Fwd: Nanoengineer

[Lee Nelson]

Bryan, Tom, Thomas


Great Bryan. does this mean that you are the official NE-1 maintainer now - or is this a fork? I did not realize that you were active with NE-1.

Tom was the first person I saw use NE-1.
http://machine-phase.blogspot.com/
Thomas was packaging NE-1 for fedora.
http://web.archiveorange.com/archive/v/OxMZLboVlcHlFDIaa4yo

---------- Forwarded message ----------
From: Bryan Bishop <kan...@gmail.com>
Date: Wed, Nov 24, 2010 at 6:13 PM
Subject: Nanoengineer
To: Lee Nelson <technol...@gmail.com>, Bryan Bishop <kan...@gmail.com>


Hey Lee,

I have been able to acquire the development repository for ne-1.

http://diyhpl.us/cgit/nanoengineer
git clone git://diyhpl.us/nanoengineer

I'll be maintaining the project from now on. My next step is to
acquire and deploy the original bugzilla database that Nanorex was
using. You should subscribe to the -dev mailing list:

http://groups.google.com/group/nanoengineer-dev

- Bryan
http://heybryan.org/
1 512 203 0507

[Bryan Bishop]

On Wed, Nov 24, 2010 at 6:27 PM, Lee Nelson wrote:
> Great Bryan. does this mean that you are the official NE-1 maintainer now -

Right. Nanorex has closed their doors. I pinged Mark and asked if I
could help make this happen, so he's letting me run with this.

> or is this a fork? I did not realize that you were active with NE-1.

Heh. Lee, how did you think I spontaneously solved your ne-1 python
problems last year? On the spot, without a reference- over at your
house? Actually I was just winging that.. but yeah, that's how you and
I met I think.

Tom & Thomas:

http://diyhpl.us/cgit/nanoengineer
git clone git://diyhpl.us/nanoengineer

[Lee Nelson]

Is there a place on the wiki for this roadmap? Will we use the old wiki?

I advocate using a short (2-4 week) sprint cycle - like they used to. They always seemed to make a lot of progress between sprints.

They used Wind IDE for development.
http://www.nanoengineer-1.net/mediawiki/index.php?search=IDE&go=Go

Since Netbeans has a python plugin, I think netbeans should be used (it is free)
http://www.google.com/search?q=netbeans


A linux installer/ package is needed to make NE1 accessible to the linux crowd.
There is a new version of BitRock Install builder available.
http://bitrock.com/

I see there was some change to the build requirements notes regarding QT, PyQt and Sip. This is really the only part that prevents a linux install. I see the build for Mac but not linux on this Page
http://nanoengineer-1.net/mediawiki/index.php?title=PreReq_Builds

There was a DNA origami Feature. That should be returned.

The movie feature should make AVIs, preferably without needing POV-Ray and Picture2AVI as separate programs

On Wed, Nov 24, 2010 at 6:54 PM, Tom <moor...@gmail.com> wrote:

Hi Guys,

It's good to see some interest in NE1 again. Do you have any sort of road map for development yet?

Best,

Tom

[Mark Sims]

On Wed, Nov 24, 2010 at 8:55 PM, Lee Nelson <technol...@gmail.com> wrote:
> Is there a place on the wiki for this roadmap? Will we use the old wiki?
>
> I advocate using a short (2-4 week) sprint cycle - like they used to. They
> always seemed to make a lot of progress between sprints.

I'd like to suggest creating a new sprint backlog for this group
(which everyone can comment on) and not put a time limit on it. It
will take everyone a while to set up a development environment, get
oriented with the code and start productive coding work.

Here is a quick, short list of the things I believe should be
considered for the 1st sprint:

1. Wiki pages for setting up a NE1 developer's environment for
Windows, MacOSX and Linux. Currently we have these wiki page, but they
need to be updated:

http://nanoengineer-1.net/mediawiki/index.php?title=NE1_Build_and_Release_System_Overview

2. Epydoc install/config on the server to (re)generate NE1 API docs like these:

http://www.nanoengineer-1.com/snapshots/NE1_Documentation/

3. Updated wiki pages for creating NE1 install packages for Windows,
MacOSX and Linux.

4. Set up Bugzilla for NE1 on server (I'm working on this with Bryan
-- stay tuned).

5. Update (and clean up) the NE1 Wiki with new info (i.e. where to get
the code, setting up a NE1 dev environment, etc.) . I've started this,
but more to be done.

These 5 projects would be a good start for the first sprint.

>
> They used Wind IDE for development.
> http://www.nanoengineer-1.net/mediawiki/index.php?search=IDE&go=Go

We used Wing IDE (www.wingware.com). The Personal Edition is $35 and
worth it. I use the Professional Edition and love it.

