Re: General advice beyond Org

Re: General advice beyond Org

[edgar]

For posterity: I have answered to the messages on this thread elsewhere. 
Thanks!

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General advice beyond Org

[edgar]

Hello,

_I_ need help. I am in graduate school, and I keep having issues with my 
advisor for my strong inclination to use free software. I am obviously 
not in position to refuse, but she dislikes to have discussions about 
it. She pays a stipend to me every month, and my tuition is waved.

Is anyone here aware of a place where they do computational human 
biomechanics, mechanics, materials or finite elements where I could 
interact with free software? (having github, LaTeX, Python, etc.; avoid 
Micro$oft products, Matlab, Mathematica, etc.). Is there no place where 
one can simply use free software on a daily basis?

It seems from her comments that I am, otherwise, a good researcher. She 
is a nice person, but I fear that this may become an issue in the future 
for me (whether with her or other people).

As a student or junior faculty, how do you go about this? Do you just 
nod and wave your freedom good bye?

Thank you! (I will post this in other fora as well; don't let that to 
discourage you from answering, please).

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Re: General advice beyond Org

[Peter Neilson]

On Thu, 17 May 2018 20:28:22 -0400, <edgar@openmail.cc> wrote:

> Hello,
>
> _I_ need help. I am in graduate school, and I keep having issues with my  
> advisor for my strong inclination to use free software. I am obviously  
> not in position to refuse, but she dislikes to have discussions about  
> it. She pays a stipend to me every month, and my tuition is waved.
>
> Is anyone here aware of a place where they do computational human  
> biomechanics, mechanics, materials or finite elements where I could  
> interact with free software? (having github, LaTeX, Python, etc.; avoid  
> Micro$oft products, Matlab, Mathematica, etc.). Is there no place where  
> one can simply use free software on a daily basis?
>
> It seems from her comments that I am, otherwise, a good researcher. She  
> is a nice person, but I fear that this may become an issue in the future  
> for me (whether with her or other people).
>
> As a student or junior faculty, how do you go about this? Do you just  
> nod and wave your freedom good bye?
>
> Thank you! (I will post this in other fora as well; don't let that to  
> discourage you from answering, please).

What is your field? In some areas of research the foremost software tools  
have been developed on a MS platform and there is no escape unless you go  
and develop your own tools.

Allow me to illustrate from a non-software perspective, in two different  
directions. I happen to own a substantial number of horses, and thus find  
myself employing the services of a farrier. That's the person who trims  
the hooves and fits shoes. My previous farrier, now retired, made some of  
his own tools and avoided using the top, well-known brand, GE. (It's GE  
Forge & Tools, NOT General Electric!) "Too expensive," he said. "Not worth  
all that extra money." My current farrier works three times as fast as the  
other guy, and uses nothing but GE tools. Clearly, he can fit in perhaps  
twice the number of customers a day, and the tools pay for themselves. He  
could make his own, as can anyone who owns a forge, an anvil, and hammers,  
but why bother? He makes perhaps $300 an hour when working on horses, and  
nearly nothing when trying to build tools.

I also get questions from young folks between the ages of 8 and 16 who  
love horses, and want a career working with horses. They hope for a job  
where they will clean stalls and exercise horses, and maybe help with  
training. My suggestion to them is to find a profession such as accounting  
or medicine where they will be able to make enough money to own several  
horses. After a day cleaning stalls and brushing horses at minimum wage or  
less, who wants to saddle up Yet Another Horse and go riding? The  
accountant who can fathom the intricacies of expenses for a Thoroughbred  
race stable will be well rewarded, and may even get invited to ride.

These words are rather far afield from your actual question, but I think  
you do need to reflect carefully on where your interests actually lie.

So back to free software itself. Read, if you have not already done so,  
this article by rms:  
https://www.gnu.org/philosophy/open-source-misses-the-point.en.html . Then  
ponder whether you want your career to follow his delightfully weird  
footsteps, or whether your field requires a totally different approach.  
I'm sure that rms would disagree with me--he has every time I've spoken  
with him--but his is not the only philosophy available.

Re: General advice beyond Org

[S. Champailler]

Be aware that free software is politcally loaded. It's just not a matter of having the right or best tools, it' sometimes a question of ideal, that is something that is *very* hard to negociate about...

Moreover, if the people you work with use, say Word, it's pretty tough to bring in, say Latex. Because you'll disrupt the organisation of the team.

In the case of emacs, though, things are easier : it's made to work with text files and that is quite compatible with any other proprietary software. You won't affect anybody's job with that.

Here at my job, I don't control any of the software I use (I have to use Oracle, Windows, Skype), but I can choose the software that *I* use for myself. So it's a balance.

Changing other's mind, or methods is super hard, what you experience is just the normal. It'd be nice to know why your advisor rejects free software equivalents (lack of features ? fear of legal battles ? organisational ...)

