Re: [sage-support] Apparently Sage lost Python

[rana-aere]

Dear Dima,

I found something strange in this error message.

anirojas@MacBook-de-Anita ~ % /Applications/SageMath/sage --notebook=export 
--list

File "/Applications/SageMath/local/bin/sagenb-export"

File 
"/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/cmdline.py",

File 
"/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/actions.py",

File 
"/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/actions.py",

File 
"/Applications/SageMath/local/lib/python3.7/site-packages/sagenb_export/sagenb_reader.py"


On MacOS, normally, we see

-

/Applications/SageMath-9.0.app/sage --notebook=export --list

/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/sagenb_export/...



I do not understand why "Contents/Resources/sage/" disappeared.

More strangely, functions defined in these files are actually executed.

Is it possible some problem in setting PATH leads to python3 bundled with 
Catalina controls

Sagemath instead of python3.7 included in Sagemath?


I do not have Catalina installed. So, I cannot verify anything on it.

I only heard Catalina now has python3 not python2.

The default shell changed to zsh instead of bash.

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Re: [sage-support] Re: Slow Computations in Quotient Rings

[rana-aere]

Dear Vincent ,

I am tempted to do so.
But, for now, I must focus on trouble of Sagemath start-up in MacOS.

I have fixed a trick of Sagemath (double click) hands over the ticket to 
the browser.
At the same time, I fixed some part of the trouble of error messages 
truncated.

I have an idea on some other problem with getcwd.

I have an idea on fixing problematic validation on MacOS 
HighSierra--Mojave--Catalina.
 This turned out much more difficult than I expected.

I must also fix deprecation warnings, which makes us hard to consult new 
users installing Sagemath.
 Most of this turns out upstream problem so I must find a way to 
reproduce warnings.

I accept to work on the ring but please allow me to be very slow.

In any event I take your welcome message.
Thank you. 

2020年4月7日火曜日 2時09分21秒 UTC+9 vdelecroix:
>
> Dear rana-aere, 
>
> If you think this is an issue, then *you* should be working on it. 
> Every SageMath developers is a volunteer that does not take orders 
> and think by herself or himself what is relevant to do. Note that 
> helping others is indeed a concern for most of them. 
>
> As a start: 
>
> - you can check whether there is already an existing ticket 
>on https://trac.sagemath.org/ for this problem, and if not 
>open one which tracks down the problem to its essence (for 
>example it has nothing to do with elliptic curves). 
>
> - If you have a *concrete suggestion* in favor of an improvement 
>but does not know how to implement it, this could be discussed 
>on the sage-devel mailing list. 
>
> SageMath developers are mature enough to read the messages on this 
> list and figure out what is relevant to do without your call. 
>
> Best 
> Vincent 
>
> Le 05/04/2020 à 17:38, rana-aere a écrit : 
> > I think it is an issue to be reported. 
> > So, I wait for someone to respond this question. 
> > 
> > To developers of the SageMath module of rings: 
> > Please verify the program in this question, with debugging messages I 
> added. 
> > we ran into a weakness of SageMath either 
> >   in formula processing producing too complicated denominators 
> >   or in SageMath module of quotient of rings, which fail to reduce the 
> > element of the ring. 
> > I believe the code reported here is an important entry for new students 
> to 
> > SageMath. 
> > Please program what is going for this program. 
> > 
> > 2020年4月5日日曜日 5時56分25秒 UTC+9 finotti: 
> >> 
> >> Thanks for the reply! 
> >> 
> >> On Saturday, April 4, 2020 at 1:00:12 PM UTC-4, rana-aere wrote: 
> >>> 
> >>> I modified the code and tried to trace computation. 
> >>> 
> >>> I think you stepped over the weakness of Sagemath. 
> >>> 
> >> 
> >> I was afraid that that would be the case... 
> >>   
> >> 
> >>> 
> >>> The modified code is quoted below. 
> >>> The line with many minus signs is meant to separate the program in 
> >>> different cells of jupyter notebook. 
> >>> My impression is that the program computes R, P + Q, LHS = (P + Q) + R 
> >>> and then Q + R for RHS. 
> >>> After that the data for the outer call of P + (Q + R) becomes too big 
> so 
> >>> that Sagemath cannot pass the parameters to add_EC. 
> >>> 
> >> 
> >> Thanks for taking the time to do that! I really appreciate.  I wonder 
> if 
> >> this is an issue that I should report or if it simply "how it is"... 
> >> 
> >> I think we will just stick with Magma for now.  I try to use (and teach 
> >> with) Sage whenever possible, but in this case I think I will have to 
> stick 
> >> with Magma. 
> >> 
> >> Thanks again! 
> >> 
> > 
>

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Re: [sage-support] Apparently Sage lost Python

[rana-aere]

I am sorry for I might have given you extra work, which produced nothing.
I agree it is not a good time to use SageMath on Catalina.


