Merge pull request #5600 from MFraters/add_typos_tester

Add typos spell checker.

.github/workflows/typos.yml

@@ -0,0 +1,55 @@
+name: Spell Check with Typos
+on:
+ push:
+ branches:
+ - 'main'
+ pull_request:
+
+concurrency:
+ group: ${{ github.actor }}-${{ github.ref }}-typos
+ cancel-in-progress: true
+
+permissions: write-all
+
+jobs:
+ typos-check:
+ name: Check for new typos
+ runs-on: ubuntu-latest
+ timeout-minutes: 5
+ steps:
+ - name: Checkout the Checkout Actions Repository
+ uses: actions/checkout@v4
+ with:
+ persist-credentials: false
+ - name: Check spelling with typos
+ #uses: crate-ci/typos@master
+ env:
+ GH_TOKEN: "${{ github.token }}"
+ run: |
+ mkdir -p "${{ runner.temp }}/typos"
+ RELEASE_ASSET_URL="$(
+ gh api /repos/crate-ci/typos/releases/latest \
+ --jq '."assets"[] | select(."name" | test("^typos-.+-x86_64-unknown-linux-musl\\.tar\\.gz$")) | ."browser_download_url"'
+ )"
+ wget --secure-protocol=TLSv1_3 --max-redirect=1 --retry-on-host-error --retry-connrefused --tries=3 \
+ --quiet --output-document=- "${RELEASE_ASSET_URL}" \
+ | tar -xz -C "${{ runner.temp }}/typos" ./typos
+ "${{ runner.temp }}/typos/typos" --version
+
+ "${{ runner.temp }}/typos/typos" --config .typos.toml --format json >> ${{ runner.temp }}/typos.jsonl || true
+ 
+
+ python -c '
+ import sys, json
+ old = set()
+ clean = True
+ with open(sys.argv[1]) as file:
+ for line in file:
+ new = json.loads(line)
+ if new["type"] == "typo":
+ clean = False
+ print("::warning file={},line={},col={}::perhaps \"{}\" should be \"{}\".".format(
+ new["path"], new["line_num"], new["byte_offset"],
+ new["typo"], " or ".join(new["corrections"])))
+ sys.exit(1 if not clean else 0)' "${{ runner.temp }}/typos.jsonl"
+

.typos.toml

@@ -20,8 +20,10 @@ extend-exclude = [
  "*.vtu",
  "contrib/catch/*",
  "contrib/world_builder/*",
+ "tests/world_builder_declarations*",
  "*.bib", # bib entries contain many arbitrary abbreviations
  "parameters.*", # parameters should be corrected in the original source
  "doc/sphinx/parameters/*", # parameters should be corrected in the original source
  "tests/prmbackslash*", # this test purposefully breaks words on different lines
+ "contrib/python/env-py_aspect.yml", # this contains random strings which may trip up typos
  ] 

CONTRIBUTING.md

@@ -118,7 +118,7 @@ you can find it [here](https://sourceforge.net/projects/astyle/files/astyle/asty
 An easy way to install it is through using the following command in Linux (do not do this in the aspect directory):
 `mkdir astyle && cd astyle && wget 'https://sourceforge.net/projects/astyle/files/astyle/astyle 2.04/astyle_2.04_linux.tar.gz' && tar -zxvf astyle_2.04_linux.tar.gz && cd astyle/build/gcc && make && sudo make install`.
 This will create a new directory called astyle, download, unpack, compile and install it.
-When you add the bin direcoty to to your path, the indent command should find astyle.
+When you add the bin directory to to your path, the indent command should find astyle.
 
 ### Changelog entries
 

benchmarks/buiter_et_al_2016_jsg/exp_1.prm

@@ -35,7 +35,7 @@ subsection Geometry model
 end
 
 # Mesh refinement specifications
-# AMR is not used since model X,Y repititions are defined.
+# AMR is not used since model X,Y repetitions are defined.
 subsection Mesh refinement
  set Initial adaptive refinement = 0
  set Initial global refinement = 0

benchmarks/shear_bands/plot_hist_and_porosity.py

@@ -10,7 +10,7 @@
 # 'band_angle_adaptive.csv' that contain the number of degrees of 
 # freedom for a given model, the standard deviation and the mean band
 # angle, which can be used to plot the convergence of the band angle
-# unsing the script 'plot_band_angle_dofs.py'. 
+# using the script 'plot_band_angle_dofs.py'. 
 
