From f14c361e017d4ed7d46b6c08160d17905b203cd9 Mon Sep 17 00:00:00 2001 From: laurentheirendt Date: Wed, 24 May 2017 15:09:28 +0200 Subject: [PATCH] Redirect links --- .github/CONTRIBUTING.md | 6 +++--- .github/PULL_REQUEST_TEMPLATE.md | 4 ++-- README.md | 18 +++++++++--------- docs/source/_templates/README.html | 2 +- docs/source/conf.py | 2 +- docs/source/contributing.rst | 7 +++---- docs/source/faq.rst | 3 +-- docs/source/funding.rst | 7 ------- docs/source/guides/testGuide.md | 4 ++-- docs/source/installation.rst | 8 ++++---- docs/source/installation/requirements.md | 2 +- docs/source/modules/multiSpeciesModelling.rst | 10 ---------- docs/source/notes/FAQ.md | 10 +++++----- initCobraToolbox.m | 4 ++-- src/base/solvers/changeCobraSolver.m | 6 +++--- src/base/solvers/configEnvVars.m | 2 +- 16 files changed, 38 insertions(+), 57 deletions(-) delete mode 100644 docs/source/modules/multiSpeciesModelling.rst diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index b2769c3295..d7666e8a70 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,8 +9,8 @@ How to contribute :bulb: **Check out the [MATLAB.devTools](https://github.com/opencobra/MATLAB.devTools) - and contribute the smart way!** -- Please follow the [Style Guide](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/STYLEGUIDE.md). -- More information on writing a **test** is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/TESTGUIDE.md) and a template is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/testTemplate.m). -- A guide for reporting an **issue** or submitting a **pull request (PR)** is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/ISSUEGUIDE.md). +- Please follow the [Style Guide](https://opencobra.github.io/cobratoolbox/docs/styleGuide.html). +- More information on writing a **test** is [here](https://opencobra.github.io/cobratoolbox/docs/testGuide.html) and a template is [here](https://opencobra.github.io/cobratoolbox/docs/testTemplate.html). +- A guide for reporting an **issue** or submitting a **pull request (PR)** is [here](https://opencobra.github.io/cobratoolbox/docs/issueGuide.html). If you want to use `git` via the command line interface and need help, these [training slides](https://uni-lu.github.io/slides/) will get you started. This [guide](https://www.digitalocean.com/community/tutorials/how-to-create-a-pull-request-on-github) or the official [GitHub guide](https://help.github.com/articles/creating-a-pull-request/) also come in handy. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index cec5c9c9d1..021c4fbe2d 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -3,8 +3,8 @@ **I hereby confirm that I have:** -- [ ] Selected `develop` as a target branch (top left drop-down menu) - [ ] Tested my code on my own machine -- [ ] Followed the guidelines in the [Contributing Guide](https://github.com/opencobra/cobratoolbox/blob/master/.github/CONTRIBUTING.md) +- [ ] Followed the guidelines in the [Contributing Guide](https://opencobra.github.io/cobratoolbox/docs/contributing.html) +- [ ] Selected `develop` as a target branch (top left drop-down menu) *(Note: You may replace [ ] with [X] to check the box)* diff --git a/README.md b/README.md index 5ad130d71d..ad155c904e 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@

