put opentree on conda-forge

[harmsm]

This library is extraordinarily useful. Would you be willing to make it installable by conda as well as pip? My lab is working on an ancestral sequence reconstruction pipeline that relies on opentree, as well as some conda-only packages. It would be useful to be able to give users an option to install the whole pipeline with conda.

I would be happy to take point on submitting to conda-forge if helpful and okay with you.

Thanks!

[harmsm]

I just submitted a PR with a draft meta.yaml file, if helpful.

[snacktavish]

Thanks! I merged it to development and updated it.
https://github.com/OpenTreeOfLife/python-opentree/blob/development/meta.yaml

I have started walking through the steps at https://conda-forge.org/docs/maintainer/adding_pkgs.html

Was there a reason you used v0.0.3 for the meta.yml? I figured I would just submit it with v1.0.1, (honestly it reminds me that we should submit a newer release to pypi... but one thing at time) but if there is a reason to start with the 0.0.3 that is fine too.

[harmsm]

Oops, copied in wrong version number when making the template. No reason at all, in other words….

…

On Aug 15, 2022, at 11:51 AM, Emily Jane McTavish ***@***.***> wrote: Thanks! I merged it to development and updated it. https://github.com/OpenTreeOfLife/python-opentree/blob/development/meta.yaml <https://github.com/OpenTreeOfLife/python-opentree/blob/development/meta.yaml> I have started walking through the steps at https://conda-forge.org/docs/maintainer/adding_pkgs.html <https://conda-forge.org/docs/maintainer/adding_pkgs.html> Was there a reason you used v0.0.3 for the meta.yml? I figured I would just submit it with v1.0.1, (honestly it reminds me that we should submit a newer release to pypi... but one thing at time) but if there is a reason to start with the 0.0.3 that is fine too. — Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABFZA6VLDEL5YY57R2HTD53VZKGR5ANCNFSM555K47KQ>. You are receiving this because you authored the thread.

[snacktavish]

Ah - it's because we tagged it but never created a new release on GitHub! I just fixed that.

[harmsm]

👍

…

On Aug 15, 2022, at 12:53 PM, Emily Jane McTavish ***@***.***> wrote: Ah - it's because we tagged it but never created a new release on GitHub! I just fixed that. — Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABFZA6R2I2XJ2MRYPORI2LTVZKN35ANCNFSM555K47KQ>. You are receiving this because you authored the thread.

[snacktavish]

I am trying to locally test my recipe before submitting a PR to staged recipes (as described in https://conda-forge.org/docs/maintainer/adding_pkgs.html#staging-test-locally).
I have forked the repo, and updated the recipe in /recipes in https://github.com/snacktavish/staged-recipes

However, when I try to run the tests using
python build-locally.py
from the top level dir, a bunch of stuff runs (I could share output), but at the end I get "There are no tempfile(s) to remove.
There are no logfile(s) to remove.
Found no recipes to build".

Any ideas?

[snacktavish]

gave up on local testing, submitted a PR and am letting the CI test it! conda-forge/staged-recipes#20097

[harmsm]

🤞 Thanks for working on it!

…

On Aug 16, 2022, at 3:01 PM, Emily Jane McTavish ***@***.***> wrote: gave up on local testing, submitted a PR and am letting the CI test it! conda-forge/staged-recipes#20097 <conda-forge/staged-recipes#20097> — Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABFZA6SY5XKVRWNTYT7P7A3VZQFTLANCNFSM555K47KQ>. You are receiving this because you authored the thread.

[harmsm]

I noticed this is stalled out on conda-forge. When I requested the conda-forge repo I did not realize that all dependencies had to be on conda-forge, rather than just visible on conda via some channel. It seems like bioconda will be a more flexible option given dendropy is already on bioconda, not conda-forge.

I created a recipe file for bioconda and have a fork ready for a PR against bioconda master. If you like, I can do the PR. (I tried to test locally, but bioconda-utils seems to be very, very broken. It relies on an apparently abandoned GO program to interface with docker???)

Thanks!

[snacktavish]

Ah nice! I will take a look this week. I was away last week and am digging out!