>
> Since Netbeans has a python plugin, I think netbeans should be used (it is
> free)
> http://www.google.com/search?q=netbeans

I'll take a look at NetBeans. Can you create a "Getting Started with
NetBeans IDE" wiki page explaining what module(s)/plugin(s) to
download and any relevant configuration info.

>
>
> A linux installer/ package is needed to make NE1 accessible to the linux
> crowd.
> There is a new version of BitRock Install builder available.
> http://bitrock.com/

Agreed.

>
> I see there was some change to the build requirements notes regarding QT,
> PyQt and Sip. This is really the only part that prevents a linux install. I
> see the build for Mac but not linux on this Page
> http://nanoengineer-1.net/mediawiki/index.php?title=PreReq_Builds

Maybe Thomas could add something about building NE1 for Fedora on that page?

>
> There was a DNA origami Feature. That should be returned.

The DNA Origami feature was superseded by "Build DNA" and all
sub-commands. Tom Moore actually designed a new origami structure
using NE1 that was eventually synthesized by Paul Rothemund. It was
painful for Tom since NE1 is so slow with large models. It is
imperative to get the graphics optimization in NE1 working (more on
that later).

>
> The movie feature should make AVIs, preferably without needing POV-Ray and
> Picture2AVI as separate programs

This is a feature request. Add it here:

http://www.nanoengineer-1.net/mediawiki/index.php?title=Feature_requests#Other_renderers

>
>
>
>
> On Wed, Nov 24, 2010 at 6:54 PM, Tom <moor...@gmail.com> wrote:
>>
>> Hi Guys,
>>
>> It's good to see some interest in NE1 again. Do you have any sort of road
>> map for development yet?
>>
>> Best,
>>
>> Tom
>
>

--
-----------------
Mark Sims
248-227-6681(cell)

[Lee Nelson]

I will do the following: (and I will try Wing)

> create a "Getting Started with
> NetBeans IDE" wiki page explaining what module(s)/plugin(s) to
> download and any relevant configuration info.

How do I create a New Page?

My suggestion is essentially the same as this one from the list:
http://www.nanoengineer-1.net/mediawiki/index.php?title=Making_simulation_videos_and_DVDs

[Mark Sims]

On Thu, Nov 25, 2010 at 1:33 PM, Lee Nelson <technol...@gmail.com> wrote:
> I will do the following: (and I will try Wing)
>
>> create a "Getting Started with
>> NetBeans IDE" wiki page explaining what module(s)/plugin(s) to
>> download and any relevant configuration info.
>
> How do I create a New Page?

First, go to http://www.nanoengineer-1.net and click "Create an
account or log in" link in the upper left corner. Click the "Create
New Account" button and create an account for yourself.

Then go to:

http://www.nanoengineer-1.net/mediawiki/index.php?title=Development_tools_for_Python

and click the Edit tab/button and add these 2 lines *after* the Wing
IDE section:

==== [http://netbeans.org/ NetBeans] ====
* [[NetBeans for NE1 Python development]]

After you save the page, you'll notice that the "NetBeans for NE1
Python development" link is red, indicating it is a new (empty) page.
Click on it and it will take you to an empty page where you can begin
editing the page.

NOTE: There is an MYSQL error when you click save every time. Just
click on the "Article" tab after you save and you'll notice that edits
were indeed saved. I'm looking into this problem and will let you know
when I have it fixed.

>
> My suggestion is essentially the same as this one from the list:
> http://www.nanoengineer-1.net/mediawiki/index.php?title=Making_simulation_videos_and_DVDs
>
>>> The movie feature should make AVIs, preferably without needing POV-Ray
>>> and
>>> Picture2AVI as separate programs
>>
>> This is a feature request. Add it here:
>>
>>
>> http://www.nanoengineer-1.net/mediawiki/index.php?title=Feature_requests#Other_renderers
>>
>>
>

--
-----------------
Mark Sims
248-227-6681(cell)

[Lee Nelson]

> How do I create a New Page?

I do NOT see the "Edit Tab" while the article is open
I do see the "Edit Tab" when I click the "Discussion Tab"
 

http://www.nanoengineer-1.net/mediawiki/index.php?title=Development_tools_for_Python

and click the Edit tab/button and add these 2 lines *after* the Wing
IDE section:

For clarity, i would like to add it under Free IDEs
Maybe making it item 1.2.9 would be appropriate
 

[Mark Sims]

On Thu, Nov 25, 2010 at 2:21 PM, Lee Nelson <technol...@gmail.com> wrote:
>
>> > How do I create a New Page?
>>
>
> I do NOT see the "Edit Tab" while the article is open
> I do see the "Edit Tab" when I click the "Discussion Tab"

Did you create an account and log in first?

You should also see "Edit" links for each section on the page to the
right of the section header. You can click on that, too, and append
the text at the end of the section and save. The new section
(NetBeans) should show up -- then you can click the Edit link to edit
just that section.

