Move the graphic user interface to ocbe-uio/trajpy-ui

.github/workflows/python-app.yml

@@ -36,4 +36,4 @@ jobs:
         uv run ruff check .
     - name: Test with pytest
       run: |
-        uv run pytest --cov=src tests/
+        uv run pytest --cov=trajpy tests/

Makefile

@@ -0,0 +1,19 @@
+.PHONY: check-format fix test lint type-check all
+
+check-format:
+	.venv/bin/ruff format trajpy --check
+
+fix:
+	.venv/bin/ruff format trajpy
+	.venv/bin/ruff check trajpy --fix
+
+test:
+	.venv/bin/python -m pytest -s tests
+
+lint:
+	.venv/bin/ruff check trajpy
+
+type-check:
+	.venv/bin/pyright trajpy
+
+all: lint type-check check-format fix test

README.md

@@ -32,7 +32,7 @@ the generator for building your own database.
 
 We have the package hosted at PyPi, for installing use the command line: 
 ```bash
-pip3 install trajpy
+pip3 install trajpy trajpy-ui
 ```
 If you want to test the development version, clone the repository at your local directory from your terminal:
 ```bash
@@ -46,23 +46,13 @@ python setup.py --install
 ## Basic Usage Example
 
 ### Using the Graphic User Interface (GUI)
+Since the version 1.4.4 we moved the user interface to a separate package named `trajpy-ui`.
 
 Open a terminal and execute the line bellow
 ```bash
-python3 -m trajpy.gui
+python3 -m trajpy_ui.ui
 ```
-
-1 - You can open one file at time clicking on `Open file...` or process several files in the same director with `Open directory...`
-
-2 - Select the features to be computed by ticking the boxes
-
-3 - Click on `Compute`
-
-4 - Select the directory and file name where the results will be stored
-
-The processing is ready when the following message appears in the text box located at the bottom of the GUI:
-
-`Results saved to /path/to/results/output.csv`
+Check the respository [trajpy-ui](https://ocbe-uio.github.io/trajpy-ui/) for more details about the GUI.
 
 ### File formats
 

data/samples/sample_lammps.yml

@@ -16,8 +16,8 @@ box:
 keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
 data:
   - [     1 , 1 ,  0.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0 , 0 , 0, ]
-  - [     2 , 1 ,  8.397981e-01 ,  8.397981e-01 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0 , 0 , 0, ]
-  - [     3 , 1 ,  8.397981e-01 ,  0.000000e+00 ,  8.397981e-01 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0 , 0 , 0, ]
+  - [     2 , 1 ,  0.000000e+00 ,  5.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  0.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0, 0 , 0, ]
 ---
 timestep: 100
 units: lj
@@ -34,9 +34,9 @@ box:
   - [ 0, 0, 0 ]
 keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
 data:
-  - [     1 , 1 ,  0.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0 , 0 , 0, ]
-  - [     2 , 1 ,  8.397981e-01 ,  8.397981e-01 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0 , 0 , 0, ]
-  - [     3 , 1 ,  8.397981e-01 ,  0.000000e+00 ,  8.397981e-01 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0 , 0 , 0, ]
+  - [     1 , 1 ,  1.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  1.000000e+00 ,  6.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  -1.000000e+00 ,  1.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0, 0 , 0, ]
 ---
 timestep: 200
 units: lj
@@ -53,9 +53,9 @@ box:
   - [ 0, 0, 0 ]
 keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
 data:
-  - [     1 , 1 ,  0.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0 , 0 , 0, ]
-  - [     2 , 1 ,  8.397981e-01 ,  8.397981e-01 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0 , 0 , 0, ]
-  - [     3 , 1 ,  8.397981e-01 ,  0.000000e+00 ,  8.397981e-01 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0 , 0 , 0, ]
+  - [     1 , 1 ,  2.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  2.000000e+00 ,  7.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  -2.000000e+00 ,  1.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0, 0 , 0, ]
 ---
 timestep: 300
 units: lj
@@ -72,6 +72,234 @@ box:
   - [ 0, 0, 0 ]
 keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
 data:
-  - [     1 , 1 ,  0.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0 , 0 , 0, ]
-  - [     2 , 1 ,  8.397981e-01 ,  8.397981e-01 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0 , 0 , 0, ]
-  - [     3 , 1 ,  8.397981e-01 ,  0.000000e+00 ,  8.397981e-01 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0 , 0 , 0, ]