[harmsm]

Unfortunately, I’m my package is also my first conda-forge submission. I didn’t even get to that step before I hit the snag of having a few non-conda packages in my dependency tree. I’ve done a fair amount in conda, so maybe I would have ideas seeing output. Could you post output spew? Thanks!

…

On Aug 15, 2022, at 12:58 PM, Emily Jane McTavish ***@***.***> wrote: I am trying to locally test my recipe before submitting a PR to staged recipes (as described in https://conda-forge.org/docs/maintainer/adding_pkgs.html#staging-test-locally <https://conda-forge.org/docs/maintainer/adding_pkgs.html#staging-test-locally>). I have forked the repo, and updated the recipe in /recipes in https://github.com/snacktavish/staged-recipes <https://github.com/snacktavish/staged-recipes> However, when I try to run the tests using python build-locally.py from the top level dir, a bunch of stuff runs (I could share output), but at the end I get "There are no tempfile(s) to remove. There are no logfile(s) to remove. Found no recipes to build". Any ideas? — Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABFZA6T4UJQNATKBOQPH3X3VZKONDANCNFSM555K47KQ>. You are receiving this because you authored the thread.

[snacktavish]

Hi Mike,
Sorry for dropping the ball on this! I suspect there is just an issue with my setup that it isn't even trying to build this recipe when I run build-locally.py, but here's all the output.

It doesn't seem like it is even trying any of the recipes 🤔 (the other ones happened to be in staged-recipes when I forked it)

$ ls recipes/
example  perl-file-chdir  perl-mime-base64  python-opentree

Click to expand verbose output

$ python build-locally.py 
valid configs are {'win64', 'linux64_cuda102', 'linux64', 'osx64', 'linux64_cuda110', 'linux64_cuda111', 'linux64_cuda112'}
config not selected, please choose from the following:

1. linux64
2. linux64_cuda102
3. linux64_cuda110
4. linux64_cuda111
5. linux64_cuda112
6. osx64
7. win64

> 1
selected linux64
Client:
Context:    default
Debug Mode: false

Server:
Containers: 16
 Running: 0
 Paused: 0
 Stopped: 16
Images: 97
Server Version: 20.10.12
Storage Driver: overlay2
 Backing Filesystem: extfs
 Supports d_type: true
 Native Overlay Diff: true
 userxattr: false
Logging Driver: json-file
Cgroup Driver: systemd
Cgroup Version: 2
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.runtime.v1.linux runc io.containerd.runc.v2
Default Runtime: runc
Init Binary: docker-init
containerd version: 
runc version: 
init version: 
Security Options:
 apparmor
 seccomp
  Profile: default
 cgroupns
Kernel Version: 5.15.0-48-generic
Operating System: Ubuntu 22.04.1 LTS
OSType: linux
Architecture: x86_64
CPUs: 8
Total Memory: 15.31GiB
Name: byatt
ID: YN25:ULNR:5DVO:HSYD:WVKW:FMBM:ZEZ2:YQZE:R6QW:BL5U:KHSD:BFEY
Docker Root Dir: /var/lib/docker
Debug Mode: false
Username: mctavishlab
Registry: https://index.docker.io/v1/
Labels:
Experimental: false
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. Trying to parse with coreutils
Using default tag: latest
latest: Pulling from condaforge/linux-anvil-cos7-x86_64
2d473b07cdd5: Already exists 
dadc05df4b32: Pull complete 
Digest: sha256:1c1b355ecab912c157741dcd971f1db9d6d6fe9f0393f13e0b54828e6f85bb57
Status: Downloaded newer image for quay.io/condaforge/linux-anvil-cos7-x86_64:latest
quay.io/condaforge/linux-anvil-cos7-x86_64:latest
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 24
drwxr-xr-x  6 conda conda 4096 Oct 11 17:13 .
drwxr-xr-x 10 conda conda 4096 Oct 11 17:13 ..
drwxr-xr-x  2 conda conda 4096 Oct 11 17:13 example
drwxr-xr-x  2 conda conda 4096 Oct 11 17:13 perl-file-chdir
drwxr-xr-x  2 conda conda 4096 Oct 11 17:13 perl-mime-base64
drwxr-xr-x  2 conda conda 4096 Oct 11 17:13 python-opentree
+ echo 'Finding recipes merged in main and removing them from the build.'
Finding recipes merged in main and removing them from the build.
+ pushd /home/conda/staged-recipes/recipes
+ '[' False == True ']'
+ git ls-tree --name-only main -- .
+ xargs -I '{}' sh -c 'rm -rf ~/staged-recipes-copy/recipes/{} && echo Removing recipe: {}'
Removing recipe: example
Removing recipe: perl-file-chdir
Removing recipe: perl-mime-base64
Removing recipe: python-opentree
+ popd
+ conda index /home/conda/staged-recipes/build_artifacts
+ mamba install --yes --quiet 'conda>4.7.12' 'conda-forge-ci-setup=3.*' conda-forge-pinning networkx=2.4 'conda-build>=3.16' boa                                                                             
                                                                                                                                                                                                            
                 __    __    __    __                                                                                                                                                                       
                /  \  /  \  /  \  /  \               
               /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
             /  / \   / \   / \   / \  \____
            /  /   \_/   \_/   \_/   \    o \__,
           / _/                       \_____/  `
           |/
       ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
       ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
       ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
       ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
       ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
       ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

       mamba (0.27.0) supported by @QuantStack

       GitHub:  https://github.com/mamba-org/mamba
       Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

 Package                             Version  Build              Channel                   Size
──────────────────────────────────────────────────────────────────────────────────────────────────
 Install:
──────────────────────────────────────────────────────────────────────────────────────────────────

 + click                               8.1.3  py310hff52083_0    conda-forge/linux-64     152kB
 + conda-env                           2.6.0  1                  conda-forge/noarch         2kB
 + conda-forge-ci-setup               3.21.0  py310hce54274_100  conda-forge/linux-64      44kB
 + conda-forge-pinning   2022.10.11.03.04.53  hd8ed1ab_0         conda-forge/noarch        22kB
 + decorator                           5.1.1  pyhd8ed1ab_0       conda-forge/noarch        12kB
 + jq                                    1.6  h36c2ea0_1000      conda-forge/linux-64     354kB
 + networkx                              2.4  py_1               conda-forge/noarch         1MB
 + oniguruma                           6.9.8  h166bdaf_0         conda-forge/linux-64     440kB
 + shyaml                              0.6.2  pyhd3deb0d_0       conda-forge/noarch        22kB

 Summary:

 Install: 9 packages

 Total download: 2MB

──────────────────────────────────────────────────────────────────────────────────────────────────

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/linux64.yaml
+ source run_conda_forge_build_setup
++ export PYTHONUNBUFFERED=1
++ PYTHONUNBUFFERED=1
++ conda config --env --set show_channel_urls true
++ conda config --env --set auto_update_conda false
++ conda config --env --set add_pip_as_python_dependency false
++ conda config --env --append aggressive_update_packages ca-certificates
++ conda config --env --remove-key aggressive_update_packages
++ conda config --env --append aggressive_update_packages ca-certificates
++ conda config --env --append aggressive_update_packages certifi
++ export CONDA_BLD_PATH=/home/conda/staged-recipes/build_artifacts
++ CONDA_BLD_PATH=/home/conda/staged-recipes/build_artifacts
++ set +u
++ [[ '' == \d\r\o\n\e ]]
++ [[ '' == \g\i\t\h\u\b\_\a\c\t\i\o\n\s ]]
++ export CPU_COUNT=2
++ CPU_COUNT=2
+++ cat /home/conda/staged-recipes/conda-forge.yml
+++ shyaml get-value channel_priority strict
++ conda config --env --set channel_priority strict
++ [[ ! -z '' ]]
++ '[' '!' -z linux64 ']'
++ '[' '!' -z '' ']'
++ cat /home/conda/staged-recipes-copy/.ci_support/linux64.yaml
c_compiler:
- gcc
cxx_compiler:
- gxx
fortran_compiler:
- gfortran
target_platform:
- linux-64
channel_sources:
- conda-forge
docker_image:
- quay.io/condaforge/linux-anvil-cos7-x86_64
cuda_compiler_version:
- None
++ 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/linux64.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
++++ conda info --json
++++ jq -r .platform
+++ BUILD_PLATFORM=linux-64
+++ '[' -f /home/conda/staged-recipes-copy/.ci_support/linux64.yaml ']'
++++ cat /home/conda/staged-recipes-copy/.ci_support/linux64.yaml
++++ shyaml get-value target_platform.0 linux-64
+++ HOST_PLATFORM=linux-64
+++ HOST_PLATFORM=linux-64
+++ [[ linux-64 != \l\i\n\u\x\-\6\4 ]]
++ '[' -f /home/conda/staged-recipes-copy/.ci_support/linux64.yaml ']'
+++ cat /home/conda/staged-recipes-copy/.ci_support/linux64.yaml
+++ shyaml get-value MACOSX_DEPLOYMENT_TARGET.0 0
++ 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 : /opt/conda/.condarc
                         /home/conda/.condarc
         conda version : 22.9.0
   conda-build version : 3.22.0
        python version : 3.10.6.final.0
      virtual packages : __linux=5.15.0=0
                         __glibc=2.17=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 : None
          channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                         https://conda.anaconda.org/conda-forge/noarch
         package cache : /home/conda/staged-recipes/build_artifacts/pkg_cache
                         /opt/conda/pkgs
      envs directories : /opt/conda/envs
                         /home/conda/.conda/envs
              platform : linux-64
            user-agent : conda/22.9.0 requests/2.28.1 CPython/3.10.6 Linux/5.15.0-48-generic centos/7.9.2009 glibc/2.17
               UID:GID : 1000:1000
            netrc file : None
          offline mode : False