Stefan


> Le 18 mai 2018 à 02:28, edgar@openmail.cc a écrit :
> 
> 
> Hello,
> 
> _I_ need help. I am in graduate school, and I keep having issues with my 
> advisor for my strong inclination to use free software. I am obviously 
> not in position to refuse, but she dislikes to have discussions about 
> it. She pays a stipend to me every month, and my tuition is waved.
> 
> Is anyone here aware of a place where they do computational human 
> biomechanics, mechanics, materials or finite elements where I could 
> interact with free software? (having github, LaTeX, Python, etc.; avoid 
> Micro$oft products, Matlab, Mathematica, etc.). Is there no place where 
> one can simply use free software on a daily basis?
> 
> It seems from her comments that I am, otherwise, a good researcher. She 
> is a nice person, but I fear that this may become an issue in the future 
> for me (whether with her or other people).
> 
> As a student or junior faculty, how do you go about this? Do you just 
> nod and wave your freedom good bye?
> 
> Thank you! (I will post this in other fora as well; don't let that to 
> discourage you from answering, please).
> 
> -------------------------------------------------
> 
> ONLY AT VFEmail! - Use our Metadata Mitigator to keep your email out of the NSA's hands!
> $24.95 ONETIME Lifetime accounts with Privacy Features!  
> 15GB disk! No bandwidth quotas!
> Commercial and Bulk Mail Options!  
>

Re: General advice beyond Org

[edgar]

On 2018-05-18 07:12, S. Champailler wrote:
> Be aware that free software is politcally loaded. It's just not a
> matter of having the right or best tools, it' sometimes a question of
> ideal, that is something that is *very* hard to negociate about...
> 
> Moreover, if the people you work with use, say Word, it's pretty tough
> to bring in, say Latex. Because you'll disrupt the organisation of the
> team.
> 
> In the case of emacs, though, things are easier : it's made to work
> with text files and that is quite compatible with any other
> proprietary software. You won't affect anybody's job with that.
> 
> Here at my job, I don't control any of the software I use (I have to
> use Oracle, Windows, Skype), but I can choose the software that *I*
> use for myself. So it's a balance.
> 
> Changing other's mind, or methods is super hard, what you experience
> is just the normal. It'd be nice to know why your advisor rejects free
> software equivalents (lack of features ? fear of legal battles ?
> organisational ...)
> 
> Stefan

Merci, Stefan. I have tried to understand her point, and I can dissect 
it into:

1. She does not see the advantage of having to learn how to use anything 
else. It works well for her, why change and waste time on doing it?

2. She likes and is used to the "features" of the software (today, I 
discovered that one of these is the so-called "track changes"; I swear I 
have tried to introduce her to Git, not that she cares).

3. I think that she is used to the interface.

4. She says (and I have no reason to question) that the whole department 
uses the proprietary software that she uses. It is an imposition to 
others (including her) to ask them to use something different.

It is only when we have to collaborate directly that the issue arises. I 
guess that it's a similar situation as you are having (programming? she 
does not care, I can do whatever I want; publication abstract? she wants 
a DOCX or DOC). What I find unfathomable is that I can produce the 
format that she needs (even with style) with free software (thanks 
community!), but what I perceive as her reluctance to my software (or 
just plain miscommunication) prevents her from informing me or me 
understanding what exactly it is that she considers important. In other 
words, she does not seem to want to deal with it in any way.

I'm sorry, I didn't want to make this very long. I hope that I explained 
myself.

The count goes like this (so that everyone knows that I am listening, 
the count is by far the least important):
- Yield partially (1) :: You will have to work with proprietary software 
in some way, but not always.
- There is no escape (1) :: You will have to work with proprietary 
software

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Re: General advice beyond Org

[Diego Zamboni]

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Hi Edgar,

As in many other contexts, it’s important to keep the big picture in mind. As a grad student, is your goal to learn about your field, to do interesting work/research, and to eventually graduate? Or is it to defend your ideals and use the software you like? If it’s the second, by all means the software you use should be a central consideration (to the point of looking for other places of study, as suggested in your original post). But if it’s the first (as it should, IMO), then the central considerations change: is your professor good/nice/competent (insert your own criteria here)? Does she foster your work/research in productive ways? Does she give you good challenges and research topics? Only you can answer those questions.

You can always compromise. Not all of us get to use only the tools we like all day long. In my case, I like my job very much, despite the fact that I have to use tools like Exchange, Sharepoint and Jira. But at home, during my free time, I get to code and use whatever tools I want (e.g. Emacs, org-mode, Elvish, Hammerspoon).  I get to use some of them at work too, but I am aware that I have to stick to the accepted standards of communication and collaboration with others.

From what you say, the tools your advisor uses are the recognized/accepted ones for doing the work. You could try to challenge this status quo, given enough time and energy. But again, think about what your goals are. You have to choose your battles. In any case, after you graduate, you can go on an be much more selective about (or even, define yourself) the tools with which you work.

As a former grad student myself, I can give you two pieces of wisdom I received over the years, one from my Ph.D. advisor, and one from one of my colleagues. Both express the same feeling:

“You may think now that getting your Ph.D. is the goal, but it’s only the beginning. The Ph.D. only opens the door for whatever you want to do next”
“The goal of a Ph.D. is to finish it”

