Docker - #3
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iankronquist wants to merge 43 commits into
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Docker#3iankronquist wants to merge 43 commits into
iankronquist wants to merge 43 commits into
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Modified BinSortSQL's template to support wraparound plots by adding 360 to field values that wrap around when calculating bins. Removed old wraparound plot code.
The check for field being less than 0 was changed to field being less than min which should work for any range.
Removed unnecessary comparison in aggregate template.
Missed this piece of failed wraparound code from rendering bins.
This bugfix was user-visible so it goes on the news page.
A previous bugfix corrected the 180/-180 issues on plots, so a new plot was generated to replace the old example plot.
Added import statements as appropriate, and also changed requirements.txt to include reference to cairocffi. Documentation will need to be changed after this patch is committed. refs #15621
The two missing lines were added, and the registration line was changed. refs #15615
refs #15615
Conflicts: pgd/requirements.txt
Added Sphinx to requirements and created the required directory structure. refs #15999
refs #15999 Copied all of the code to rst files. Formatted them to hopefully look like the wiki, but haven't actually seen how they look, yet.
refs #15999 Liberation fonts is required for pgd to be installed, but was not in the package requirements
refs #16353 Added an if statement checking whether or not the pdb directory exists, and creating it if it doesn't
refs #16353 Added an if statement checking whether or not the pdb directory exists, and creating it if it doesn't
Rebasing branch because I accidently branched off of master instead of develop
refs #15999 Modified the files to get rid of the errors when building. Usually just indentation errors. Also modified headings, so that only the major ones are in the index
Conflicts: pgd/requirements.txt
Added LICENSE.txt which contains the software license for the project.
The previous repository stored everything one directory lower for no apparent reason.
If a residue has chi corrections and both atoms in the dictionary are absent, the code attempts to delete non-existent keys. The code has been changed to pop the keys, which will prevent the KeyError from being thrown. Refs #17229
The PDB contains files for proteins that treat selenocysteine as an amino acid, but DSSP does not yet support this condition. Temporary files generated for DSSP will now be modified if they have ATOM lines that contain SEC. Refs #17223
After discussion with Dale and Ken, this change can be merged into develop. Refs #17229
The PDB contains files for proteins that treat selenocysteine as an amino acid, but DSSP does not yet support this condition. Temporary files generated for DSSP will now be modified if they have ATOM lines that contain SEC. Refs #17223
Periodic changes in develop require rebasing.
Selenocysteine is now considered an amino acid by the PDB and DSSP folks, so the "amino acid" checks for HETATM lines have been changed. In addition, a new check for ATOM lines has been added. Refs #17223
The amino_present function explicitly checked for selenocysteine which caused other proteins to not import correctly. Leaving it out makes all the proteins import correctly. Refs #17223.
Some PDB files have ATOM lines for SEC (selenocysteine). SEC is a relatively new addition to the amino acid family, and the PGD code does not generally acknowledge SEC as an amino acid. The code that parses PDB files was modified to support SEC in ATOM lines.
Addresses #17799
Optional of course. An environment based config makes dockerization much easier.
By default it falls back to previous values.
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Should have made this against develop. Closing and making a new pr. |
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This was referenced Apr 28, 2017
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This is very preliminary. The Dockerfile works, but I need to add docs.
The biggest change is that I added a dependency, python-decouple, which was recommended by @mythmon as a way to use and environment variable based config. Mozilla uses it in a couple projects, and it looks like a clean solution.
I also changed the settings.py.dist to use decouple.
Sample docker commands might look like:
$ docker build -t osl_test/pgd . $ docker run --name pgd_mysql -e MYSQL_ROOT_PASSWORD=pgd_mysql -e MYSQL_USER=root -e MYSQL_PASSWORD=pgd_db -e MYSQL_DATABASE=pgd_db -d mysql $ docker run --name pgd --link pgd_mysql:mysql osl_test/pgd