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    Iskandar Pashayev
    @ispashayev
    I'll be there
    lkapitana
    @lkapitana
    Hi, is there anything involving use cases or documentation?
    Reece Hart
    @reece
    Perhaps. Do you have a biocommons environment installed (hgvs, seqrepo, bioutils)?
    lkapitana
    @lkapitana
    Yes, installed a few months ago
    Reece Hart
    @reece
    Great. I knew that you installed some, but wasn't sure you had gotten everything working.
    If you're still able/willing to help, how about let's work on documentation for bioutils. It's reasonably self-contained and short on documentation. Sound good?
    Kevin McCurdy
    @khmccurdy
    Forgot to post this last time - inspired by the JBrowse example Reece posted a while ago:
    Shifting acids
    lkapitana
    @lkapitana
    @reece is there something specific you can point me towards? I can't make it tonight but if you think of something specific for me to look at I can take a shot, likely late this week or next week
    I can't make it tonight
    was thinking that working on use cases in a team might be a good idea
    Reece Hart
    @reece
    @lkapitana : Sure. Main repo is here: https://github.com/biocommons/bioutils. Look at function definitions in https://github.com/biocommons/bioutils/blob/master/src/bioutils/assemblies.py as an example. Then, read https://sphinxcontrib-napoleon.readthedocs.io/en/latest/ on formatting doc strings. The goal is to document bioutils functions using Google-style described in the napoleon link. At the same time, I'd love other eyes on the prose that's there to improve it. Make sense? Interested in that?
    @khmccurdy I can't quite tell what those graphics are showing, but I suspect I'm missing something. Show in person?
    Kevin McCurdy
    @khmccurdy
    Here's an ebook about Bioinformatics: https://www.biostarhandbook.com/
    Kevin McCurdy
    @khmccurdy
    @reece The lines surrounding the center bar indicate gene sequence (ATGAACGAAAAT... on the bottom, TACTTGCTTTTA... on the top); the symbols directly above and below indcate codons - the animation shifts between possible groupings of codons; the symbols at the top and bottom represent the amino acids formed by said codons (appearing as the codon symbol with other codons for that acid superimposed on top)
    lkapitana
    @lkapitana
    @reece thank you, will look into this!
    Reece Hart
    @reece
    General info: The three most frequently-used sources of common bioinformatics data (e.g., sequences, transcripts, variation, taxonomy, etc) are NCBI (National Center for Biotechnology Information, part of National Library of Medicine), Ensembl (European Bioinformatics Institute), and UC Santa Cruz Genome Center. Tools from each of them have been stuck in the 2000s for a while. I just got a link to a very pre-release of the ensembl web site at it looks awesome. Check it out: http://2020.ensembl.org/app/browser/GRCh38_demo/ENST00000589042.5?region=2:178616861-178617118. It's so prerelease that the data are mock, so you won't be able to do too much.
    Iskandar Pashayev
    @ispashayev
    @reece I thought of a test case I wanted to run for normalization. I'm trying to create the dev environment for bioutils, but I'm having some issues with running make devready. Looks like it has something to do with the ensurepip package:
    Failing command: ['/home/iskandar/GitHub/bioutils/venv/3.7/bin/python3.7', '-Im', 'ensurepip', '--upgrade', '--default-pip']
    Also it specifically tells me that ensurepip is not available and to install python3-venv, but I already have python3-venv installed
    Reece Hart
    @reece
    @ispashayev: Please rm -fr venv, then try again. The only thing I can think of is that your environment is incomplete or not being activated. Removing the venv will try from scratch. If that doesn't work, would you please upload the full transcript here? I just tried on Py 3.7 and it works fine.
    Also, by the time this command gets executed, the environment is no longer the system environment, which means that python3-venv is irrelevant. (The error message and remedy are misleading, and provides a good example of why packages should be really careful about proscribing how to manage outer environments.)
    Also, please try this:
    Reece Hart
    @reece
    deactivate
    python3.7 -m venv venv/3.7
    source venv/3.7/bin/activate
    python3.7 -Im ensurepip
    lkapitana
    @lkapitana
    Hi all, sorry delayed with other work and haven't had time to get back into this, hope to have more time in August
    Iskandar Pashayev
    @ispashayev
    I had to install python3.7-venv
    It gets further, but now I am getting another error when it runs python setup.py egg_info
    Traceback:
    ERROR: Complete output from command python setup.py egg_info:
        ERROR: Traceback (most recent call last):
          File "<string>", line 1, in <module>
          File "/home/iskandar/GitHub/bioutils/setup.py", line 3, in <module>
            setup(use_scm_version=True)