All the best,

—Diego


> On 18 May 2018, at 10:10, edgar@openmail.cc wrote:
> 
> On 2018-05-18 07:12, S. Champailler wrote:
>> Be aware that free software is politcally loaded. It's just not a
>> matter of having the right or best tools, it' sometimes a question of
>> ideal, that is something that is *very* hard to negociate about...
>> Moreover, if the people you work with use, say Word, it's pretty tough
>> to bring in, say Latex. Because you'll disrupt the organisation of the
>> team.
>> In the case of emacs, though, things are easier : it's made to work
>> with text files and that is quite compatible with any other
>> proprietary software. You won't affect anybody's job with that.
>> Here at my job, I don't control any of the software I use (I have to
>> use Oracle, Windows, Skype), but I can choose the software that *I*
>> use for myself. So it's a balance.
>> Changing other's mind, or methods is super hard, what you experience
>> is just the normal. It'd be nice to know why your advisor rejects free
>> software equivalents (lack of features ? fear of legal battles ?
>> organisational ...)
>> Stefan
> 
> Merci, Stefan. I have tried to understand her point, and I can dissect it into:
> 
> 1. She does not see the advantage of having to learn how to use anything else. It works well for her, why change and waste time on doing it?
> 
> 2. She likes and is used to the "features" of the software (today, I discovered that one of these is the so-called "track changes"; I swear I have tried to introduce her to Git, not that she cares).
> 
> 3. I think that she is used to the interface.
> 
> 4. She says (and I have no reason to question) that the whole department uses the proprietary software that she uses. It is an imposition to others (including her) to ask them to use something different.
> 
> It is only when we have to collaborate directly that the issue arises. I guess that it's a similar situation as you are having (programming? she does not care, I can do whatever I want; publication abstract? she wants a DOCX or DOC). What I find unfathomable is that I can produce the format that she needs (even with style) with free software (thanks community!), but what I perceive as her reluctance to my software (or just plain miscommunication) prevents her from informing me or me understanding what exactly it is that she considers important. In other words, she does not seem to want to deal with it in any way.
> 
> I'm sorry, I didn't want to make this very long. I hope that I explained myself.
> 
> The count goes like this (so that everyone knows that I am listening, the count is by far the least important):
> - Yield partially (1) :: You will have to work with proprietary software in some way, but not always.
> - There is no escape (1) :: You will have to work with proprietary software
> 
> -------------------------------------------------
> 
> ONLY AT VFEmail! - Use our Metadata Mitigator to keep your email out of the NSA's hands!
> $24.95 ONETIME Lifetime accounts with Privacy Features!  15GB disk! No bandwidth quotas!
> Commercial and Bulk Mail Options!  


[-- Attachment #2: Type: text/html, Size: 6478 bytes --]

Re: General advice beyond Org

[Aaron Ecay]

Hi Edgar,

2018ko maiatzak 18an, -ek idatzi zuen:

> It is only when we have to collaborate directly that the issue
> arises. 

It sounds like the issue you are having is about collaboration workflow,
and not about the usage of free software per se.  Reading between the
lines, it sounds like your biggest difficulty is with Microsoft Word.
Itʼs very unlikely that you will be able to convince your advisor to
switch to another program when writing with you.  As Diego said, it is
ultimately up to you whether you can live with this.  But there are
certainly compromises you could entertain that might make it easier.

There are important benefits, to a field and to individual researchers,
of open analyses.  On the other hand, what maters about a scientific
publication is principally the words themselves and where they are
published – not the workflow that was used to create them, which mostly
passes into irrelevance once they become part of the scientific record.
So you might find pragmatic benefits to focusing on free software
analysis tools and programming languages, and on the importance of
publicly releasing analysis materials (whether based on free software or
not) at an appropriate stage of the research, rather than on document
authorship workflow where your advisor seems to have a particularly
entrenched position.

Another suggestion to reach out to other graduate students, who have the
surplus of time* and lack of pre-established workflow habits conducive to
learning new techniques.  This wonʼt directly solve your issues with
your advisor, but if you are contributing to the success of free
software in other areas you might feel like your sacrifices with her are
being balanced out.

(*Having been a graduate student, Iʼm only too aware of the falsity of
the premise that grad students have ample free time in an absolute
sense.  But relative to other career stages, grad students are probably
the best situated in that regard.  Itʼs also true that there are many
things that grad students need to learn that could be learned either
with free or nonfree software.  The marginal time cost of replacing
nonfree software in that learning with free software is likely to be
small.)

Itʼs also true that free software has network effects.  Once someone is
using R or Python, they are introduced to things like Jupyter or knitr
(which are literate programming systems) – or even org mode.  They also
get exposed to VCS (like git), free text editors (like emacs, or RStudio),
and other tools that do not directly replace Word but contribute to an
alternate ecosystem.  They might eventually be induced to switch their
writing software of choice because of the features of such environments.
So by evangelizing the pieces of free software that are most appetizing
to others in your field, you are laying the groundwork for subsequent
improvements that might initially be a harder sell.

Finally, a very pragmatic suggestion.  You might suggest to your advisor
that you and her collaborate via Google Docs rather than MS Word.  This
is something I have found helpful with colleagues of mine who are not
otherwise prepared to change their writing habits.  The Google Docs
interface is very similar to Word (but actually avoids some of the
radical UI changes that MS has made recently, which might make it even
more appetizing to certain users).  While Gdocs is not free software (as
itʼs important to point out), it enables me to use less proprietary
software, on average.  Iʼve never been able to get Libreoffice to work
satisfactorily for iterative edits to a Word doc; I find that it too
often loses formatting, included images, or otherwise doesnʼt
interoperate with Word well enough.  So in the absence of Google Docs I
would have to maintain a Windows system on which to use Word.  With
Gdocs I have one browser tab that runs unfree JS, but the rest of my
system is GNU/Linux.  (There are also benefits to the online-first
nature of Google Docs, which avoids the emailing back and forth of
dueling versions of a Word document that I have sometimes encountered in
groups that primarily use Word – but these are orthogonal to the
free/nonfree distinction.)

