[Biopython] [PATCH] Use https:// instead of git:// in examples

[Peter Cock]

Hi Adam,

A pull request via GitHub would be easiest for us, but if you have
philosophical issues with their new ownership, I can understand that.

As to the issue at hand, I've had problems both ways round depending
on the network, but still lean to the git protocol by default.

What are other people's thoughts?

Thanks,

Peter

On Thu, Oct 3, 2019 at 2:17 PM Adam Sjøgren <asjo at koldfront.dk> wrote:
>
> A number of places - companies - have firewalled outgoing access to
> the git:// protocol, while https:// is open, so to make it easier to
> get started, it makes sense to use the https:// variant.
> ---
>
>   Hi,
>
> Here is a suggested patch for biopython.github.io - I wasn't sure where
> to submit it (I don't want to create a Microsoft Github account).
>
> It should be possible to apply the patch by saving the email and running
> "git am saved_email.txt".
>
>   Best regards,
>
>     Adam
>
>  wiki/Building_a_release.md |  2 +-
>  wiki/GitUsage.md           | 16 ++++++++--------
>  wiki/SourceCode.md         |  2 +-
>  3 files changed, 10 insertions(+), 10 deletions(-)
>
> diff --git a/wiki/Building_a_release.md b/wiki/Building_a_release.md
> index d59cadc..8d1c724 100644
> --- a/wiki/Building_a_release.md
> +++ b/wiki/Building_a_release.md
> @@ -105,7 +105,7 @@ Making and testing the tar-ball
>  10. check out clean version somewhere else:
>
>      ``` bash
> -    drevil:~tmp1/> git clone git://github.com/biopython/biopython.git
> +    drevil:~tmp1/> git clone https://github.com/biopython/biopython.git
>      drevil:~tmp1/> cd biopython
>      ```
>
> diff --git a/wiki/GitUsage.md b/wiki/GitUsage.md
> index 77befd9..ceaeada 100644
> --- a/wiki/GitUsage.md
> +++ b/wiki/GitUsage.md
> @@ -157,7 +157,7 @@ Getting a copy of the repository (called "cloning" in Git terminology)
>  without GitHub account is very simple:
>
>  ``` bash
> -git clone git://github.com/biopython/biopython.git
> +git clone https://github.com/biopython/biopython.git
>  ```
>
>  This command creates a local copy of the entire Biopython repository on
> @@ -209,7 +209,7 @@ You may want to also link your branch with the official distribution
>  (see below on how to keep your copy in sync):
>
>  ``` bash
> -git remote add upstream git://github.com/biopython/biopython.git
> +git remote add upstream https://github.com/biopython/biopython.git
>  ```
>
>  To add additional contributors to your repository on GitHub (i.e. people
> @@ -347,7 +347,7 @@ official Biopython branch) to your repository.
>  Assuming you have issued this command (you only need to do this once):
>
>  ``` bash
> -git remote add upstream git://github.com/biopython/biopython.git
> +git remote add upstream https://github.com/biopython/biopython.git
>  ```
>
>  Then all you need to do is:
> @@ -430,13 +430,13 @@ core developers, or anyone accepting changes on a branch.
>  For example, suppose Eric has some interesting changes on his public
>  repository:
>
> -git://github.com/etal/biopython.git
> +https://github.com/etal/biopython.git
>
>  You must tell git about this by creating a reference to this remote
>  repository:
>
>  ``` bash
> -git remote add eric git://github.com/etal/biopython.git
> +git remote add eric https://github.com/etal/biopython.git
>  ```
>
>  Now we can fetch *all* of Eric's public repository with one line:
> @@ -448,7 +448,7 @@ remote: Compressing objects: 100% (105/105), done.
>  remote: Total 105 (delta 77), reused 0 (delta 0)
>  Receiving objects: 100% (105/105), 27.53 KiB, done.
>  Resolving deltas: 100% (77/77), completed with 24 local objects.
> -From git://github.com/etal/biopython
> +From https://github.com/etal/biopython
>   * [new branch]      bug2754    -> eric/bug2754
>   * [new branch]      master     -> eric/master
>   * [new branch]      pdbtidy    -> eric/pdbtidy
> @@ -632,12 +632,12 @@ giving you a URL. Typically this will be on GitHub (but it may be any
>  public git url). Let us assume that the url is (which happens to be my
>  clone of Biopython):
>
> -git://github.com/barwil/biopython.git
> +https://github.com/barwil/biopython.git
>
>  First, you need to get the code from this repository:
>
>  ``` bash
> -git remote add Bartek git://github.com/barwil/biopython.git
> +git remote add Bartek https://github.com/barwil/biopython.git
>  git fetch Bartek
>  ```
>
> diff --git a/wiki/SourceCode.md b/wiki/SourceCode.md
> index 8607977..306df9c 100644
> --- a/wiki/SourceCode.md
> +++ b/wiki/SourceCode.md
> @@ -56,7 +56,7 @@ is very simple using the git command line tool, you don't need an
>  account or password:
>
>  ``` bash
> -git clone git://github.com/biopython/biopython.git
> +git clone https://github.com/biopython/biopython.git
>  ```
>
>  This command creates a local copy of the entire Biopython repository on
> --
> 2.7.4
>
> --
>  "We're not unreasonable, I mean, noone's going to eat        Adam Sjøgren
>   your eyes"                                             asjo at koldfront.dk
>
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