Add Spell Checker (#1168)

* first attempt at spellchecker, listing all file types and excluding some known exceptions

* Move file to repo root

* Exclude JSON and R files as we are less sure if they can be corrected

* Add common abbreviations to avoid false positives

* Fix "releative"

* Fix "permision"

* Fix "Setings"

* Fix "untill"

* Fix "buttom"

* Fix "alloted"

* Fix "controling"

* Fix "auxiliary"

* Fix "constriant"

* Fix most typos in non-code files

* Change config file path in GHA workflow

* Fix "seperate"

* Fix "excpetion"

* Fix "handeling"

* Fix "deafult(s)"

* Fix typos in code comments or strings

* Add exclusions for typos for identifiers in non-internal scopes

* Fix typos in code

* Fix typo in figure name

* Fix "thershold"

* Format code

* Fix "NoInteractiveSer"

* Fix "ghostOuput"

* Uncommit and ignore Pipfile

---------

Co-authored-by: Ludovico Bianchi <lbianchi@lbl.gov>
Co-authored-by: Keith Beattie <ksbeattie@lbl.gov>

.github/workflows/checks.yml

@@ -47,9 +47,19 @@ jobs:
       - name: Run Black to verify that the committed code is formatted
         run: |
           black --check .
+  spell-check:
+    name: Check Spelling
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v3
+      - name: Run Spell Checker
+        uses: crate-ci/typos@master
+        with: 
+          config: .typos.toml
   pytest:
     name: pytest (py${{ matrix.python-version }}/${{ matrix.os }})
-    needs: [code-formatting]
+    needs: [code-formatting, spell-check]
     runs-on: ${{ matrix.os-version }}
     strategy:
       fail-fast: false

.gitignore

@@ -24,6 +24,7 @@ eggs/
 *.lib
 *.suo
 *.zip
+Pipfile
 
 # OSX
 *.DS_Store

.typos.toml

@@ -0,0 +1,43 @@
+[files]
+extend-exclude = [
+    "*.smp",
+    "*.ui",
+    "*.html",
+    "*.css",
+    "*.js",
+    "*.svg",
+    "*.foqus",
+    "*.bkp",
+    "*.acmf",
+    "*.for",
+    "*.his",
+    "*.def",
+    "*.ads",
+    "*.pt",
+    "*.pkl",
+    "*.R",
+    "*.json",
+]
+
+[default.extend-words]
+# Ignore IDAES
+IDAES = "IDAES"
+FO = "FO"  # TODO: probably an abbreviation?
+sur = "sur"  # abbreviation for 'surrogate'
+nd = "nd"  # used as a variable name in sdoeAnalysisDialog
+astroid = "astroid"  # Python package name
+# proper nouns
+Gess = "Gess"
+# false positives
+strat = "strat"  # abbreviation of "strategy" used by Hypothesis
+
+[default.extend-identifiers]
+# false positives
+strngComps = "strngComps"  # strng = strongly (connected)
+# true positives that are part of the API
+userInterupt = "userInterupt"
+maxTimeInterupt = "maxTimeInterupt"
+PyCodeInterupt = "PyCodeInterupt"
+simin_nam = "simin_nam"
+simout_nam = "simout_nam"
+displayAvailablityWarning = "displayAvailablityWarning"

README.md

@@ -34,13 +34,13 @@ See our [FAQ](FAQs.md) for frequently asked questions and answers
 See also the list of [contributors](../../graphs/contributors) who participated in this project.
 
 ## Development Practices
-* Code development will be peformed in a forked copy of the repo. Commits will not be 
+* Code development will be performed in a forked copy of the repo. Commits will not be 
   made directly to the repo. Developers will submit a pull request that is then merged
   by another team member, if another team member is available.
 * Each pull request should contain only related modifications to a feature or bug fix.  
 * Sensitive information (secret keys, usernames etc) and configuration data 
   (e.g database host port) should not be checked in to the repo.
-* A practice of rebasing with the main repo should be used rather that merge commmits.
+* A practice of rebasing with the main repo should be used rather that merge commits.
 
