recipes-copy/.ci_support/linux64.yaml
Attempting to finalize metadata for pygbif
INFO conda_build.metadata:finalize_outputs_pass(748): Attempting to finalize metadata for pygbif
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
BUILD START: ['pygbif-0.5.0-pyh6c4a22f_0.tar.bz2']
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/conda/staged-recipes/build_artifacts/pygbif_1622587822896/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac


The following NEW packages will be INSTALLED:

    _libgcc_mutex:    0.1-conda_forge          conda-forge
    _openmp_mutex:    4.5-1_gnu                conda-forge
    ca-certificates:  2021.5.30-ha878542_0     conda-forge
    certifi:          2021.5.30-py39hf3d152e_0 conda-forge
    ld_impl_linux-64: 2.35.1-hea4e1c9_2        conda-forge
    libffi:           3.3-h58526e2_2           conda-forge
    libgcc-ng:        9.3.0-h2828fa1_19        conda-forge
    libgomp:          9.3.0-h2828fa1_19        conda-forge
    libstdcxx-ng:     9.3.0-h6de172a_19        conda-forge
    ncurses:          6.2-h58526e2_4           conda-forge
    openssl:          1.1.1k-h7f98852_0        conda-forge
    pip:              21.1.2-pyhd8ed1ab_0      conda-forge
    python:           3.9.4-hffdb5ce_0_cpython conda-forge
    python_abi:       3.9-1_cp39               conda-forge
    readline:         8.1-h46c0cb4_0           conda-forge
    setuptools:       49.6.0-py39hf3d152e_3    conda-forge
    sqlite:           3.35.5-h74cdb3f_0        conda-forge
    tk:               8.6.10-h21135ba_1        conda-forge
    tzdata:           2021a-he74cb21_0         conda-forge
    wheel:            0.36.2-pyhd3deb0d_0      conda-forge
    xz:               5.2.5-h516909a_1         conda-forge
    zlib:             1.2.11-h516909a_1010     conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Source cache directory is: /home/conda/staged-recipes/build_artifacts/src_cache
INFO conda_build.source:download_to_cache(44): Source cache directory is: /home/conda/staged-recipes/build_artifacts/src_cache
Downloading source to cache: pygbif-0.5.0_342988e96f.tar.gz
INFO conda_build.source:download_to_cache(69): Downloading source to cache: pygbif-0.5.0_342988e96f.tar.gz
Downloading https://pypi.io/packages/source/p/pygbif/pygbif-0.5.0.tar.gz
INFO conda_build.source:download_to_cache(83): Downloading https://pypi.io/packages/source/p/pygbif/pygbif-0.5.0.tar.gz
Success
INFO conda_build.source:download_to_cache(94): Success
Extracting download
source tree in: /home/conda/staged-recipes/build_artifacts/pygbif_1622587822896/work
export PREFIX=/home/conda/staged-recipes/build_artifacts/pygbif_1622587822896/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac
export BUILD_PREFIX=/home/conda/staged-recipes/build_artifacts/pygbif_1622587822896/_build_env
export SRC_DIR=/home/conda/staged-recipes/build_artifacts/pygbif_1622587822896/work
Using pip 21.1.2 from $PREFIX/lib/python3.9/site-packages/pip (python 3.9)
Non-user install because user site-packages disabled
Ignoring indexes: https://pypi.org/simple
Created temporary directory: /tmp/pip-ephem-wheel-cache-w46zhc41
Created temporary directory: /tmp/pip-req-tracker-6c0x8lcn
Initialized build tracking at /tmp/pip-req-tracker-6c0x8lcn
Created build tracker: /tmp/pip-req-tracker-6c0x8lcn
Entered build tracker: /tmp/pip-req-tracker-6c0x8lcn
Created temporary directory: /tmp/pip-install-8wa295w3
Processing $SRC_DIR
  Created temporary directory: /tmp/pip-req-build-jmpg1lev
  DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
   pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555.
  Added file://$SRC_DIR to build tracker '/tmp/pip-req-tracker-6c0x8lcn'
    Running setup.py (path:/tmp/pip-req-build-jmpg1lev/setup.py) egg_info for package from file://$SRC_DIR
    Created temporary directory: /tmp/pip-pip-egg-info-l8js60ig
    Running command python setup.py egg_info
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-req-build-jmpg1lev/setup.py", line 5, in <module>
        from pygbif import package_metadata
      File "/tmp/pip-req-build-jmpg1lev/pygbif/__init__.py", line 38, in <module>
        from .occurrences import search, get, count, download
      File "/tmp/pip-req-build-jmpg1lev/pygbif/occurrences/__init__.py", line 21, in <module>
        from .search import search
      File "/tmp/pip-req-build-jmpg1lev/pygbif/occurrences/search.py", line 3, in <module>
        from pygbif.gbifutils import gbif_baseurl, bool2str, requests_argset, gbif_GET
      File "/tmp/pip-req-build-jmpg1lev/pygbif/gbifutils.py", line 1, in <module>
        import requests
    ModuleNotFoundError: No module named 'requests'
WARNING: Discarding file:///home/conda/staged-recipes/build_artifacts/pygbif_1622587822896/work. Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Exception information:
Traceback (most recent call last):
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in _main
    status = self.run(options, args)
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 204, in wrapper
    return func(self, options, args)
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 318, in run
    requirement_set = resolver.resolve(
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 103, in resolve
    r = self.factory.make_requirement_from_install_req(
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 444, in make_requirement_from_install_req
    raise self._build_failures[ireq.link]
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 200, in _make_candidate_from_link
    self._link_candidate_cache[link] = LinkCandidate(
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 306, in __init__
    super().__init__(
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 151, in __init__
    self.dist = self._prepare()
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 234, in _prepare
    dist = self._prepare_distribution()
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 317, in _prepare_distribution
    return self._factory.preparer.prepare_linked_requirement(
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 508, in prepare_linked_requirement
    return self._prepare_linked_requirement(req, parallel_builds)
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 570, in _prepare_linked_requirement
    dist = _get_prepared_distribution(
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 60, in _get_prepared_distribution
    abstract_dist.prepare_distribution_metadata(finder, build_isolation)
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/distributions/sdist.py", line 36, in prepare_distribution_metadata
    self.req.prepare_metadata()
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/req/req_install.py", line 563, in prepare_metadata
    self.metadata_directory = self._generate_metadata()
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/req/req_install.py", line 538, in _generate_metadata
    return generate_metadata_legacy(
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/operations/build/metadata_legacy.py", line 67, in generate_metadata
    call_subprocess(
  File "$PREFIX/lib/python3.9/site-packages/pip/_internal/utils/subprocess.py", line 244, in call_subprocess
    raise InstallationSubprocessError(proc.returncode, command_desc)
pip._internal.exceptions.InstallationSubprocessError: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Removed file://$SRC_DIR from build tracker '/tmp/pip-req-tracker-6c0x8lcn'
Removed build tracker: '/tmp/pip-req-tracker-6c0x8lcn'
Traceback (most recent call last):
  File "/home/conda/staged-recipes-copy/.ci_support/build_all.py", line 175, in <module>
    build_all(os.path.join(root_dir, "recipes"), args.arch)
  File "/home/conda/staged-recipes-copy/.ci_support/build_all.py", line 100, in build_all
    build_folders(recipes_dir, folders, arch, channel_urls)
  File "/home/conda/staged-recipes-copy/.ci_support/build_all.py", line 156, in build_folders
    conda_build.api.build([recipe], config=get_config(arch, channel_urls))
  File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 186, in build
    return build_tree(
  File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3068, in build_tree
    packages_from_this = build(metadata, stats,
  File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2191, in build
    utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env,
  File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 412, in check_call_env
    return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
  File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 392, in _func_defaulting_env_to_os_environ
    raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/home/conda/staged-recipes/build_artifacts/pygbif_1622587822896/work/conda_build.sh']' returned non-zero exit status 1.