I hope that some of this comes as useful advice.

-- 
Aaron Ecay

Re: General advice beyond Org

[Stefan Monnier]

> It is only when we have to collaborate directly that the issue
> arises.  I guess that it's a similar situation as you are having
> (programming? she does not care, I can do whatever I want; publication
> abstract? she wants a DOCX or DOC).

Collaborating on an article does require a fairly "deep" integration of
various people's tools, so some compromise often need to be made.

If she's used to using Word to edit documents, then it's likely going to
be difficult to convince her to use something else, at least during your
tenure as student.  What I do usually in those cases is the following:

- I refuse to install proprietary software, so in the worst case I'll edit
  a .docx document with LibreOffice (I don't see why she'd object to
  that under the imperfect compatibility between LibreOffice and Word
  gets in the way).
  [ BTW, If imperfect compatibility between LibreOffice and Word gets in the
  way, you might try and look for some other version of Word than hers,
  and find other incompatibilities (the various Word versions also
  suffer from imperfect compatibility), so as to show her that the issue
  is not just due to your use of Free Software.  ]

- You can try and get her to install the ODT plugin for Word so she can
  open ODT documents as well as .docx in her Word program.
  I often make the effort to only send ODT documents, even when it's
  a modification of a document that was sent to me in .docx format (on
  the premise that I shouldn't be the only one to bear the brunt of the
  format war).

- Depending on how many changes/annotations she contributes to the
  document, you might be able to keep your original in your favorite
  format (LaTeX, Org, you name it); convert it to ODT or .docx before
  sending it to her; and then integrating her changes/annotations by
  hand into your original document.

Using Git with ODT/.docx documents is about as pleasant as pulling teeth
in my experience, so there's no point trying to convince her to try it
out as long as she sticks to such WYSIWYG thingies.

Of course, the real problems start when she wants to use some *really*
poorly supported format like Apple's Pages.


        Stefan

Re: General advice beyond Org

[Yuri Khan]

On Fri, May 18, 2018 at 7:29 AM <edgar@openmail.cc> wrote:

> _I_ need help. I am in graduate school, and I keep having issues with my
> advisor for my strong inclination to use free software. I am obviously
> not in position to refuse, but she dislikes to have discussions about
> it. She pays a stipend to me every month, and my tuition is wa[i]ved.

> Is anyone here aware of a place where they do computational human
> biomechanics, mechanics, materials or finite elements where I could
> interact with free software? (having github, LaTeX, Python, etc.; avoid
> Micro$oft products, Matlab, Mathematica, etc.). Is there no place where
> one can simply use free software on a daily basis?

Are you required to pay for licenses for proprietary software you are asked
to use? Chances are, your school is getting academic discounts, and you get
to use it for no charge.

Your instructors and professors probably have a lot of experience with
those tools. They are understandably reluctant to switch, because the tools
work well enough for them.

Also, as a student, you do not have sufficient influence to convert
everybody at your school to free software.

> As a student or junior faculty, how do you go about this? Do you just
> nod and wave your freedom good bye?

The point of education is to get exposed to many tools, techniques and
workflows. By limiting yourself to free software only, you will miss out.

Be a scout in the proprietary camp. Learn the tools your instructors are
willing to teach. Learn what it takes to achieve the same results with free
software. Learn the difference in workflows and user experience.

You will find something you can do with free software that you don’t know
how to do with proprietary tools. Ask your teachers. They will either point
you at something you missed (and then you can study it); or they will admit
that feature is nice but their tool doesn’t have it (and then you have
demonstrated the merits of free software); or they will say it’s not
important.

You will also likely find more than a few points where non-free software
delivers better UX. Use that knowledge to improve free software so that it
can compete with proprietary software on UX terms, not only on the issue of
freedom.

Re: General advice beyond Org

[S. Champailler]

This is a super wise advice :

>> Be a scout in the proprietary camp. Learn the tools your instructors are
>> willing to teach. Learn what it takes to achieve the same results with free
>> software. Learn the difference in workflows and user experience.

Comparing stuff in scenarios you don't invent yourself is super enlightening. Once you don't define the scenario, all sorts of edge/unexpected situations arise.

For example, if you work with math stuff, I'm sure you'll find interesting differences between computations results (e.g. matlab equations solving versus say Octave).

