Merge pull request #92 from ess-dmsc-dram/fix-typos

Fix typos and run checks in CI

.github/workflows/deploy-book.yml

@@ -9,6 +9,22 @@ on:
 
 # This job installs dependencies, builds the book, and pushes it to `gh-pages`
 jobs:
+  formatting:
+    name: Formatting and static analysis
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --all-files
+      - uses: pre-commit-ci/[email protected]
+        if: always()
+        with:
+          msg: Apply automatic formatting
+
   deploy-book:
     runs-on: ubuntu-latest
     timeout-minutes: 45

.pre-commit-config.yaml

@@ -0,0 +1,18 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: detect-private-key
+      - id: end-of-file-fixer
+        exclude: '\.idea/'
+      - id: trailing-whitespace
+        args: [ --markdown-linebreak-ext=md ]
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.24.5
+    hooks:
+      - id: typos

1-python/python_basics/basic_language_principles.ipynb

@@ -127,7 +127,7 @@
    "metadata": {},
    "source": [
     "**Exercise (3)** <br>\n",
-    "Using the variable assigment code shown above, first initialize a variable to `2` and then increment it by 2.\n",
+    "Using the variable assignment code shown above, first initialize a variable to `2` and then increment it by 2.\n",
     "Then assign to the variable x the string value `\"my string\"`."
    ]
   },
@@ -161,7 +161,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "You are most likely seeing the error similar to one bellow:\n",
+    "You are most likely seeing the error similar to one below:\n",
     "\n",
     "```python\n",
     "---------------------------------------------------------------------------\n",

1-python/using_external_libraries/matplotlib.ipynb

@@ -1434,7 +1434,7 @@
    "source": [
     "### Interactive linked scatter and histogram\n",
     "\n",
-    "In this example, we use the `RectangleSelector` to select points in a 2D scatter plots that represent the x and y coordinates of some data points. The points also have a 3rd dimension/property, e.g., temperature. The temperature of all the points is histogrammed in the right-hand side panel. The histogram for only the selected points is overlayed with a red color and updated every time the selector is moved/resized."
+    "In this example, we use the `RectangleSelector` to select points in a 2D scatter plots that represent the x and y coordinates of some data points. The points also have a 3rd dimension/property, e.g., temperature. The temperature of all the points is histogrammed in the right-hand side panel. The histogram for only the selected points is overlaid with a red color and updated every time the selector is moved/resized."
    ]
   },
   {

1-python/using_external_libraries/numpy.ipynb

@@ -121,7 +121,7 @@
     "### Data types\n",
     "\n",
     "Numpy arrays support a variety of data-types (`dtype`).\n",
-    "The most commonly used ones are integers and floating-point numbers in either double-precison or single-precision.\n",
+    "The most commonly used ones are integers and floating-point numbers in either double-precision or single-precision.\n",
     "By default `dtype` is inferred from the values used for initialization.\n",
     "To control it, many functions support a `dtype` keyword argument.\n",
     "For explicit conversion `astype()` can be used:"

1-python/using_external_libraries/pandas.ipynb

@@ -1667,7 +1667,7 @@
     "\n",
     "- Dealing with missing values  \n",
     "```\n",
-    "df_to_write_to_file.to_csv('simple_file.csv', na_rep='Unkown') # missing value saved as 'Unknown'\n",
+    "df_to_write_to_file.to_csv('simple_file.csv', na_rep='Unknown') # missing value saved as 'Unknown'\n",
     "```\n",
     "\n",
     "- Specifying the precision of the data written to file\n",

1-python/using_external_libraries/unit_testing.ipynb

@@ -316,7 +316,7 @@
     "As an example, we are going to look at the Zeeman effect.\n",
     "Let us start by reminding ourselves of the formula.\n",
     "\n",
-    "The coupling of the spin and orbital angular momentum of an electron to an external magentic field $B$ shifts the energy level of that electron by\n",
+    "The coupling of the spin and orbital angular momentum of an electron to an external magnetic field $B$ shifts the energy level of that electron by\n",
     "\n",
     "$$\n",
     "\\Delta E = \\mu_B g_j m_j B ,\n",

