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A conda-smithy repository for mdtraj.

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

mdtraj-feedstock's Introduction

About mdtraj-feedstock

Feedstock license: BSD-3-Clause

Home: https://github.com/mdtraj/mdtraj

Package license: LGPL-2.1-or-later

Summary: A modern, open library for the analysis of molecular dynamics trajectories

Development: https://github.com/mdtraj/mdtraj

Documentation: http://mdtraj.org/

MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories and perform a variety of analyses, including fast RMSD, solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj is the wide variety of molecular dynamics trajectory file formats which are supported, including RCSB pdb, GROMACS xtc, tng, and trr, CHARMM / NAMD dcd, AMBER binpos, AMBER NetCDF, AMBER mdcrd, TINKER arc and MDTraj HDF5.

Current build status

Azure

Variant	Status
linux_64_numpy1.22python3.10.____cpythonpython_implcpython
linux_64_numpy1.22python3.8.____cpythonpython_implcpython
linux_64_numpy1.22python3.9.____cpythonpython_implcpython
linux_64_numpy1.23python3.11.____cpythonpython_implcpython
linux_64_numpy1.26python3.12.____cpythonpython_implcpython
osx_64_numpy1.22python3.10.____cpythonpython_implcpython
osx_64_numpy1.22python3.8.____cpythonpython_implcpython
osx_64_numpy1.22python3.9.____cpythonpython_implcpython
osx_64_numpy1.23python3.11.____cpythonpython_implcpython
osx_64_numpy1.26python3.12.____cpythonpython_implcpython
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.____cpythonpython_implcpython
win_64_numpy1.22python3.8.____cpythonpython_implcpython
win_64_numpy1.22python3.9.____cpythonpython_implcpython
win_64_numpy1.23python3.11.____cpythonpython_implcpython
win_64_numpy1.26python3.12.____cpythonpython_implcpython

Current release info

Name	Downloads	Version	Platforms

Installing mdtraj

Installing mdtraj 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, mdtraj can be installed with conda:

conda install mdtraj

or with mamba:

mamba install mdtraj

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

conda search mdtraj --channel conda-forge

or with mamba:

mamba search mdtraj --channel conda-forge

Alternatively, mamba repoquery may provide more information:

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

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

# List dependencies of `mdtraj`:
mamba repoquery depends mdtraj --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 mdtraj-feedstock

If you would like to improve the mdtraj 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/mdtraj-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

mdtraj-feedstock's People

Contributors

Stargazers

Watchers

Forkers

conda-forge-admin mpharrigan marscher kain88-de ocefpaf regro-cf-autotick-bot mattwthompson eguarnera rmcgibbo sroet giorginolab clonker chrisburr jeremyleung521 mlund simonboothroyd

mdtraj-feedstock's Issues

Remove me as feedstock maintainer

I'm not involved in conda-forge anymore, and i've left the github organization. If someone could remove me as maintainer from the recipe, that would be great.

Build on `linux-aarch64`

This would be nice to have for running Docker on Apple Silicon without Rosetta.

Support M1 Macs

This will probably require a new release; I think mdtraj/mdtraj#1679 might be the first indication of it actually building on M1 in development environments

New build is not prefered

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

Issue:
When running conda create -n test python=3.8 mdtraj it defaults to pull in the broken combo of build 0 with astunparse 1.6.3 instead of the latest build 1 with astunparse 1.6.2, (which the fixed pin added in #30)
explicitly calling:
conda create -n test python=3.8 astunparse=1.6.2 mdtraj does pull in the correct build...

Reading through the docs, I think a patch should be submitted to https://github.com/conda-forge/conda-forge-repodata-patches-feedstock , I will see if I can generate one

Add `mda-xdrlib` to `meta.yml`

Comment:

Just a reminder for the next release since mdtraj/mdtraj#1911 and mdtraj/mdtraj#1913 have been merged.

Python 3.12 build uses distutils

Solution to issue cannot be found in the documentation.

I checked the documentation.

Issue

The following env brings a package that uses setuptools:

$ mamba create -n test python==3.12 mdtraj

This is causing an error when importing it in the NNPOps feedstock:

______________________ ERROR collecting TestBatchedNN.py _______________________
ImportError while importing test module '$PREFIX/share/nnpops/tests/TestBatchedNN.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
TestBatchedNN.py:24: in <module>
    import mdtraj
../../../lib/python3.12/site-packages/mdtraj/__init__.py:30: in <module>
    from .formats.registry import FormatRegistry
../../../lib/python3.12/site-packages/mdtraj/formats/__init__.py:9: in <module>
    from .netcdf import NetCDFTrajectoryFile
../../../lib/python3.12/site-packages/mdtraj/formats/netcdf.py:40: in <module>
    from distutils.version import StrictVersion
E   ModuleNotFoundError: No module named 'distutils'

In my system this error does not arise, when digging a little into it I found out this is because python is looking into my system folders for it instead of the conda ones (where it is not present).

Installed packages

$ mamba list
# packages in environment at /home/raul/miniforge3/envs/test:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               hc2324a3_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.28.1               hd590300_0    conda-forge
c-blosc2                  2.14.4               hb4ffafa_1    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
hdf5                      1.14.3          nompi_h4f84152_101    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h55db66e_0    conda-forge
libaec                    1.1.3                h59595ed_0    conda-forge
libblas                   3.9.0           22_linux64_openblas    conda-forge
libcblas                  3.9.0           22_linux64_openblas    conda-forge
libcurl                   8.7.1                hca28451_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h77fa898_7    conda-forge
libgfortran-ng            13.2.0               h69a702a_7    conda-forge
libgfortran5              13.2.0               hca663fb_7    conda-forge
libgomp                   13.2.0               h77fa898_7    conda-forge
liblapack                 3.9.0           22_linux64_openblas    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.27          pthreads_h413a1c8_0    conda-forge
libsqlite                 3.45.3               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               hc0a3c3a_7    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              hd590300_1001    conda-forge
mdtraj                    1.9.9           py312hadb1fa1_1    conda-forge
ncurses                   6.5                  h59595ed_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
numexpr                   2.9.0           py312hed3a10b_100    conda-forge
numpy                     1.26.4          py312heda63a1_0    conda-forge
openssl                   3.3.0                hd590300_0    conda-forge
packaging                 24.0               pyhd8ed1ab_0    conda-forge
pandas                    2.2.2           py312h1d6d2e6_1    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
py-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
pytables                  3.9.2           py312h96d95ec_2    conda-forge
python                    3.12.0          hab00c5b_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-tzdata             2024.1             pyhd8ed1ab_0    conda-forge
python_abi                3.12                    4_cp312    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
scipy                     1.13.0          py312hc2bc53b_1    conda-forge
setuptools                69.5.1             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.2.0                hdb0a2a9_1    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zlib-ng                   2.0.7                h0b41bf4_0    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

Environment info

N/A