[DOC] move doc to main website and apply simple pre-commit hooks

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = .git,*.pdf,*.svg
+ignore-words-list = ans

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+---
+repos:
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-json
+    -   id: check-ast
+    -   id: check-added-large-files
+    -   id: pretty-format-json
+    -   id: check-case-conflict
+
+
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    -   id: codespell
+
+-   repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+    rev: 0.2.3
+    hooks:
+    -   id: yamlfmt
+        args: [--mapping, '4', --sequence, '4', --offset, '0']

.travis.yml

@@ -1,6 +1,7 @@
+---
 # vim ft=yaml
 # travis-ci.org definition for MOxUnit build (based on CoSMoMVPA,
-# which is based on PyMVPA, which is based on nipype configuration, 
+# which is based on PyMVPA, which is based on nipype configuration,
 # which in turn was based on nipy)
 #
 # We pretend to be java because we need GNU Octave which is not
@@ -10,54 +11,42 @@ language: java
 dist: trusty
 sudo: required
 cache:
-  - apt
+-   apt
 env:
- global:
-    - OCTAVE=octave
- matrix:
-    - WITH_COVERAGE=
-    - WITH_COVERAGE=true
+    global:
+    -   OCTAVE=octave
+    matrix:
+    -   WITH_COVERAGE=
+    -   WITH_COVERAGE=true
 before_install:
     # to prevent IPv6 being used for APT
-    - sudo bash -c "echo 'Acquire::ForceIPv4 \"true\";' > /etc/apt/apt.conf.d/99force-ipv4"
-    - travis_retry sudo apt-get -y -qq update
-    - travis_retry sudo apt-get install -y -qq software-properties-common python-software-properties
-    - travis_retry sudo apt-add-repository -y ppa:octave/stable
-    - travis_retry sudo apt-get -y -qq update
+-   sudo bash -c "echo 'Acquire::ForceIPv4 \"true\";' > /etc/apt/apt.conf.d/99force-ipv4"
+-   travis_retry sudo apt-get -y -qq update
+-   travis_retry sudo apt-get install -y -qq software-properties-common python-software-properties
+-   travis_retry sudo apt-add-repository -y ppa:octave/stable
+-   travis_retry sudo apt-get -y -qq update
     # get Octave 4,0
-    - travis_retry sudo apt-get -y -qq install octave liboctave-dev
+-   travis_retry sudo apt-get -y -qq install octave liboctave-dev
     # install MOxUnit
-    - cd ..
-    - rm -rf MOxUnit
-    - git clone https://github.com/MOxUnit/MOxUnit.git
-    - make -C MOxUnit install
+-   cd ..
+-   rm -rf MOxUnit
+-   git clone https://github.com/MOxUnit/MOxUnit.git
+-   make -C MOxUnit install
     # install MOcov
-    - rm -rf MOcov
-    - git clone https://github.com/MOcov/MOcov.git
-    - make -C MOcov install
-    # cd back to original directory 
-    - cd MOdox
+-   rm -rf MOcov
+-   git clone https://github.com/MOcov/MOcov.git
+-   make -C MOcov install
+    # cd back to original directory
+-   cd MOdox
     # show .octaverc
-    - cat ~/.octaverc
+-   cat ~/.octaverc
 
 script:
-    - if [[  "$WITH_COVERAGE" == "true" ]]; then
-          TEST_ARGS=WITH_COVERAGE=true;
-          COVER_ARGS=COVER=`pwd`/MOdox;
-
-          if [[  "$SHIPPABLE" == "true"  ]]; then
-              OUTPUT_ARGS=COVER_XML_FILE=${SHIPPABLE_BUILD_DIR}/shippable/codecoverage/coverage.xml;
-              AFTER_SCRIPT="find ${SHIPPABLE_BUILD_DIR}/shippable/;cat ${SHIPPABLE_BUILD_DIR}/shippable/codecoverage/coverage.xml;which reports";
-          elif [[  "$TRAVIS" == "true"  ]]; then
-              OUTPUT_ARGS=COVER_JSON_FILE=`pwd`/coveralls.json;
-              AFTER_SCRIPT="curl --verbose -F json_file=@`pwd`/coveralls.json https://coveralls.io/api/v1/jobs";
-          fi;
-      elif [[  "$SHIPPABLE" == "true"  ]]; then
-          RESULT_ARGS=JUNIT_XML_FILE=${SHIPPABLE_BUILD_DIR}/shippable/testresults/test_results.xml;
-      fi
-    - echo Test arguments $TEST_ARGS $COVER_ARGS $OUTPUT_ARGS $RESULT_ARGS
-    - make test $TEST_ARGS $COVER_ARGS $OUTPUT_ARGS $RESULT_ARGS
-    - eval $AFTER_SCRIPT
-
-
-
+-   "if [[  \"$WITH_COVERAGE\" == \"true\" ]]; then TEST_ARGS=WITH_COVERAGE=true; COVER_ARGS=COVER=`pwd`/MOdox;\nif [[  \"$SHIPPABLE\" == \"true\"  ]];\
+    \ then OUTPUT_ARGS=COVER_XML_FILE=${SHIPPABLE_BUILD_DIR}/shippable/codecoverage/coverage.xml; AFTER_SCRIPT=\"find ${SHIPPABLE_BUILD_DIR}/shippable/;cat\
+    \ ${SHIPPABLE_BUILD_DIR}/shippable/codecoverage/coverage.xml;which reports\"; elif [[  \"$TRAVIS\" == \"true\"  ]]; then OUTPUT_ARGS=COVER_JSON_FILE=`pwd`/coveralls.json;\
+    \ AFTER_SCRIPT=\"curl --verbose -F json_file=@`pwd`/coveralls.json https://coveralls.io/api/v1/jobs\"; fi; elif [[  \"$SHIPPABLE\" == \"true\"  ]];\
+    \ then RESULT_ARGS=JUNIT_XML_FILE=${SHIPPABLE_BUILD_DIR}/shippable/testresults/test_results.xml; fi"
+-   echo Test arguments $TEST_ARGS $COVER_ARGS $OUTPUT_ARGS $RESULT_ARGS
+-   make test $TEST_ARGS $COVER_ARGS $OUTPUT_ARGS $RESULT_ARGS
+-   eval $AFTER_SCRIPT

