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A conda-smithy repository for pymol-open-source.

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

Python 100.00%

pymol-open-source-feedstock's Introduction

About pymol-open-source-feedstock

Feedstock license: BSD-3-Clause

Home: https://pymol.org/

Package license: LicenseRef-PyMOL

Summary: A user-sponsored molecular visualization system. PyMOL is a trademark of Schrodinger, LLC.

Development: https://github.com/schrodinger/pymol-open-source/

Documentation: https://pymolwiki.org/

PyMOL is a molecular visualization software with a Python based command line. This is a user-created build based on the open-source variant of the PyMOL software. PyMOL is a trademark of Schrodinger, LLC.

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
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
win_64_numpy1.22python3.10.____cpython
win_64_numpy1.22python3.8.____cpython
win_64_numpy1.22python3.9.____cpython
win_64_numpy1.23python3.11.____cpython
win_64_numpy1.26python3.12.____cpython

Current release info

Name	Downloads	Version	Platforms

Installing pymol-open-source

Installing pymol-open-source 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, pymol-open-source can be installed with conda:

conda install pymol-open-source

or with mamba:

mamba install pymol-open-source

It is possible to list all of the versions of pymol-open-source available on your platform with conda:

conda search pymol-open-source --channel conda-forge

or with mamba:

mamba search pymol-open-source --channel conda-forge

Alternatively, mamba repoquery may provide more information:

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

# List packages depending on `pymol-open-source`:
mamba repoquery whoneeds pymol-open-source --channel conda-forge

# List dependencies of `pymol-open-source`:
mamba repoquery depends pymol-open-source --channel conda-forge

About conda-forge

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

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

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

For more information please check the conda-forge documentation.

Terminology

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

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

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

Updating pymol-open-source-feedstock

If you would like to improve the pymol-open-source 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/pymol-open-source-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

pymol-open-source-feedstock's People

Contributors

Stargazers

Watchers

Forkers

regro-cf-autotick-bot padix-key jaimergp bkpoon liamjwang

pymol-open-source-feedstock's Issues

Conflict with ambertools conda-forge package

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

Issue:

Details about conda and system ( conda info ):

$ conda info
    active environment : base
    active env location : /home/sdoerr/miniconda3
            shell level : 1
       user config file : /home/sdoerr/.condarc
 populated config files : 
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.8.5.final.0
       virtual packages : __cuda=11.2=0
                          __linux=5.11.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/sdoerr/miniconda3  (writable)
      conda av data dir : /home/sdoerr/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : 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 : /home/sdoerr/miniconda3/pkgs
                          /home/sdoerr/.conda/pkgs
       envs directories : /home/sdoerr/miniconda3/envs
                          /home/sdoerr/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.3 requests/2.24.0 CPython/3.8.5 Linux/5.11.0-40-generic ubuntu/20.04.2 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Hi I am trying to install ambertools package together with pymol-open-source. There is a conflict in the latest versions:

$ conda create -n test_install ambertools=21.11 pymol-open-source=2.5.0 python=3.7 -c conda-forge
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: \ 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                         

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package python conflicts for:
ambertools=21.11 -> cython -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|3.4.*|3.7.*|3.9.*|3.8.*']
ambertools=21.11 -> python[version='>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0']
python=3.7

Package mkl conflicts for:
pymol-open-source=2.5.0 -> numpy[version='>=1.19.5,<2.0a0'] -> mkl[version='>=2019.4,<2020.0a0|>=2019.4,<2021.0a0|>=2021.2.0,<2022.0a0|>=2021.3.0,<2022.0a0']
ambertools=21.11 -> libblas[version='>=3.8.0,<4.0a0'] -> mkl[version='2019.1.*|>=2019.0,<2020.0a0|>=2020.0,<2021.0a0|>=2020.4,<2021.0a0|>=2021.2.0,<2022.0a0|>=2021.3.0,<2022.0a0|>=2021.4.0,<2022.0a0|>=2019.4,<2021.0a0|>=2019.3,<2021.0a0|>=2019.1,<2021.0a0|>=2018.0.3,<2019.0a0|>=2018.0.2,<2019.0a0|>=2018.0.1,<2019.0a0|>=2018.0.0,<2019.0a0|>=2019.4,<2020.0a0']

Package setuptools conflicts for:
python=3.7 -> pip -> setuptools
ambertools=21.11 -> cython -> setuptoolsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.31=0
  - feature:|@/linux-64::__glibc==2.31=0
  - ambertools=21.11 -> libgfortran-ng -> __glibc[version='>=2.17']
  - python=3.7 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

Requesting for pymol-open-source=2.4.0 solves the conflict. This command works

$ conda create -n test_install ambertools=21.11 pymol-open-source=2.4.0 python=3.7 -c conda-forge

If I install first ambertools and then pymol-open-source it tries to downgrade the following packages:

  Downgrade:
───────────────────────────────────────────────────────────────────────────────────────

  - ambertools            21.11  py37h5d2b9b6_0       installed                      
  + ambertools            20.15  py37hc295af0_1       conda-forge/linux-64      96 MB
  - hdf5                 1.12.1  nompi_h2750804_101   installed                      
  + hdf5                 1.10.6  nompi_h6a2412b_1114  conda-forge/linux-64       3 MB
  - icu                    69.1  h9c3ff4c_0           installed                      
  + icu                    68.2  h9c3ff4c_0           conda-forge/linux-64      13 MB
  - libnetcdf             4.8.1  nompi_hb3fd0d9_101   installed                      
  + libnetcdf             4.7.4  nompi_h56d31a8_107   conda-forge/linux-64       1 MB

Could not load the Qt platform plugin "xcb" in "" even though it was found.