3-mcstas/Simulation.ipynb

@@ -56,7 +56,7 @@
     "### Programming language\n",
     "The McStas core and components are all written using the C programming language, though the user interface for assembling the instrument is a meta-language built upon C. This means C code is allowed in parts the file, but it also has a section for adding these components with their parameters and physical positions / rotations with a simple syntax. There also exists a McStas python API called McStasScript, this is what will be used during this course.\n",
     "\n",
-    "### Coordiante system\n",
+    "### Coordinate system\n",
     "To use McStas effectively it is important to understand the coordinate system. The beam direction is generally along the z direction, y points upwards against gravity and x to the left when looking in the beam direction. Furthermore each component will have its own coordinate system, and components can be placed relative to one another. The McStas core handles this complexity so each component can work in a simple local coordinate system.\n",
     "\n",
     "### Units\n",

3-mcstas/Talk.ipynb

@@ -212,7 +212,7 @@
     "tags": []
    },
    "source": [
-    "### Coordiante system\n",
+    "### Coordinate system\n",
     "- x: left, looking in the beam direction\n",
     "- y: upwards, against gravity\n",
     "- z: beam direction "

3-mcstas/make_SANS_instrument.py

@@ -217,7 +217,7 @@ def mu_gas(sigma, bars, temperature_C):
     ref.set_AT([0, 0.5*casing.yheight, 0], RELATIVE=detector_position)
     """
 
-    # Parmeters for time of flight limits
+    # Parameters for time of flight limits
     instrument.add_declare_var("double", "t_min")
     instrument.add_declare_var("double", "t_max")
     instrument.add_declare_var("double", "t_max_pulses")

3-mcstas/mcstas-qens.ipynb

@@ -851,7 +851,7 @@
     "The next task is to specify the physical location of the component, this is done using the `set_AT` method on the component object.\n",
     "This method takes a list of 3 numbers, corresponding to the `x`, `y` and `z` coordinates of the component.\n",
     "\n",
-    "One can also specify in what coordinate system one wants to work, which can be that of any preceeding component.\n",
+    "One can also specify in what coordinate system one wants to work, which can be that of any preceding component.\n",
     "Use the `RELATIVE` keyword to work in the `source` coordinate system.\n",
     "The position of the chopper is needed for calculating phase, so it is available as a variable in the instrument, use this variable to set the position."
    ]
@@ -1072,7 +1072,7 @@
     "### Time resolution\n",
     "Using the plotted data above its possible to get a estimate of the time resolution of the instrument.\n",
     "\n",
-    "Use the curser to zoom and read of values for the time resolution of the instrument (FWHM). Insert the found time in the question below as a value in seconds."
+    "Use the cursor to zoom and read of values for the time resolution of the instrument (FWHM). Insert the found time in the question below as a value in seconds."
    ]
   },
   {

3-mcstas/mcstas-sans.ipynb

@@ -847,7 +847,7 @@
    "source": [
     "## Run improved instrument\n",
     "\n",
-    "Its time to run the improved instrument. We will use the same parameters as earlier, but now also set `integration_time` to $5\\times 10^4$, corresponding to 13.8 hours. This is suposed to emulate a long measurement of the instrument background only done rarely. We use the integration time in the continued workflow to estimate the error on the measured signal.\n",
+    "Its time to run the improved instrument. We will use the same parameters as earlier, but now also set `integration_time` to $5\\times 10^4$, corresponding to 13.8 hours. This is supposed to emulate a long measurement of the instrument background only done rarely. We use the integration time in the continued workflow to estimate the error on the measured signal.\n",
     "\n",
     "Store the returned data in a variable called `background_data`. Name the generated data folder \"SANS_without_sample_1_pulse\" using the *output_path* argument in the `settings` method of the instrument."
    ]

