A Python wrapper around Bacting

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Overview

pybacting

Tests PyPI PyPI - License PyPI - Python Version Code style: black DOI

Python wrapper around bacting.

Usage

Based on the example from the bacting page, you can do:

from pybacting import cdk

print(cdk.fromSMILES("COC"))

Or you can use some of the more pythonic functions that wrap the functions exposed through the pybacting.cdk object:

import pybacting

print(pybacting.from_smiles("COC"))

Installation

Before installing, you'll need to make sure Maven (mvn) is available on your path. If you're on mac, use brew install maven.

$ pip install pybacting

Install the latest code from GitHub:

$ pip install git+https://github.com/cthoyt/pybacting

Download and install from source in development mode:

$ git clone https://github.com/cthoyt/pybacting
$ cd pybacting
$ pip install --editable .
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Comments
  • README instructions correct?

    README instructions correct?

    Following the README which writes:

    Download and install from source in development mode:

```shell
$ git clone https://github.com/cthoyt/pybacting
$ cd pybacting
$ pip install --editable .

    ... I get this error:

    pybacting$ pip install --editable .
ERROR: File "setup.py" not found. Directory cannot be installed in editable mode: /home/egonw/var/Projects/hub/pybacting
(A "pyproject.toml" file was found, but editable mode currently requires a setup.py based build.)
    opened by egonw 4
  • ScyJava does not pick up the correct dependencies

    ScyJava does not pick up the correct dependencies

    Eclipse had a dependency issue which they recently fixed, removing archives from Maven Central. Bacting 0.0.40 was updated, giving the fixed dependency tree:

    [INFO] |  \- io.github.egonw.bacting:bioclipse-core:jar:2.8.0.16:compile
[INFO] |     +- org.eclipse.platform:org.eclipse.core.runtime:jar:3.25.0:compile
[INFO] |     |  +- org.eclipse.platform:org.eclipse.osgi:jar:3.18.0:compile (version selected from constraint [3.17.0,4.0.0))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.common:jar:3.16.100:compile (version selected from constraint [3.16.0,))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.core.jobs:jar:3.13.0:compile (version selected from constraint [3.13.0,4.0.0))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.registry:jar:3.11.100:compile (version selected from constraint [3.11.0,4.0.0))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.1:compile (version selected from constraint [3.10.0,4.0.0))
[INFO] |     |  |  \- org.osgi:org.osgi.service.prefs:jar:1.1.2:compile (version selected from constraint [1.1.0,1.2.0))

    Here, org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.1 is the fixed library (see https://github.com/eclipse-equinox/equinox.bundles/issues/54), but when installing pybacting it still depends on 3.10.0:

    [Error: ] Failed to execute goal on project managers-inchi-BOOTSTRAPPER: Could not resolve dependencies for project 
io.github.egonw.bacting-BOOTSTRAPPER:managers-inchi-BOOTSTRAPPER:jar:0: Failed to collect dependencies at 
io.github.egonw.bacting:managers-inchi:jar:0.0.40 -> io.github.egonw.bacting:bacting-core:jar:0.0.40 -> 
io.github.egonw.bacting:bioclipse-core:jar:2.8.0.16 -> org.eclipse.platform:org.eclipse.core.runtime:jar:3.25.0 -> 
org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.0 -> org.osgi.service:org.osgi.service.prefs:jar:[1.1.0,1.2.0):
No versions available for org.osgi.service:org.osgi.service.prefs:jar:[1.1.0,1.2.0) within specified range -> [Help 1]

    Note how it does pick up org.eclipse.platform:org.eclipse.core.runtime:jar:3.25.0 but then is happy with the broken org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.0 where version 3.10.1 should be used instead.

    This leaves pybacting uninstallable for now. It is yet unclear how to fix this.

    opened by egonw 1
  • Update deps

    Update deps

    Closes #4 if new JGO is installed. Some of the artifacts were POM only and were excluded (see https://github.com/scijava/scyjava/issues/30#issuecomment-892061823). For the rest, I added the managers.

    opened by cthoyt 1
  • Enable importing all bacting build artifacts

    Enable importing all bacting build artifacts

    Blocked by https://github.com/scijava/scyjava/issues/30 and transitively https://github.com/scijava/jgo/issues/31#issuecomment-548056700

    To fix this, we'll have to wait for a new release of jgo which includes the finished PR https://github.com/scijava/jgo/pull/62. Then, the issue with scyjava will magically go away. This issue can be closed with an update to pybacting's setup.cfg file to include a minimum version of jgo

    opened by cthoyt 1
Releases(v0.2.9)
Owner
Charles Tapley Hoyt
Bio/cheminformatician, open scientist, maintainer of @pybel and @pykeen, part of @indralab (he/him)
Charles Tapley Hoyt
GitHub Repository
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