examples: fixed paths

Author: BitterB0NG0

docs/source/examples/do.md

@@ -6,7 +6,7 @@ PyMCNP enables common workflows using `pyvista`, `pandas`, `subprocesss`, `matpl
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_00.inp>`_.
+   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_00.inp>`_.
 ```
 
 Code:
@@ -18,14 +18,14 @@ Code:
 
 Output:
 
-    Checking INP file: `PyMCNP/files/inp/example_00.inp`
-    Fixing and writing to INP file: `PyMCNP/files/inp/example_00.inp`
+    Checking INP file: `example_00.inp`
+    Fixing and writing to INP file: `example_00.inp`
 
 ## Converting OUTP Files
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_00.outp <https://github.com/FSIBT/PyMCNP/blob/master/files/outp/example_00.outp>`_.
+   This example requires `example_00.outp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_00.outp>`_.
 ```
 
 Code:
@@ -44,7 +44,7 @@ Output:
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_00.outp <https://github.com/FSIBT/PyMCNP/blob/master/files/outp/example_00.outp>`_.
+   This example requires `example_00.outp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_00.outp>`_.
 ```
 
 Code:
@@ -68,7 +68,7 @@ Output:
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_00.inp>`_, `example_01.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_01.inp>`_, and `example_02.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_02.inp>`_.
+   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_00.inp>`_, `example_01.inp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_01.inp>`_, and `example_02.inp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_02.inp>`_.
 ```
 
 Code:
@@ -97,7 +97,7 @@ Output:
 
 ```{eval-rst}
 .. note:: 
-   This example requires `valid_29.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/valid_29.inp>`_.
+   This example requires `example_05.inp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_05.inp>`_.
 ```
 
 Code:
@@ -109,16 +109,16 @@ Code:
 
 Output:
 
-    Visualizing all surfaces from `PyMCNP/files/inp/valid_29.inp`.
-    Writing visualizations of all surfaces from `PyMCNP/files/inp/valid_29.inp` to `valid_29-surfaces.pdf`
+    Visualizing all surfaces from `example_05.inp`.
+    Writing visualizations of all surfaces from `example_05.inp` to `example_05-surfaces.pdf`
 
 ![do_visualize](../images/do_visualize.png)
 
 ## Parameter Scan
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_01.outp <https://github.com/FSIBT/PyMCNP/blob/master/files/outp/example_01.outp>`_ and `example_04.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_04.inp>`_.
+   This example requires `example_01.outp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_01.outp>`_ and `example_04.inp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_04.inp>`_.
 ```
 
 Code:

docs/source/examples/read.md

@@ -6,7 +6,7 @@ PyMCNP provides endpoints to read MCNP files.
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_00.inp>`_.
+   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_00.inp>`_.
 ```
 
 Code:
@@ -18,7 +18,7 @@ Code:
 
 Output:
 
-    Reading INP from `PyMCNP/files/inp/example_00.inp`:
+    Reading INP from `example_00.inp`:
     Isotropic neutron source over lunar regolith with two gamma detectors
     c
     c cell cards
@@ -34,7 +34,7 @@ Output:
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_00.inp>`_.
+   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_00.inp>`_.
 ```
 
 Code:
@@ -46,14 +46,14 @@ Code:
 
 Output:
 
-    Reading cell from `PyMCNP/files/inp/example_00.inp`:
+    Reading cell from `example_00.inp`:
     100 100 -1.54 -1 imp:P,N 1
 
 ## Reading INP Material
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_00.inp>`_.
+   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_00.inp>`_.
 ```
 
 Code:
@@ -65,7 +65,7 @@ Code:
 
 Output:
 
-    Reading material from `PyMCNP/files/inp/example_00.inp`:
+    Reading material from `example_00.inp`:
     m100 013027 -0.1701 020040 -0.131742819 020042 -0.000879273 020044 &
           -0.002834874 026054 -0.00086506 026056 -0.013579592 026057 -0.000313612 &
           008016 -0.45489192 019039 -0.0001865162 019041 -0.0000134604 012024 &
@@ -78,7 +78,7 @@ Output:
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/files/inp/example_00.inp>`_.
+   This example requires `example_00.inp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_00.inp>`_.
 ```
 
 Code:
@@ -90,14 +90,14 @@ Code:
 
 Output:
 
-    Reading surface from `PyMCNP/files/inp/example_00.inp`:
+    Reading surface from `example_00.inp`:
     2  rcc 50 0 0 0 0 7.62 3.81
 
 ## Reading OUTP
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_00.outp <https://github.com/FSIBT/PyMCNP/blob/master/files/outp/example_00.outp>`_.
+   This example requires `example_00.outp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_00.outp>`_.
 ```
 
 Code:
@@ -123,7 +123,7 @@ Output:
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_00.outp <https://github.com/FSIBT/PyMCNP/blob/master/files/outp/example_00.outp>`_.
+   This example requires `example_00.outp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_00.outp>`_.
 ```
 
 Code:
@@ -155,7 +155,7 @@ Output:
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_03.outp <https://github.com/FSIBT/PyMCNP/blob/master/files/outp/example_03.outp>`_.
+   This example requires `example_03.outp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_03.outp>`_.
 ```
 
 Code:
@@ -187,7 +187,7 @@ Output:
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_02.outp <https://github.com/FSIBT/PyMCNP/blob/master/files/outp/example_02.outp>`_.
+   This example requires `example_02.outp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_02.outp>`_.
 ```
 
 Code:
@@ -219,7 +219,7 @@ Output:
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_01.outp <https://github.com/FSIBT/PyMCNP/blob/master/files/outp/example_01.outp>`_.
+   This example requires `example_01.outp <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_01.outp>`_.
 ```
 
 Code:
@@ -251,7 +251,7 @@ Output:
 
 ```{eval-rst}
 .. note:: 
-   This example requires `example_02.ptrac <https://github.com/FSIBT/PyMCNP/blob/master/files/ptrac/example_02.ptrac>`_.
+   This example requires `example_02.ptrac <https://github.com/FSIBT/PyMCNP/blob/master/examples/example_02.ptrac>`_.
 ```
 
 Code:

examples/do_check.py

@@ -10,7 +10,7 @@
 import pymcnp
 
 # Initializing `Check`.
-path = pathlib.Path(__file__).parent.parent / 'files' / 'inp' / 'example_00.inp'
+path = pathlib.Path('example_00.inp')
 checker = pymcnp.Check(path)
 
 # Checking.

examples/do_convert.py

@@ -12,7 +12,7 @@
 TALLY = '1'
 
 # Reading OUTP.
-path = pathlib.Path(__file__).parent.parent / 'files' / 'outp' / 'example_00.outp'
+path = pathlib.Path('example_00.outp')
 outp = pymcnp.Outp.from_file(path)
 
 # Initializing `Convert`.

examples/do_parameter_scan.py

@@ -20,7 +20,7 @@
 class MyRun(pymcnp.Run):
     def posthook_file(self, path, index):
         # Copying OUTP (ECHO used for demo).
-        path_copy = pathlib.Path(__file__).parent.parent / 'files' / 'outp' / 'example_01.outp'
+        path_copy = pathlib.Path('example_01.outp')
         path_outp = path / f'run-{index}.outp'
 
         with path_outp.open('w') as file_outp:
@@ -44,7 +44,7 @@ def posthook_batch(self, path):
 
 
 # Reading INP.
-path_inp = pathlib.Path(__file__).parent.parent / 'files' / 'inp' / 'example_04.inp'
+path_inp = pathlib.Path('example_04.inp')
 inp = pymcnp.Inp.from_file(path_inp)
 
 # Scanning.

examples/do_plot.py

@@ -14,7 +14,7 @@
 TALLY = '1'
 
 # Reading OUTP.
-path = pathlib.Path(__file__).parent.parent / 'files' / 'outp' / 'example_00.outp'
+path = pathlib.Path('example_00.outp')
 outp = pymcnp.Outp.from_file(path)
 
 # Initializing `Plot`

examples/do_run.py

@@ -31,9 +31,9 @@ def posthook_batch(self, path):
 
 
 # Reading INP.
-path0 = pathlib.Path(__file__).parent.parent / 'files' / 'inp' / 'example_00.inp'
-path1 = pathlib.Path(__file__).parent.parent / 'files' / 'inp' / 'example_01.inp'
-path2 = pathlib.Path(__file__).parent.parent / 'files' / 'inp' / 'example_02.inp'
+path0 = pathlib.Path('example_00.inp')
+path1 = pathlib.Path('example_01.inp')
+path2 = pathlib.Path('example_02.inp')
 inp0 = pymcnp.Inp.from_file(path0)
 inp1 = pymcnp.Inp.from_file(path1)
 inp2 = pymcnp.Inp.from_file(path2)

examples/do_visualize.py

@@ -1,7 +1,7 @@
 """
 Example visualizing INP files using `Visualize`.
 
-This example visualizes the surfaces in `valid_29.inp` INP file using
+This example visualizes the surfaces in `example_05.inp` INP file using
 `to_show_surfaces`, and it generates a PDF file containing the images.
 """
 
@@ -10,7 +10,7 @@
 import pymcnp
 
 # Reading INP.
-path = pathlib.Path(__file__).parent.parent / 'files' / 'inp' / 'valid_29.inp'
+path = pathlib.Path('example_05.inp')
 inp = pymcnp.Inp.from_file(path)
 
 # Visualizing surfaces.
@@ -19,5 +19,5 @@
 visualizer.to_show_surfaces().show()
 
 # Converting to PDF.
-print(f'Writing visualizations of all surfaces from `{path}` to `valid_29-surfaces.pdf`')
-visualizer.to_pdf_surfaces('valid_29-surfaces.pdf')
+print(f'Writing visualizations of all surfaces from `{path}` to `example_05-surfaces.pdf`')
+visualizer.to_pdf_surfaces('example_05-surfaces.pdf')