2020年4月6日月曜日 3時14分47秒 UTC+9 Anita Rojas:
>
> Thanks a lot for your support and patience but I gave up. I can not 
> succeed. There are too many difficulties that I am not going to be able of 
> solving: My older routines lost, my files with computations and examples. I 
> do not know how to recover them. Perhaps I will try again in next future, 
> with less anxiety and more energy.
> Thanks again.
> Best regards
>
> On Sat, Apr 4, 2020 at 12:13 AM Dima Pasechnik  > wrote:
>
>>
>>
>> On Sat, 4 Apr 2020, 11:11 Anita Rojas, > 
>> wrote:
>>
>>> Hi! I am far away of being a OSX guru, but I managed to get my SAGE 
>>> working. 
>>>
>>> It use to work properly but now I got the following message:
>>>
>>>
>>> Error: Tried to use Sage's Python which was not yet installed.
>>>
>>> If this was called from an spkg-install script for another 
>>>
>>> package you should add $(PYTHON) as a dependency in 
>>>
>>> build/pkgs//dependencies
>>>
>>>
>>> I looked for solutions but I could not find answers. I would appreciate 
>>> help.
>>>
>>
>> Probably a MacOS update broke your Sage installation.
>>
>> If so, reinstalling might be the only  known way to fix this.
>>
>>
>>> Best,
>>>
>>> Anita
>>>
>>> -- 
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>>>  
>>> 
>>> .
>>>
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>>  
>> 
>> .
>>
>
>
> -- 
> Anita M. Rojas
> Departamento de Matemáticas
> Facultad de Ciencias
> Universidad de Chile
>
> https://sites.google.com/a/u.uchile.cl/mat-ciencias-prof-anita-rojas/
>

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[sage-support] Re: Slow Computations in Quotient Rings

[rana-aere]

I think it is an issue to be reported.
So, I wait for someone to respond this question.

To developers of the SageMath module of rings:
Please verify the program in this question, with debugging messages I added.
we ran into a weakness of SageMath either
 in formula processing producing too complicated denominators
 or in SageMath module of quotient of rings, which fail to reduce the 
element of the ring.
I believe the code reported here is an important entry for new students to 
SageMath.
Please program what is going for this program.

2020年4月5日日曜日 5時56分25秒 UTC+9 finotti:
>
> Thanks for the reply!
>
> On Saturday, April 4, 2020 at 1:00:12 PM UTC-4, rana-aere wrote:
>>
>> I modified the code and tried to trace computation.
>>
>> I think you stepped over the weakness of Sagemath.
>>
>
> I was afraid that that would be the case...
>  
>
>>
>> The modified code is quoted below.
>> The line with many minus signs is meant to separate the program in 
>> different cells of jupyter notebook.
>> My impression is that the program computes R, P + Q, LHS = (P + Q) + R 
>> and then Q + R for RHS.
>> After that the data for the outer call of P + (Q + R) becomes too big so 
>> that Sagemath cannot pass the parameters to add_EC.
>>
>
> Thanks for taking the time to do that! I really appreciate.  I wonder if 
> this is an issue that I should report or if it simply "how it is"...
>
> I think we will just stick with Magma for now.  I try to use (and teach 
> with) Sage whenever possible, but in this case I think I will have to stick 
> with Magma.
>
> Thanks again!
>

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Re: [sage-support] Apparently Sage lost Python

[rana-aere]

I guess it is about the page of title "Home".
We do not have access to sagenb notebooks.
Instead we have access to jupyter notebooks.
For the current situation, you do not have any noebooks.
That is why no notebook is listed in the page.
You can try "New" button at the upper right corner below the grey 
horizontal line.
If you play with some little program in the new notebook,
it might be a good chance to test upgrading sagenb notebooks.

This "upgrade" is only possible from command line.
The two relevant "sage --notebook=export --list" and "sage 
--notebook=export ipynb TARGETFILENAME admin:NN". The former prints a 
list of sagenb notebooks.
An example is here.

```

Unique ID   | Notebook Name

---

admin:0 | Save 30% by Sagemath  (~/Manuals/SageTutorial9.0.pdf)

admin:1 | "Rabbit's population" $F_n$ is like $((1+\sqrt{5})/2)^n$!

admin:2 | Integral #1: $f(x)=\frac{1}{\sqrt{1-x^2}}$, $|x| < 1$.

admin:3 | Integral #2: why is f(x) = x * sqrt(1-x^2), (x in [-1,1]) 
easier?

admin:4 | Oval body & `tail' of @rana-aerea

admin:5 | Calculus of log|x|, x > 0.

admin:6 | mycalc

admin:7 | mycalc

```


The other command upgrades the notebook.

For example,

"sage --notebook=export ipynb mycalc-a admin:6"

converts the notebook with title "mycalc" with the unique id "admin:6".

It is possible some notebooks of yours have unique id of the form "guest:0"

or some other "user name". I guess 

"sage --notebook=export ipynb guestnotebook guest:0"

also works.

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Re: [sage-support] Apparently Sage lost Python

[rana-aere]

Yes, version <= 8.9 is the solution for now.
If the number of notebooks is not too large, upgrading sagenb notebooks to 
jupyter notebooks
might be a good idea.
In the next release, the error messages will not be missing.
In that time please try "sage --notebook=export --list"
and "sage --notebook=export ipynb TARGETFILENAME admin:NN"
for upgrading notebooks.