stF







> Le 18 mai 2018 à 12:54, Yuri Khan <yurivkhan@gmail.com> a écrit :
> 
> 
> On Fri, May 18, 2018 at 7:29 AM <edgar@openmail.cc> wrote:
> 
> > _I_ need help. I am in graduate school, and I keep having issues with my
> > advisor for my strong inclination to use free software. I am obviously
> > not in position to refuse, but she dislikes to have discussions about
> > it. She pays a stipend to me every month, and my tuition is wa[i]ved.
> 
> > Is anyone here aware of a place where they do computational human
> > biomechanics, mechanics, materials or finite elements where I could
> > interact with free software? (having github, LaTeX, Python, etc.; avoid
> > Micro$oft products, Matlab, Mathematica, etc.). Is there no place where
> > one can simply use free software on a daily basis?
> 
> Are you required to pay for licenses for proprietary software you are asked
> to use? Chances are, your school is getting academic discounts, and you get
> to use it for no charge.
> 
> Your instructors and professors probably have a lot of experience with
> those tools. They are understandably reluctant to switch, because the tools
> work well enough for them.
> 
> Also, as a student, you do not have sufficient influence to convert
> everybody at your school to free software.
> 
> > As a student or junior faculty, how do you go about this? Do you just
> > nod and wave your freedom good bye?
> 
> The point of education is to get exposed to many tools, techniques and
> workflows. By limiting yourself to free software only, you will miss out.
> 
> Be a scout in the proprietary camp. Learn the tools your instructors are
> willing to teach. Learn what it takes to achieve the same results with free
> software. Learn the difference in workflows and user experience.
> 
> You will find something you can do with free software that you don’t know
> how to do with proprietary tools. Ask your teachers. They will either point
> you at something you missed (and then you can study it); or they will admit
> that feature is nice but their tool doesn’t have it (and then you have
> demonstrated the merits of free software); or they will say it’s not
> important.
> 
> You will also likely find more than a few points where non-free software
> delivers better UX. Use that knowledge to improve free software so that it
> can compete with proprietary software on UX terms, not only on the issue of
> freedom.
>

Re: General advice beyond Org

[Kevin Buchs]

As a student, you simply need to go along with your supervisor's
recommendations. You are not in a position to dictate the terms. Using the
proprietary tools will not hurt you, unless you need to buy your own. If it
were the case that you needed to buy your own, then I would ask your
supervisor for another solution.

Even as a Junior faculty member, you may be in close collaboration with
other faculty and should follow the consensus. That is how you work with
other people effectively. You don't keep asserting that your solution is
better. When you are calling the shots, you can use the tools you wish.

So, you need to adjust your attitude. It may be that you are presenting the
issue of principles - I prefer free, you prefer proprietary, but that is
not really the true issue. Maybe you don't know the proprietary tools and
don't want to learn them or feel you can't learn them. Choice of tools you
use is no reason to switch graduate programs.

This is entirely a matter of getting along with other people, not being
selfish, etc. These are life skills we are talking about.

Kevin Buchs

On Thu, May 17, 2018 at 7:28 PM, <edgar@openmail.cc> wrote:

> Hello,
>
> _I_ need help. I am in graduate school, and I keep having issues with my
> advisor for my strong inclination to use free software. I am obviously not
> in position to refuse, but she dislikes to have discussions about it. She
> pays a stipend to me every month, and my tuition is waved.
>
> Is anyone here aware of a place where they do computational human
> biomechanics, mechanics, materials or finite elements where I could
> interact with free software? (having github, LaTeX, Python, etc.; avoid
> Micro$oft products, Matlab, Mathematica, etc.). Is there no place where one
> can simply use free software on a daily basis?
>
> It seems from her comments that I am, otherwise, a good researcher. She is
> a nice person, but I fear that this may become an issue in the future for
> me (whether with her or other people).
>
> As a student or junior faculty, how do you go about this? Do you just nod
> and wave your freedom good bye?
>
> Thank you! (I will post this in other fora as well; don't let that to
> discourage you from answering, please).
>
> -------------------------------------------------
>
> ONLY AT VFEmail! - Use our Metadata Mitigator to keep your email out of
> the NSA's hands!
> $24.95 ONETIME Lifetime accounts with Privacy Features!  15GB disk! No
> bandwidth quotas!
> Commercial and Bulk Mail Options!
>

Re: General advice beyond Org

[hymie!]

In our last episode, the evil Dr. Lacto had captured our hero,
  edgar@openmail.cc <edgar@openmail.cc>, who said:

> I am in graduate school, and I keep having issues with my 
> advisor for my strong inclination to use free software. [...]
>
> Is anyone here aware of a place where they do computational human 
> biomechanics, mechanics, materials or finite elements where I could 
> interact with free software?

First question -- it sounds like you are doing very specific research
with very specific tools, software, equations, and things like that.
Are you sure that free software exists that will do what you want?

For example, good luck finding free software that will do your taxes.

> Do you just nod and wave your freedom good bye?

Second question -- you keep using that word "free".  Are you really "free"
in this situation?  You said you are getting tuition covered and a
stipend.  The way employment typically works is that, in return for
salary and/or compensation, you give your full devotion to your employer's
wants and needs instead of your own.  Using your employer's software is
not a huge jump.

I don't mean this as a personal attack.  That's how it works.  I am
"free" to wear a t-shirt that says "F**K THE POLICE" on it, but the
person who pays my salary would prefer if, for 40 hours each week, I
wear a different shirt.  I am "free" to ignore his request.  He is "free"
to stop paying my salary.

So I'm afraid that's my answer.  Suck it up and do what the nice person
who is giving you lots of money wants you to do, they way he/she wants
you to do it.

--hymie!     http://lactose.homelinux.net/~hymie    hymie@lactose.homelinux.net

Re: General advice beyond Org

[Marcin Borkowski]

On 2018-05-18, at 15:50, hymie! <hymie@lactose.homelinux.net> wrote:

> For example, good luck finding free software that will do your taxes.

I, for that matter, do not use any proprietary software to do my taxes.
(And BTW, I'm not religiously following the "only use free software"
mantra, in fact, I feel some distance to the FSF ideals.)

