Add MMCIF reading and writing with gzip compression

[marcom]

Add MMCIF reading and writing with gzip compression

This adds a gzip keyword in the same manner as the MMTF functions have.

Sorry that the patch for the tests is rather noisy and hard to compare, but that was the easiest way to test many things without adding a lot of extra code. Let me know if you want it changed in any way.

I also didn't add anything to the downloadpdb... functions. Not sure what the best way do that would be, perhaps a decompress=true keyword. I personally don't use those functions at the moment (using the PDB rsync).

I have not checked any influence on performance, hoping that there is none.

Types of changes

This PR implements the following changes: (Please tick any or all of the following that are applicable)

• [x] :sparkles: New feature (A non-breaking change which adds functionality).
• [ ] :bug: Bug fix (A non-breaking change, which fixes an issue).
• [ ] :boom: Breaking change (fix or feature that would cause existing functionality to change).

:clipboard: Additional detail

• If you have implemented new features or behaviour

  • Provide a description of the addition in as many details as possible. See above

  • Provide justification of the addition. Makes it easier to work with gzip-compressed mmcif files, as in the mmtf case.

  • Provide a runnable example of use of your addition.

At the shell:

    $ wget https://files.rcsb.org/download/1AKI.cif.gz

In Julia:

using BioStructures
cif = MMCIFDict("1AKI.cif.gz"; gzip=true)

• Does your change alter APIs or existing exposed methods/types? This adds a new keyword argument to mmcif functions, which (i believe) shouldn't affect existing usage.

:ballot_box_with_check: Checklist

Note: the julia style guide link and the documentation style guide links don't work.

• [ ] :art: The changes implemented is consistent with the julia style guide.
• [x] :blue_book: I have updated and added relevant docstrings, in a manner consistent with the documentation styleguide.
• [x] :blue_book: I have added or updated relevant user and developer manuals/documentation in docs/src/.
• [x] :ok: There are unit tests that cover the code changes I have made.
• [x] :ok: The unit tests cover my code changes AND they pass.
• [ ] :pencil: I have added an entry to the [UNRELEASED] section of the manually curated CHANGELOG.md file for this repository.
• [x] :ok: All changes should be compatible with the latest stable version of Julia.
• [x] :thought_balloon: I have commented liberally for any complex pieces of internal code.

[codecov[bot]]

Codecov Report

Merging #25 into master will increase coverage by 0.04%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master      #25      +/-   ##
==========================================
+ Coverage   94.55%   94.60%   +0.04%     
==========================================
  Files           6        6              
  Lines        1507     1520      +13     
==========================================
+ Hits         1425     1438      +13     
  Misses         82       82              

Impacted Files	Coverage Δ
src/mmtf.jl	99.24% <ø> (ø)
src/mmcif.jl	98.81% <100.00%> (+0.06%)	:arrow_up:

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[jgreener64]

Thanks a lot for adding this, it was on the todo list but I didn't get round to it. It looks good to me as is.

[jgreener64]

Available in v0.11.3.