3-mcstas/monte_carlo.py

@@ -7,47 +7,47 @@
 def plot_points(square_side_length, circle_radius,n=100):
     global points_inside_circle, total_points, estimates, estimate
     global points_x_inside, points_y_inside, points_x_outside, points_y_outside
-    
+
     for _ in range(n):
         x, y = np.random.rand(2)*square_side_length  # Random points x, y between 0 and 1
         distance = np.sqrt((x-0.5*square_side_length)**2 + (y-0.5*square_side_length)**2)
-        
+
         total_points += 1
-        
+
         if distance <= circle_radius:
             points_inside_circle += 1
             points_x_inside.append(x)
             points_y_inside.append(y)
         else:
             points_x_outside.append(x)
             points_y_outside.append(y)
-        
+
         # area of circle = pi*circle_radius**2
         # area of box = side_length**2
         # estimate =
-        
+
         estimate = square_side_length**2/circle_radius**2 * points_inside_circle / total_points
         estimates.append(estimate)
-        
+
     # Update scatter plots
     scatter_inside.set_offsets(np.c_[points_x_inside, points_y_inside])
     scatter_outside.set_offsets(np.c_[points_x_outside, points_y_outside])
-    
+
     # Update line plot
     line.set_data(range(len(estimates)), estimates)
     if len(estimates) == 0:
         line_pi.set_data([0, 1], [np.pi, np.pi])
     else:
         line_pi.set_data([0, len(estimates)], [np.pi, np.pi])
-    
+
     ax[1].relim()
     ax[1].autoscale_view()
-    
+
 
     ax[1].set_title(f'Estimate of Pi: {estimate}')
     ax[1].set_xlabel('Number of Points')
     ax[1].set_ylabel('Estimate Value')
-    
+
     # Update the figure
     fig.canvas.draw()
 
@@ -87,7 +87,7 @@ def example(points=100, square_side_length=1, circle_diameter=1):
     # Initial Plot
     plot_points(square_side_length, circle_radius, 100)
 
- 
+
     plt.tight_layout()
 
 
@@ -126,44 +126,44 @@ def example_interactive(square_side_length=1, circle_diameter=1):
     def plot_points(n=1):
         global points_inside_circle, total_points, estimates, estimate
         global points_x_inside, points_y_inside, points_x_outside, points_y_outside, scatter_inside, scatter_outside
-        
+
         for _ in range(n):
             x, y = np.random.rand(2)*square_side_length  # Random points x, y between 0 and 1
             distance = np.sqrt((x-0.5*square_side_length)**2 + (y-0.5*square_side_length)**2)
-            
+
             total_points += 1
-            
+
             if distance <= circle_radius:
                 points_inside_circle += 1
                 points_x_inside.append(x)
                 points_y_inside.append(y)
             else:
                 points_x_outside.append(x)
                 points_y_outside.append(y)
-            
+
             # area of circle = pi*circle_radius**2
             # area of box = side_length**2
             # estimate =
-            
+
             estimate = square_side_length**2/circle_radius**2 * points_inside_circle / total_points
             estimates.append(estimate)
-            
+
         # Update scatter plots
         scatter_inside.set_offsets(np.c_[points_x_inside, points_y_inside])
         scatter_outside.set_offsets(np.c_[points_x_outside, points_y_outside])
-        
+
         # Update line plot
         line.set_data(range(len(estimates)), estimates)
         if len(estimates) == 0:
             line_pi.set_data([0, 1], [np.pi, np.pi])
         else:
             line_pi.set_data([0, len(estimates)], [np.pi, np.pi])
-        
+
         ax[1].relim()
         ax[1].autoscale_view()
         ax[1].set_xlabel('Number of Points')
         ax[1].set_ylabel('Estimate Value')
-        
+
         # Update the figure
         fig.canvas.draw()
 

