Regarding License

[Rauf Salamzade]

Hello,

On the PAML website it states the following:

"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang."

However, I cannot find any information about whether it would be ok for me to use it for commercial research. Note, I am NOT planning on incorporating the program in a package or something which I will then sell, but simply want to use it to perform some research at the private company I work for. I look forward to a response. Thank you for your time.

Best regards,

Rauf

[Andreas Tille]

Hi,

I would like the authors to reconsider the license in general as I just wrote in my posting on the Debian Med mailing list to enable a free distribution of PAML inside Debian.

Kind regards

         Andreas.

[Ziheng]

I think if you are just using it, it should be fine.

i'll need to talk to someone about the license in general.

ziheng

[Andreas Tille]

Hi,

Am Freitag, 19. Februar 2016 15:39:39 UTC+1 schrieb Ziheng:

I think if you are just using it, it should be fine.

As I tried to explain in the linkes posting: "using" is not a defined term.  The usage should not be restricted for any purpose of use nor any group of users.  It also needs to contain a permission to change and distribute the code.
 

i'll need to talk to someone about the license in general.

This would be *really* welcome.  It would be also great if you (or the persons you need to ask) could answer my question on the Debian Med mailing list.
 

ziheng

Thanks for considering

          Andreas.

[Rauf Salamzade]

Hi Ziheng,

Thank you for the reply. Yes, please let me know of any updates regarding the use of the software for internal research.

Much appreciated,
Rauf

[Andreas Tille]

Hi,
did you succeeded in talking to some responsible person?
Kind regards
    Andreas.

[Ziheng]

I intend to copy the GPL narrative into the paml code, but have not got time to do so.
There seem to be endless emergencies to deal with.
If you are trying to do something with paml, you can assume the GPL for paml.
ziheng

[Andreas Tille]

Hi,

thanks for the very good news about GPL license.  I updated the Debian packaging to the latest version and uploaded it to the Debian New queue where it needs to pass another check by the Debian ftpmasters after the licensing change.  While I have linked to the statement in your thread meanwhile it could helpful if you state the GPL license at thePAML homepage.  There is no real need to touch every single file (even if this is the better long term solution) but an explicite statement replacing the

"distributed for academic use free of charge"

which remains at the text on the homepage would be probably very helpful to convince ftpmasters of the license change.  They might refuse otherwise due to the conflict between website and your statement here.

As a remark for future versions:  I needed to add some patches to your source code which you can find in our packaging Git repository.  Feel free to take these over into your next release.

Kind regards and thanks a lot for your cooperation

      Andreas.


   

[Andreas Tille]

Hi again,

unfortunately (but not surprisingly) our ftpmaster rejected my upload of PAML to Debian main:
     https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-May/042129.html
I wonder if you could at least adapt the web page to reflect the license change - there is no urgent need to adapt the code as well.

Kind regards and thanks for your cooperation

          Andreas.

[Andreas Tille]

Hi,

as I said it would be super helpful if you would adapt the PAML web page to reflect what you said here in this thread and replace the "distributed for academic use free of charge" string by "distributed under the GNU General Public License version 3, or at your opinion any later version" or something like this (whatever version of the GPL you might prefer or whether you want to allow automatic license upgrades or not.  Without this explicit statement on the web page the Debian ftpmaster will not allow to distribute PAML as official Debian package.

Thanks a lot for your cooperation

         Andreas.

[Andreas Tille]

Hi,

sorry for getting on your nerves but it would be super helpful if you could do the one line change on your website to update the licensing information to GPL (with version - preferably 2 or 3) what you said here in this thread.  The issue is so important to me since other packages in Debian depend from PAML or are using PAML code and we could free these as well.

[Ziheng]

I'm sorry for being hopelessly slow.
I'll try to get this done.
Ziheng.

[Andreas Tille]

Hi again,

I'm sorry if I might get on your nerves but the issue becomes urgent now.  If you will not manage to change this very tiny bit on your homepage we will not manage to include paml in the next stable Debian release.  As I wrote previously I'd volunteer to sent a patch for the HTML text - if you would only confirm that this is static html and not some generated page.  Please, pretty please take those few minutes to change the text from

     distributed for academic use free of charge

to

     distributed under GPL version <put your choice here>

and you are done.

Thanks a lot for considering

        Andreas

[Andreas Tille]

dear andreas,

I edited the web site.  is it good enough.

I think I should also edit the documentation pamlDOC.pdf to be consistent. 

what about the following, or should I delete "© Copyright 1993-2015 by HZiheng Yang"?

best,

ziheng

© Copyright 1993-2015 by HZiheng Yang

The software package is provided "as is" without warranty of any kind. In no event shall the author or his employer be held responsible for any damage resulting from the use of this software, including but not limited to the frustration that you may experience in using the package.  The program package, including source codes, example data sets, executables, and this documentation, is maintained by Ziheng Yang and distributed under the GNU GPL v3.

 

Dear Ziheng,

the copyright statement is fine since the copyright is definitely yours.  The GPL license gives permission to the users and enables Debian to distribute it freely.