 ## Versioning
 We use [SemVer](http://semver.org/) for versioning. For the versions available, 

cloud/aws/README.md

@@ -140,8 +140,7 @@ PSParentPath          : Microsoft.PowerShell.Core\Registry::HKEY_LOCAL_MACHINE\S
 PSChildName           : Windows
 PSDrive               : HKLM
 PSProvider            : Microsoft.PowerShell.Core\Registry
-PS C:\Users\Administrator> Set-ItemProperty -path HKLM:\SYSTEM\CurrentControlSet\Control\Windows\ -Name NoInteractiveSer
-vices -Value 0
+PS C:\Users\Administrator> Set-ItemProperty -path HKLM:\SYSTEM\CurrentControlSet\Control\Windows\ -Name NoInteractiveServices -Value 0
 ```
 ##### Registry set NoInteractiveServices
 ```

cloud/aws/cloudformation/FOQUS_SLM_instance_in_subnet.py

@@ -78,7 +78,7 @@ def _create_template(
     t.add_version("2010-09-09")
     t.add_description(
         """Template to create SLM instance and bind to
-    passed in Newtork Interface\
+    passed in Network Interface\
     """
     )
 

docs/source/chapt_dev/index.rst

@@ -3,7 +3,7 @@
 Developer Documentation
 =======================
 
-Since the `source code for all of FOQUS is publically available
+Since the `source code for all of FOQUS is publicly available
 <https://github.com/CCSI-Toolset/FOQUS>`_, the more adventurous user may wish to look at the
 inner-workings of FOQUS to get a better understand how it works, contribute a fix to a bug, or add
 new features to the source tree. Other members of our CCSI partnership (national laboratories,

docs/source/chapt_flowsheet/reference/settings.rst

@@ -22,7 +22,7 @@ FOQUS** tab.
 
 Options in the **Settings, FOQUS** tab are described below.
 
-#. **Save settings to working directoy**, when checkbox is selected the
+#. **Save settings to working directory**, when checkbox is selected the
    settings file will be read from the specified working directory. This
    setting is useful for running multiple copies of FOQUS to ensure the
    settings do not conflict. When starting additional copies of FOQUS,

docs/source/chapt_install/run_foqus.rst

@@ -58,4 +58,4 @@ e.g., for the Bash shell:
 
 If, on the contrary, a graphical interface *is* desired but the errors above occur, it is possible that the system is not yet configured to support graphical applications.
 In this case, try installing the :code:`libgl1-mesa-glx` and/or :code:`libxkbcommon-x11-0` packages using
-the package manager appropriate for your Linux distrubution (i.e. :code:`apt-get install` on Ubuntu).
+the package manager appropriate for your Linux distribution (i.e. :code:`apt-get install` on Ubuntu).

docs/source/chapt_matlab/reference/matlab_foqus_intro.rst

@@ -54,7 +54,7 @@ If the MATLAB engine package was installed correctly, a similar message to the F
 
 .. figure:: ../figs/terminal_window_msg.png
 
-   Figure 1 - Terminal window message after installating the MATLAB engine package
+   Figure 1 - Terminal window message after installing the MATLAB engine package
 
 Now, to run MATLAB models within FOQUS follow the steps below:
 

docs/source/chapt_odoe/tutorial-createcand.rst

@@ -111,7 +111,7 @@ In this example, the user will generate a new candidate set.
 
    Browse and load the EvaluationSet.csv file from the examples folder. Similar to the candidate set
    section, the user can select the evaluation set and click on the **Delete Selection** button in
-   case they want to delete the evaulation set. To visualize the data, just click the **View**
+   case they want to delete the evaluation set. To visualize the data, just click the **View**
    button under the **Visualize** column.
 
    .. figure:: figs/9b_ODoE_Cand&EvalSets.png

docs/source/chapt_odoe/tutorial-loadcand.rst

@@ -98,7 +98,7 @@ In this example, the user will provide an existing candidate set.
 
    Browse and load the EvaluationSet.csv file from the examples folder. Similar to the candidate set
    section, the user can select the evaluation set and click on the **Delete Selection** button in
-   case they want to delete the evaulation set. To visualize the data, just click the **View**
+   case they want to delete the evaluation set. To visualize the data, just click the **View**
    button under the **Visualize** column.
 