CITATION.cff

@@ -0,0 +1,27 @@
+# schema: https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md
+
+cff-version: 1.2.0
+
+title: MOdox
+
+abstract: MOdox is documentation test ("doctest") framework for Matlab and GNU Octave.
+
+version: 0.1.0
+
+license: MIT
+
+repository-code: https://github.com/MOxUnit/MOdox.git
+
+message: If you use this software, please cite it as below.
+
+keywords:
+  - testing-framework
+  - MATLAB
+  - octave
+
+authors:
+  - given-names: Nikolaas N.
+    family-names: Oosterhof
+    email: n.oosterhof@gmail.com
+  - given-names: Oliver
+    family-names: Heimlich

LICENSE

@@ -0,0 +1,22 @@
+(The MIT License)
+
+Copyright (c) 2015-2023 Nikolaas N. Oosterhof
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction,
+including without limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of the Software,
+and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

MOdox/@MOdoxDocTestParser/MOdoxDocTestParser.m

@@ -2,4 +2,4 @@
 % Instaniate MOdoxDocTestParser object
 
     s=struct();
-    obj=class(s,'MOdoxDocTestParser');
+    obj=class(s,'MOdoxDocTestParser');

MOdox/@MOdoxDocTestParser/getDocTestLines.m

@@ -17,7 +17,7 @@
 %                           with indentation removed. If no documentation
 %                           is found, then the output is an empty cell
 %                           array.
-%                           If a parsing error occured, then this is a
+%                           If a parsing error occurred, then this is a
 %                           string with the error message.
 %   doctest_idxs            the indices of the lines with doctests, i.e.
 %                           lines{doctest_idxs}==doctest_lines.
@@ -230,4 +230,3 @@ function check_inputs(obj,lines)
     if ~(iscell(lines) && all(cellfun(empty_or_string,lines)))
         error('Second input must be cell string');
     end
-

MOdox/@MOdoxDocTestParser/getHelpLines.m

@@ -81,5 +81,3 @@
     cleaner=onCleanup(@()fclose(fid));
     lines_vec=fread(fid,'char=>char')';
     lines=regexp(lines_vec,sprintf('\n'),'split');
-
-

MOdox/@MOdoxDocTestParser/getOutputPrefix.m

@@ -8,4 +8,4 @@
 %   s                       string that indicates that line contains
 %                           expected output
 
-    s='%||';
+    s='%||';

MOdox/@MOdoxDocTestParser/parseLines.m

@@ -29,7 +29,7 @@
     [doc_lines,doc_idxs]=getDocTestLines(obj,all_lines);
 
     if ischar(doc_lines)
-        % unparseable expression
+        % unparsable expression
         reason=doc_lines;
         line_number=max([1,doc_idxs(find(doc_idxs,1))]);
         location=MOdoxMFileLocation(mfile_name,line_number);
@@ -140,9 +140,3 @@
     escaped_prefix=regexptranslate('escape',prefix);
 
     pat=['^\s*' escaped_prefix '(.*)$'];
-
-
-
-
-
-

MOdox/@MOdoxExpression/MOdoxExpression.m

@@ -3,4 +3,3 @@
 
     s=struct();
     obj=class(s,'MOdoxExpression');
-

MOdox/@MOdoxMFileLocation/disp.m

@@ -1,4 +1,4 @@
 function disp(obj)
 % display the object
 
-    fprintf('%s\n',str(obj));
+    fprintf('%s\n',str(obj));

MOdox/@MOdoxMFileLocation/getFilename.m

@@ -1,4 +1,4 @@
 function filename=getFilename(obj)
 % return filename
 
-    filename=obj.filename;
+    filename=obj.filename;

MOdox/@MOdoxMFileLocation/getLineNumber.m

@@ -1,4 +1,4 @@
 function line_number=getLineNumber(obj)
 % return line number
 
-    line_number=obj.line_number;
+    line_number=obj.line_number;

