diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 3575d00..53248ca 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -34,14 +34,3 @@ _(Please tick any or all of the following that are applicable)_ - If you are implementing changes that are intended to increase performance, you should provide the results of a simple performance benchmark exercise demonstrating the improvement. Especially if the changes make code less legible. - -## :ballot_box_with_check: Checklist - -- [ ] :art: The changes implemented is consistent with the [julia style guide](https://docs.julialang.org/en/stable/manual/style-guide/). -- [ ] :blue_book: I have updated and added relevant docstrings, in a manner consistent with the [documentation styleguide](https://docs.julialang.org/en/stable/manual/documentation/). -- [ ] :blue_book: I have added or updated relevant user and developer manuals/documentation in `docs/src/`. -- [ ] :ok: There are unit tests that cover the code changes I have made. -- [ ] :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. -- [ ] :ok: All changes should be compatible with the latest stable version of Julia. -- [ ] :thought_balloon: I have commented liberally for any complex pieces of internal code. diff --git a/NEWS.md b/NEWS.md index 3c84ed2..cee1c7e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,10 @@ BioStructures.jl release notes ============================== +## v0.11.3 - Sep 2020 + +* Gzip support is added for reading and writing mmCIF files via the `gzip` keyword argument. + ## v0.11.2 - Sep 2020 * Add `get` method for `MMCIFDict`. diff --git a/Project.toml b/Project.toml index 9276fa6..627e10a 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "BioStructures" uuid = "de9282ab-8554-53be-b2d6-f6c222edabfc" authors = ["Joe G Greener "] -version = "0.11.2" +version = "0.11.3" [deps] BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e" diff --git a/docs/src/documentation.md b/docs/src/documentation.md index e6ef89e..2278759 100644 --- a/docs/src/documentation.md +++ b/docs/src/documentation.md @@ -461,7 +461,7 @@ Various options can be set through optional keyword arguments when parsing PDB/m | `remove_disorder::Bool=false` | Whether to remove atoms with alt loc ID not ' ' or 'A' | | `read_std_atoms::Bool=true` | Whether to read standard ATOM records | | `read_het_atoms::Bool=true` | Whether to read HETATOM records | -| `gzip::Bool=false` | Whether the file is gzipped (MMTF and MMCIF files only) | +| `gzip::Bool=false` | Whether the file is gzipped (MMTF and mmCIF files only) | Use [`retrievepdb`](@ref) to download and parse a PDB file into a Structure-Model-Chain-Residue-Atom framework in a single line: @@ -517,8 +517,8 @@ writepdb("1EN2_out.pdb", struc, backboneselector) ``` To write mmCIF format files, use the [`writemmcif`](@ref) function with similar arguments. -A [`MMCIFDict`](@ref) can also be written using [`writemmcif`](@ref): The `gzip` keyword argument, default `false`, determines whether to gzip the written file. +A [`MMCIFDict`](@ref) can also be written using [`writemmcif`](@ref): ```julia writemmcif("1EN2_out.dic", mmcif_dict) diff --git a/test/runtests.jl b/test/runtests.jl index de10162..339bde9 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -5,12 +5,12 @@ using Test using BioAlignments using BioSequences import BioCore # Imported to avoid clash with BioGenerics distance +using CodecZlib using DataFrames using Format using LightGraphs using MetaGraphs using RecipesBase -using CodecZlib using BioStructures using BioStructures: