Is it possible that 'Number Points' blue background goes behind the white marker and axis letters correctly positioned?

Remove the usage of farseer_user_variables.py file.
farseermain.py should load directly from .json file and only one file containing all the variables should exist, so that adding a new variable or variable group (dictionary) can be done by editing a single file.

in the default_conf.json the font type and weight values are strings configure to such as 'Arial' or 'normal'.
I see that that does not relate to the configuration appear in the menus.

I remember before you had numbers in the default_config.json and I changed it to the string values some commits ago. My fault.

I can revert the font weight to numbers so that they fit the indexes in gui.utils.py line 54. But, where is the font list so I can set 'Arial' correctly.

When saving the configuration file nothing happens. No file is saved an no message is printed in the Terminal.

If user loads the peaklists by drag&drop to the left area in PeakList Selection tab,

What is the meaning of the Spectrum Path in the Settings tabs?
Should the parsed peaklists (and folder tree) be placed in the Calculation Output Folder? 👍

we have changed this couple of times and I got lost :-P

When Drag&Drop hierarchic folders to the left Peaklist area:

1. Dropping two folder at the same level - OK
2. Dropping a parent folder with two folders inside - OKAY, same result as (1)
3. Dropping two folders simmultaneously like in (2) - CRASHES

Traceback (most recent call last):
  File "/home/joao/Dropbox/labo-documents/Projects/Programming/FarSeer/git/gui/components/Sidebar.py", line 37, in dropEvent
    self.load_from_path(filePath)
  File "/home/joao/Dropbox/labo-documents/Projects/Programming/FarSeer/git/gui/components/Sidebar.py", line 45, in load_from_path
    self.load_peaklist(path)
  File "/home/joao/Dropbox/labo-documents/Projects/Programming/FarSeer/git/gui/components/Sidebar.py", line 70, in load_peaklist
    number = int(self.peakLists.keys()[-1].split('_')[1])+1
TypeError: 'odict_keys' object does not support indexing
Aborted (core dumped)

4. Dropping full spectra/ hierarchy - CRASHES with same error as in (3).

I do not mean this is a bug. To discuss what should be the behaviour of the left area panel. If some options should be blocked, therefore a WET message should popup to inform the user and avoid core dump failures.

in main.py it reads

from current.farseermain import read_user_variables, run_farseer
        fsuv, cwd = read_user_variables(spectrum_path)
        run_farseer('{}/spectra'.format(cwd), fsuv)

run_farseer() from farseermain.py now takes only one argument, fsuv, as returned from read_user_variables() that takes only the path argument

Most likely this is due to the changes in the variable files. Some menus are broken:

• PRE Settings
• Dpre Settings
• CS Scatter
• CS Scatter Flower

when we are together you have too teach me some more about how are the variables configured so I can help you out on this :-)

I have deleted the file in examples/artificial_dataset_generator.

The updated farseer_user_variables files should only be that in current.

I guess the versions we are using are not compatible. Specially when generating default_config.json. How do you generate that file? So that I can update it according to the latest farseer_user_variable.py

stylesheet needs fixing for interface top and axis labels.

In default_config.json, changing the flag:

"applyFASTA": true
or
"expand_lost_yy": true,

actually activates by default the corresponding flags in the GUI.

Doing the same for do_cond1-3 does not activate the corresponding flag. Mismatch in variable names?

Saving settings by Save Setting button works correctly.

user_config.json saved when hitting Run Analysis button do not store the actual user settings.
I had deactivated the FASTA flag and still it remained true when hit the Run started.

},
    "fasta_settings": {
        "FASTAstart": 1,
        "applyFASTA": true

incorrect and inconsistent keys appearing in config when tree created and saved.

Selecting a folder that contains all the peaklists inside BUT also contains other files like a blank new file or a .fasta file or anything is not a .csv file crashed the GUI with the following.

Invalid file: /home/fbssps/joao/debugging_farseer/GUI_1D/spec-load/4000.csv
Traceback (most recent call last):
  File "../../FarSeer-NMR/main.py", line 477, in set_spectrum_path
    self.set_spectrum_path_text(path)
  File "../../FarSeer-NMR/main.py", line 469, in set_spectrum_path_text
    self.parent().parent().parent().load_peak_lists(path)
  File "../../FarSeer-NMR/main.py", line 111, in load_peak_lists
    self.interface.sideBar.load_from_path(path)
  File "/home/fbssps/joao/FarSeer-NMR/gui/components/Sidebar.py", line 55, in load_from_path
    name, path = self.load_peaklist(path)
TypeError: 'NoneType' object is not iterable
Aborted (core dumped)

Suggestion/Correction:
Spectrum Path browser should parse only .csv files to the left side bar in PeakList Tab.

