Pdfmorph web-page #23

RomanMatthew · 2019-07-09T17:52:34Z

sbillinge

great job....

Is there a way to preview how it will look when it is built?

products/PDFmorph.rst

RomanMatthew · 2019-07-09T18:10:44Z

@chiahaoliu @CJ-Wright @sbillinge Sorry to be tagging you guys so fervently in all this stuff but I just want to make sure that I did the right stuff. What do you think?

CJ-Wright · 2019-07-09T18:14:02Z

@sbillinge if you look at the code there is a button on the file name line which looks like a document, that will render the rst to the best of its ability.

….github.io into pdfmorph_web

products/PDFmorph.rst

RomanMatthew · 2019-07-09T18:23:44Z

products/PDFmorph.rst

+independent way. The program was designed to help a researcher answer the question: 
+"has my material undergone a phase transition between these two measurements?"
+
+PDFmorph makes use of several data manipulation techniques to correct for benign


@sbillinge I shortened the description a little bit here - please let me know if it's too detrimental to the content itself!

It is good. Make sure there is a pointer to the user manual documentation

btw, please make an issue to check all the docstrings.

There's no manual in the diffpy.pdfmorph master, so I assume I'll have to link that once I make it, right? and will do on the docstrings issue! Would that be for this particular PR?

package specific doc should go to diffpy.pdfmorph repo in a different PR.

You will need to create a special branch named `gh-pages so github will build the website for you automatically. We can talk about more details in person.

Sounds good! I'll grab you when you come back

package specific doc should go to diffpy.pdfmorph repo in a different PR.
You will need to create a special branch named `gh-pages so github will build the website for you automatically.

actually the best would be to publish package docs on readthedocs.io, for example the docs for diffpy.structure are at https://diffpystructure.readthedocs.io/en/stable.

I have a TODO issue #22 to stop hosting manual at the gh-pages branch and move it over to RTD. This should eventually happen for all diffpy packages.

I'll get started on that! Thank you @pavoljuhas. So publishing on rtd is what we would want to do for the documentation for all of diffpy? Sounds like a decent project!

So publishing on rtd is what we would want to do for the documentation for all of diffpy?

Yes, I think it would save a lot of work and keep the manuals in sync with the source code.

@pavoljuhas would you mind providing the source for the diffpy.structure that was published on readthedocs? That would be really helpful, thanks!

The RTD page is rebuild on pushes to https://github.com/diffpy/diffpy.structure repo with the manual sources in doc/manual. There is a small control file .readthedocs.yml to setup the manual compilation at RTD.

Setting up an RTD build for PDFmorph should be an issue in the pdfmorph project.
Here we should create documentation links pointing to the RTD pages - once they are up.

sbillinge

few small things

products/PDFmorph.rst

pavoljuhas · 2019-07-09T19:23:50Z

I suggest to use lowercase filenames for the new pages.
This would make it easier to link them from other pages and less error prone to type the URL directly.

Please rename

products/PDFmorph.rst --> products/pdfmorph.rst
products/pdfmorphLICENSE.rst --> products/pdfmorph_license.rst

make clean html complains that pdfmorphlicense.rst is not included at all, please check
please link to the new pdfmorph page from _templates/menu01.html so we link it from the menu
whitespace - please fix issues reported from git diff --check source pdfmorph_web.
Consider activating a commit hook that would prevent these in a first place:
```
cd .git/hooks
cp pre-commit.sample pre-commit
```

products/pdfmorph.rst

products/pdfmorph_license.rst

RomanMatthew · 2019-07-16T20:25:53Z

@pavoljuhas I fixed some of the problems but caused more in products/pythonpackages.rst. Could you help me figure out how to solve the issues I caused? I've been trying for a bit

Temporary merge of main line, please rebase.

pavoljuhas · 2019-07-16T23:11:28Z

@RomanMatthew - I have fixed the conflicts by a temporary merge with the parent source branch.
Also there was an extra blank line in the table which broke the syntax.

I recommend to merge this PR using "Rebase and Merge" so it is easier to later on understand what changes it brings in.

RomanMatthew · 2019-07-17T15:11:08Z

@pavoljuhas @sbillinge Does that mean that it should be ready to merge now?

pavoljuhas · 2019-07-17T15:44:34Z

Does that mean that it should be ready to merge now?

Let me give it a quick read.

pavoljuhas · 2019-07-17T17:52:38Z

BTW, we need to hold on with this merge until PDFmorph is really out.

sbillinge

few comments

products/pdfmorph.rst

sbillinge · 2019-07-18T11:38:49Z

products/pdfmorph.rst

+
+		conda create --name=<env_name> python=3
+
+	You can give the environment any name you like but it should


the python=3 ensures it will have python 3 installed so remove "but it should have some Python version 3 installed (though PDFmorph also works on Python 2.7)." This is just confusing.

Probably the best is at the top say "PDFmorph will run on python 3 and also python 2.7 or higher, but we recommend.....virtual environment. Here we give instructions for installing the python 3 version. With Anaconda...."

I would suggest to drop instructions for creating new environment, it is not really needed as pdfmorph is quite lightweight package.