2020年4月5日日曜日 23時17分02秒 UTC+9 Anita Rojas:
>
> Thanks. I tried "sage -n Jupyter", and my browser opened but without 
> success in entering SAGE.
> I will install SAGA 8.1 to see if it works. 
> Here is the message I got once typing "sage -n":
> ---
>
> sage: notebook()
>
> ---
>
> ModuleNotFoundError   Traceback (most recent call 
> last)
>
>  in ()
>
> > 1 notebook()
>
>
>
> ModuleNotFoundError: No module named 'sagenb'
> ...
>

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Re: [sage-support] Apparently Sage lost Python

[rana-aere]

I guess your computer is left vulnerable.
So you should use
```
sudo spctl --master-enable
```

We are fixing slow start-up of Sagemath and also problems of permissions.
SageMath-8.9 is OK for MacOS upto MacOS Mojave.
SageMath-9.0 needs techniques for installation on MacOS Mojave.
Many people complains problems of SageMath-9.0 on MacOS Catalina.
I only understood two or three symptoms reported but I located one 
essential problem.

So, we are in a rather transient situation.

For the user's of sagenb notebook, I'd rather recommend to use SageMath-8.9 
while
waiting for SageMath get OK with Catalina. I think you are in this category.

For MacOS freak, I recommend to try the following procedure in the same 
account:
(This works for MacOS Mojave. On the other hand, no one reported it to work 
on Catalina.)
(1) Copy SageMath-9.0 from disk-image to /Applications. Do not double click 
it at this moment.
(2) Open /Applications/Utilities/Terminal.app
(3) In the terminal window, issue the following command
```
myhome$ /Applications/SageMath-9.0.app/sage
```
(4) Quit sage after the sage-prompt asks you for input something.
(5) Diable verification by "sudo spctl --master-disable".
(6) Double click /Applications/SageMath-9.0.app
(7) Specify your folder for Sagemath when a dialogue asks it.
 This folder is something close to the folder tree  ~/.sage of 
notebooks.
 But it must be different from ~/.sage.
 Sagemath does not start-up on Catalina if this folder is not specified 
at the dialogue.
(8) If Sagemath opened a web-page of jupyter notebook
 and you verify this page accept programs of Sagemath (e.g. 
print("hello") ),
 then quit Sagemath by the menu.
(9) Use " sudo spctl --master-enable" to restart protection.

I guess this explanation gives an impression of a gap between (7) and (8).
This is because we are still fighting the problem behind (7).

If you are in this category, I welcome claims from you.

Alternatively, if you want to go to new versions of Sagemath,
please wait for Sagemath-9.1.


2020年4月4日土曜日 13時25分46秒 UTC+9 Anita Rojas:
>
> Thanks. I did:
>
> sudo spctl --master-disable
>
> and it worked. I have a question: Did I leave my computer vulnerable by 
> doing so?
>
> Second: I was used to use notebook() but it did not work. 
>
> Deep thanks for your help
> Anita
>
> ...
>

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[sage-support] Re: Slow Computations in Quotient Rings

[rana-aere]

I modified the code and tried to trace computation.

I think you stepped over the weakness of Sagemath.

The modified code is quoted below.
The line with many minus signs is meant to separate the program in 
different cells of jupyter notebook.
My impression is that the program computes R, P + Q, LHS = (P + Q) + R and 
then Q + R for RHS.
After that the data for the outer call of P + (Q + R) becomes too big so 
that Sagemath cannot pass the parameters to add_EC.
I introduced local variable myA. This should represent A instead of the 
coordinate a of P.

Please verify the output.

```
def add_EC(vE, P, Q):
print("add_EC is called with");
print("P = ", P);
print("Q = ", Q);
if P == 0:
print("P == 0, returning Q");
return Q
print("P != 0");
if Q == 0:
print("Q == 0, returning P");
return P
print("Q != 0");

# avoid confusion of a of elliptic curve with a of P.
myA = vE[0]
# I gues we are not using b of the equation.
# myB = vE[1]
x1 = P[0]
y1 = P[1]
x2 = Q[0]
y2 = Q[1]
print("Copied actual parameters in local variables");
if P == Q:
print("P==Q");
if y1 == 0:
print("y1 == 0, returning 0");
return 0
else:
print("y1 != 0, comuting m");
m = (3*x1^2 + myA)/(2*y1)
print("P==Q && y1 != 0");
else:
print("P != Q");
if x1 == x2:
print("x1 == x2, returning 0");
return 0
else:
print("x1 != x2, computing m");
m = (y2 - y1)/(x2 - x1)
print("P!=Q && x1!=x2");
print("Main case: intermediate variable m already computed");
print("m = ", m);
c = y1 - m*x1
print("c = ", c);
x3 = m^2 - x1 - x2
print("x3 = ", x3);
y3 = m*x3 + c
print("y3= ", y3);
return [x3, -y3]
#--
R. = PolynomialRing(QQ)

eq1 = b^2 - a^3 - A*a - B
eq2 = d^2 - c^3 - A*c - B

S = R.quo([eq1, eq2])
F = FractionField(S)

vE = [F(A), F(B)]
P  = [F(a), F(b)]
Q  = [F(c), F(d)]
#--
R = add_EC(vE, P, Q)
#--
R
#--
LHS = add_EC(vE, add_EC(vE, P, Q), R)
#--
LHS
#--
# Sagemath cannot handle the next step.
# Make sure you are ready to terminate Sagemath,
# before uncommenting the next line.
# RHS = add_EC(vE, P, add_EC(vE, Q, R))
#--
# RHS
#--
# LHS==RHS
```

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[sage-support] Re: deprecation warning about "`\QQ`" and "\*"

[rana-aere]

I just began learning development of Sagemath.
And reference manual of Sagemath looks like combination of original 
documentation
and collection of documentation from source code.
I do not know how modification of source influence the entire system, which 
include reference manuals.

