Merge pull request #213 from Remi-Gau/init

[ENH] update initialisation

Author: Remi-Gau

.all-contributorsrc

@@ -7,7 +7,7 @@
   "contributors": [
     {
       "login": "CerenB",
-      "name": "CerenB",
+      "name": "Ceren Battal",
       "avatar_url": "https://avatars1.githubusercontent.com/u/10451654?v=4",
       "profile": "https://github.com/CerenB",
       "contributions": [
@@ -21,7 +21,7 @@
     },
     {
       "login": "marcobarilari",
-      "name": "marcobarilari",
+      "name": "Marco Barilari",
       "avatar_url": "https://avatars3.githubusercontent.com/u/38101692?v=4",
       "profile": "https://github.com/marcobarilari",
       "contributions": [
@@ -64,7 +64,7 @@
     },
     {
       "login": "iqrashahzad14",
-      "name": "iqrashahzad14",
+      "name": "Iqra Shahzad",
       "avatar_url": "https://avatars.githubusercontent.com/u/75671348?v=4",
       "profile": "https://github.com/iqrashahzad14",
       "contributions": [

checkCppBidsDependencies.m

@@ -1,65 +1,16 @@
-% (C) Copyright 2020 CPP_BIDS developers
-
 function checkCppBidsDependencies(cfg)
-    %
-    % Adds dependencies to the Matlab / Octave path and make sure we got all of them.
-    %
-    % USAGE::
-    %
-    %   checkCppBidsDependencies(cfg)
-    %
-    % :param cfg: Configuration. See ``checkCFG()``.
-    % :type cfg: structure
-
-    if nargin < 1
-        cfg.verbose = 2;
-    end
-
-    global CPP_BIDS_INITIALIZED
-
-    if isempty(CPP_BIDS_INITIALIZED)
-
-        GITHUB_WORKSPACE = getenv('GITHUB_WORKSPACE');
-
-        if strcmp(GITHUB_WORKSPACE, '/github/workspace')
-
-            pth = GITHUB_WORKSPACE;
-            addpath(genpath(fullfile(pth, 'lib')));
-
-        elseif isempty(GITHUB_WORKSPACE)  % local
+    % (C) Copyright 2020 CPP_BIDS developers
 
-            pth = fullfile(fileparts(mfilename('fullpath')));
-
-            addpath(pth);
-
-            checkSubmodule(fullfile(pth, 'lib', 'JSONio'));
-            checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'));
-
-            addpath(genpath(fullfile(pth, 'src')));
-
-        end
-
-        printCreditsCppBids(cfg);
-
-        CPP_BIDS_INITIALIZED = true();
-
-    else
-        if ~isfield(cfg, 'versbose') || cfg.verbose
-            fprintf(1, '\n\nCPP_BIDS already initialized\n\n');
-        end
+    warning(sprintf(['\n\nDEPRECATION WARNING:\n', ...
+                     '"checkCppBidsDependencies" is deprecated ', ...
+                     'and will be removed in a future release.\n', ...
+                     '\nPlease use "cpp_bids(''init'')" instead.'])); %#ok<SPWRN>
 
+    verbose = false;
+    if nargin > 0 && ~isempty(cfg) && isfield(cfg, 'verbose') && ~isempty(cfg.verbose)
+        verbose = cfg.verbose;
     end
 
-end
+    cpp_bids('init', 'verbose', verbose);
 
-function checkSubmodule(pth)
-    % If external dir is empty throw an exception
-    % and ask user to update submodules.
-    if numel(dir(pth)) <= 2 % Means that the external is empty
-        error(['Git submodules are not cloned!', ...
-               'Try this in your terminal:', ...
-               ' git submodule update --recursive ']);
-    else
-        addpath(pth);
-    end
 end