 import numpy as np
 import numpy.fft as fft

cookbooks/grain_size_ridge/doc/grain_size_ridge.md

@@ -91,7 +91,7 @@ Finally, we use a second Order Runge Kutta integrator to advect the particles.
 We run the model for 200 million years. In the first few tens of millions of years
 there are no large changes in the temperature structure, except that the
 thermal boundary layer increases slightly in thickness. In addition, the grain
-size evolves from its intially constant value, with the grain size being
+size evolves from its initially constant value, with the grain size being
 reduced due to deformation. This leads to a band of particularly low grain
 size in the lowermost part of the oceanic plate. Grain size is also reduced
 in the asthenesphere, but to a lesser degree.

cookbooks/inner_core_convection/doc/inner_core_traction.part.1.prm

@@ -4,7 +4,7 @@ subsection Material model
  # The 'inner core material' model also contains a function that
  # represents the resistance to melting/freezing at the inner core
  # boundary.
- # For P-->inifinity, the boundary is a free slip boundary, and for
+ # For P-->infinity, the boundary is a free slip boundary, and for
  # P-->0, the boundary is an open boundary (with zero normal stress).
  subsection Inner core
  subsection Phase change resistance function

cookbooks/inner_core_convection/inner_core_traction.prm

@@ -37,7 +37,7 @@ subsection Material model
  # velocity and normal stress. The relation between the two scales
  # with the phase change number P, which is given in the 'Function
  # expression'.
- # For P-->inifinity, the boundary is a free slip boundary, and for
+ # For P-->infinity, the boundary is a free slip boundary, and for
  # P-->0, the boundary is an open boundary (with zero normal stress).
 
  # For time dependence, the variable names have to have dim+1 entries,

cookbooks/steinberger/steinberger.prm

@@ -108,7 +108,7 @@ subsection Material model
  set Minimum viscosity = 1e20
 
  # We base our viscosity profile on the adiabat computed based on the
- # material porperties used in the model rather than the laterally
+ # material properties used in the model rather than the laterally
  # averaged temperature.
  set Use lateral average temperature for viscosity = false
 

cookbooks/tomography_based_plate_motions/plugins/tomography_based_plate_motions.cc

@@ -1113,7 +1113,7 @@ namespace aspect
  prm.declare_entry ("Phase transition temperatures", "",
  Patterns::List (Patterns::Double(0)),
  "A list of temperatures where phase transitions occur. Higher or lower "
- "temperatures lead to phase transition ocurring in smaller or greater "
+ "temperatures lead to phase transition occurring in smaller or greater "
  "depths than given in Phase transition depths, depending on the "
  "Clapeyron slope given in Phase transition Clapeyron slopes. "
  "List must have the same number of entries as Phase transition depths. "

cookbooks/tomography_based_plate_motions/plugins/tomography_based_plate_motions.h

@@ -49,7 +49,7 @@ namespace aspect
  * fault boundaries and in continental regions at locations defined
  * by the the compositional field 'faults' or 'cratons', respectively.
  * The material model also allows the option to compute and use
- * equilibirum grain size following paleowattmeter approximation
+ * equilibrium grain size following paleowattmeter approximation
  * by Austin and Evans, (2007), Paleowattmeters: "A scaling relation for
  * dynamically recrystallized grain size", Geology, 35, 343.
  * Other material parameters are either based on (1) an input tomography
@@ -246,9 +246,9 @@ namespace aspect
  std::vector<double> average_viscosity_profile;
 
  /**
- * Variable returned to determine if the evaluate () funciton is called and
+ * Variable returned to determine if the evaluate () function is called and
  * viscosities are computed. Initially, it is set to false and then updated
- * to true in the update () funciton.
+ * to true in the update () function.
  */
  bool initialized;
 
@@ -477,7 +477,7 @@ namespace aspect
  double lithosphere_thickness;
 
  /**
- * Parameter used to decribe the uppermost mantle based on Tutu (2018).
+ * Parameter used to describe the uppermost mantle based on Tutu (2018).
  */
  double depth_to_base_of_uppermost_mantle;
 

data/material-model/steinberger/visc.m

@@ -22,7 +22,7 @@
 0.264E+23 0.9843
 ];
 
-% values are for the middle of the inveral, so shift the x values
+% values are for the middle of the interval, so shift the x values
 
 len = size(mat,1);
 for i=1:size(mat,1)-1

doc/modules/changes/20230718_lhy11009

@@ -1,3 +1,3 @@
-Improved: The iteration scheme in the diffusion dislocation material model now uses the derivative of the logarithm of the strain rate to the logarithm of the stress. This improves efficiency and stablility of the iterative scheme. The parameter "Strain rate residual tolerance" now corresponds to the residual for the logarithm of the strain rate (which close to the solution corresponds to the relative residual).
+Improved: The iteration scheme in the diffusion dislocation material model now uses the derivative of the logarithm of the strain rate to the logarithm of the stress. This improves efficiency and stability of the iterative scheme. The parameter "Strain rate residual tolerance" now corresponds to the residual for the logarithm of the strain rate (which close to the solution corresponds to the relative residual).
 <br>
 (Haoyuan Li and Bob Myhill, 2023/07/18)