I have rearranged variable names in defaul_config.json regarding PRE representation in the plots. Variable names were misleading and were placed in the wrong dictionaries.
These should be updated on the GUI.
May be I can deal with it tomorrow with your help :-)
See changes in the following commit.

After configuring Settings options,
Save Configuration button actually saves a .json file but with the default values and not with the values configured in the GUI.

for the future.
to discuss

or not calculated or not plotted.

I tried to run the main.py from another directory and it crashed.

How should he handle this? Correct it? Is there a way to simulate running from script folder with a shortcut/link file?

Traceback (most recent call last):
  File "/home/joao/Dropbox/labo-documents/Projects/Programming/FarSeer/git/main.py", line 800, in <module>
    gui_settings, stylesheet = gui_utils.deliver_settings(screen_resolution)
  File "/home/joao/Dropbox/labo-documents/Projects/Programming/FarSeer/git/gui/gui_utils.py", line 65, in deliver_settings
    stylesheet = open('gui/stylesheet_1k.qss').read()
FileNotFoundError: [Errno 2] No such file or directory: 'gui/stylesheet_1k.qss'
15:11 1D] 

Starting from a blank folder, and Loading a config.json file from a previous run, should populated spectra/ folder and all parameters and perfectly reproduce the run.
Original peaklists should be in original absolute file path, that's should be up to the user.

Exporting CS Scatter series if only CSP is calculated, with PosF1 and PosF2 calc flags False do no export the data used and can not be retrieved. Data should any way be exported into the CS Scatter folder.

If a user wants to substitute a peaklist in the tree he/she should «Delete» it and then drag&drop the new one.

If FASTA Flag is Checked and not fasta files are selected GUI should warns the user.

This is already implemented in the main farseer code, so, anyway, the run won't crash.

If possible,
Farseer-NMR should be delivered with its own miniconda distribution so that user does not have to install anaconda or python libraries in the system.

Directly Run without pre configuring the spectra

Traceback (most recent call last):
  File "../../FarSeer-NMR/main.py", line 579, in run_farseer_calculation
    self.parent().parent().parent().run_farseer_calculation()
  File "../../FarSeer-NMR/main.py", line 131, in run_farseer_calculation
    run_msg = create_directory_structure(output_path, self.variables, peakLists)
  File "/home/fbssps/joao/FarSeer-NMR/current/setup_farseer_calculation.py", line 17, in create_directory_structure
    if variables["fasta_files"][y_key]:
KeyError: '0'
Aborted (core dumped)
[fbssps@fbscpcu234 GUI_1D]$ 

Can we block the user from running in case spectra have not loaded as you did if the spectra/ already existed?

When Run Farseer button and settings were not saved, settings should be saved as user_config.json.

Having loaded a config file the user should be able to repopulate the experimental tree without loosing the other configuration settings.

Same if the user loads a configuration without information on the peaklists, he/she should be able to populate the peaklist tree maintaining the configuration.

Drag and dropping a folder to the left area in the Peaklist Selection tab prints to the terminal

Invalid file: /home/joao/Desktop/git_trials/farseer_dev_desktop/templates_dev/debugging_farseer/1D_GUI_spectra/spectra/dia/L1/0500.csv
Invalid file: /home/joao/Desktop/git_trials/farseer_dev_desktop/templates_dev/debugging_farseer/1D_GUI_spectra/spectra/dia/L1/0125.csv
Invalid file: /home/joao/Desktop/git_trials/farseer_dev_desktop/templates_dev/debugging_farseer/1D_GUI_spectra/spectra/dia/L1/0000.csv
Invalid file: /home/joao/Desktop/git_trials/farseer_dev_desktop/templates_dev/debugging_farseer/1D_GUI_spectra/spectra/dia/L1/0250.csv

Started GUI
created a tree
saved config
restarted gui
load config.

<gui.components.Sidebar.SideBar object at 0x7fe8b67a3708>
Traceback (most recent call last):
  File "../../FarSeer-NMR/main.py", line 489, in load_config
    self.load_variables()
  File "../../FarSeer-NMR/main.py", line 603, in load_variables
    sself.output_path.field.setText(general["output_path"])
NameError: name 'sself' is not defined
Aborted (core dumped)
[fbssps@fbscpcu234 GUI_1D]$ 

for example, all Y axis scales in Restraint Calculation menu or Bar Plot - Bar Alpha.

