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shortDOI support & update environment on 2019-02-06

Merges #174

* Environment update on 2019-02-06

Does not upgrade weasyprint or cairo, due to the following error during
WeasyPrint execution:
OSError: dlopen() failed to load a library: cairo / cairo-2 / cairo-gobject-2

Specify cairocffi dependency in environment.yml, since v0.9 from PyPI
seemed to trigger the OSError.

* Add shortDOI support & usage

Update repo to https://github.com/manubot/manubot
greenelab/manubot relocated to manubot/manubot as per
manubot/manubot#94.

02.delete-me.md still references greenelab/manubot,
however it is not worth creating merge conflicts to
update just this.
  • Loading branch information...
dhimmel committed Feb 6, 2019
1 parent 658bcd7 commit f559600ff1965899b20874e71874794c05787087
Showing with 12 additions and 7 deletions.
  1. +2 −2 .travis.yml
  2. +5 −1 USAGE.md
  3. +5 −4 build/environment.yml
@@ -5,15 +5,15 @@ branches:
only:
- master
before_install:
- wget https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh
- wget https://repo.continuum.io/miniconda/Miniconda3-4.5.12-Linux-x86_64.sh
--output-document miniconda.sh
- bash miniconda.sh -b -p $HOME/miniconda
- source $HOME/miniconda/etc/profile.d/conda.sh
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda info --all
install:
- conda env create --quiet --file build/environment.yml
- conda list --name manubot
- conda activate manubot
script:
- sh build/build.sh
@@ -76,6 +76,10 @@ Therefore, citations must be of the following form: `@source:identifier`, where
When choosing which source to use for a citation, we recommend the following order:

1. DOI (Digital Object Identifier), cite like `@doi:10.15363/thinklab.4`.
Shortened versions of DOIs can be created at [shortdoi.org](http://shortdoi.org/).
shortDOIs begin with `10/` rather than `10.` and can also be cited.
For example, Manubot will expand `@doi:10/993` to the DOI above.
We suggest using shortDOIs to cite DOIs containing forbidden characters, such as `(` or `)`.
2. PubMed Central ID, cite like `@pmcid:PMC4497619`.
3. PubMed ID, cite like `@pmid:26158728`.
4. _arXiv_ ID, cite like `@arxiv:1508.06576v2`.
@@ -165,7 +169,7 @@ Note that `affiliations` should be a list to allow for multiple affiliations per

## Manubot feedback

If you experience any issues with the Manubot or would like to contribute to its source code, please visit [`greenelab/manubot`](https://github.com/greenelab/manubot) or [`greenelab/manubot-rootstock`](https://github.com/greenelab/manubot-rootstock).
If you experience any issues with the Manubot or would like to contribute to its source code, please visit [`manubot/manubot`](https://github.com/manubot/manubot) or [`greenelab/manubot-rootstock`](https://github.com/greenelab/manubot-rootstock).

## Examples

@@ -3,20 +3,21 @@ channels:
- conda-forge
dependencies:
- conda-forge::cairo=1.14.12
- conda-forge::cairocffi=0.8.0
- conda-forge::cffi=1.11.5
- conda-forge::ghp-import=0.5.5
- conda-forge::jinja2=2.10
- conda-forge::jsonschema=2.6.0
- conda-forge::pandas=0.23.4
- conda-forge::pandoc=2.5
- conda-forge::pandas=0.24.0
- conda-forge::pandoc=2.6
- conda-forge::pango=1.40.14
- conda-forge::python=3.6.5
- conda-forge::python=3.6.7
- conda-forge::pyyaml=3.13
- conda-forge::requests=2.21.0
- conda-forge::watchdog=0.8.3
- pip:
- errorhandler==2.0.1
- git+https://github.com/greenelab/manubot@552dd99aaa148365a29a87176fedd626d4642d3c
- git+https://github.com/manubot/manubot@4505db3fd8a9dc1ba26c36f3fea9accbf02d47d8
- jsonref==0.2
- opentimestamps-client==0.6.0
- opentimestamps==0.3.0

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