doc/modules/to-2.5.0.h

@@ -169,7 +169,7 @@
  * (Elodie Kendall and Anne Glerum, 2022/07/29)
  *
  * <li> Changed: Models that use a strain-dependent rheology
- * can now use an interative Advection scheme, which was
+ * can now use an interactive Advection scheme, which was
  * confirmed not to cause unrealistic accumulation of
  * strain in compositional fields during nonlinear iterations.
  * <br>

include/aspect/material_model/utilities.h

@@ -334,7 +334,7 @@ namespace aspect
 
  private:
  /**
- * The StucturedDataLookup object that stores the material data.
+ * The StructuredDataLookup object that stores the material data.
  */
  std::unique_ptr<Utilities::StructuredDataLookup<2>> material_lookup;
  };

include/aspect/mesh_deformation/fastscape.h

@@ -309,7 +309,7 @@ namespace aspect
 
  /**
  * Flag for having FastScape advect/uplift the surface. If the free surface is used
- * in conjuction with FastScape, this can be set to false, then FastScape will only
+ * in conjunction with FastScape, this can be set to false, then FastScape will only
  * apply erosion/deposition to the surface and not advect or uplift it.
  */
  bool fastscape_advection_uplift;
@@ -374,7 +374,7 @@ namespace aspect
  unsigned int left;
 
  /**
- * Paramters that set the fastscape boundaries periodic even though the ghost nodes are set 'fixed'
+ * Parameters that set the fastscape boundaries periodic even though the ghost nodes are set 'fixed'
  */
  bool topbottom_ghost_nodes_periodic;
  bool leftright_ghost_nodes_periodic;

include/aspect/postprocess/crystal_preferred_orientation.h

@@ -71,7 +71,7 @@ namespace aspect
  std::pair<std::string,std::string> execute (TableHandler &statistics) override;
 
  /**
- * This funcion ensures that the particle postprocessor is run before
+ * This function ensures that the particle postprocessor is run before
  * this postprocessor.
  */
  std::list<std::string>

include/aspect/simulator.h

@@ -752,7 +752,7 @@ namespace aspect
  * Assemble and solve the temperature equation.
  * This function returns the residual after solving.
  *
- * If the `redidual` argument is not a `nullptr`, the function computes
+ * If the `residual` argument is not a `nullptr`, the function computes
  * the residual and puts it into this variable. The function returns
  * the current residual divided by the initial residual given as the
  * first argument. The two arguments may point to the same variable,
@@ -770,7 +770,7 @@ namespace aspect
  * (fields or particles). This function returns the residuals for
  * all fields after solving.
  *
- * If the `redidual` argument is not a `nullptr`, the function computes
+ * If the `residual` argument is not a `nullptr`, the function computes
  * the residual and puts it into this variable. The function returns
  * the current residual divided by the initial residual given as the
  * first argument. The two arguments may point to the same variable,
@@ -787,7 +787,7 @@ namespace aspect
  * Assemble and solve the Stokes equation.
  * This function returns the nonlinear residual after solving.
  *
- * If the `redidual` argument is not a `nullptr`, the function computes
+ * If the `residual` argument is not a `nullptr`, the function computes
  * the residual and puts it into this variable. The function returns
  * the current residual divided by the initial residual given as the
  * first argument. The two arguments may point to the same variable,

source/mesh_deformation/fastscape.cc

@@ -1516,10 +1516,10 @@ namespace aspect
  // Now load the last output at time of restart.
  // this allows us to correctly track when to call
  // FastScape to make new VTK files.
- std::ifstream in_last_ouput_time(restart_filename_time);
- AssertThrow (in_last_ouput_time, ExcIO());
+ std::ifstream in_last_output_time(restart_filename_time);
+ AssertThrow (in_last_output_time, ExcIO());
  {
- in_last_ouput_time >> last_output_time;
+ in_last_output_time >> last_output_time;
  }
  }
 
@@ -1698,7 +1698,7 @@ namespace aspect
  "Deposition coefficient for bedrock.");
  prm.declare_entry("Sediment deposition coefficient", "-1",
  Patterns::Double(),
- "Deposition coefficient for sediment, -1 sets this to teh same as the bedrock deposition coefficient.");
+ "Deposition coefficient for sediment, -1 sets this to the same as the bedrock deposition coefficient.");
  prm.declare_entry("Bedrock river incision rate", "1e-5",
  Patterns::Double(),
  "River incision rate for bedrock in the Stream Power Law. Units: $\\{m^(1-2*drainage_area_exponent)/yr}$");

source/postprocess/crystal_preferred_orientation.cc

@@ -591,7 +591,7 @@ namespace aspect
  prm.declare_entry ("Random number seed", "1",
  Patterns::Integer (0),
  "The seed used to generate random numbers. This will make sure that "
- "results are reproducable as long as the problem is run with the "
+ "results are reproducible as long as the problem is run with the "
  "same amount of MPI processes. It is implemented as final seed = "
  "random number seed + MPI Rank. ");
 