++ conda config --env --show-sources
==> /opt/conda/.condarc <==
add_pip_as_python_dependency: False
auto_update_conda: False
aggressive_update_packages:
 - ca-certificates
 - certifi
channel_priority: strict
channels:
 - conda-forge
show_channel_urls: True

==> /home/conda/.condarc <==
pkgs_dirs:
 - /home/conda/staged-recipes/build_artifacts/pkg_cache
 - /opt/conda/pkgs
channels:
 - conda-forge
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                       2_gnu    conda-forge
anaconda-client           1.8.0              pyhd8ed1ab_0    conda-forge
anyio                     3.6.1              pyhd8ed1ab_1    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
boa                       0.12.0             pyha770c72_4    conda-forge
brotlipy                  0.7.0           py310h5764c6d_1004    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.9.24            ha878542_0    conda-forge
certifi                   2022.9.24          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_0    conda-forge
chardet                   5.0.0           py310hff52083_0    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
click                     8.1.3           py310hff52083_0    conda-forge
clyent                    1.2.2                      py_1    conda-forge
colorama                  0.4.5              pyhd8ed1ab_0    conda-forge
commonmark                0.9.1                      py_0    conda-forge
conda                     22.9.0          py310hff52083_1    conda-forge
conda-build               3.22.0          py310hff52083_2    conda-forge
conda-env                 2.6.0                         1    conda-forge
conda-forge-ci-setup      3.21.0          py310hce54274_100    conda-forge
conda-forge-pinning       2022.10.11.03.04.53      hd8ed1ab_0    conda-forge
conda-package-handling    1.9.0           py310h5764c6d_0    conda-forge
cryptography              38.0.1          py310h597c629_0    conda-forge
curl                      7.85.0               h7bff187_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
expat                     2.4.9                h27087fc_0    conda-forge
filelock                  3.8.0              pyhd8ed1ab_0    conda-forge
future                    0.18.2          py310hff52083_5    conda-forge
gettext                   0.19.8.1          h27087fc_1009    conda-forge
git                       2.38.0          pl5321h5fbbf19_0    conda-forge
glob2                     0.7                        py_0    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.4          py310hff52083_0    conda-forge
importlib_resources       5.10.0             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.2.0              pyhd8ed1ab_0    conda-forge
jq                        1.6               h36c2ea0_1000    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.16.0             pyhd8ed1ab_0    conda-forge
jupyter_core              4.11.1          py310hff52083_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
libarchive                3.5.2                hb890918_3    conda-forge
libcurl                   7.85.0               h7bff187_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
liblief                   0.12.2               h27087fc_0    conda-forge
libmamba                  0.27.0               h0dd8ff0_0    conda-forge
libmambapy                0.27.0          py310hab0e683_0    conda-forge
libnghttp2                1.47.0               hdcd2b5c_1    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libsolv                   0.7.22               h6239696_0    conda-forge
libsqlite                 3.39.4               h753d276_0    conda-forge
libssh2                   1.10.0               haa6b8db_3    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libxml2                   2.9.14               h22db469_4    conda-forge
libzlib                   1.2.12               h166bdaf_4    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     0.27.0          py310hf87f941_0    conda-forge
markupsafe                2.1.1           py310h5764c6d_1    conda-forge