MOdox/@MOdoxMFileLocation/str.m

@@ -1,4 +1,4 @@
 function s=str(obj)
 % return string representation number
 
-    s=sprintf('%s: %d',getFilename(obj),getLineNumber(obj));
+    s=sprintf('%s: %d',getFilename(obj),getLineNumber(obj));

MOdox/@MOdoxSeparatorExpression/MOdoxSeparatorExpression.m

@@ -3,4 +3,3 @@
 
     s=struct();
     obj=class(s,'MOdoxSeparatorExpression',MOdoxExpression());
-

MOdox/@MOdoxSeparatorExpression/isEvaluable.m

@@ -1,4 +1,4 @@
 function tf=isEvaluable(obj)
 % Returns true
 
-    tf=false;
+    tf=false;

MOdox/@MOdoxSeparatorExpression/isValid.m

@@ -1,4 +1,4 @@
 function tf=isValid(obj)
 % Returns true
 
-    tf=true;
+    tf=true;

MOdox/@MOdoxSeparatorExpression/str.m

@@ -1,3 +1,3 @@
 function s=str(obj)
 % Return string representation of expression
-    s=repmat('-',1,20);
+    s=repmat('-',1,20);

MOdox/@MOdoxTestCase/getExpressions.m

@@ -9,4 +9,4 @@
 % Output:
 %   expr           cell with MOdoxExpression instances
 
-    expr=obj.expressions;
+    expr=obj.expressions;

MOdox/@MOdoxTestCase/run.m

@@ -63,7 +63,7 @@
         DXD__expression=DXD__expressions{DXD__i};
 
         if ~isValid(DXD__expression)
-            % unparseable expression
+            % unparsable expression
             DXD__reason=getReason(DXD__expression);
             DXD__outcome_args=DXD__build_error_struct(DXD__reason,...
                                             DXD__expression);
@@ -187,7 +187,3 @@
 
 function line=remove_ans_eq(line)
     line=regexprep(line,'^\s*ans\s*=','');
-
-
-
-

MOdox/@MOdoxTestCaseExpression/MOdoxTestCaseExpression.m

@@ -7,7 +7,7 @@
 %   location                MOdoxMFileLocation instance
 %   lines                   cellstring with matlab code
 %   output_prefix           (optional) string prefix for output
-%   output                  cellstring with expectd output
+%   output                  cellstring with expected output
 
 
     check_inputs(location,code,output_prefix,output)

MOdox/@MOdoxTestCaseExpression/disp.m

@@ -1,3 +1,3 @@
 function disp(obj)
     s=str(obj);
-    fprintf('%s:\n%s',class(obj),s);
+    fprintf('%s:\n%s',class(obj),s);

MOdox/@MOdoxTestCaseExpression/getCode.m

@@ -1,4 +1,4 @@
 function code=getCode(obj)
 % Return code (without prefix)
 
-    code=obj.code;
+    code=obj.code;

MOdox/@MOdoxTestCaseExpression/getLocation.m

@@ -1,4 +1,4 @@
 function location=getLocation(obj)
 % Return location
 
-    location=obj.location;
+    location=obj.location;

MOdox/@MOdoxTestCaseExpression/getOutput.m

@@ -1,4 +1,4 @@
 function code=getOutput(obj)
 % Return code (without prefix)
 
-    code=obj.output;
+    code=obj.output;

MOdox/@MOdoxTestCaseExpression/getOutputPrefix.m

@@ -1,4 +1,4 @@
 function prefix=getOutputPrefix(obj)
 % Return prefix
 
-    prefix=obj.output_prefix;
+    prefix=obj.output_prefix;

MOdox/@MOdoxTestCaseExpression/isEvaluable.m

@@ -1,4 +1,4 @@
 function tf=isEvaluable(obj)
 % Returns true
 
-    tf=true;
+    tf=true;

MOdox/@MOdoxTestCaseExpression/isValid.m

@@ -1,4 +1,4 @@
 function tf=isValid(obj)
 % Returns true
 
-    tf=true;
+    tf=true;

MOdox/@MOdoxTestSuite/MOdoxTestSuite.m

@@ -21,5 +21,3 @@
 
     s=struct();
     obj=class(s,class_name,MOxUnitTestSuite(name));
-
-

MOdox/@MOdoxTestSuite/addFromFile.m

@@ -45,4 +45,3 @@
             end
         end
     end
-

MOdox/@MOdoxUnparseableExpression/getLocation.m

@@ -1,4 +1,4 @@
 function location=getLocation(obj)
 % Return location
 
-    location=obj.location;
+    location=obj.location;

MOdox/@MOdoxUnparseableExpression/getReason.m

@@ -1,4 +1,4 @@
 function reason=getReason(obj)
 % return parse error reason
 
-    reason=obj.reason;
+    reason=obj.reason;

MOdox/@MOdoxUnparseableExpression/isEvaluable.m

@@ -1,4 +1,4 @@
 function tf=isEvaluable(obj)
 % Returns true
 
-    tf=true;
+    tf=true;