Best,

-- 
Marcin Borkowski
http://mbork.pl

Re: General advice beyond Org

[Adonay Felipe Nogueira]

2018-05-18T00:28:22+0000 edgar@openmail.cc wrote:
> Hello,
>
> _I_ need help. I am in graduate school, and I keep having issues with

I'm undergraduating (seeking a bachelor's degree in organization
management). :D

> _I_ need help. I am in graduate school, and I keep having issues with
> my advisor for my strong inclination to use free software. I am
> obviously not in position to refuse, but she dislikes to have

At first glance I would recommend you to keep using free/libre software
only, and advocating for it where you live, work and study. But please
read on...

> discussions about it. She pays a stipend to me every month, and my
> tuition is waved.

... Now this is a tricky challenge. Not that difficult, but as far as I
can see these are the options:

a) worst: make the compromise and use these non-free tools in your
   computer (the same applies when using a virtual machine or a
   container), because all-in-alll, it's still your personal
   computer. Besides, the virtual machine or container can misbehave and
   impact your real system or personal files.

   You will still have to deal with side-effects caused by loss of
   control over your own computing, let alone the need to learn
   how to use that non-free tool;

b) somewhat better, although slow: use another computer (or get one from
   a rent) to do the work, and only do the work with that machine.

   The same case described in the second paragraph of (a) applies here;

c) better: do it with only free/libre software, and perhaps even teach
   or show the people involved how to make use of tools that support
   your workflow. For example Software Carpentry has awesome
   collaborative material on the basics of VCS using Git and of
   statistics wih R.

   If you don't have time to teach, make use of a tool that eases *them*
   participating in their terms.

   As an example, I'm writing my final course work using Org-mode, LaTeX
   and TikZ/PGF (this last one is for graphics), and whenever I want to
   send a snapshot for review to my advisor I do so through making a
   .pdf, but there is even more...

   The .pdf files don't actually track changes, so I must go into the
   extra step of doing the following:

   --8<---------------cut here---------------start------------->8--- #
   # Convert old .pdf work snapshot to text. Makes a .txt file of the same
   # name, minus ".pdf". Caution here because if you don't specify a name or
   # path to place the .txt file, `pdftotext' will put it in the same
   # directory where the original is, contrary to what most commands do in
   # GNU+Linux. In Trisquel 8.0 Flidas, `pdftotext' comes from the
   # "poppler-utils" package.

   pdftotext "Documents/Work_---_2018-05-01.pdf"

   # Same for current .pdf which will be sent.

   pdftotext "Work.pdf"

   # Use GNU `diff' to produce Unified diff for text-only content.  For us
   # who use GNU+Linux or GNU-with-Linux computers (GC) the diff files
   # commonly have .diff or .patch extensions, but we use .txt here so that
   # users of Windows computers (WC) can open those with ease in their
   # default plain text editor.

   diff -u "Work_---_2018-05-01.txt" "Work.txt" > "Work_diff.txt"

   # Among other unknown reasons, WCs make use of "\r\n" (carriage return
   # followed by line feed, commonly known as "CRLF" or "CR+LF") in the end
   # of each line to distinguish these plain text files from binary files.
   # WCs' default notepad will open a non-CRLF file but with all lines
   # joined, so we correct that using the `sed' line below. The side-effect
   # for us GC users is that some editing software might present two line
   # breaks.

   sed -i '/\r$/! { s/\($\)/\r\1/g }' "Work_diff.txt"
   --8<---------------cut here---------------end--------------->8---

   Then send them both the .pdf and the diff file (the one which has
   .txt extension of course). And explain to them that the .txt is plain
   text that can be opened in plain text editor (usually called
   "Notepad" in Windows), and mention that it essentially shows the
   difference between old and new versions, and that:

   - Lines that begin with "+ " is new content;

   - ... "- " old content being removed;

   - ... "@@ -old_start,count_old +new_start,count_new @@" a line jump to
     given "old_start" line in the old file.

   With all that said, the advantages of .pdf files is that the advisors
   can highlight and annote/comment on these, save the changes and send
   it back to you (they can't change the structure or content of the
   document itself, but can at least give you hints).

With all the options I presented, there is still another issue which is
quite common at least in the college I study: the advisors don't
actually orient people that well here, so even if someone theoretically
decides to "suck it up and use non-free software anyways" this doesn't
stop the advisor from being too vague as to give comments such as "it's
not compliant with the institutional norms" (what exactly is not
compliant?! And how?!).

> As a student or junior faculty, how do you go about this? Do you just
> nod and wave your freedom good bye?

Particularly I would make use of (b) or (c), but not (a).

I hope this has shed some light.


Respectfully, Adonay.

-- 
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Re: General advice beyond Org

[Marcin Borkowski]

On 2018-05-18, at 21:57, Adonay Felipe Nogueira <adfeno@hyperbola.info> wrote:

> c) better: do it with only free/libre software, and perhaps even teach
>    or show the people involved how to make use of tools that support
>    your workflow. For example Software Carpentry has awesome
>    collaborative material on the basics of VCS using Git and of
>    statistics wih R.
>
>    If you don't have time to teach, make use of a tool that eases *them*
>    participating in their terms.
>
>    As an example, I'm writing my final course work using Org-mode, LaTeX
>    and TikZ/PGF (this last one is for graphics), and whenever I want to
>    send a snapshot for review to my advisor I do so through making a
>    .pdf, but there is even more...
>
>    The .pdf files don't actually track changes, so I must go into the
>    extra step of doing the following:

Or use latexdiff (in case of LaTeX).