nbformat                  5.6.1              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
networkx                  2.4                        py_1    conda-forge
oniguruma                 6.9.8                h166bdaf_0    conda-forge
openssl                   1.1.1q               h166bdaf_0    conda-forge
patch                     2.7.6             h7f98852_1002    conda-forge
patchelf                  0.15.0               h58526e2_0    conda-forge
pcre2                     10.37                hc3806b6_1    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pip                       22.2.2             pyhd8ed1ab_0    conda-forge
pkginfo                   1.8.3              pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.31             pyha770c72_0    conda-forge
prompt_toolkit            3.0.31               hd8ed1ab_0    conda-forge
psutil                    5.9.2           py310h5764c6d_0    conda-forge
py-lief                   0.12.2          py310hd8f1fbe_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.3           py310h5764c6d_1010    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_1    conda-forge
pyrsistent                0.18.1          py310h5764c6d_1    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.6          h582c2e5_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python-libarchive-c       4.0             py310hff52083_1    conda-forge
python_abi                3.10                    2_cp310    conda-forge
pytz                      2022.4             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0             py310h5764c6d_4    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
reproc                    14.2.3               h7f98852_0    conda-forge
reproc-cpp                14.2.3               h9c3ff4c_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
rich                      12.6.0             pyhd8ed1ab_0    conda-forge
ripgrep                   13.0.0               h2f28480_2    conda-forge
ruamel.yaml               0.17.21         py310h5764c6d_1    conda-forge
ruamel.yaml.clib          0.2.6           py310h5764c6d_1    conda-forge
ruamel_yaml               0.15.80         py310h5764c6d_1007    conda-forge
setuptools                65.4.1             pyhd8ed1ab_0    conda-forge
shyaml                    0.6.2              pyhd3deb0d_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
su-exec                   0.2               h166bdaf_1003    conda-forge
tini                      0.19.0               h166bdaf_1    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tqdm                      4.64.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.4.0              pyhd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022d                h191b570_0    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
watchgod                  0.8.2              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.7.0                h27087fc_2    conda-forge
zipp                      3.8.1              pyhd8ed1ab_0    conda-forge
zstd                      1.5.2                h6239696_4    conda-forge
+ find /home/conda/staged-recipes-copy/recipes -mindepth 2 -maxdepth 2 -type f -name yum_requirements.txt
+ xargs -n1 cat
+ grep -v -e '^#' -e '^$'
+ xargs -r /usr/bin/sudo -n yum install -y
+ test 1 == 1
+ python /home/conda/staged-recipes-copy/.ci_support/build_all.py
Updating build index: /home/conda/staged-recipes/build_artifacts

Will remove 9 (2.2 MB) tarball(s).
Will remove 1 index cache(s).
Will remove 26 (495.5 MB) package(s).
There are no tempfile(s) to remove.
There are no logfile(s) to remove.
Found no recipes to build
+ touch /home/conda/staged-recipes/build_artifacts/conda-forge-build-done

[snacktavish]

Aha! Progress. Verbose below, but the key part is:

Unsatisfiable dependencies for platform linux-64: {'nosetests', 'm2r', "dendropy[version='>=4.4.0']
m2r is just for the docs, and nose is for testing which presumably doesn't have to happen on conda, but dendropy is pivotal.