Perhaps the installation instructions should be

conda install --channel=diffpy diffpy.pdfmorph

or if you use conda-forge

conda install --channel=conda-forge diffpy.pdfmorph

its for novice users who are not familiar with conda. Maybe start this section out from right below the license information:

"PDFmorph is distribute and is best installed using conda. It should run in most python 3 conda environments and can be directly installed in an existing environment (using the commands listed below). If you do not currently have conda installed, here are some lightweight instructions for getting started:

download and install Anaconda or mini-conda from continuum <https://www.continuum.io>__."

create a python 3 environment with the command

conda create --name=<env_name> python=3

where you can give the environment any name you like.

You only need to create the environment once,
but every time you want to use PDFmorph you will have to
reactivate the environment in which it is installed by typing ::

...and so on

Simon could you guve the new version a look?

products/pdfmorph.rst

sbillinge · 2019-07-18T11:42:44Z

products/pdfmorph_license.txt

@@ -0,0 +1,36 @@
+This program is part of the DiffPy open-source project at Columbia


Is it possible to connect directly to the license file in the package top level directory? This would be more robust/maintainable than having two license files hanging around. What if they are different? Which one is the correct one?

Is it possible to connect directly to the license file in the package top level directory? This would be more robust/maintainable than having two license files hanging around. What if they are different?

For diffpy-cmi packages I use a dedicated license branch at
https://github.com/diffpy/diffpy-release/tree/license.
I make any text updates in the "license" branch and merge it to each package just before release, e.g., here.

Perhaps we could add a new license-pdfmorph branch to the "diffpy-release" repo and keep on merging it to this webpage sources and to the "diffpy.pdfmorph" master as well. If license files come from a common upstream branch, they will stay in sync.

is this something that would be top-priority upon release?

sbillinge

yes, these changes are all good. @pavoljuhas, waiting for your approval on this.

Include only when used.

Fix issues from `git diff --check`.

List compatible Python versions. Suggest pip rather than easy_install.

pavoljuhas · 2019-07-18T20:02:29Z

Here is my take on that page - RomanMatthew/diffpy.github.io@pdfmorph_web...pavoljuhas:pdfmorph_web_pj
and here is the page rendered - http://pavoljuhas.github.io/diffpy.github.io/products/pdfmorph.html.

If that looks OK, please pull

git pull https://github.com/pavoljuhas/diffpy.github.io.git pdfmorph_web_pj

RomanMatthew · 2019-07-19T18:58:39Z

@pavoljuhas The changes should be implemented now!

pavoljuhas

This looks good to me, but let's hold on with publishing until the release is out.

RomanMatthew and others added 3 commits July 9, 2019 13:48

Added infrastructure for PDFmorph web-page

3cd884f

Added relevant PDFmorph web-page files

59c2995

Update pdfmorph_license.txt

726a7b1

sbillinge reviewed Jul 9, 2019

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RomanMatthew added 2 commits July 9, 2019 14:14

Removed xPDFsuite paragraph from pdfmorph.rst

27a78fc

Merge branch 'pdfmorph_web' of https://github.com/RomanMatthew/diffpy…

b05ea1a

….github.io into pdfmorph_web

CJ-Wright reviewed Jul 9, 2019

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Fixed version name and CLI reference in pdfmorph.rst

afcd519

RomanMatthew commented Jul 9, 2019

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RomanMatthew commented Jul 9, 2019

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RomanMatthew added 2 commits July 9, 2019 14:32

Fix graph label, spelling errors, and virtual env directions

92d28ed

Fix CLI note

87f5b62

RomanMatthew mentioned this pull request Jul 9, 2019

check docstrings in PR #23 #24

Open

Fix xPDFsuite comment

46364ae

RomanMatthew and others added 4 commits July 9, 2019 16:25

Fixed filenames

9b51ea7

Rename PDFmorph.rst to pdfmorph.rst

9408726

Add link to PDFmorph in dropdown menu and fixed index pointer

2300e7c

Fixed license reference in pdfmorph.rst

d87c500

sbillinge reviewed Jul 11, 2019

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RomanMatthew added 2 commits July 11, 2019 11:46

Update virtual environment instructions and fix typos

1ee2756

Fixed structure issues

13435df

pavoljuhas added 2 commits July 16, 2019 19:01

BUG: fix table - remove offending blank line

aaa81dd

DROPME - Merge branch 'source' into pdfmorph_web

4bc49b4

Temporary merge of main line, please rebase.

MNT: remove trailing blanks

612a7b9

sbillinge reviewed Jul 18, 2019

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RomanMatthew added 2 commits July 18, 2019 12:49

Update installation section

76f0294

Update installation instructions

54417fd

sbillinge reviewed Jul 18, 2019

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pavoljuhas added 4 commits July 18, 2019 14:48

Drop unused include of abbreviations

ea9dcec

Include only when used.

pdfmorph - typo and small rewording

13c79ea

MNT: clean up trailing blanks

02628b0

Fix issues from `git diff --check`.

pdfmorph - remove conda environment creation

e5bccef

List compatible Python versions. Suggest pip rather than easy_install.

pavoljuhas approved these changes Jul 19, 2019

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Pdfmorph web-page #23

Pdfmorph web-page #23

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		conda create --name=<env_name> python=3

		You can give the environment any name you like but it should

		@@ -0,0 +1,36 @@
		This program is part of the DiffPy open-source project at Columbia

Pdfmorph web-page #23

Are you sure you want to change the base?

Pdfmorph web-page #23

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