Hth,

-- 
Marcin Borkowski
http://mbork.pl

Re: General advice beyond Org

[Samuel Wales]

perhaps we can start thinking about improving registration between formats?

if you export org [you posted to org mailng list] to a foreign format,
you want your collaborator to be able to edit, save, send back without
raising a sweat.

now you have to integrate the changes.  you want to do this without annoyance.

suppose you export comments in the foreign format that contain the
equivalent of persistent markers.  you might or might not be willing
to put org id or custom id on every heading, but there might be
workarounds that are not so intrusive.  maybe your source can contain
comments with markers.  dunno.

if your exported document is a subtree within a huge org file that you
edit all the time, registration allows your software to identify that
subtree, so you're not trying to change anything outside that subtree.
that alone is a win.

but maybe we can do more.  the markers can register sections or even
paragraphs if you're doing intensive collaboration.  the tricky part
might be getting standard tools to understand that the mapping of
markers takes precedence over everything else.

details of this handwavey and possibly impossible brainstorm are left
as an exercise for the reader.

Re: General advice beyond Org

[Adonay Felipe Nogueira]

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Just an update to let you know that I decided to migrate from
Org-mode+LaTeX to ODF-and-related, particularly because of LPPL+GPL
incompatibility, caused by LaTeX and related projects and because
ODF-and-related are easier for the other people to participate and see
the changes (no need to compile a .pdf nor to download 4 GiB of software).

ODF 1.2 (which is used by default at least in LibreOffice 5) is good and
offers many features similar to Org-mode, including adding files to each
other, interacting with spreadsheets (look for "relative DDE link"), and
also offers bibliography/reference manageemnt, along many other things.

Although I do want to point out that you might want to go to View ->
Disable "Show figures", so that LibreOffice Writer .odt documents are
more editable and less slow.

Also, note that you must recommend people to use LibreOffice to open the
files. Microsoft says to have support, but it's not excellent.

You may also want to import other .odt/.rtf/.doc/.docx files inside the
main one. The tricks are that if you do so using "Insert" -> "Section"
and tick "Link", the inserted section will use the main document's
styles, not their own. Besides, for these files, since they *do* have
notion of what is a "page break", then they will inevitably start in the
next page. Also, inserting them this way may replace or add document
metadata/properties (look in "File" -> "Properties"). at the same time,
some files that you want to add are actually drawings made in
LibreOffice Draw. In all the cases you might want to keep their own
styling. To do this export them to .pdf.

I use this:

------------------------------------------------------------------------
# Please close any running LibreOffice, or `soffice' silently fails.
# No need to specify target file name.
while read each_file
do
  soffice --headless \
	-convert-to pdf \
	"${each_file}"
done <<end_of_list
Preserve styles.docx
Contract.doc
Multi-page document with spaces in name.odt
Drawing.odg
end_of_list
------------------------------------------------------------------------

After this, if you happen to need to import these .pdf files into your
document, use ImageMagick's `convert' command to do the conversion to
.png. For example:

------------------------------------------------------------------------
# `-units' and `-density' are important to be set before .pdf input
# according to what I will do, otherwise there will be loss of quality.
while read pdf_file
do
  convert -units PixelsPerInch \
	-density 300 \
	"${pdf_file}" \
	"$(echo "${pdf_file}" | sed 's/\.pdf$/.png/g')"
done <<end_of_list
Preserve styles.pdf
Multi-page document with spaces in name.pdf
Drawing.pdf
end_of_list
------------------------------------------------------------------------

This will take care of multi-page .pdfs, since the .png files will be
like "Original name-0.png", "Original name-1.png", "Original
name-2.png", and so on. Zero (0) is the first page.

After this conversion, go to the main document, "Insert" ->
"Figure"/"image", tick the box that has "Link" and select the image that
you want to insert. Do this for each .png image.

The "link" options are important so that the main document picks any
change made to the .png image, otherwise LibreOffice will insert the
entire image in the .odt, which will also make it more heavier to attach
in e-mails (but requires the other person to also have the linked file
in the same place).

A caveat of the manual .png insertion is that if a .pdf happens to have
more or less pages than the last conversion to .png, then you will need
to add or delete the related links and their corresponding figures in
the main .odt file. If someone has better solution please share.

Additionally, one can't do "Insert" -> "OLE Object" to insert .odg or
.ods files because these *cannot* break across pages, and don't look
good when printing. This OLE feature wasn't made for printing purpose,
but to facilitate editing without leaving the same program. If I recall
correctly, it's a Microsoft kludge.

As for tabular/table results produced by R, use and abuse of
`write.csv'. Besides, make R output graphics to a .png image (use the
`png' command/device). For all of this, write an .R/.r file and use
Rscript to run it.

The R-produced .png files can be inserted in the main .odt document I
described earlier, no need to repeat the explanation. What you need to
tweak in the `png' R command/device is the `pointsize' and `res'
arguments. Something like this would do:

------------------------------------------------------------------------
## The variables are here just for explanation.

## The standard DPI/`res' of the `png' command/device.
R_img_dpi <- 72

## The standard pointsize of the `png' command/device.
R_pointsize <- 12

## The new DPI/`res' of our image, to make things sharp.
## Just changing `width' or `height' isn't enough.
sharp_img_dpi <- 90

png(file="Plot.png",
	height = 768,
	pointsize = R_pointsize * sharp_img_dpi / R_img_dpi,
	res = sharp_img_dpi,
	width = 1024)

plot(something)
## ... or output some graphic.