    .. figure:: figs/9a-2_ODoE_Cand&EvalSets.png

docs/source/chapt_opt/reference/optimization.rst

@@ -173,7 +173,7 @@ Python expressions.
 
 #. The **Penalty Factor** contains the coefficient :math:`a` used in calculating
    the penalty for a constraint violation, see Equations
-   :eq:`eq.linear.constriant` to :eq:`eq.step.constriant`.
+   :eq:`eq.linear.constraint` to :eq:`eq.step.constraint`.
 
 #. The **Form** column contains a selection of different methods to
    calculate a constraint penalty.
@@ -186,10 +186,10 @@ Python expressions.
    The variables are provided without the sample index.
 
 The calculations for each type of constraint penalty are given in
-Equations :eq:`eq.linear.constriant` to :eq:`eq.step.constriant`.
+Equations :eq:`eq.linear.constraint` to :eq:`eq.step.constraint`.
 
 .. math::
-   :label: eq.linear.constriant
+   :label: eq.linear.constraint
 
    \text{Linear penalty form:  }p_i =
    \begin{cases}
@@ -198,7 +198,7 @@ Equations :eq:`eq.linear.constriant` to :eq:`eq.step.constriant`.
    \end{cases}
 
 .. math::
-   :label: eq.quadratic.constriant
+   :label: eq.quadratic.constraint
 
    \text{Quadratic penalty form:  }p_i =
    \begin{cases}
@@ -207,7 +207,7 @@ Equations :eq:`eq.linear.constriant` to :eq:`eq.step.constriant`.
    \end{cases}
 
 .. math::
-   :label: eq.step.constriant
+   :label: eq.step.constraint
 
    \text{Step penalty form:  }p_i =
    \begin{cases}

docs/source/chapt_sdoe/basics-runorder.rst

@@ -2,7 +2,7 @@ Efficient Implementation of Experimental Run Order
 ==================================================
 
 Once designs have been created, it is often important to optimize the run order to efficiently reach equilibrium and 
-allow for the maximum number of runs to be implemented within a constrainted budget or time period. While statisticians 
+allow for the maximum number of runs to be implemented within a constrained budget or time period. While statisticians 
 generally recommend using a randomized order for the experimental runs, it can sometimes mean the difference of a small 
 randomized experiment versus a larger non-randomized experiment. 
 

docs/source/chapt_sinter/tutorial/gproms.rst

@@ -404,7 +404,7 @@ configuration can be done.
    Default Initialization page will display. Here the default values of
    the vectors may be edited.
 
-   .. figure:: ../figs/gPROMS/25_Vectorss.png
+   .. figure:: ../figs/gPROMS/25_Vectors.png
       :alt: Editing Vectors
       :name: fig.sinter.gproms.vectors
 

docs/source/chapt_surrogates/tutorial/alamo.rst

@@ -139,7 +139,7 @@ data is provided and adaptive sampling is used.
 
    Sample Distributions
 
-19. The **Sampling schem\ e** dialog should display (Figure
+19. The **Sampling scheme** dialog should display (Figure
     :ref:`fig.tut.sur.new.uq.sample2`).
     Select “Latin Hypercube” from the list.
 
@@ -216,15 +216,15 @@ other and for the model building, selecting one output is the same as
 selecting more.
 
 30. Select the **Variable\ s** tab (Figure
-    :ref:`fig.tut.sur.vaiables`).
+    :ref:`fig.tut.sur.variables`).
 
 31. Select the checkbox for both input variables.
 
 32. Select the checkbox for both output variables.
 
 .. figure:: ../figs/variables.svg
    :alt: Variable Selection
-   :name: fig.tut.sur.vaiables
+   :name: fig.tut.sur.variables
 
    Variable Selection
 

docs/source/chapt_vector_support/example2/Aspen_Model_Vectors_Handling.rst

@@ -77,8 +77,8 @@ Vectorize" will be displayed as shown in Figure 3.
           elements required as a part of the vector.
 