3-mcstas/quizlib/QENS_quiz.py

@@ -193,7 +193,7 @@ def question_8(self, answer=None):
         which is done using the *set_AT* component. This method takes a list
         of 3 numbers, corresponding to the *x*, *y* and *z* coordinates of
         the component. One can also specify in what coordinate system one
-        wants to work, which can be that of any preceeding component. Use
+        wants to work, which can be that of any preceding component. Use
         the *RELATIVE* keyword to work in the *source* coordinate system.
         The position of the chopper is needed for calculating phase, so it
         is available as a variable in the instrument, use this variable to
@@ -259,7 +259,7 @@ def question_9(self, answer=None):
         self.insert_value(answer, 0.000246,
                           feedback_correct=success_msg,
                           feedback_below=below_msg, feedback_above=above_msg,
-                          tollerance_factor=0.2)
+                          tolerance_factor=0.2)
 
     def question_10(self, answer=None):
         """
@@ -275,7 +275,7 @@ def question_10(self, answer=None):
         self.insert_value(answer, 0.00126,
                           feedback_correct=success_msg,
                           feedback_below=below_msg, feedback_above=above_msg,
-                          tollerance_factor=0.25)
+                          tolerance_factor=0.25)
 
     def question_11(self, answer=None):
         """
@@ -289,4 +289,4 @@ def question_11(self, answer=None):
         self.insert_value(answer, 8.238,
                           feedback_correct=success_msg,
                           feedback_below=below_msg, feedback_above=above_msg,
-                          tollerance_factor=0.20)
+                          tolerance_factor=0.20)

3-mcstas/quizlib/quiz.py

@@ -55,7 +55,7 @@ def multiple_choice(self, answer, correct_answer, feedback):
             correct = answer in correct_answer
         else:
             correct = answer == correct_answer
-        
+
         if answer not in feedback:
             message = "This multiple choice question did not contain that option!"
             valid = False
@@ -67,26 +67,26 @@ def multiple_choice(self, answer, correct_answer, feedback):
 
     def insert_value(self, answer, correct_answer,
                      feedback_correct="", feedback_below="", feedback_above="",
-                     tollerance_factor=None, tollerance_interval=None):
+                     tolerance_factor=None, tolerance_interval=None):
 
         if answer is None:
             print("Insert your answer in the question above.")
             return
 
-        if tollerance_interval is not None and tollerance_factor is not None:
-            print("Question bug, use only tollerance_factor or tollerance_interval!")
+        if tolerance_interval is not None and tolerance_factor is not None:
+            print("Question bug, use only tolerance_factor or tolerance_interval!")
 
         lower_limit = correct_answer
-        if tollerance_factor is not None:
-            lower_limit *= 1 - tollerance_factor
-        if tollerance_interval is not None:
-            lower_limit -= 0.5*tollerance_interval
+        if tolerance_factor is not None:
+            lower_limit *= 1 - tolerance_factor
+        if tolerance_interval is not None:
+            lower_limit -= 0.5*tolerance_interval
 
         upper_limit = correct_answer
-        if tollerance_factor is not None:
-            upper_limit *= 1 + tollerance_factor
-        if tollerance_interval is not None:
-            upper_limit += 0.5*tollerance_interval
+        if tolerance_factor is not None:
+            upper_limit *= 1 + tolerance_factor
+        if tolerance_interval is not None:
+            upper_limit += 0.5*tolerance_interval
 
         if not isinstance(answer, (float, int)):
             message = "This question needs a value as the answer"
@@ -269,20 +269,3 @@ def last_component_in_instr_check(self, answer, comp_type_str, required_pars=Non
             print_box(success_msg, True)
 
         return True
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-

3-mcstas/ray_tracer_examples.py

@@ -39,4 +39,3 @@ def large():
 
 
     return sim
-