## Close/save the .png image.
dev.off()
------------------------------------------------------------------------

Now you ask, how to insert the .csv files in the main .odt document as
tables in a dynamic way (such that if the .csv contents are changed by a
external application, LibreOffice picks the modifocation)?

To partially answer that question, I suggest you to make a new .ods
spreadsheet set/document, and for each .csv, use "Spreadsheet" ->
"Insert spreadsheet from file", select the .csv, enable/tick "Link",
save the .ods. With that done, go to the spreadsheet/tab in LibreOffice
Calc that you want to insert in your main .odt, click on the square
between the column name A and which is above row name 1 (this will
select the entire spreadsheet), copy (Ctrl + C), and Ctrl + Shift + V in
the .odt, select "DDE link".

To style the table, do it in the .odt document, not in the .ods
spreadsheet. Particularly, if you want to make tables with consistent
formating, make the first example table according to your needs then use
the "Table" -> "Style and formating" -> "Add" option to make that
formatting into a new table style. Note however that applying this to
other tables doesn't establish a "style" relationship as is done in the
case of other elements in LibreOffice, so I cannot expect every "Black
1"-styled table to change if I ever update/remake the "Black 1" table
style, so my advice is that these styles deal with display of
tables/cells/rows/columns themselves, not their contents/text. For these
you are better off changing the "Table content" and "Table
title/heading" paragraph styles.

Another caveat of this method is that the DDE column/row references are
absolute ("take from 1 to 3") and as far as I know there is no way to
say "take the entire spreadsheet even if new columns/rows are added".

Again, if someone has a better method that addresses both caveats,
please share.

Finally, there is a known bug[1] in LibreOffice Writer in which DDE
links from Calc .ods files are inserted referring to the absolute path
of the file. So after doing the "Ctrl + Shift + V, select 'DDE link'",
go to "Edit" -> "Links", double-click in the corresponding "soffice"
link to the .ods file, and in "File" field, and change that to relative
path, inserting "file:./" at the start, like so:

Old path: /home/adfeno/Docs/Work/Spreadsheets in the same directory.ods
New path: file:./Spreadsheets in the same directory.ods

Or if the spreadsheets are in some parent directory, use "file:../",
like so:

Old path: /home/adfeno/Docs/Spreadsheets in parent directory.ods
New path: file:../Spreadsheets in parent directory.ods

And so on for traversing to outer directories:

Old path: /home/adfeno/Docs/Contract/Spreadsheets in contract.ods
New path: file:../Contract/Spreadsheets in contract.ods

Similarly:

Old path: /home/adfeno/Spreadsheets at home.ods
New path: file:../../Spreadsheets at home.ods


All in all, the command-line steps are great because you can append
these in the main .odt itself (to be printed verbatim) using "Insert" ->
"Section", and since they are plain text files, it won't make the text
start in new page (so you can write a section title before them).

Happy hacking! :D


[1] https://bugs.documentfoundation.org/show_bug.cgi?id=47223


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Re: General advice beyond Org

[Marco]

Hey fellow orgers,

I started as post-doc almost 10 years ago, I made a point in having
linux on my desktop and only use software I see fit - and know - such
R, and LaTeX to write papers. The occasional word/excel document I
opened with libreoffice/wps office or more frequently remotely on a
windows server / on a virtualbox, same with the occasional
windows-only piece of software I needed to use.
After 8-9 years of mockery, my whole departement is now switching to
LiNuX/LaTeX/python/R/jupyter, with the exception of a few specialized
softwares which are windows-only and will run on selected
machines/servers. Point is, also the secretary has to migrate, she was
the greatest advocate against the change.
No luck yet with emacs + org with my colleagues, but hey, one step at a time ;)
If your research and daily work involves programming/modelling I
actually don't see any point in staying on windows. Unices have LOTS
of advantages. The best general-purpose research tools nowadays are
free/libre software (since 3D FEM was named: openfoam, moose,
opencascade/salome, code_aster just to name a few... ), that is, if
you are developing something and not just running models, their steep
learning curve pays off immediately. If it's just a matter of running
specific models maybe there are other specialized softwares which may
be more efficient (e.g., avizo for 3D microtomography, eclipse /
petrel for geological modelling and reservoir engineering). In the
realm of statistics/machine learning/AI it's all linux-based free
software (think about keras + tensorflow with R and Python, but loads
and loads of other similar stuff out there).
So in my opinion in a research environment there are 2 kinds of
activities: computational/programming stuff, where unix and free
software have a clear advantage both on desktops and of course on HPC
(of course it depends how it looks like in your domain AND in your
research group), and on the other side wiriting documents and
interacting with others (reports, proposals, data exchange, papers).
You should have 100% control of the first category, but still have to
factor in cooperation with colleagues (i.e.: if everyoen is working on
matlab and you are supposed to extend and re-use their developments...
probably you should too. At least try sci-lab and octave); but you can
definitely compromise on the second.
Cheers and good luck,
domanov

Re: General advice beyond Org

[Grant Rettke]

On Wed, Jun 6, 2018 at 3:58 AM, Marco <domanov@gmail.com> wrote:
> I started as post-doc almost 10 years ago,

Thanks for your share Marco.