Nose and dendropy can be installed using:
conda install -c bioconda dendropy
conda install -c conda-forge nose

But on a quick google I don't see how to add channels to the meta.yml

Click to expand verbose output

conda build python-opentree/
No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.16
WARNING:conda_build.metadata: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:Adding in variants from internal_defaults
Attempting to finalize metadata for python-opentree
INFO:conda_build.metadata:Attempting to finalize metadata for python-opentree
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
BUILD START: ['python-opentree-1.0.1-py_0.tar.bz2']
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/ejmctavish/.conda/envs/testenv/conda-bld/python-opentree_1665510019295/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p


The following NEW packages will be INSTALLED:

    _libgcc_mutex:    0.1-main                
    _openmp_mutex:    5.1-1_gnu               
    ca-certificates:  2022.07.19-h06a4308_0   
    certifi:          2022.9.24-py37h06a4308_0
    ld_impl_linux-64: 2.38-h1181459_1         
    libffi:           3.3-he6710b0_2          
    libgcc-ng:        11.2.0-h1234567_1       
    libgomp:          11.2.0-h1234567_1       
    libstdcxx-ng:     11.2.0-h1234567_1       
    ncurses:          6.3-h5eee18b_3          
    openssl:          1.1.1q-h7f8727e_0       
    pip:              22.2.2-py37h06a4308_0   
    python:           3.7.13-h12debd9_0       
    readline:         8.1.2-h7f8727e_1        
    setuptools:       63.4.1-py37h06a4308_0   
    sqlite:           3.39.3-h5082296_0       
    tk:               8.6.12-h1ccaba5_0       
    wheel:            0.37.1-pyhd3eb1b0_0     
    xz:               5.2.6-h5eee18b_0        
    zlib:             1.2.12-h5eee18b_3       

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

Leaving build/test directories:
  Work:
 /home/ejmctavish/.conda/envs/testenv/conda-bld/work 
  Test:
 /home/ejmctavish/.conda/envs/testenv/conda-bld/test_tmp 
Leaving build/test environments:
  Test:
source activate  /home/ejmctavish/.conda/envs/testenv/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh 
  Build:
source activate  /home/ejmctavish/.conda/envs/testenv/conda-bld/_build_env 


Traceback (most recent call last):
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/environ.py", line 799, in get_install_actions
    actions = install_actions(prefix, index, specs, force=True)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/common/io.py", line 86, in decorated
    return f(*args, **kwds)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/plan.py", line 476, in install_actions
    txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 159, in solve_for_transaction
    should_retry_solve)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 200, in solve_for_diff
    force_remove, should_retry_solve)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 317, in solve_final_state
    ssc = self._add_specs(ssc)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 607, in _add_specs
    explicit_pool = ssc.r._get_package_pool(self.specs_to_add)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 556, in _get_package_pool
    pool = self.get_reduced_index(specs)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/common/io.py", line 86, in decorated
    return f(*args, **kwds)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 577, in get_reduced_index
    explicit_specs, features = self.verify_specs(explicit_specs)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 289, in verify_specs
    raise ResolvePackageNotFound(bad_deps)
conda.exceptions.ResolvePackageNotFound: 
  - nosetests
  - m2r
  - dendropy[version='>=4.4.0']

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ejmctavish/.conda/envs/testenv/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 496, in main
    execute(sys.argv[1:])
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 487, in execute
    verify=args.verify, variants=args.variants, cache_dir=args.cache_dir)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/api.py", line 195, in build
    variants=variants
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 3096, in build_tree
    notest=notest,
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 2131, in build
    create_build_envs(top_level_pkg, notest)
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 2009, in create_build_envs
    raise e
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 1999, in create_build_envs
    channel_urls=tuple(m.config.channel_urls))
  File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/environ.py", line 801, in get_install_actions
    raise DependencyNeedsBuildingError(exc, subdir=subdir)
conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {'nosetests', 'm2r', "dendropy[version='>=4.4.0']"}

[harmsm]

Thanks for working on this! (This stuff is no fun, so I really appreciate it). One question: are you trying to get this up on conda-forge or on bioconda? I originally suggested conda-forge, but that *only* allows dependencies on conda-forge, which is basically impossible on my end as well. Bioconda lists the following for their dependencies (https://bioconda.github.io/contributor/guidelines.html#bioconda-recipe-checklist) <paste> There is currently no mechanism to define, in the meta.yaml file, that a particular dependency should come from a particular channel. This means that a recipe must have its dependencies in one of the following: as-yet-unbuilt recipes in the repo but that will be included in the PR conda-forge channel bioconda channel default Anaconda channel </paste> Mike