@@ -623,7 +623,7 @@ namespace aspect
  "over the rotation matrix since they only require to write 3 values instead "
  "of 9. If the list is empty, this file will not be written."
  "Furthermore, the entries will be written out in the order given, "
- "and if entries are entered muliple times, they will be written "
+ "and if entries are entered multiple times, they will be written "
  "out multiple times.");
 
  prm.declare_entry ("Write out draw volume weighted cpo data",
@@ -642,11 +642,11 @@ namespace aspect
  "over the rotation matrix since they only require to write 3 values instead "
  "of 9. If the list is empty, this file will not be written. "
  "Furthermore, the entries will be written out in the order given, "
- "and if entries are entered muliple times, they will be written "
+ "and if entries are entered multiple times, they will be written "
  "out multiple times.");
  prm.declare_entry ("Compress cpo data files", "true",
  Patterns::Bool(),
- "Wether to compress the raw and weighted cpo data output files with zlib.");
+ "Whether to compress the raw and weighted cpo data output files with zlib.");
  }
  prm.leave_subsection ();
  }
@@ -721,7 +721,7 @@ namespace aspect
 
  AssertThrow(split_raw_cpo_instructions.size() == 2,
  ExcMessage("Value \""+ write_raw_cpo_list[i] +"\", set in \"Write out raw cpo data\", is not a correct option "
- + "because it should contain a mineral identification and a output specifier seprated by a colon (:). This entry "
+ + "because it should contain a mineral identification and a output specifier separated by a colon (:). This entry "
  + "does not follow those rules."));
 
  // get mineral number
@@ -764,7 +764,7 @@ namespace aspect
 
  AssertThrow(split_draw_volume_weighted_cpo_instructions.size() == 2,
  ExcMessage("Value \""+ write_draw_volume_weighted_cpo_list[i] +"\", set in \"Write out draw volume weighted cpo data\", is not a correct option "
- + "because it should contain a mineral identification and a output specifier seprated by a colon (:). This entry "
+ + "because it should contain a mineral identification and a output specifier separated by a colon (:). This entry "
  + "does not follow those rules."));
 
  // get mineral number
@@ -832,7 +832,7 @@ namespace aspect
  "is recommended for plotting against real data. For both representations"
  "the specific output fields and their order can be set."
  "The work of this postprocessor should better be done by the main particles "
- "postprocessor, however we need to be able to process the data before outputing it, "
+ "postprocessor, however we need to be able to process the data before outputting it, "
  "which does not work with that postprocessor. If this is added to the other "
  "postprocessor in the future this one becomes obsolete.")
  }

tests/box_simple_log_viscosity_depth_average.prm

@@ -8,7 +8,7 @@ set Pressure normalization = surface
 set Surface pressure = 0
 
 # Geometry of the domain. In order to test the depth averaging,
-# we use the X and Y repititions such that four equal depth
+# we use the X and Y repetitions such that four equal depth
 # layers of visocisty are created in the depth-dependent material
 # model.
 subsection Geometry model

tests/drucker_prager_derivatives_2d.cc

@@ -75,7 +75,7 @@ void f(const aspect::SimulatorAccess<dim> &simulator_access,
  /**
  * We can't take to small strain-rates, because then the difference in the
  * visocisty will be too small for the double accuracy which stores
- * the visocity solutions and the finite diference solution.
+ * the visocity solutions and the finite difference solution.
  */
  in_base.strain_rate[0] = SymmetricTensor<2,dim>();
  in_base.strain_rate[0][0][0] = 1e-12;

tests/drucker_prager_derivatives_3d.cc

@@ -75,7 +75,7 @@ void f(const aspect::SimulatorAccess<dim> &simulator_access,
  /**
  * We can't take to small strain-rates, because then the difference in the
  * visocisty will be too small for the double accuracy which stores
- * the visocity solutions and the finite diference solution.
+ * the visocity solutions and the finite difference solution.
  */
  in_base.strain_rate[0] = SymmetricTensor<2,dim>();
  in_base.strain_rate[0][0][0] = 1e-12;

tests/entropy_initial_lookup_wb.wb

@@ -22,7 +22,7 @@
  "features": [
  {
  "model": "oceanic plate",
- "name": "Overiding plate",
+ "name": "Overriding plate",
  "max depth": 150000.0,
  "min depth": -100000.0,
  "coordinates": [