Thanks a lot

         Andreas.

[Andreas Tille]

dear andreas,I edited the web site.  is it good enough.

Unfortunately just editing only the web page did not yet convinced the Debian ftpmaster.  Could you please also change the README.txt in the same manner as the web page and release a new tarball?
Thanks a lot
        Andreas.

[Ziheng]

just posted 4.9c, with the license statement copied in a few places. 

hope this is good enough.

best,

ziheng

[Andreas Tille]

Hi Ziheng,

thanks for your effort to assemble a new version with the GPL license.  I noticed the change in src/README.txt.  Unfortunately the "academic use only" string remains in the most prominent file README.txt which was the reason for the rejection of Debian ftpmaster.  Would you mid changing also this file?

BTW., your tarball contains some files with wrong permissions.  It would be helpful also for other users if you would do
 

chmod 600 examples/lysozyme/codeml.ctl
chmod 600 examples/lysozyme/lysozymeSmall.trees
chmod 600 src/README.txt

[Ziheng]

is it possible that your version is still the old one.  I looked at the version I posted and it seems fine.

I am having some issues with windows file permissions.  I transferred the files onto a Linux box, chmod the files and then created the tar ball.  I hope this has fixed the problem with file permissions.

thanks,

ziheng

[Andreas Tille]

Hi,

I just downloaded
   http://abacus.gene.ucl.ac.uk/software/paml4.9c.tgz
untared it and found

$ grep academic paml4.9c/README.txt
PAML is distributed free of charge for academic use only.

while in the src dir it is

$ grep GPL paml4.9c/src/README.txt

Yang and distributed under the GNU GPL v3.

Debian ftpmaster wants you to change all mentions of the "academic use only" clause.

The file permissions are a minor issue which I can deal with - that was only a hint.

Thanks for your cooperation, Andreas.

[Andreas Tille]

Hi Ziheng,

I have understood your time to deal with this issue is limited but I hope you were able to verify that the main README.txt file remains with the old license.  If you are interested in having PAML distributed in the next Debian release  there is probably only one week left to meet this.  It would be really great if you could fix this README.txt file since I expect more users and thus more response about the code for you if it would be distributed with official Debian.

Kind regards

      Andreas.

[Andreas Tille]

Hi again,

time is running really fast and the window to distribute paml inside Debian is about to close very soon.  If I might help saving your time by some script that would be sufficient to do to create the next release.  Please consider running it and publish the resulting tarball on your web site.  Its simply replacing the old licensing text in README.txt by the phrase you are using in src/README.txt:


#!/bin/sh -e
wget http://abacus.gene.ucl.ac.uk/software/paml4.9c.tgz
tar xaf paml4.9c.tgz
sed -i~ 's/PAML is distributed free of charge for academic use only./The software package is provided "as is" without warranty of any \

kind. In no event shall the author or his employer be held responsible \
for any damage resulting from the use of this software, including but \
not limited to the frustration that you may experience in using the \
package.  The program package, including source codes, example data \

sets, executables, and this documentation, is maintained by Ziheng \
Yang and distributed under the GNU GPL v3./' paml4.9c/README.txt
diff -u paml4.9c/README.txt~ paml4.9c/README.txt || true
rm paml4.9c/README.txt~
mv paml4.9c paml4.9d
GZIP=-9 tar --owner=root --group=root --mode=a+rX -czf paml4.9d.tgz paml4.9d
rm -rf paml4.9d



Thanks for considering

       Andreas.

[Andreas Tille]

Hi,
yesterday was the first aniversary for my joining of this thread.  I was hoping that my little script would have saved you some time to fix the remaining issue.  While I assumed that it was to late for paml making it into the next Debian stable release I see some very small chance that it might be possible if you run the script I've posted in my last message and publish the tarball.
I'd be really happy about your cooperation, Andreas.

[Carnë Draug]

I just happened to email Professor Yang yesterday, offering my help to solve this issue.
Here's the email I sent:

```
I want to use PAML on my own software but PAML's unclear licensing
state prevents it.  Some of the files on the last release mention
GPL but other files say "academic use only" while the actual source
files says nothing.

It is my understanding that you do want to make it available under
GPL.  I am offering my help to fix this issue which is also
preventing the inclusion of PAML in Linux distributions and
indirectly makes my own software more difficult to install too.

Ideally, I would send you a patch for some repository but I couldn't
find any.  I can send you patch against a specific release too,
whatever you prefer.  Please let me know.
```

[Sascha Steinbiss]

Hi,

I would just like to state that I would also very much like to see PAML in Debian. Hence I am also kindly asking to make the necessary remaining adjustments to the code. Given the popularity of PAML it would help a lot!

Many thanks

Sascha

[Andreas Tille]

Hi again,
I wonder if this script might have been of any use?  My point was to save your time since the intention of your recent change was clear it was just incomplete.  It would be really helpful if this issue could be settled.
Thanks a lot, Andreas.