Subject: Re: Latest version of Ale?

From: Loredana Lo Conte <[email-masked]>
Date: Thu, 8 Aug 2002 07:53:03 +0100 (BST)

On 7 Aug 2002, Jim Blandy wrote:

> So, Loredana, can you check out a copy of this version and see if it
> makes the problems you observed go away?

I will. From messages following this one, I see Karl is still making
changes. Do me a favor. Tell me when you are happy with the current
version and I will try it.

>
> You'll need to install a client for the Subversion version control
> system.  http://subversion.tigris.org  If this is too much trouble for
> you, we can make a tar for you, but it would really be much nicer if
> you were working with the current sources.

I will install the Subversion client and use it. However, I'l need your
help if it does not work smoothly. We have a firewall, will this cause
problems?

Loredana

---

From: Karl Fogel <[email-masked]>
Date: 07 Aug 2002 22:49:37 -0500

> version and I will try it.

Don't worry about my changes -- they're just tweaks.  Try it right
now :-).

In general, we should be keeping the repository version stable.  Any
change checked in is ready to be tried.  So you should never worry
because you see activity, unless someone's log message explicitly says
"Wait, I'm still working here, don't use this revision" or something.

> help if it does not work smoothly. We have a firewall, will this cause

It may or may not cause a problem.  Do you have a proxy?  Subversion
can go through the proxy; we'll help you configure that if you need
to.

-Karl

---

From: Loredana Lo Conte <[email-masked]>
Date: Thu, 8 Aug 2002 09:03:41 +0100 (BST)

Ok, I will try it later on today. Need to talk to the system manager about
the firewall, I don't know myself how it is configured. If you want to
make sure that I'l try soon,  perhaps it is safer to make a tarball
available somewhere.

BTW, I am getting duplicated messages. Send to [email-masked], don't cc
to me.

Loredana

---

From: Jim Blandy <[email-masked]>
Date: 08 Aug 2002 09:29:42 -0500

> version and I will try it.

No, that is not The Way.  :)

As Karl says, we (and you) will make every effort to keep it working
after every commit, and you should be running the very bleeding edge.
This is the best way to get a decent testing cycle going.  If it does
happen that you don't like a change, it's very easy to backdate your
sources to the last time it worked.  But I'll point out that, at the
moment, the bleeding edge is better than what you've got.  :)

If we want to make some big change, we don't tear apart the main
sources and keep anyone else from contributing and testing their work
until we're done.  Everything has to be done incrementally.  People
can use branches for heavy experimentation, if they want.

---

From: Loredana Lo Conte <[email-masked]>
Date: Thu, 8 Aug 2002 18:06:30 +0100 (BST)

I don't run red had 7.x. I don't use rpm. I am an affectionate user of
debian gnu/linux and gnu software that can be installed with three
commands. Sorry :)

I understand that it would be kind of me to use Subversion, but I got lost
in your installation page. It seems to imply that I have to learn how to
use rpm, find the right packages and so on.

Here is what I got to start with:

% rpm -i apache-libapr-2.0.40-0.7.i386.rpm

error: failed dependencies:
        rpmlib(PayloadFilesHavePrefix) <= 4.0-1 is needed by
apache-libapr-2.0.40-0.7
        rpmlib(CompressedFileNames) <= 3.0.4-1 is needed by
apache-libapr-2.0.40-0.7
        libc.so.6(GLIBC_2.2)   is needed by apache-libapr-2.0.40-0.7

Can you make a tarball for once, just to start with? I would be happy to
test Ale.

Loredana

---

From: Jim Blandy <[email-masked]>
Date: 09 Aug 2002 12:16:16 -0500

> debian gnu/linux and gnu software that can be installed with three

Subversion can be installed with `configure; make; make install'.  You
don't have to use RPM.  Karl runs Debian, too.  We're not hosers.