JWCook · 2021-06-02T00:12:45Z

Looks like you just need to add the requirements from your setup.py to
requirements.run:

requirements:
    host:
        - python
        - pip
    run:
        - requests >=2.7
        - etc.

JWCook · 2021-06-02T00:31:13Z

Oh, one small problem, though: looks like geojson_rewind and geomet don't have conda packages available, so those would need to be published first.

@pjgoodall If you wanted to give that a try, there's a handy tool called grayskull that can grab package metadata from PyPI and generate a Conda recipe from it. It usually requires a bit of manual adjustment after that, but it does about 80% of the work for you.

Alternatively, you could probably get away with publishing pygbif without those dependencies, and do without the wkt_rewind utils in the Conda version for now. It looks like those are optional features, right?

pjgoodall · 2021-06-10T07:07:09Z

Thanks @JWCook will put this on my list. I need to learn how to do this anyway.

JWCook · 2021-06-10T14:09:23Z

If/when you submit PRs for those, feel free to ping me if you run into any problems.

sckott · 2021-06-11T22:34:09Z

looks like geojson_rewind and geomet don't have conda packages available, so those would need to be published first.

Thanks, so I should wait for this, correct?

JWCook · 2021-06-11T22:45:17Z

Right, there's nothing else to do until those dependencies are published.

sckott · 2021-06-11T23:18:46Z

thanks. ran again after adding deps to the meta file - and ran into the missing geojson_rewind - so will wait for that

Rassine · 2024-02-15T15:02:50Z

thanks. ran again after adding deps to the meta file - and ran into the missing geojson_rewind - so will wait for that

If I'm not mistaken, geojson_rewind exist now as a conda package under the name geojson-rewind here, Are you still planning on building pygbif on conda ?

I would be happy to help but I'm still learning to do conda recepe on tools that needs pygbif

sckott · 2024-02-15T17:28:34Z

i no longer maintain this. @CecSve ?

CecSve · 2024-02-16T08:08:57Z

Thank you - we will look into it!

CecSve assigned jhnwllr Mar 1, 2024

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No current publication of pygbif on conda-forge #83

No current publication of pygbif on conda-forge #83

pjgoodall commented May 31, 2021

sckott commented Jun 1, 2021

JWCook commented Jun 2, 2021

JWCook commented Jun 2, 2021 •

edited

pjgoodall commented Jun 10, 2021

JWCook commented Jun 10, 2021

sckott commented Jun 11, 2021

JWCook commented Jun 11, 2021

sckott commented Jun 11, 2021

Rassine commented Feb 15, 2024

sckott commented Feb 15, 2024

CecSve commented Feb 16, 2024

No current publication of pygbif on conda-forge #83

No current publication of pygbif on conda-forge #83

Comments

pjgoodall commented May 31, 2021

sckott commented Jun 1, 2021

JWCook commented Jun 2, 2021

JWCook commented Jun 2, 2021 • edited

pjgoodall commented Jun 10, 2021

JWCook commented Jun 10, 2021

sckott commented Jun 11, 2021

JWCook commented Jun 11, 2021

sckott commented Jun 11, 2021

Rassine commented Feb 15, 2024

sckott commented Feb 15, 2024

CecSve commented Feb 16, 2024

JWCook commented Jun 2, 2021 •

edited