>
>>
>>
>> http://www.nanoengineer-1.net/mediawiki/index.php?title=Development_tools_for_Python
>>
>> and click the Edit tab/button and add these 2 lines *after* the Wing
>> IDE section:
>>
>
> For clarity, i would like to add it under Free IDEs
> Maybe making it item 1.2.9 would be appropriate

Sounds good.

>
>>
>> ==== [http://netbeans.org/ NetBeans] ====
>> * [[NetBeans for NE1 Python development]]
>>
>> After you save the page, you'll notice that the "NetBeans for NE1
>> Python development" link is red, indicating it is a new (empty) page.
>> Click on it and it will take you to an empty page where you can begin
>> editing the page.
>>
>

--
-----------------
Mark Sims
248-227-6681(cell)

[Mark Sims]

Lee,

I notice the page is currently protected -- it was probably spammed a
while ago. Hopefully, you can edit it if you log into your account
first. If not, let me know.

Mark

[Lee Nelson]

Thanks,
Yes I have had an account for some time.
I am logged in.
I can see my "Watch List".

Did you create an account and log in first?

I noticed there are no "Edit Links" for the sections.
Can anyone verify this?
http://www.nanoengineer-1.net/mediawiki/index.php?title=Development_tools_for_Python

I looked at a page from "Recent Changes" and a few others.
http://www.nanoengineer-1.net/mediawiki/index.php?title=NE1_Server_Build_Notes&rcid=50076
These other pages DO have the edit links.
Is it just something about the Wing Page?
 

You should also see "Edit" links for each section on the page to the
right of the section header. You can click on that, too, and append
the text at the end of the section and save. The new section
(NetBeans) should show up -- then you can click the Edit link to edit
just that section.

 
This Just in:

I logged out and back in - still no "Edit Tab"

[Tom]

The page is locked for editing.

Mark, unlock the page.

Best,

Tom

[Tom]

yeah, page is locked to prevent editing

[Mark Sims]

Lee,

The page is now unlocked. Sorry about that -- I thought logging in
would allow you to edit it.

I'm off to have Thanksgiving dinner, so I'll be offline until late this evening.

Happy Thanksgiving,
Mark

--
-----------------
Mark Sims
248-227-6681(cell)

[Lee Nelson]

Thanks. The Page now exists

http://www.nanoengineer-1.net/mediawiki/index.php?title=Development_tools_for_Python&action=edit&section=15

[Lee Nelson]

ok- I found:

NanoEngineer-1 v1.1.1/source/cad/src/experimental/domoapp_0.1/main.py

I do not think this is the right file.
Can anyone tell me where the main.py is in windows?

[Mark Sims]

Lee,

It is cad/src/main.py

Mark

--
-----------------
Mark Sims
248-227-6681(cell)

[Lee Nelson]

Thanks,
I found it at:

C:\Program Files\Nanorex\NanoEngineer-1 v1.1.1\source\cad\src\main.py

Lee,

It is cad/src/main.py

[Reza M. Zadegan]

Dear Mark,

I need to re-install nanoengineer v 1.1.12, but the website is down and i cant download it anymore. Please let me know if you have this version and if you can send it to me. Please use my email reza.m.zadegan @ uky.edu or contact me on 859 359 8726

Thanks in advance

Reza

[Bryan Bishop]

On Thu, Dec 5, 2013 at 10:05 AM, Reza M. Zadegan <reza.moham...@gmail.com> wrote:

Dear Mark,

I need to re-install nanoengineer v 1.1.12, but the website is down and i cant download it anymore. Please let me know if you have this version and if you can send it to me. Please use my email reza.m.zadegan @ uky.edu or contact me on 859 359 8726

Here you go:

http://diyhpl.us/~bryan/irc/nanoengineer/snapshots/

[Bryan Bishop]

On Thu, Dec 5, 2013 at 10:20 AM, Reza M. Zadegan <reza.m....@gmail.com> wrote:

Thanks, but version 1.1.12 that I m looking for is corrupted. I imagine its uploaded as it was faulty. Can you provide me another link?

What is the problem with the files I linked to?

[Reza M. Zadegan]

I can download load it but as trying to install it I get an error indicating the file is corrupted. I guess the original file should weight something about 30 mb and this one is 10 mb.

--
Reza M. Zadegan, PhD

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[Bryan Bishop]

On Thu, Dec 5, 2013 at 10:26 AM, Reza M. Zadegan <reza.m....@gmail.com> wrote:

I can download load it but as trying to install it I get an error indicating the file is corrupted. I guess the original file should weight something about 30 mb and this one is 10 mb.

 

Which exact file are you using? Also, show me the md5 sum of the file you have downloaded:

$ md5sum myfile.tar.gz