- +

The COBRA Toolbox
COnstraint-Based Reconstruction and Analysis Toolbox @@ -32,12 +32,12 @@ The COBRA Toolbox
COnstraint-Based Reconstruction and Analysis Toolbox System Requirements ------------------- -warning Please follow [this guide](https://github.com/opencobra/cobratoolbox/blob/master/.github/REQUIREMENTS.md) in order to configure your system properly. +warning Please follow [this guide](https://opencobra.github.io/cobratoolbox/docs/requirements.html) in order to configure your system properly. Solver Installation ------------------- -The default solver is `glpk` (for `LP` and `MILP`). You can install `TOMLAB`, `IBM ILOG CPLEX`, `GUROBI`, or `MOSEK` by following these **[detailed instructions](https://github.com/opencobra/cobratoolbox/blob/master/.github/SOLVERS.md)**. +The default solver is `glpk` (for `LP` and `MILP`). You can install `TOMLAB`, `IBM ILOG CPLEX`, `GUROBI`, or `MOSEK` by following these **[detailed instructions](https://opencobra.github.io/cobratoolbox/docs/solvers.html)**. Installation ------------ @@ -68,7 +68,7 @@ Support and Documentation - The documentation is available [here](http://opencobra.github.io/cobratoolbox). This version is in development, but the legacy version of the documentation is [here](http://opencobra.github.io/cobratoolbox/deprecated/docs/index.html). -- Answers to Frequently Asked Questions (**FAQ**) are [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/FAQ.md). +- Answers to Frequently Asked Questions (**FAQ**) are [here](https://opencobra.github.io/cobratoolbox/docs/FAQ.html). - If you need support, please feel free to post your question in our . @@ -83,14 +83,14 @@ How to contribute bulb **Check out the [MATLAB.devTools](https://github.com/opencobra/MATLAB.devTools) - and contribute the smart way!** -- Please follow the [Style Guide](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/STYLEGUIDE.md). -- More information on writing a **test** is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/TESTGUIDE.md) and a template is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/testTemplate.m). -- A guide for reporting an **issue** or submitting a **pull request (PR)** is [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/ISSUEGUIDE.md). +- Please follow the [Style Guide](https://opencobra.github.io/cobratoolbox/docs/styleGuide.html). +- More information on writing a **test** is [here](https://opencobra.github.io/cobratoolbox/docs/testGuide.html) and a template is [here](https://opencobra.github.io/cobratoolbox/docs/testTemplate.html). +- A guide for reporting an **issue** or submitting a **pull request (PR)** is [here](https://opencobra.github.io/cobratoolbox/docs/issueGuide.html). If you want to use `git` via the command line interface and need help, these [training slides](https://uni-lu.github.io/slides/) will get you started. This [guide](https://www.digitalocean.com/community/tutorials/how-to-create-a-pull-request-on-github) or the official [GitHub guide](https://help.github.com/articles/creating-a-pull-request/) also come in handy. How to cite `The COBRA Toolbox` ---------------- +------------------------------- When citing `The COBRA Toolbox`, it is important to cite the original paper where an algorithm was first reported, as well as its implementation in `The COBRA Toolbox`. This is important, because the objective of `The COBRA Toolbox` is to amalgamate and integrate the functionality of a wide range of COBRA algorithms and this will be undermined if contributors of new algorithms do not get their fair share of citations. The following is one example how to approach this within the methods section of a paper (**not** the supplemental material please): @@ -110,7 +110,7 @@ For convenience, we provide the [`SBMLToolbox 4.1.0`](http://sbml.org/Software/S [Binaries](https://github.com/opencobra/COBRA.binary) for these libraries are provided in a submodule for Mac OS X 10.6 or later (64-bit), GNU/Linux Ubuntu 10.0 (64-bit), and Microsoft Windows 7 (64-bit). For unsupported OS, please refer to their respective building instructions ([`glpk_mex`](https://github.com/blegat/glpkmex#instructions-for-compiling-from-source), [`libSBML`](http://sbml.org/Software/libSBML/5.13.0/docs//cpp-api/libsbml-installation.html)). -Read more on the compatibility with SBML-FBCv2 [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/NOTES.md). +Read more on the compatibility with SBML-FBCv2 [here](https://opencobra.github.io/cobratoolbox/docs/notes.html). Disclaimer ---------- diff --git a/docs/source/_templates/README.html b/docs/source/_templates/README.html index 57df9fef6d..29a4a52815 100644 --- a/docs/source/_templates/README.html +++ b/docs/source/_templates/README.html @@ -2,7 +2,7 @@

Documentation
COnstraint-Based Reconstruction
and A

- View The COBRA Toolbox source code on . + View The COBRA Toolbox source code on .


diff --git a/docs/source/conf.py b/docs/source/conf.py index 342b7573cd..53b367aca8 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -188,7 +188,7 @@ def linkcode_resolve(domain, info): # The name of an image file (relative to this directory) to place at the top # of the sidebar. # -html_logo = '_static/logo.png' +html_logo = '_static/images/logos/logo.png' # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 4c2ba8c15e..77e9ba0c33 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -9,9 +9,9 @@ How to contribute

bulb Check out the MATLAB.devTools - and contribute the smart way!

If you want to use git via the command line interface and need help, these training slides will get you started. This guide or the official GitHub guide also come in handy.

How to cite The COBRA Toolbox

@@ -23,4 +23,3 @@ How to contribute

[2] = Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. 2011 Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0. Nature Protocols 6:1290-1307.