Download:
http://subversion.tigris.org/files/documents/15/578/subversion-r2667.tar.gz
and do the usual thing.

You don't need Apache or Berkeley DB, since you're not going to build
a server.

---

From: Loredana Lo Conte <[email-masked]>
Date: Fri, 9 Aug 2002 19:36:56 +0100 (BST)

> No, that is not The Way.  :)

Ok, you know the Way. You show me the Way :)

---

From: Loredana Lo Conte <[email-masked]>
Date: Fri, 9 Aug 2002 20:01:38 +0100 (BST)

> don't have to use RPM.  Karl runs Debian, too.  We're not hosers.

Time for you to know about my origins: I am Italian. Don't know what
a "hoser" is. Hope it is not too bad :)

I went to:
http://subversion.tigris.org/servlets/ProjectDocumentList?folderID=87&maxDepth=true

and clicked on "i386", which looked the right place to go. There I got
lost in the red hat stuff. Perhaps it is of some use for you to know.
Someone else may be as stupid as me.

> http://subversion.tigris.org/files/documents/15/578/subversion-r2667.tar.gz

Done. I must go now, but will work on it during the weekend.

> You don't need Apache or Berkeley DB, since you're not going to build

Ok.

Loredana

---

From: Jim Blandy <[email-masked]>
Date: 09 Aug 2002 16:22:03 -0500

> don't have to use RPM.  Karl runs Debian, too.  We're not hosers.

Um, my text doesn't read quite the way I meant, so let me expand:

Karl and I both very much come from GNU and Debian territory, and we
both very much prefer programs that can be built with `configure; make
install'.  We both strongly agree with you that that's the way things
should be.  And we both want Subversion to be widely used outside of
Red Hat Linux and the other RPM-based distributions; we see RPM as a
convenience for the large body of Red Hat users out there, but not at
all a complete solution.

Someone who posts portable software as an RPM and considers the job
done is being a bit myopic --- thus the "we're not hosers" remark.

I think the Subversion web site is a bit confusing, so I'm not
surprised you went astray looking for a set of sources you could
download.

---

From: Jim Blandy <[email-masked]>
Date: 09 Aug 2002 16:29:40 -0500

> Ok, you know the Way. You show me the Way :)

Okay. :)

I'm hoping that you aren't the only person interested in using Ale,
and that Karl and I aren't the only people who could maintain it
(because we don't want the commitment).  If this is the case, then Ale
could be resuscitated, which would make both of us very happy.

So in this situation, The Way is for you to run our very latest Ale
sources, so that you can try out any fixes we make quickly, and send
us reports of bugs we haven't already fixed.

If the three of us can use Subversion to manage the sources, this will
be much easier.

---

From: Karl Fogel <[email-masked]>
Date: 10 Aug 2002 09:51:14 -0500

> make sure that I'l try soon,  perhaps it is safer to make a tarball

We should set up a tarball distribution area eventually, but you'll
need to have a working copy anyway, so you can easily update to the
latest sources, to try things out and fix bugs.

As Subversion 0.14.1 has just been released, this would be a good time
to set yourself up.  It's very easy:

First, grab:

  http://subversion.tigris.org/files/documents/15/690/subversion-r2927.tar.gz

Unpack it, build and install the `svn' client:

  $ zcat subversion-r2927.tar.gz | tar xvf -
  $ cd subversion-r2927
  $ ./configure --disable-shared
  $ make
  $ make check   ### this is optional; also, it can take a long time
  # make install
  $ 

Now you should have `/usr/local/bin/svn', so you can:

  $ cd wherever/you/keep/your/projects
  $ svn co http://svn.red-bean.com:8080/ale/trunk ale

That's it -- you now have a working copy of Ale.

The recipe to build ale from a working copy is:

   $ ./autogen.sh
   $ ./configure
   $ make
   # make install

(Of course you must have Emacs 21 installed on the system already).