+  - [     1 , 1 ,  3.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  3.000000e+00 ,  8.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  -3.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0, 0 , 0, ]
+---
+timestep: 300
+units: lj
+time: 2.0
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  4.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  2.000000e+00 ,  9.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  -4.000000e+00 ,  2.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0, 0 , 0, ]
+---
+timestep: 400
+units: lj
+time: 2.5
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  5.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  1.000000e+00 ,  10.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  -4.000000e+00 ,  3.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0, 0 , 0, ]
+---
+timestep: 500
+units: lj
+time: 3.0
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  6.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  2.000000e+00 ,  11.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  -3.000000e+00 ,  2.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0, 0 , 0, ]
+---
+timestep: 600
+units: lj
+time: 3.5
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  7.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  3.000000e+00 ,  12.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  -2.000000e+00 ,  1.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0, 0 , 0, ]
+---
+timestep: 700
+units: lj
+time: 4.0
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  8.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  2.000000e+00 ,  13.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  -1.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0, 0 , 0, ]
+---
+timestep: 800
+units: lj
+time: 4.5
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  9.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  3.000000e+00 ,  14.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  -1.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0, 0 , 0, ]
+---
+timestep: 900
+units: lj
+time: 5.0
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  10.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  4.000000e+00 ,  15.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  -1.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0, 0 , 0, ]
+---
+timestep: 1000
+units: lj
+time: 5.5
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  11.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  5.000000e+00 ,  16.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  0.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0 , 0 , 0, ]
+---
+timestep: 1100
+units: lj
+time: 6.0
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  12.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  4.000000e+00 ,  17.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  0.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0 , 0 , 0, ]
+---
+timestep: 1200
+units: lj
+time: 6.5
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  13.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  3.000000e+00 ,  17.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  0.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0 , 0 , 0, ]
+---
+timestep: 1300
+units: lj
+time: 7.0
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  14.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  2.000000e+00 ,  17.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  0.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0 , 0 , 0, ]
+---
+timestep: 1400
+units: lj
+time: 7.5
+natoms: 3
+boundary: [ p, p, p, p, p, p, ]
+thermo:
+  - keywords: [ Step, Temp, E_pair, E_mol, TotEng, Press, ]
+  - data: [ 0, 0, -27093.472213010766, 0, 0, 0, ]
+box:
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 16.795961913825074 ]
+  - [ 0, 0, 0 ]
+keywords: [ id, type, x, y, z, vx, vy, vz, ix, iy, iz,  ]
+data:
+  - [     1 , 1 ,  15.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.841579e-01 , -9.710036e-01 , -2.934617e+00 , 0, 0 , 0, ]
+  - [     2 , 1 ,  1.000000e+00 ,  17.000000e+00 ,  0.000000e+00 ,  -1.799591e+00 ,  2.127197e+00 ,  2.298572e+00 , 0, 0 , 0, ]
+  - [     3 , 1 ,  0.000000e+00 ,  0.000000e+00 ,  0.000000e+00 ,  -1.807682e+00 , -9.585130e-01 ,  1.605884e+00 , 0 , 0 , 0, ]

pyproject.toml

@@ -18,9 +18,7 @@ keywords = [
 dependencies = [
     "numpy>=1.14.3",
     "scipy>=1.7.1",
-    "ttkthemes>=2.4.0",
-    "Pillow>=8.1.0",
-    "PyYAML>=5.3.1",
+    "PyYAML>=5.3.1"
 ]
 
 [project.urls]