- diff --git a/docs/source/faq.rst b/docs/source/faq.rst index 273ab18ac0..5a25d1444d 100644 --- a/docs/source/faq.rst +++ b/docs/source/faq.rst @@ -1,7 +1,6 @@ Support ======= -Answers to Frequently Asked Questions (**FAQ**) are `here `_. +Answers to Frequently Asked Questions (**FAQ**) are `here `_. If you need support, please feel free to post your question in our `forum `_. - diff --git a/docs/source/funding.rst b/docs/source/funding.rst index 2e8eb1e082..e1d61deca9 100644 --- a/docs/source/funding.rst +++ b/docs/source/funding.rst @@ -29,11 +29,4 @@ Funding
-
-
-
-

Principal investigators -

- Ronan Fleming ― Ines Thiele ― Thomas Sauter

- diff --git a/docs/source/guides/testGuide.md b/docs/source/guides/testGuide.md index 11504ad96d..7f58bc14c0 100644 --- a/docs/source/guides/testGuide.md +++ b/docs/source/guides/testGuide.md @@ -1,6 +1,6 @@ # Guide for writing a test -Before starting to write a test on your own, it might be instructive to follow common test practices in `/test/verifiedTests`. A style guide on how to write tests is given [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/STYLEGUIDE.md). +Before starting to write a test on your own, it might be instructive to follow common test practices in `/test/verifiedTests`. A style guide on how to write tests is given [here](https://opencobra.github.io/cobratoolbox/docs/styleGuide.html). ## Test if an output is correct @@ -55,7 +55,7 @@ Note that this allows the error message to be thrown without failing the test. ## Test template -A test template is readily available [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/testTemplate.m). The following sections shall be included in a test file: +A test template is readily available [here](https://opencobra.github.io/cobratoolbox/docs/testTemplate.html). The following sections shall be included in a test file: #### 1. Header ````Matlab diff --git a/docs/source/installation.rst b/docs/source/installation.rst index f015e9d432..e7e6049f87 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -6,12 +6,12 @@ Installation
System Requirements: - Please follow this guide in order to configure your system properly. + Please follow this guide in order to configure your system properly.
- +
Solver Installation: - The default solver is glpk (for LP and MILP). You can install TOMLAB, IBM ILOG CPLEX, GUROBI, or MOSEK by following these detailed instructions. + The default solver is glpk (for LP and MILP). You can install TOMLAB, IBM ILOG CPLEX, GUROBI, or MOSEK by following these detailed instructions.
  1. @@ -38,4 +38,4 @@ Binaries and Compatibility

    For convenience, we provide the SBMLToolbox 4.1.0, and glpk_mex in external/toolboxes, libSBML-5.13.0-matlab in src/io/utilities.

    Binaries for these libraries are provided in a submodule for Mac OS X 10.6 or later (64-bit), GNU/Linux Ubuntu 10.0 (64-bit), and Microsoft Windows 7 (64-bit).
    For unsupported OS, please refer to their respective building instructions (glpk_mex, libSBML).

    -

    Read more on the compatibility with SBML-FBCv2 here.

    +

    Read more on the compatibility with SBML-FBCv2 here.