I have a tendency to run into bugs other programmers/researchers do not 
encounter.
This means I will report many bugs.
So, I should learn to propose how to fix the bugs.

On the other hand,  my major was software engineering.
So, it is more creative for me to consider the whole system when I propose 
fixing bugs.

This is why I asked how I can test the influence of rewriting docstring.

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Re: [sage-support] Re: Sage 9.0 macOS Jupyter Server failed to start

[rana-aere]

I solved the first form of bug reported here.
By accident I wrote it 
in https://groups.google.com/forum/#!topic/sage-support/WP473oaAulE .
Another one about getcwd seems to be an issue specific to Catalina.
I will work on it.

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[sage-support] Re: Does a deprecation warning prevent start-up of jupyter server of Double clickable application SageMath-X.X?

[rana-aere]

I think another trouble of SageMath-9.0.app was about failure of getcwd.
I have an idea on this problem.
I will check it.

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[sage-support] Re: Does a deprecation warning prevent start-up of jupyter server of Double clickable application SageMath-X.X?

[rana-aere]

I finally made it to make a disk-image-file of SageMath-9.1.app with 
updates of https://trac.sagemath.org/ticket/29371.

The issue of failing start-up with partial record of patching files is 
solved.
I explain what was happening.
Mac application SageMath-9.0.app set-up bash command using pipes:
Roughly speaking it is
"sage starting jupyter server | tee for recording log | grep in 2 stages 
for ticket of jupyter".
There were some problem in the last two stages so that grep terminated by 
error.
Hence, the pipe got stuck.
This prevented tee from writing logs beyond some amount of bytes.
Another effect was probably tee command also terminated and sage command 
also terminated.
This problem will be solved in SageMath-9.1.

Current work-around is here:
Start /Applications/SageMath-9.0.app/sage by command line.
Then patching will be done.
Exit sage after sage-prompt comes up.

Then, double click Mac Application SageMath-9.0.app.
This solution has a problem of sage terminates unexpectedly when huge 
amount of logging takes place
for one invocation of jupyter-server.
I admit this.
If you are not in a hurry, waiting for SageMath-9.1 will be an easier 
solution.

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[sage-support] Re: Does a deprecation warning prevent start-up of jupyter server of Double clickable application SageMath-X.X?

[rana-aere]

I forgot to mention one thing.

Patching in SageMath-9.1beta8 was on libraries not on source codes.
This might be another difference from the distribution of SageMath-9.0.

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[sage-support] Re: Does a deprecation warning prevent start-up of jupyter server of Double clickable application SageMath-X.X?

[rana-aere]

I edited the code back to original and tested how SageMath starts up.
Deprecation warning does not block start-up.
There remains some more mystery in start-up of double clickable 
SageMath.app of MacOS.

For possible users who encounter the same symptom of SageMath, I leave some 
record.

Step 1: I copied SageMath9.1beta8.app in /Users/Shared/SagemathTestground.
Step 2: I double clicked the copy  /Users/Shared/SagemathTestground/ 
SageMath9.1beta8.app
> Mac dialogue appeared an reported failure of jupyter server to 
start.
Step 3: I used "view log" to read the log. The log was incomplete. It 
seemed patching was on the way.
Step 4: I started  /Users/Shared/SagemathTestground/ 
SageMath9.1beta8.app/sage from the command line.
> Plenty of messages on patching were displayed.
> Then, a deprecation warning on \Q in the definition of 
_macaulay2_init_ appeared.
> sage prompt appeared.
Step 5: I quitted sage and edited the relevant file and silenced that 
warning.
Step 6: I invoked sage from command line and verified warning message is 
silenced.
Step 7: I double clicked  /Users/Shared/SagemathTestground/ 
SageMath9.1beta8.app.
> Jupyter server started up and Sagemath was OK.
Step 8: I put the code back in original for testing the software for 
sage-support-group.
Step 9: I quitted /Users/Shared/SagemathTestground/ SageMath9.1beta8.app 
and double clicked it again.
> Jupyter server started up and Sagemath was OK.

Lesson?   Patching at the initial invocation might fail occasionally. And, 
retrying initial invocation of SageMath several times might help. 
Deprecation warning seems not the real obstruction.

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[sage-support] Re: deprecation warning about "`\QQ`" and "\*"

[rana-aere]

Thank you for clear instructions.
I used the codes to compare how doctoring of the method _macaulay2_init_ is 
displayed. 

sage-8.9 (command line and jupyter)

```
Init docstring: x.__init__(...) initializes x; see help(type(x)) for 
signature
File:   
/Applications/SageMath-8.9.app/Contents/Resources/sage/local/lib/python2.7/site-packages/sage/structure/sage_object.pyx
Type:   builtin_function_or_method
```

sage-9.0 (command line and jupyter )

```
Signature:  S._macaulay2_init_(macaulay2=None)
Docstring: 
   EXAMPLES:

   Quotients of multivariate polynomial rings over QQ, ZZ and a
   finite field:
```

sage-9.1 (command line and jupyter)

```
Signature:  S._macaulay2_init_(macaulay2=None)
Docstring: 
   EXAMPLES:

   Quotients of multivariate polynomial rings over \QQ, \ZZ and a
   finite field:
```

All three have different behaviors.