Additional, all colour alpha should be topped to 1.00, wich are:
Bar Plot - Bar Alpha
Bar Plot - Stdv Threeshold Alpha
Titration Plot Settings - Y Grid Alpha
Residue Evolution Plot - Shade transparency

The GUI should load a .fasta file for each Y data point.

In the final spectra/ folder (the one used for in terminal runs) the .fasta files are placed in the last folder, together with the peaklists .csv files. And there should be one for each folder. .fastas do not need to be named the same along Y folders, but they should along Z.

Remove the word 'Plot' because the flags are to "calculate" and not to "plot".

there is a typo error in the main gui at the bottlon left.
where it reads Arbescu should read Arbesú.

At present there is no check to make sure that all exp conditions along an axis are unique. If there are not an error would be raised in drawing the tree

Check ticks and font colour in file choosing windows are in very light grey colours.

Farseer calculations depend on spectra/ folder which requires a very curated structure. Performing a run from the GUI adds the new defined peaklists to the spectra/ folder without removing existent files. This should stay like that but an issue should rise warning the user that a spectra/ folder already exists and this is not compatible with FarseerNMR.

PRE Analysis should not be active unless Height or Volume are active.

PRE plots should not be active unless PRE Analysis is.

two issues in one:

1. When clicking Alpha by residue window crashes. I guess is a question on how the dictionary is written in the default_config.* files. You are more familar with the .json format, could you check this?

2. Can the default values that appear for each residue for every residue be filled with the value in variable csp_res4alpha ? I think this won't affect the calculation is a question to show the user that is going to be used.

bug in calls for parameters

Tried to create conda env from the env.yml but anaconda complains.

Could you check in a spec file created from conda list --explicit > spec-file.txt?

Needs update to be consistent with issues #32 and #33.

Issue description

If a .fasta file that should start at residue 30 is configured with 1 with 'FASTA start' variable, the last residues of the peaklist will be probably truncated by 30 residues because on FarseerCube.seq_expand() peaklist index is reindexed based on the fasta

Solution

Farseer-NMR should identify that the last residue of the fasta is prior to the last residue of the protein and output and error/warning message. Message should be listed in WET list.

Conditions variable full of zeros after config loaded and calculation executed

Apart from the issues already posted, there are two main development major issues to deal with, and that we should do it together:

1. the previous issue we discussed on how to handle loading peaklist,
2. how to handle repeating a calculation; peaklists path maybe should be stored in config.json so that loading that would load eveything else.
3. Define well how to handle the user variables. I think now the GUI routines are handicapped by the way I programmed the terminal version and that makes no sense. I can easily adapt the terminal version to better fit the GUI requirements, maybe deprecrating the farseer_user_variables.py. I absolutely want users to use only the GUI, me included.

Another thing, as you well said, we need to share our code architecture so that both can work on every part of the code :-) That would be perfect for next week also. At the end, we are going to have a beer together tomorrow :-D

After that, I guess we are really close make a full run.

Regarding the publication,
I didn't have time to start drafting. But I did almost complete the Documentation Wiki. I still need to change one thing that I could do even today and than we need to add documentation on the GUI. I think we should finished everything before starting the publication writting. I really care about your feedback on the documentation. This is the first time I write docs. I tried to make them as short as possible and as explanatory as possible. I guess the words there can alse serve a publication means; specially the pictures.

What is your feeling?

I created the tree drag&dropping from left panel after Spectrum Path.
Save the config file. Close and re-open the program.
Load config file.
crashed

Traceback (most recent call last):
  File "../../FarSeer-NMR/main.py", line 487, in load_config
    self.variables = self.parent().parent().parent().load_config()
  File "../../FarSeer-NMR/main.py", line 104, in load_config
    self.interface.peakListArea.updateTree(variables)
  File "/home/fbssps/joao/FarSeer-NMR/gui/components/PeakListArea.py", line 136, in updateTree
    self.sideBar().removeItem(pl_name)
  File "/home/fbssps/joao/FarSeer-NMR/gui/components/Sidebar.py", line 100, in removeItem
    sip.delete(result[0])
IndexError: list index out of range
Aborted (core dumped)
[fbssps@fbscpcu234 GUI_1D]$ 

so that we can directly give users hyperlinks to the error messages.