           In this case, "B_TEMP" is the variable name corresponding to the
-          liquid phase temerature along the absorber column, and "TVAP" is the
-          variable name corresponding to the vapor phase temerature along the
+          liquid phase temperature along the absorber column, and "TVAP" is the
+          variable name corresponding to the vapor phase temperature along the
           absorber column, according to their path in SimSinter.
           These vector variables are indexed over the absorber stages, which is
           why the number of elements in each of them would be 90.
@@ -104,7 +104,7 @@ steps 3 and 4 with the correct user inputs. If it is created, open the json file
 directly to check whether it has been modified correctly.
 
 In the json file, the dictionary corresponding to the "outputs" key must contain
-180 scalar variables 90 each corrsponding to the vector variables "B_TEMP" and
+180 scalar variables 90 each corresponding to the vector variables "B_TEMP" and
 "TVAP". Each scalar output variable corresponding to the vector must contain a
 "vector" field which includes the vector variable it is associated with, and an
 "index" field, which defines its location in the vector. The indices range from

docs/source/conf.py

@@ -60,7 +60,7 @@
     #    'sphinx-jsonschema'
 ]
 
-# Avoid duplicating heading labels across parallely constructed documentation
+# Avoid duplicating heading labels across parallelly constructed documentation
 autosectionlabel_prefix_document = True
 
 # Add any paths that contain templates here, relative to this directory.

examples/test_files/Smoke_Tests/fs_smoke_test.py

@@ -33,7 +33,7 @@ def go(sleep=0.25, MainWin=MainWin):
 
 
 def getButton(w, label):
-    """Get a buttom in window w labeled label"""
+    """Get a button in window w labeled label"""
     blist = w.buttons()
     for b in blist:
         if b.text().replace("&", "") == label:
@@ -700,13 +700,13 @@ def timerWait(timer, sleep=0.25, n=40, go=go, timers=timers, tf=testOutFile):
             return True
     timers[timer].stop()  # Timer never did it's thing so just shut it down
     with open(tf, "a") as f:  # file to write test results to
-        f.write("ERROR: timer {} didn't stop in alloted time\n".format(timer))
+        f.write("ERROR: timer {} didn't stop in allotted time\n".format(timer))
     return False  # return False to stop script.  Something is wrong
 
 
 # make the timers that will be needed just start and stop as needed
 # need to make sure that when this script exits all timers are stopped
-# or some crazy stuff may happen untill you exit FOQUS.
+# or some crazy stuff may happen until you exit FOQUS.
 addTimer("time_out", MainWin.helpDock.setStopTrue)  # stop script if too long
 addTimer("msg_okay", msg_okay)  # click OK on mgsbox
 addTimer("msg_no", msg_no)  # click No on msgbox

examples/test_files/Smoke_Tests/optimization_smoke_test.py

@@ -36,7 +36,7 @@ def go(sleep=0.25, MainWin=MainWin):
 
 
 def getButton(w, label):
-    """Get a buttom in window w labeled label"""
+    """Get a button in window w labeled label"""
     blist = w.buttons()
     for b in blist:
         if b.text().replace("&", "") == label:
@@ -177,13 +177,13 @@ def timerWait(timer, sleep=0.25, n=40, go=go, timers=timers, tf=errorFile):
             return True
     timers[timer].stop()  # Timer never did it's thing so just shut it down
     with open(tf, "a") as f:  # file to write test results to
-        f.write("ERROR: timer {} didn't stop in alloted time\n".format(timer))
+        f.write("ERROR: timer {} didn't stop in allotted time\n".format(timer))
     return False  # return False to stop script.  Something is wrong
 