I think true and meaningful difference should be observed in conversion to 
tutorial, wiki or manual
If someone knows how to test it, please tell me the result.
I will find a way to make a ticket for it.

For now I proceed to check issues on "sqrt?"

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[sage-support] Does a deprecation warning prevent start-up of jupyter server of Double clickable application SageMath-X.X?

[rana-aere]

I am testing binary-pkg.

This question is relevant to the previous one on deprecation warning on 
`\QQ`.
But, the focus is different.

I made SageMath-9.1beta8 by binary-pkg.
Then, I  copied SageMath-9.1beta8 out of the disk-image-file mounted of 
MacOS.
I ejected the disk-image.
And double clicked SageMath-9.1beta8.
There was an error message (dialogue) on failure on invoking jupyter server.

So, I invoked command-line version SageMath-9.1beta8/sage on Terminal 
(bash).
There were messages on patching and then there was a deprecation warning.
For command line, this was just one deprecation warning one can ignore.
I found the source code which is responsible for this warning.
I made a correction in the relocated folder tree of SageMath-9.1beta9.
Then, I reinvoked sage through command line and verified that the warning 
does not show up again.

I quitted sage and double clicked the Mac application.
This time, jupyter server started up normally.

Is it possible Mac application is designed to stop invocation even for a 
deprecation warning?

I am currently investigating trouble of Mac application with error messages.
(Trouble like adding three extra diagnosis message prevents Mac application 
of SageMath-9.0 from normal start-up.)
So, any information on the question 4 lines above is helpful.

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[sage-support] deprecation warning about "`\QQ`" and "\*"

[rana-aere]

I am compiling binary-pkg and encountered a deprecation warning.
The warning appeared when I invoked sage from command line.
(Technically, it was after messages of patching.)

The warning reads

```
.../quotient_ring.py:1350: DeprecationWarning: invalid escape sequence \Q
```

I read the file quotient_ring.py located at 
SageMath-9.1.beta8.app/Contents/Resources/sage/local/lib/python3.7/site-packages/sage/rings.

The description (line 1300--1350) of _macaulay2_init contains a line

```
Quotients of multivariate polynomial rings over `\QQ`, `\ZZ` and
```

So, I inserted 'r' before """ on line 1300. (""" -> r""").

After reinvocation of sage, the previous warning is gone.
Unfortunately, I cannot test the effect of the change on description.
I tried typing "_macaulay2_init_?". This did not work.

How can I test it? (Question 1.)

I thought  function name with "?" might not be the right syntax.
So, I tested "sqrt?". It gave me a series of deprecation warnings like

```
.../sessions.py:565: DeprecationWarning: invalid escape sequence \*
```

They make the screen to scroll one page.

These warnings for sessions.py are also descriptions of functions enclosed 
by """...""" pair inserted of r"""...""".
Yes, the recommended style was r"""..."" for description containing latex 
expressions.
The warnings for sessions.py might be regular expressions intended to be 
displayed by "function_name?"
or may be "*" are really escaped so that enclosing by r"""...""" and 
changing "\*" with "*" might help.
I do not have knowledge to distinguish these two.

(Question 2.) Is there any body who can tell which correction is suitable 
for sessions.py?
Option 1. """...""" -> r"""..."""
Option ". """... \*...""" -> r"""... *..."""

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Re: [sage-support] Re: Sage 9.0 macOS Jupyter Server failed to start

[rana-aere]

Thank you for your reply.
I am trying to compile Sagemath.
I will verify my proposed code.


2020年3月20日金曜日 18時57分22秒 UTC+9 Dima Pasechnik:
>
> On Fri, Mar 20, 2020 at 4:45 PM rana-aere  > wrote: 
> > 
> > Thank you for making the ticket and making a patch. 
> > 
> > I think the code is now right. 
> > I am still unable to compile it for test. 
>
> Why is that? I suppose with a complete installation of Xcode and its 
> command-line tools, 
> it should work, using src/mac-app/Makefile 
> But it might be you'd need to have Sage built from source first. For 
> this, it's probably 
> easiest to do it using Conda or Homebrew, so that many packages from 
> either Conda or 
> Homebrew may be used. 
>
>

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Re: [sage-support] Re: Sage 9.0 macOS Jupyter Server failed to start

[rana-aere]

Thank you for making the ticket and making a patch.

I think the code is now right.
I am still unable to compile it for test.

Here is a partial method for test.
```
$ cat sage.log | grep -i --line-buffered --context=1 'Notebook is running 
at' | grep --line-buffered -o -e "http://.*";
```

(Another minor change is insertion of "-e". This change does affect the 
action in normal circumstances.
But I found it when I tested the code again.)

Do I need to take part in GitHub for reviewing the patch?
And may be I should ask someone to invite me in Sagemath developer's group?