…

On Oct 11, 2022, at 10:54 AM, Emily Jane McTavish ***@***.***> wrote: Aha! Progress. Verbose below, but the key part is: Unsatisfiable dependencies for platform linux-64: {'nosetests', 'm2r', "dendropy[version='>=4.4.0'] m2r is just for the docs, and nose is for testing which presumably doesn't have to happen on conda, but dendropy is pivotal. Nose and dendropy can be installed using: conda install -c bioconda dendropy conda install -c conda-forge nose But on a quick google I don't see how to add channels to the meta.yml conda build python-opentree/ No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16 WARNING:conda_build.metadata: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:Adding in variants from internal_defaults Attempting to finalize metadata for python-opentree INFO:conda_build.metadata:Attempting to finalize metadata for python-opentree Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done BUILD START: ['python-opentree-1.0.1-py_0.tar.bz2'] Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/ejmctavish/.conda/envs/testenv/conda-bld/python-opentree_1665510019295/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p The following NEW packages will be INSTALLED: _libgcc_mutex: 0.1-main _openmp_mutex: 5.1-1_gnu ca-certificates: 2022.07.19-h06a4308_0 certifi: 2022.9.24-py37h06a4308_0 ld_impl_linux-64: 2.38-h1181459_1 libffi: 3.3-he6710b0_2 libgcc-ng: 11.2.0-h1234567_1 libgomp: 11.2.0-h1234567_1 libstdcxx-ng: 11.2.0-h1234567_1 ncurses: 6.3-h5eee18b_3 openssl: 1.1.1q-h7f8727e_0 pip: 22.2.2-py37h06a4308_0 python: 3.7.13-h12debd9_0 readline: 8.1.2-h7f8727e_1 setuptools: 63.4.1-py37h06a4308_0 sqlite: 3.39.3-h5082296_0 tk: 8.6.12-h1ccaba5_0 wheel: 0.37.1-pyhd3eb1b0_0 xz: 5.2.6-h5eee18b_0 zlib: 1.2.12-h5eee18b_3 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed Leaving build/test directories: Work: /home/ejmctavish/.conda/envs/testenv/conda-bld/work Test: /home/ejmctavish/.conda/envs/testenv/conda-bld/test_tmp Leaving build/test environments: Test: source activate /home/ejmctavish/.conda/envs/testenv/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh Build: source activate /home/ejmctavish/.conda/envs/testenv/conda-bld/_build_env Traceback (most recent call last): File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/environ.py", line 799, in get_install_actions actions = install_actions(prefix, index, specs, force=True) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/common/io.py", line 86, in decorated return f(*args, **kwds) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/plan.py", line 476, in install_actions txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 159, in solve_for_transaction should_retry_solve) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 200, in solve_for_diff force_remove, should_retry_solve) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 317, in solve_final_state ssc = self._add_specs(ssc) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 607, in _add_specs explicit_pool = ssc.r._get_package_pool(self.specs_to_add) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 556, in _get_package_pool pool = self.get_reduced_index(specs) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/common/io.py", line 86, in decorated return f(*args, **kwds) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 577, in get_reduced_index explicit_specs, features = self.verify_specs(explicit_specs) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 289, in verify_specs raise ResolvePackageNotFound(bad_deps) conda.exceptions.ResolvePackageNotFound: - nosetests - m2r - dendropy[version='>=4.4.0'] During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/ejmctavish/.conda/envs/testenv/bin/conda-build", line 11, in <module> sys.exit(main()) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 496, in main execute(sys.argv[1:]) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 487, in execute verify=args.verify, variants=args.variants, cache_dir=args.cache_dir) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/api.py", line 195, in build variants=variants File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 3096, in build_tree notest=notest, File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 2131, in build create_build_envs(top_level_pkg, notest) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 2009, in create_build_envs raise e File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 1999, in create_build_envs channel_urls=tuple(m.config.channel_urls)) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/environ.py", line 801, in get_install_actions raise DependencyNeedsBuildingError(exc, subdir=subdir) conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {'nosetests', 'm2r', "dendropy[version='>=4.4.0']"} — Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABFZA6RQZ4CHCFDYX6TRULTWCWSU5ANCNFSM555K47KQ>. 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