    diff --git a/docs/source/installation/requirements.md b/docs/source/installation/requirements.md index 25d3ea6683..c4459a5076 100644 --- a/docs/source/installation/requirements.md +++ b/docs/source/installation/requirements.md @@ -39,5 +39,5 @@ In order to install `git`, install the [Xcode Command Line Tools](http://osxdail Please download the `git` tools for Windows from [here](https://git-scm.com/download). During the installation process, please ensure that you select **Use Git from the Windows Command Prompt**. In addition, please make sure that you select **Checkout as-is, commit Unix-style line endings**.
    -   . +   .
    diff --git a/docs/source/modules/multiSpeciesModelling.rst b/docs/source/modules/multiSpeciesModelling.rst deleted file mode 100644 index c22c848d66..0000000000 --- a/docs/source/modules/multiSpeciesModelling.rst +++ /dev/null @@ -1,10 +0,0 @@ - -.. _multiSpeciesModelling: - - -MultiSpeciesModelling ---------------------- - -.. automodule:: src.modelAnalysis.multiSpecies - :members: - diff --git a/docs/source/notes/FAQ.md b/docs/source/notes/FAQ.md index b173703d7e..17346f14e7 100644 --- a/docs/source/notes/FAQ.md +++ b/docs/source/notes/FAQ.md @@ -5,7 +5,7 @@ Frequently Asked Questions (FAQ) **What do all these labels mean?** -A comprehensive list of labels and their description for the issues and pull requests is given [here](https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/LABELS.md). +A comprehensive list of labels and their description for the issues and pull requests is given [here](https://opencobra.github.io/cobratoolbox/docs/labels.html). ## Reconstruction @@ -32,9 +32,9 @@ git rm --cached external/lusolMex64bit When running cobra code in a parfor loop, solvers (and other global variables) are not properly set. -**Answer**: This is an issue with global variables and the matlab parallel computing toolbox. +**Answer**: This is an issue with global variables and the matlab parallel computing toolbox. Global variables are not passed on to the workers of a parallel pool. -To change cobra global settings for a parfor loop, it is necessary to +To change cobra global settings for a parfor loop, it is necessary to reinitialize the global variables on each worker. The easiest way to do this is as follows: ```Matlab global CBT_SOLVER_LP @@ -45,5 +45,5 @@ parfor 1:2 optimizeCbModel(model); end ``` -By requesting the current global variable before the parfor loop and assigning it to a local variable, that variable is passed on to the workers, -which can then use it to set up the correct solver (or other variable). \ No newline at end of file +By requesting the current global variable before the parfor loop and assigning it to a local variable, that variable is passed on to the workers, +which can then use it to set up the correct solver (or other variable). diff --git a/initCobraToolbox.m b/initCobraToolbox.m index 9597843188..8a533782f4 100644 --- a/initCobraToolbox.m +++ b/initCobraToolbox.m @@ -530,7 +530,7 @@ function checkGit() end else fprintf(result_gitVersion); - fprintf([' > Please follow the guidelines on how to install git ', hyperlink('https://github.com/opencobra/cobratoolbox/blob/master/.github/REQUIREMENTS.md.', 'here', 'here: '), '.\n']); + fprintf([' > Please follow the guidelines on how to install git ', hyperlink('https://opencobra.github.io/cobratoolbox/docs/requirements.html.', 'here', 'here: '), '.\n']); error(' > git is not installed.'); end end @@ -565,7 +565,7 @@ function checkGit() else if throwError fprintf(result_curl); - fprintf([' > Please follow the guidelines on how to install curl ', hyperlink('https://github.com/opencobra/cobratoolbox/blob/master/.github/REQUIREMENTS.md.', 'here', 'here: '), '.\n']); + fprintf([' > Please follow the guidelines on how to install curl ', hyperlink('https://opencobra.github.io/cobratoolbox/docs/requirements.html.', 'here', 'here: '), '.\n']); error(' > curl is not installed.'); else if ENV_VARS.printLevel diff --git a/src/base/solvers/changeCobraSolver.m b/src/base/solvers/changeCobraSolver.m index e4a56051ec..1e5992cfbd 100644 --- a/src/base/solvers/changeCobraSolver.m +++ b/src/base/solvers/changeCobraSolver.m @@ -159,7 +159,7 @@ end return end - + if isempty(SOLVERS) || isempty(OPT_PROB_TYPES) ENV_VARS.printLevel = false; @@ -207,7 +207,7 @@ tmpVar = 'MOSEK_PATH'; end if printLevel > 0 && (strcmpi(solverName, 'gurobi') || strcmpi(solverName, 'ibm_cplex') || strcmpi(solverName, 'tomlab_cplex') || strcmpi(solverName, 'cplex_direct') || strcmpi(solverName, 'mosek')) - error(['The global variable `', tmpVar, '` is not set. Please follow ', hyperlink('https://git.io/v92Vi', 'these instructions', 'the instructions on '), ' to set the environment variables properly.']); + error(['The global variable `', tmpVar, '` is not set. Please follow ', hyperlink('https://opencobra.github.io/cobratoolbox/docs/solvers.html', 'these instructions', 'the instructions on '), ' to set the environment variables properly.']); end end end @@ -441,6 +441,6 @@ if exist(fileName, 'file') >= 2 solverOK = true; elseif printLevel > 0 - error(['Solver ', solverName, ' is not installed. Please follow ', hyperlink('https://git.io/v92Vi', 'these instructions', 'the instructions on '), ' in order to install the solver properly.']) + error(['Solver ', solverName, ' is not installed. Please follow ', hyperlink('https://opencobra.github.io/cobratoolbox/docs/solvers.html', 'these instructions', 'the instructions on '), ' in order to install the solver properly.']) end end diff --git a/src/base/solvers/configEnvVars.m b/src/base/solvers/configEnvVars.m index a654d7549b..be593cd6f7 100644 --- a/src/base/solvers/configEnvVars.m +++ b/src/base/solvers/configEnvVars.m @@ -143,7 +143,7 @@ function configEnvVars(printLevel) % if the solver variable is still empty, then give instructions on how to proceed if isempty(eval(solverPaths{k, 1})) if printLevel > 0 - solversLink = 'https://git.io/v92Vi'; % curl -i https://git.io -F "url=https://github.com/opencobra/cobratoolbox/blob/master/.github/SOLVERS.md" + solversLink = 'https://opencobra.github.io/cobratoolbox/docs/solvers.html'; if usejava('desktop') solversLink = ['instructions']; end