2020年3月20日金曜日 17時08分40秒 UTC+9 Dima Pasechnik:
>
>
>
> On Friday, March 20, 2020 at 3:27:18 AM UTC+8, rana-aere wrote:
>>
>> Yes, I am aware of it.
>> I have intension to help developing Mac Application.
>> In August, I can spare time to try compilation and rewriting Mac specific 
>> codes.
>> Currently, I am hesitating because of so may prerequisites or 
>> dependencies.
>>
>
> The patch you propose is now on
> https://trac.sagemath.org/ticket/29371
>
> Would be great if someone reviewed it.
>

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Re: [sage-support] Re: Sage 9.0 macOS Jupyter Server failed to start

[rana-aere]

Yes, I am aware of it.
I have intension to help developing Mac Application.
In August, I can spare time to try compilation and rewriting Mac specific 
codes.
Currently, I am hesitating because of so may prerequisites or dependencies.

2020年3月20日金曜日 3時39分05秒 UTC+9 Dima Pasechnik:
>
> as a matter of fact, we might currently be lacking developers with 
> knowledge of these MacOS-specific things. (I suggest that 
> SageMath-*.app should not be used, instead use terminal-based ways to 
> start Sage) 
>
> On Fri, Mar 20, 2020 at 2:35 AM rana-aere  > wrote: 
>
>

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[sage-support] Re: Sage 9.0 macOS Jupyter Server failed to start

[rana-aere]

I am interested in one aspect.
For "security", MacOS might restrict softwares access to directories.
If someone tries this and find some difference, maybe some more users will 
be helped.

Step 1. Remove the /Applications/SageMath-9.0.app which does not work.
(This test is for such SageMath-9.0.app. If it is working do not remove it 
since the test does not make sense anyway.) The application might be 
shown /Applications/SageMath-9.0 in Finder.

Step 2. In the Terminal window of an administrator's account, use this 
command:
$ cd /Applications/SageMath-9.0.app/Contents/Resources/sage
$ open -a /Applications/SageMath-9.0.app

The first command changes the working directory to SAGE_ROOT.
The second command tells the full pathname to the application and invoke it.

I surfed through the internet and found the error message is from bash.
It tells bash found no current working directory when it is invoked.

If Step 2 is OK, please proceed to the next step.

Step 3. Quit SageMath.app and the browser. Then, double click 
/Applications/SageMath-9.0.app.

If Step 3 fails, then please proceed to the next step.

Step 4. Try the procedure of Step 2 again.

I will try to find what is going on there on the isolated island Catalina.

2020年3月18日水曜日 0時04分16秒 UTC+9 Steve Emmett:
>
> I am having maybe a similar issue. Im on MacOS 10.15.3  I've successfully 
> used 8.9 for quite a while.  I downloaded 
> *sage-9.0-OSX_10.15.2-x86_64.app.dmg 
> .*
> I did the install selected SageMath-9.0.app in Applications.
>
> Safari starts up and overlaid on that screen is the following error 
> message:
>
> [image: Screen Shot 2020-03-17 at 101002 .png]
>
> The only log entry is:
>
>
> shell-init: error retrieving current directory: getcwd: cannot access 
> parent directories: Operation not permitted.
>
>
> Maybe not exactly like your but I would tend to agree that something that 
> was hooked up in pre Sage 9.x is now not there in Sage 9.x
>
>
>
>
>
> On Sunday, January 5, 2020 at 2:39:50 PM UTC-5, Murray Eisenberg wrote:
>>
>> When I open SageMath-9.0.app under macOS Catallina (10.15.2), I get an 
>> immediate pop-up error window saying, "Jupyter Server failed to start". 
>>
>> The log shows:
>>
>> ┌┐
>> │ SageMath version 9.0, Release Date: 2020-01-01 │
>> │ Using Python 3.7.3. Type "help()" for help.│
>> └┘
>> Please wait while the Sage Jupyter Notebook server starts...
>>
>> However, I can get the Jupyter server to start with an indirect method 
>> that was never required in earlier versions of SageMath-x.x.app, namely:
>>
>>1. In Finder, Show package contents for SageMath-9.0.app.
>>2. Navigate in Finder to Contents/MacOS.
>>3. Double-click Sage.
>>
>> That both starts the server and opens the expected client window in 
>> Safari, from which I can open and evaluate cells in an existing notebook or 
>> create a new SageMath 9.0 notebook.
>>
>> So something that used to be "hooked up" between the SageMath-x.x.app and 
>> the command to start the jupyter server has been broken with 9.0.
>>
>>
>>

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[sage-support] Re: Sage 9.0 macOS Jupyter Server failed to start

[rana-aere]

I think SageMath-9.0.app has less records in log file.
I suspect it is not anything planned.
When SageMath-9.0.app terminates abnormally, some messages for log file is 
lost.
This loss has one explanation, which is the --line-buffered option of grep 
is turned off in SageMath-9.0.app.
Since I believe this support-group is for asking things to developers, I 
propose two thing:
Dear developers, please turn on --line-buffered option in AppController.m
SageMath-9.0.app
   " grep -i --context 1 'Notebook is running at' |"
" grep -o http://.*";,
SageMath-9.1.app
   " grep -i  --line-buffered --context=1 'Notebook is 
running at' |"
   " grep  --line-buffered -o http://.*";,
Note also the character "=". This is causing an error currently.
(I myself used hex editor to fix this. But this solution is only 
recommended for programmers.)
Please turn on other switches so that the other messages for log file will 
be recorded.
Currently, I do not see version numbers of Sage-9.0 in log file.
I think informative log file will help the community to identify the real 
bottle neck.