          File "/home/iskandar/GitHub/bioutils/venv/3.7/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in setup
            return distutils.core.setup(**attrs)
          File "/usr/lib/python3.7/distutils/core.py", line 108, in setup
            _setup_distribution = dist = klass(attrs)
          File "/home/iskandar/GitHub/bioutils/venv/3.7/lib/python3.7/site-packages/setuptools/dist.py", line 444, in __init__
            k: v for k, v in attrs.items()
          File "/usr/lib/python3.7/distutils/dist.py", line 292, in __init__
            self.finalize_options()
          File "/home/iskandar/GitHub/bioutils/venv/3.7/lib/python3.7/site-packages/setuptools/dist.py", line 732, in finalize_options
            ep.load()(self, ep.name, value)
          File "/home/iskandar/GitHub/bioutils/.eggs/setuptools_scm-3.3.3-py3.7.egg/setuptools_scm/integration.py", line 17, in version_keyword
            dist.metadata.version = get_version(**value)
          File "/home/iskandar/GitHub/bioutils/.eggs/setuptools_scm-3.3.3-py3.7.egg/setuptools_scm/__init__.py", line 154, in get_version
            parsed_version, version_scheme=version_scheme, local_scheme=local_scheme
          File "/home/iskandar/GitHub/bioutils/.eggs/setuptools_scm-3.3.3-py3.7.egg/setuptools_scm/version.py", line 304, in format_version
            main_version = version_scheme(version)
          File "/home/iskandar/GitHub/bioutils/.eggs/setuptools_scm-3.3.3-py3.7.egg/setuptools_scm/version.py", line 236, in guess_next_dev_version
            return version.format_next_version(guess_next_version)
          File "/home/iskandar/GitHub/bioutils/.eggs/setuptools_scm-3.3.3-py3.7.egg/setuptools_scm/version.py", line 182, in format_next_version
            guessed = guess_next(self.tag, **kw)
          File "/home/iskandar/GitHub/bioutils/.eggs/setuptools_scm-3.3.3-py3.7.egg/setuptools_scm/version.py", line 210, in guess_next_version
            return _bump_dev(version) or _bump_regex(version)
          File "/home/iskandar/GitHub/bioutils/.eggs/setuptools_scm-3.3.3-py3.7.egg/setuptools_scm/version.py", line 223, in _bump_dev
            assert tail == "0", "own dev numbers are unsupported"
        AssertionError: own dev numbers are unsupported
        ----------------------------------------
    ERROR: Command "python setup.py egg_info" failed with error code 1 in /home/iskandar/GitHub/bioutils/
    Reece Hart
    @reece
    Okay, now do a git pull.
    Explanation: I discovered last week that setuptools doesn't permit certain Semantic Version version numbers (https://semver.org/). SemVer permits 0.1.2.dev6 (i.e., 6th dev release based on 0.1.2). PyPI requires version numbers to push code. I tagged with something like 0.5.0.dev2 and pushed, but now you can't set up. :-(
    Anyway, removed the tags. I think that git pull should update your repo so that you're not building with a devN tag. (BTW, .dev is just fine... a trailing number is the culprit).
    Iskandar Pashayev
    @ispashayev
    Did you push? I don't see new commits when I fetch or in the commit history on github
    Reece Hart
    @reece
    Weird. I just started getting this error too in a new project that didn't inherit any code. I'm still investigating.
    Reece Hart
    @reece
    Fascinating. I just worked out that python -m venv throws this error if there's a problem with setup.cfg . I'm not sure that's what's causing the issue you experience.
    Reece Hart
    @reece
    I just updated bioutils. make devready works for me. Please git pull, then make devready.
    Reece Hart
    @reece
    @lkapitana @trentwatt I added a docs directory with autodoc enabled. See biocommons/bioutils#22 for more info an instructions. I think it's ready for you two to dive in! Thanks for adding documentation!
    Reece Hart
    @reece
    That page used to be blank, so it's fair to say that that's a big win. Woot!
    Deena Blumenkrantz
    @Deena-B
    @trentwatt It looks beautiful!
    Reece Hart
    @reece
    Hey devs. Long time no talk!
    But, @trentwatt has been busy. Take a look at the docs he added:
    Thanks Trent!
    Trent Watson
    @trentwatt
    you bet @reece
    Trent Watson
    @trentwatt
    !
    Reece Hart
    @reece
    Hi devs. Who's planning on attending on Wednesday?
    Trent Watson
    @trentwatt
    cant make it, out of town
    Reece Hart
    @reece

    The biocommons SIG started a year ago this month. I had hoped to create a community with an active and enduring engagement that made meaningful contributions to biocommons efforts. Although we've had a few great contributions, we mostly haven't met that goal.

    Therefore, I intend to suspend the biocommons SIG at project night. Unfortunately, I can't be there this month to wind it down in person. Because this is the last project night of the year, we will have a long gap in meetings.

    To those of you who contributed to conversations, code, or documentation, thank you.

    And, if any of you remain genuinely interested in learning and contributing, I am still open to helping you achieve that goal. Please contact me directly.