 
 # make the timers that will be needed just start and stop as needed
 # need to make sure that when this script exits all timers are stopped
-# or some crazy stuff may happen untill you exit FOQUS.
+# or some crazy stuff may happen until you exit FOQUS.
 addTimer("time_out", MainWin.helpDock.setStopTrue)  # stop script if too long
 addTimer("msg_okay", msg_okay)  # click OK on mgsbox
 addTimer("msg_no", msg_no)  # click No on msgbox

examples/test_files/Smoke_Tests/optimization_smoke_test_BFGS.py

@@ -36,7 +36,7 @@ def go(sleep=0.25, MainWin=MainWin):
 
 
 def getButton(w, label):
-    """Get a buttom in window w labeled label"""
+    """Get a button in window w labeled label"""
     blist = w.buttons()
     for b in blist:
         if b.text().replace("&", "") == label:
@@ -177,13 +177,13 @@ def timerWait(timer, sleep=0.25, n=40, go=go, timers=timers, tf=errorFile):
             return True
     timers[timer].stop()  # Timer never did it's thing so just shut it down
     with open(tf, "a") as f:  # file to write test results to
-        f.write("ERROR: timer {} didn't stop in alloted time\n".format(timer))
+        f.write("ERROR: timer {} didn't stop in allotted time\n".format(timer))
     return False  # return False to stop script.  Something is wrong
 
 
 # make the timers that will be needed just start and stop as needed
 # need to make sure that when this script exits all timers are stopped
-# or some crazy stuff may happen untill you exit FOQUS.
+# or some crazy stuff may happen until you exit FOQUS.
 addTimer("time_out", MainWin.helpDock.setStopTrue)  # stop script if too long
 addTimer("msg_okay", msg_okay)  # click OK on mgsbox
 addTimer("msg_no", msg_no)  # click No on msgbox

examples/test_files/Smoke_Tests/optimization_smoke_test_COBYLA.py

@@ -36,7 +36,7 @@ def go(sleep=0.25, MainWin=MainWin):
 
 
 def getButton(w, label):
-    """Get a buttom in window w labeled label"""
+    """Get a button in window w labeled label"""
     blist = w.buttons()
     for b in blist:
         if b.text().replace("&", "") == label:
@@ -177,13 +177,13 @@ def timerWait(timer, sleep=0.25, n=40, go=go, timers=timers, tf=errorFile):
             return True
     timers[timer].stop()  # Timer never did it's thing so just shut it down
     with open(tf, "a") as f:  # file to write test results to
-        f.write("ERROR: timer {} didn't stop in alloted time\n".format(timer))
+        f.write("ERROR: timer {} didn't stop in allotted time\n".format(timer))
     return False  # return False to stop script.  Something is wrong
 
 
 # make the timers that will be needed just start and stop as needed
 # need to make sure that when this script exits all timers are stopped
-# or some crazy stuff may happen untill you exit FOQUS.
+# or some crazy stuff may happen until you exit FOQUS.
 addTimer("time_out", MainWin.helpDock.setStopTrue)  # stop script if too long
 addTimer("msg_okay", msg_okay)  # click OK on mgsbox
 addTimer("msg_no", msg_no)  # click No on msgbox

examples/test_files/Smoke_Tests/optimization_smoke_test_CRS2.py

@@ -36,7 +36,7 @@ def go(sleep=0.25, MainWin=MainWin):
 
 
 def getButton(w, label):
-    """Get a buttom in window w labeled label"""
+    """Get a button in window w labeled label"""
     blist = w.buttons()
     for b in blist:
         if b.text().replace("&", "") == label:
@@ -177,13 +177,13 @@ def timerWait(timer, sleep=0.25, n=40, go=go, timers=timers, tf=errorFile):
             return True
     timers[timer].stop()  # Timer never did it's thing so just shut it down
     with open(tf, "a") as f:  # file to write test results to
-        f.write("ERROR: timer {} didn't stop in alloted time\n".format(timer))
+        f.write("ERROR: timer {} didn't stop in allotted time\n".format(timer))
     return False  # return False to stop script.  Something is wrong
 
 
 # make the timers that will be needed just start and stop as needed
 # need to make sure that when this script exits all timers are stopped
-# or some crazy stuff may happen untill you exit FOQUS.
+# or some crazy stuff may happen until you exit FOQUS.
 addTimer("time_out", MainWin.helpDock.setStopTrue)  # stop script if too long
 addTimer("msg_okay", msg_okay)  # click OK on mgsbox
 addTimer("msg_no", msg_no)  # click No on msgbox