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[sage-support] Re: Cannot open sage after install.

[rana-aere]

High, you are not alone in this endeavor.
Comments in "Does SageMath work on Mac OS 10.14.6" of sage-support-group 
might help.
But first, please make sure you have not invoked sage before you movesage
to desktop.
Sage rewrites the links inside its code when it is invoked for the first 
time,
(through SageMath-X.X(.app) or through command line "./sage".)
If one moves SageMath after this invocation, Sage cannot find modules it 
uses.
If your case matches this description, I think you can fix it by installing 
SageMath again.

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Re: [sage-support] Re: Does SageMath work on Mac OS 10.14.6

[rana-aere]

Yes, giving permission to run SageMath-9.0.app is essential. But here is a 
problem. On MacOS 10.14, security control is made much strict. GUI 
interface for giving permission is now impossible for applications with 
wrong signature. (For application without signature, MacOS 10.14 behaves 
similarly to previous MacOS's. So, we can give permission to run 
SageMath-8.9.app is possible from GUI interface.)  

For SageMath-9.0.app, we should use this command.

```Console
myhome$ sudo spctl  --master-disable
```

Then, double click SageMath-9.0.app and direct to run it anyway for the 
dialog.
After that use this command

```Console
myhome$ sudo spctl  --master-enable
```

to make the machine safer again.


2020年2月26日水曜日 2時52分47秒 UTC+9 Fernando Q. Gouvea:
>
> I managed to install *sage-9.0-OSX_10.11.6-x86_64.app.dmg* 
>  
> on a Mac running OSX 10.13. The app version seems to work better than the 
> non-app version, and this one worked much better than the older 8.8 version 
> I tried first.
>
> The key is to be an administrator. That is needed at several points. 
> First, when copying the app to the Applications folder. Then I had to start 
> the program and the computer would tell me it wasn't from the Apple store 
> so it couldn't be run. Once that happened, going into the security settings 
> (and entering the admin password again) allowed me to say "run it anyway". 
> Next time I started the program it spend a good long time "verifying" it. 
> That may have required more administrator password. But eventually I got it 
> to run and correctly open a notebook.
>
> On a Windows machine, a non-administrator can install Sage "for yourself 
> only", but Macs don't seem to allow that.
>
> Fernando
> On 2/25/2020 12:18 PM, Nathan Dunfield wrote:
>
>
>
> On Tuesday, February 25, 2020 at 9:36:55 AM UTC-6, seriously wrote: 
>>
>> Seriously, has anyone got one of the current releases of Sage to work on 
>> any Mac platform? 
>>
>> I tried several times, lately with version 8.8 for 10.14.5.  I dropped 
>> the binary in Applications.
>> It can start up then - it opens a browser window which just stalls; it 
>> has a drop-down menu called "Terminal Session",
>> which doesn't do anything, and if I go directly into the App and execute 
>> ./sage, all kinds of errors appear
>> (many about permissions) and it crashes.
>>
>> Unfortunately I want to run a program built on this platform, and really 
>> need a working version.  
>> Any ideas are much appreciated.
>>
>
> I would try this version:
>
> sage-8.9-OSX_10.14.6-x86_64.tar.bz2   (1058.94 MB)
>
> as it worked fine for me on macOS 10.14.6 using the following commands in 
> the terminal:
>
> cd /Applications
> mv ~/Downloads/sage-8.9-OSX_10.14.6-x86_64.tar.bz2 .
> tar xf sage-8.9-OSX_10.14.6-x86_64.tar.bz2
> cd SageMath
> ./sage
>  
> Best,
>
> Nathan
>
> -- 
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> "sage-support" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to sage-s...@googlegroups.com .
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> https://groups.google.com/d/msgid/sage-support/93a7e77b-83fa-40f3-9687-15bd18c0cf32%40googlegroups.com
>  
> 
> .
>
> -- 
> ==
> Fernando Q. Gouvea
> Carter Professor of Mathematics  
> Colby College
> Mayflower Hill 5836
> Waterville, ME 04901 fqgo...@colby.edu  
> http://www.colby.edu/~fqgouvea
>
> What precisely is profound in Christianity is that Christ is both our
> atoner and our judge, not that one is our atoner and another our
> judge, for then we would nevertheless come to be judged, but that the
> atoner and the judge are the same.
>   -- Søren Kierkegaard, Journals
>
>
>

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[sage-support] Re: Does SageMath work on Mac OS 10.14.6

[rana-aere]

Yes, I installed SageMath-9.0.app (from disk image file) on MacOS 10.14.6.
In Ask Sagemath, I explained how I managed it.
The subject is "SageMath-9.0 authentication error".
On the other hand, I feel your SageMath-9.0.app has slightly different 
problem.

I guess there are two similar issues in SageMath-9.0.app.