cpp_bids.m

@@ -0,0 +1,171 @@
+function cpp_bids(varargin)
+    %
+    % General intro function for CPP BIDS
+    %
+    % USAGE::
+    %
+    %   cpp_bids
+    %   cpp_bids('init')
+    %   cpp_bids('uninit')
+    %   cpp_bids('dev')
+    %
+    % :param action:
+    % :type action: string
+    %
+    % :returns: - :action: (type) (dimension)
+    %
+    % Example::
+    %
+    % (C) Copyright 2022 CPP_BIDS developers
+
+    p = inputParser;
+
+    defaultAction = 'init';
+
+    addOptional(p, 'action', defaultAction, @ischar);
+    addParameter(p, 'verbose', true);
+
+    parse(p, varargin{:});
+
+    action = p.Results.action;
+    verbose = p.Results.verbose;
+
+    switch lower(action)
+
+        case 'init'
+
+            initCppBids(verbose);
+
+        case 'uninit'
+
+            uninitCppBids();
+
+        case 'run_tests'
+
+            runTests();
+
+    end
+
+end
+
+function initCppBids(verbose)
+    %
+    % Adds the relevant folders to the path for a given session.
+    % Has to be run to be able to use CPP_BIDS.
+    %
+    % USAGE::
+    %
+    %   initCppPtb()
+    %
+    % (C) Copyright 2022 CPP_BIDS developers
+
+    thisDirectory = fileparts(mfilename('fullpath'));
+
+    global CPP_BIDS_INITIALIZED
+    global CPP_BIDS_PATHS
+
+    if isempty(CPP_BIDS_INITIALIZED)
+
+        pathSep = ':';
+        if ~isunix
+            pathSep = ';';
+        end
+
+        CPP_BIDS_PATHS = fullfile(thisDirectory);
+        CPP_BIDS_PATHS = cat(2, CPP_BIDS_PATHS, ...
+                             pathSep, ...
+                             genpath(fullfile(thisDirectory, 'src')));
+        assert(isdir(fullfile(thisDirectory, 'lib', 'bids-matlab', '+bids')));
+        CPP_BIDS_PATHS = cat(2, CPP_BIDS_PATHS, pathSep, ...
+                             fullfile(thisDirectory, 'lib', 'bids-matlab'));
+        assert(isdir(fullfile(thisDirectory, 'lib', 'JSONio')));
+        CPP_BIDS_PATHS = cat(2, CPP_BIDS_PATHS, pathSep, ...
+                             fullfile(thisDirectory, 'lib', 'JSONio'));
+
+        addpath(CPP_BIDS_PATHS, '-begin');
+
+        CPP_BIDS_INITIALIZED = true();
+
+        detectCppBids();
+
+        if verbose
+            printCreditsCppBids();
+        end
+
+    else
+        if verbose
+            fprintf('\n\nCPP_BIDS already initialized\n\n');
+        end
+
+    end
+
+end
+
+function detectCppBids()
+
+    workflowsDir = cellstr(which('saveEventsFile.m', '-ALL'));
+
+    if isempty(workflowsDir)
+        error('CPP_BIDS is not in your MATLAB / Octave path.\n');
+
+    elseif numel(workflowsDir) > 1
+        fprintf('CPP_BIDS seems to appear in several different folders:\n');
+        for i = 1:numel(workflowsDir)
+            fprintf('  * %s\n', fullfile(workflowsDir{i}, '..', '..'));
+        end
+        error('Remove all but one with ''pathtool'' .\n'); % or ''spm_rmpath
+
+    end
+end
+
+function uninitCppBids()
+    %
+    % Removes the added folders from the path for a given session.
+    %
+    % USAGE::
+    %
+    %   uninitCppPtb()
+    %
+    % (C) Copyright 2021 CPP_BIDS developers
+
+    global CPP_BIDS_INITIALIZED
+    global CPP_BIDS_PATHS
+
+    if isempty(CPP_BIDS_INITIALIZED) || ~CPP_BIDS_INITIALIZED
+        fprintf('\n\nCPP_BIDS not initialized\n\n');
+        return
+
+    else
+        rmpath(CPP_BIDS_PATHS);
+
+        if isOctave
+            clear -g;
+        else
+            clearvars -GLOBAL;
+        end
+
+    end
+
+end
+
+function retval = isOctave()
+    %
+    % Returns true if the environment is Octave.
+    %
+    % USAGE::
+    %
+    %   retval = isOctave()
+    %
+    % :returns: :retval: (boolean)
+    %
+    % (C) Copyright 2020 Agah Karakuzu
+    % (C) Copyright 2022 CPP_BIDS developers
+
+    persistent cacheval   % speeds up repeated calls
+
+    if isempty (cacheval)
+        cacheval = (exist ('OCTAVE_VERSION', 'builtin') > 0);
+    end
+
+    retval = cacheval;
+end

docs/source/conf.py

@@ -12,17 +12,19 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'CPP BIDS'
-copyright = '2020, the CPP BIDS dev team'
-author = 'the CPP BIDS dev team'
+project = "CPP BIDS"
+copyright = "2020, the CPP BIDS dev team"
+author = "the CPP BIDS dev team"
 
 # The full version, including alpha/beta/rc tags
-release = 'v2.1.2dev'
+with open("../../version.txt", encoding="utf-8") as version_file:
+    release = version_file.read()
 
 
 # -- General configuration ---------------------------------------------------
@@ -31,42 +33,45 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinxcontrib.matlab',
-    'sphinx.ext.autodoc']
-matlab_src_dir = os.path.dirname(os.path.abspath('../../src'))
-primary_domain = 'mat'
+    "sphinxcontrib.matlab",
+    "sphinx.ext.autodoc",
+    "myst_parser",
+    "sphinx_copybutton",
+]
+matlab_src_dir = os.path.dirname(os.path.abspath("../../src"))
+primary_domain = "mat"
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
-html_logo = '_static/cpp_lab_logo.png'
+html_logo = "_static/cpp_lab_logo.png"
 
 # html_theme_options = {
 #     'github_user': 'cpp-lln-lab',
@@ -81,11 +86,11 @@
 # }
 
 html_sidebars = {
-    '**': [
-        'about.html',
-        'navigation.html',
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
-        'donate.html',
+    "**": [
+        "about.html",
+        "navigation.html",
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
+        "donate.html",
     ]
 }

lib/bids-matlab

@@ -2,7 +2,7 @@
 project_root
 
 line_length: 100
-regex_function_name: "[a-z]+(([A-Z]){1}[A-Za-z]+)*"
+regex_function_name: "[a-z]+(_*[a-zA-Z0-9]+[a-z]*)*"
 regex_parameter_name: "[a-z0-9]+(([A-Z]){1}[A-Za-z]+)*"
 
 exclude_dir: "lib"

miss_hit.cfg

@@ -2,6 +2,11 @@ Sphinx
 sphinxcontrib-matlabdomain
 sphinxcontrib-napoleon
 sphinx_rtd_theme
+myst-parser
+sphinx-copybutton
+
 miss_hit==0.9.29
+pre-commit
+
 notebook
 octave_kernel