Subversion's basic operations are the same as CVS's:

   "svn update"  ==  "cvs update"
   "svn commit"  ==  "cvs commit"
   "svn diff"    ==  "cvs diff"
   "svn status"  =~  "cvs status"

And you know where to ask questions... :-),
-Karl

---

From: Loredana Lo Conte <[email-masked]>
Date: Sun, 11 Aug 2002 20:26:15 +0100 (BST)

> us reports of bugs we haven't already fixed.

I installed the subversion client, ale rev 9, and emacs 21.2.1, then tried
ale both with your demo.gb file (in demo-data) and with one of my
protein sequence file.

The bugs I reported for ale-0.1.183, when I was using emacs 20.5.1, are
still there, just a little bit worse:

1) changing colour setting does not work

2) while before I was able at least to define a group with the mouse, now
I can't (i.e., selecting sequence id generates a "wrong type argument,
sequencep, 1", the menu disappears, it reappears if I click on the
sequence area, but if I click on the menu itself ale crashes). I tried to
change the lock property for few sequences to "unlock", but it does not
seem to help.

I didn't check anything else.

Can you reproduce these bugs? Better, can you fix them ? :)

Loredana

---

From: Jim Blandy <[email-masked]>
Date: 12 Aug 2002 00:27:44 -0500

> still there, just a little bit worse:

Beautiful --- this is very helpful.  (Thank you so much for taking the
effort to come this far!  I think things will go more easily from here
on.)

> Can you reproduce these bugs? Better, can you fix them ? :)

I'll try give it a shot in the next few days.

---

From: Loredana Lo Conte <[email-masked]>
Date: Wed, 21 Aug 2002 21:32:29 +0100 (BST)

This one:

Loredana

---

From: Karl Fogel <[email-masked]>
Date: 21 Aug 2002 12:52:33 -0500

> > 1) changing colour setting does not work

What exact commands/menus/keystrokes did you do, and what was the
result?

One thing to remember here is that Jim and I remember very little
about the Ale interface.  It's been seven years.  I had to read the
manual just to relearn how to mark a rectangle and move it.  So when
you say "change colour setting", I don't have any idea what you
actually tried :-), or what you expected as a result.

(A nice side effect of detailed bug reports from you will be that we
start to relearn various commands.  I will print out the manual and
read it now, but I'm sure I'll still learn a lot from detailed reports
of how you actually work).

> > change the lock property for few sequences to "unlock", but it does not

Ah.  Okay, I think I reproduced this:

I clicked mouse-1 on a sequence's name (Mc.vanniel) in the left
window, while holding down no modifier keys, and I got the error you
describe.  Is that what you did?

I will debug this now.  No, wait: first I'll run out and get a fresh
mozarella and basil sandwich, *then* I'll start debugging this.

Have you already tried to debug it at all?  (Just curious, no
pressure.)

-Karl

---

From: Loredana Lo Conte <[email-masked]>
Date: Wed, 21 Aug 2002 23:31:23 +0100 (BST)

> What exact commands/menus/keystrokes did you do, and what was the

ale demo-data/demo.gb (or any other file)
then click on settings (menu bar)
then click on anything but uncolored
What I get is wrong in all cases, but varies slightly.

NOTE: I am at home and not really doing it, this is what I remember.
I don't want to miss the chance and wait until tomorrow since you are
so well inclined right now.

How was the mozzarella? If you fix ale, I 'l sent you an original one from
Italy :)

Good night
Loredana

---

From: Karl Fogel <[email-masked]>
Date: 21 Aug 2002 15:07:11 -0500

> so well inclined right now.

Thanks, this is a *perfect* bug report!  

I just reproduced it.  Yes, those are some pretty bizarre results.
I'll see what I can do.

> How was the mozzarella? If you fix ale, I 'l sent you an original one from

It was sooooooo tasty.  And I fixed the other bug already, so that's
half a mozarella from Italy at least :-).

-K