1. After copying SageMath-9.0.app from the disk image to, say, 
/Applications, one must run SageMath-9.0.app in the same user/administrator 
account. This is because SageMath-9.0.app or SageMath-9.0.app/sage 
configure files in the directory tree of SageMath-9.0.app. I feel your 
situation for running SageMath-9.0.app looks like this.
2. In MacOS 10.14.6, Apple is getting more sensitive about security and 
refuse to accept application with wrong signature. In my case, this was the 
problem. If you pass the previous hurdle, and double click 
SageMath-9.0,app, this might cause a problem. This issue is also important 
for you. (Running unix application SageMath-9.0.app/sage in MacOS 10.14.6 
is all right. For me, the issue was about double clicking for invoking 
SageMath-9.0.) You can check this issue by the following command. I wrote 
the response on my machine.

```Console
myhome$ codesign --verify /Applications/SageMath-9.0.app/
/Applications/SageMath-9.0.app/: invalid Info.plist
(plist or signature have been modified)
In architecture: x86_64
```

3. If you pass previous two hurdles, another one might be a SageNB not 
supported any more.
3.1 A good new is SageMath-9.0.app starts very quickly now and we do 
not need to wait for 2 minutes for its web interface to come up.
3.2. Double clicking SageMath-9.0.app open jupyter notebook and 
loading-page.html. In case jupyter notebook, does not come up, you might 
double click the button `jupyter notebook`. Unfortunately, the button links 
to the wrong address `localhost:8080. Changing 8080 to  might solve 
this problem.
3.3 If one want to use old SageNB Notebook (or Sage Worksheet), the sad 
news is that Sagemath-9.0.app does not support it anymore. I checked the 
source and understood it refuses to open SageNB Notebook and I also saw 
messages on modules of sagenb notebook missing.
3.4. If you execute "SageMath-9.0.app/sage --notebook", a different 
opening page will show up. Clicking the button for SageNB Notebook leads to 
a page, which is note maintained. The message "you can run sagenb ..." is 
wrong for SageMath-9.0.app.
4. If you are moving from SageNB Notebook, you might want to convert your 
documents.
4.1. On my machine, the dialog offering upgrades does not work.
4.2. On my machine, clicking the menu of upgrading SageNB Notebook on 
the web page from "SageMath-9.0.app/sage --notebook" does not work. I 
verified the log file and found error messages.
4.3. Workaround for this is to use `SageMath-9.0.app/sage 
--notebook=export --list` for identifying the SageNB Notebook and the use 
``SageMath-9.0.app/sage --notebook=export --ipynb=YourFilename.ipynb 
admin:NN`, where YourFileName.ipynb is the file for placing the result and 
NN is the number you find by the `--list` option. The result has markdown 
sections harder to edit, but the Sagemath code is all right.

I apologize this long long answer. But SageMath-9.0.app is that complicated.

If you manage to work these around, please tell me your result of 
`codesign` command. I feel the behavior of MacOS highly depends on 
versions/revisions. It looks like binaries working on some version/revision 
is not working on older and newer versions/revisions. If we identify how 
the behavior of MacOS changes, we can help the developers and through them 
million potential users of Sagemath.


2020年2月26日水曜日 0時36分55秒 UTC+9 seriously:
>
> Seriously, has anyone got one of the current releases of Sage to work on 
> any Mac platform?
>
> I tried several times, lately with version 8.8 for 10.14.5.  I dropped the 
> binary in Applications.
> It can start up then - it opens a browser window which just stalls; it has 
> a drop-down menu called "Terminal Session",
> which doesn't do anything, and if I go directly into the App and execute 
> ./sage, all kinds of errors appear
> (many about permissions) and it crashes.
>
> Unfortunately I want to run a program built on this platform, and really 
> need a working version.  
> Any ideas are much appreciated.
>
>

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[sage-support] Re: connection to note book

[rana-aere]

I experienced a similar error.

The trouble is that loading-page.html has a incorrect address 
 localhost:8080 for jupyter notebook. The connection to Jupyter notebook is 
localhost:/ not localhost:8080 now.

I assume your started Mac Application of Sagemath by Double click, Dock or 
LaunchPad.
Please verify your opening window has heading:
"The SageNB server or Jupyter is currently starting. Please wait..."
There are buttons "SageNB interface" and "Jupyter". Both of them link to 
localhost:8080 mistakenly.

Please try opening localhost: form your browser.
Or if you are familiar with Terminal.app, please use the command
"  open http://localhost: ".
If this opens a Jupyter notebook or its login page, my workaround should be 
good for you.

My workaround is to edit loading-page.html by a text editor.
You should login MacOS with the same account as the time of your 
installation of SageMath.
If you put SageMath-9.0.app in /Applications folder, you can locate the 
loading-page.html by the following pathname.

/Applications/SageMath-9.0.app/Contents/Resources/loading-page.html

If the version is different change "9.0" with the version of your SageMath 
application.
(Form the Finder, the filename might appear SageMath-9.0 but from the 
Terminal, we have to write SageMath-9.0.app with the extension .app.)
Opening this file from the Finder needs a technique of typing the path 
/Applications/.../Resources/ in the Finder's menu of "Go".
But it is simpler to use /Applications/Utilities/Terminal.app and open the 
pathname /Applications/.../loading-page.html by your preferred text editor.

Once opened loading-page.html, search for the string 8080.
The second hit is in the following patter.

 http://localhost:8080/";>Jupyter

Change this occurrence of 8080 to .


Please tell me if it succeeds.
I am planning to tell the developers many many improvements like this.

If some developer is reading my comment, please arrange you I can report 
bugs and improvements.


2020年2月23日日曜日 4時09分44秒 UTC+9 James Traynor:
>
> I receive this response when I try to open notebook 
>
>
> safari cannot connect to local host 8080 
>

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