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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,23 @@ | ||
| # Directories to ignore: | ||
|
|
||
| *.ipynb_checkpoints/ | ||
| data/ | ||
| docs/build/ | ||
| docs/site/ | ||
| docs/src/examples/ | ||
| input/ | ||
| output/ | ||
|
|
||
| # Files to ignore: | ||
|
|
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| .DS_Store | ||
| *.aux | ||
| *.ipynb_checkpoints/ | ||
| *.jl.*.cov | ||
| *.jl.cov | ||
| *.jl.*.cov | ||
| *.jl.mem | ||
| *.log | ||
| data/ | ||
| deps/custom_preamble.tex | ||
| deps/deps.jl | ||
| deps/pdf2svg.svg | ||
| deps/showed_warning | ||
| docs/build | ||
| input/ | ||
| output/ | ||
| scratch.jl |
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|---|---|---|
| @@ -1,44 +1,49 @@ | ||
| ## Documentation: http://docs.travis-ci.com/user/languages/julia/ | ||
| language: julia | ||
|
|
||
| os: | ||
| - linux | ||
| - osx | ||
| - linux | ||
| - osx | ||
|
|
||
| julia: | ||
| - 0.6 | ||
| # - nightly | ||
| - 0.6 | ||
| - nightly | ||
|
|
||
| notifications: | ||
| email: false | ||
| email: false | ||
|
|
||
| git: | ||
| depth: 99999999 | ||
| depth: 99999999 | ||
|
|
||
| ## Allow failures on nightly julia: | ||
| matrix: | ||
| allow_failures: | ||
| - julia: nightly | ||
| allow_failures: | ||
| - julia: nightly | ||
|
|
||
| addons: | ||
| apt: | ||
| packages: | ||
| - gfortran | ||
| - pdf2svg | ||
| - pgf | ||
| - poppler-utils # provides /usr/bin/pdftoppm | ||
| - texlive-binaries | ||
| - texlive-latex-base | ||
| - texlive-latex-extra | ||
| - texlive-pictures | ||
| apt: | ||
| packages: | ||
| - gfortran | ||
| - pdf2svg | ||
| - pgf | ||
| - poppler-utils | ||
| - texlive-binaries | ||
| - texlive-latex-base | ||
| - texlive-latex-extra | ||
| - texlive-pictures | ||
|
|
||
| before_install: | ||
| # update homebrew | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi | ||
| # install mactex | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew cask install basictex; fi | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH=/Library/TeX/texbin:"$PATH"; fi | ||
| # update tlmgr | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr update --self; fi | ||
| # install tex packages | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install luatex85; fi | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install pgfplots; fi | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install standalone; fi | ||
| # install pdf2svg | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install pdf2svg; fi | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew cask install basictex; fi | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH=/Library/TeX/texbin:"$PATH"; fi | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr update --self; fi | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install luatex85; fi | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install pgfplots; fi | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install standalone; fi | ||
| - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install pdf2svg; fi | ||
|
|
||
| script: | ||
| - julia --color=yes -e 'Pkg.clone(pwd())' | ||
| - julia --color=yes -e 'Pkg.build("PredictMD")' | ||
| - julia --check-bounds=yes --color=yes -e 'Pkg.test("PredictMD", coverage=true)' | ||
|
|
||
| after_success: | ||
| - julia -e 'cd(Pkg.dir("PredictMD")); include(joinpath("docs", "deploy_docs.jl"))' |
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|---|---|---|
|
|
@@ -14,9 +14,6 @@ This document provides information on contributing to the PredictMD source code. | |
| </tr> | ||
| <tr> | ||
| <td align="left"><a href="#2-setting-up-the-predictmd-repo">2. Setting up the PredictMD repo</a></td> | ||
| </tr> | ||
| <tr> | ||
| <td align="left"><a href="#3-working-with-examples">3. Working with examples</a></td> | ||
| </tr> | ||
| </tbody> | ||
| </table> | ||
|
|
@@ -156,41 +153,3 @@ cd ~/.julia/v0.6/PredictMD | |
| ```bash | ||
| git config commit.gpgsign true && git remote set-url origin https://github.com/bcbi/PredictMD.jl.git && git remote set-url --push origin [email protected]:bcbi/PredictMD.jl.git && git checkout master && git checkout develop && git flow init -fd && git checkout develop && git fetch --all --prune | ||
| ``` | ||
|
|
||
| ## 3. Working with examples | ||
|
|
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| Some of the examples are provided as Jupyter notebooks as a convinient way to visualize and interact with the code. However, we also like to mantain corresponding plain Julia scripts that are in-sync with the notebooks. A convinient way to do so, is to add a post-save hook to your Jupyter configuration file. | ||
|
|
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| 1. Open you jupyter configuration file ~/.jupyter/jupyter_notebook_config.py. If the file does not exist you can generate it by running `jupyter notebook --generate-config` | ||
|
|
||
| 2. Add the following code to the top of the file | ||
|
|
||
| ```python | ||
| #----------------------------------------------------------------------------- | ||
| # Auto save script version of notebook | ||
| # Reference: https://svds.com/jupyter-notebook-best-practices-for-data-science/ | ||
| #----------------------------------------------------------------------------- | ||
|
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| import os | ||
| from subprocess import check_call | ||
|
|
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| def post_save(model, os_path, contents_manager): | ||
| """post-save hook for converting notebooks to .py scripts""" | ||
| if model['type'] != 'notebook': | ||
| return # only do this for notebooks | ||
| d, fname = os.path.split(os_path) | ||
| check_call(['jupyter', 'nbconvert', '--to', 'script', fname], cwd=d) | ||
|
|
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| c.FileContentsManager.post_save_hook = post_save | ||
| ``` | ||
|
|
||
| **Note:** This behavior is global. If you want to have this saving only when in a particular folder, you can create multiple configuration files as a work-around. First create a new profile name via a bash command line: | ||
| ```bash | ||
| export JUPYTER_CONFIG_DIR=~/.jupyter_profile2 | ||
| jupyter notebook --generate-config | ||
| ``` | ||
| This will create a new directory and file at `~/.jupyter_profile2/jupyter_notebook_config.py` Then run jupyter notebook and work as usual. To switch back to your default profile you will have to set (either by hand, shell function, or your .bashrc) back to: | ||
|
|
||
| ```bash | ||
| export JUPYTER_CONFIG_DIR=~/.jupyter | ||
| ``` | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| import Documenter | ||
| import PredictMD | ||
|
|
||
| ENV["PREDICTMD_IS_DEPLOY_DOCS"] = "true" | ||
|
|
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| Documenter.deploydocs( | ||
| branch = "gh-pages", | ||
| deps = Documenter.Deps.pip( | ||
| "mkdocs", | ||
| "pygments", | ||
| "python-markdown-math", | ||
| ), | ||
| julia = "0.6", | ||
| latest = "develop", | ||
| osname = "linux", | ||
| repo = "github.com/bcbi/PredictMD.jl.git", | ||
| target = "site", | ||
| ) | ||
|
|
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| ENV["PREDICTMD_IS_DEPLOY_DOCS"] = "false" |
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