testing should work now\

docs/index.md

@@ -31,6 +31,7 @@ A version of gpxrdpy is also implemented in pyiron found in the [ugent pyiron br
 
 ## Requirements
 * `pyobjcryst` - Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library <br> (see [https://github.com/diffpy/pyobjcryst]())
-* `numpy` - library for scientific computing in python
+* `numpy` - library for computing in python
 * `scipy` - library for scientific computing in python
-* `molmod` - collection of molecular modelling tools for python <br> (see [https://github.com/molmod/molmod]())
+* `matplotlib` - library for plotting in python
+* `h5py` - library for storing data in python

docs/installation.md

@@ -14,7 +14,7 @@ The easiest way to install gpxrdpy, is by first installing the pyobjcryst throug
  $ conda install -c conda-forge pyobjcryst
 ```
 
-Afterward, the gpxdpy package can be installed through pip:
+Afterward, the gpxdpy package can be installed through pip, which will install all other dependencies:
 
 ```console
  $ pip install --upgrade git+https://github.com/SanderBorgmans/gpxrdpy.git
@@ -25,7 +25,22 @@ Afterward, the gpxdpy package can be installed through pip:
 To quickly check whether the installation went smoothly, you can run the gpxrdpy-test.py script as follows:
 
 ```console
- $ gpxrdpy-test.py
+ $ gpxrd_test.py
 ```
 
-which computes the static PXRD pattern of COF-5. This will generate a `.fhkl` file with the intensities for each hkl index, and a `.tsv` file with the integrated pattern. 
+which computes the static PXRD pattern of COF-5 and compares it to a reference pattern. This will generate a `.fhkl` file with the intensities for each hkl index, and two `.dat` files with the integrated diffraction intensities as a function of the Bragg angle (2θ), and the scattering vector (q). Finally, the comparison between the calculated and the reference pattern is saved to a `xrd.pdf` file, whereas the statistical comparison is printed to the terminal:
+
+```console
+ Imported powder pattern: 2351 points, 2theta= 3.000 -> 50.000, step= 0.020
+ Guess = 3.725577310703468e-09, fit = 7.3208687727899055e-09
+
+ Statistical comparison
+ ------------------------------------------------------------------
+ Quantity | Full | LA (min-10) | HA (10-max)
+ ------------------------------------------------------------------
+ R factor (abs) | 0.942803315 | 0.845442566 | 0.985120011
+ R factor (squared) | 0.924069988 | 0.839995526 | 0.986114068
+ Weighted R factor | 0.953021538 | 0.873615415 | 0.985541226
+ Similarity index | 0.388794850 | 0.558217914 | 0.476000931
+
+```

scripts/gpxrdpy-test.py → scripts/gpxrd_test.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-
+import os
 
 deg = 0.017453292519943295 # conversion of rad to deg
 
@@ -24,7 +24,7 @@ def check_calculation():
  numpoints = 1000
  max2theta = 50 * deg
  obspattern = obspattern
- plot = True
+ plot = 'xrd'
  check_peaks = False
  detail = False # do not print detailed info for each peak
  neutron = False
@@ -42,7 +42,10 @@ def check_calculation():
  return
 
  # Check whether correct files are created
-
+ assert os.path.exists('tests/data/COF-5.dat')
+ assert os.path.exists('tests/data/COF-5_fhkl.dat')
+ assert os.path.exists('tests/data/COF-5_q.dat')
+ assert os.path.exists('tests/data/xrd.pdf')
 
 if __name__ == "__main__":
  print("Testing your gpxrdpy installation...")

setup.py

@@ -7,7 +7,7 @@
  description="PXRD pattern calculator based on pyobjcryst",
  url="https://github.com/SanderBorgmans/gpxrdpy",
  packages=setuptools.find_packages(),
- scripts=['scripts/gpxrd.py', 'scripts/gpxrd_average.sh'],
+ scripts=['scripts/gpxrd.py', 'scripts/gpxrd_average.sh', 'scripts/gpxrd_test.py'],
  classifiers=[
  "Programming Language :: Python :: 3",
  "License :: OSI Approved :: MIT License",