Comment:

Hi, I'm trying to install pymol-open-source-3.0.0 in a virtual env of miniconda3 under Ubuntu 22.04.4 LTS.
After installed, I commanded pymol, but pymol didn't start and the following message appeared.

qt.qpa.xcb: could not connect to display

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, minimal, minimalegl, offscreen, vnc, webgl, xcb.

Aborted (core dumped)

To address the problem, I tried two commands.

export DISPLAY=:0
export QT_QPA_PLATFORM_PLUGIN_PATH=/home/usr_name/miniconda3/envs/env_name/plugins/platforms/

However, pymol remains to start, and the error message is

qt.qpa.xcb: could not connect to display :0
qt.qpa.xcb: could not connect to display :0
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "/home/usr_name/miniconda3/envs/env_name/plugins/platforms/" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs (from /home/usr_name/miniconda3/envs/env_name/plugins/platforms/), minimal (from /home/usr_name/miniconda3/envs/env_name/plugins/platforms/), minimalegl (from /home/usr_name/miniconda3/envs/env_name/plugins/platforms/), offscreen (from /home/usr_name/miniconda3/envs/env_name/plugins/platforms/), vnc (from /home/usr_name/miniconda3/envs/env_name/plugins/platforms/), webgl (from /home/usr_name/miniconda3/envs/env_name/plugins/platforms/), xcb (from /home/usr_name/miniconda3/envs/env_name/plugins/platforms/), eglfs, minimal, minimalegl, offscreen, vnc, webgl, xcb.

I would like to thank you if you tell me any solution.

Build for Python 3.10 missing

Solution to issue cannot be found in the documentation.

I checked the documentation.

Issue

I found that no pymol-open-source builds are created for Python 3.10. Am I missing something obvious here or is this some kind of problem with the recipe?

Installed packages

N/A

Environment info

N/A

Molfile plugins not compiled in

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

Issue: .gro files are not supported, probably because the molfile plugins are not compiled in, as they need libnetcdf. A "{{ pin_compatible('libnetcdf', max_pin='x.x') }}" in the dependencies should do the trick (I do the same in my pymol-open-source build in the "awacha" anaconda channel). The pinning is needed because the so version changed recently.

Environment (conda list):

$ conda list
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
ca-certificates           2021.1.19            h06a4308_0  
certifi                   2020.12.5        py39h06a4308_0  
dbus                      1.13.18              hb2f20db_0  
expat                     2.2.10               he6710b0_2  
fontconfig                2.13.1               h6c09931_0  
freetype                  2.10.4               h5ab3b9f_0  
glew                      2.1.0                h9c3ff4c_2    conda-forge
glib                      2.66.1               h92f7085_0  
glm                       0.9.9.4              hc9558a2_0    conda-forge
gst-plugins-base          1.14.0               h8213a91_2  
gstreamer                 1.14.0               h28cd5cc_2  
icu                       58.2                 he6710b0_3  
jpeg                      9b                   h024ee3a_2  
ld_impl_linux-64          2.33.1               h53a641e_7  
libblas                   3.9.0                8_openblas    conda-forge
libcblas                  3.9.0                8_openblas    conda-forge
libedit                   3.1.20191231         h14c3975_1  
libffi                    3.3                  he6710b0_2  
libgcc-ng                 9.3.0               h2828fa1_18    conda-forge
libgfortran-ng            9.3.0               hff62375_18    conda-forge
libgfortran5              9.3.0               hff62375_18    conda-forge
libglu                    9.0.0                hf484d3e_1  
libgomp                   9.3.0               h2828fa1_18    conda-forge
liblapack                 3.9.0                8_openblas    conda-forge
libopenblas               0.3.12          pthreads_h4812303_1    conda-forge
libpng                    1.6.37               hbc83047_0  
libstdcxx-ng              9.3.0               h6de172a_18    conda-forge
libuuid                   1.0.3                h1bed415_2  
libxcb                    1.14                 h7b6447c_0  
libxml2                   2.9.10               hb55368b_3  
ncurses                   6.2                  he6710b0_1  
numpy                     1.20.1           py39hdbf815f_0    conda-forge
openssl                   1.1.1i               h27cfd23_0  
pcre                      8.44                 he6710b0_0  
pip                       20.3.3           py39h06a4308_0  
pymol-open-source         2.4.0            py39h20a8f2e_3    conda-forge
pyqt                      5.9.2            py39h2531618_6  
python                    3.9.1                hdb3f193_2  
python_abi                3.9                      1_cp39    conda-forge
qt                        5.9.7                h5867ecd_1  
readline                  8.1                  h27cfd23_0  
setuptools                52.0.0           py39h06a4308_0  
sip                       4.19.13          py39h2531618_0  
sqlite                    3.33.0               h62c20be_0  
tk                        8.6.10               hbc83047_0  
tzdata                    2020f                h52ac0ba_0  
wheel                     0.36.2             pyhd3eb1b0_0  
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libx11               1.6.12               h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h27cfd23_1007  
xz                        5.2.5                h7b6447c_0  
zlib                      1.2.11               h7b6447c_3