fix images issue

code/plugins/reformat_plugin.py

@@ -0,0 +1,97 @@
+import os
+import sys
+import shutil
+
+# open a text file ending with .md and append a paragraph to it
+def reformat_plugin(dirpath, plugin_name):
+    plugins_dir = '/Users/dtyoung/Documents/EEGLAB/sccn.github.io/plugins'
+    index_file = os.path.join(plugins_dir, 'index.md')
+    shutil.copyfile(os.path.join(dirpath, 'README.md'), index_file)
+    with open(index_file) as f:
+        text = f.read()
+        append_text = '''---
+layout: default
+title: {plugin_name}
+long_title: {plugin_name}
+parent: Plugins
+---
+'''.format(plugin_name=plugin_name)
+        text = append_text + text
+        with open(index_file, 'w') as out:
+            out.write(text)
+
+# open a text file ending with .md and append a paragraph to it
+# Usage: python test.py <filename>.md
+def append_to_file(filepath, filename, parent, output_file):
+    with open(filepath) as f:
+        text = f.read()
+        append_text = '''---
+layout: default
+title: {filename}
+long_title: {filename}
+parent: {parent}
+grand_parent: Plugins
+---
+'''.format(filename=filename, parent=parent)
+        text = append_text + text
+    with open(output_file, 'w') as out:
+        out.write(text)
+
+def reformat_plugin_dir(plugin_input_dir, plugin_name, plugin_type='wiki'):
+    # plugins_output_dir = '/Users/dtyoung/Documents/EEGLAB/sccn.github.io/plugins'
+    plugin_output_dir = os.path.join('/Users/dtyoung/Documents/EEGLAB/sccn.github.io/plugins', plugin_name)
+    if not os.path.exists(plugin_output_dir):
+        os.makedirs(plugin_output_dir)
+    # copy image directory from input to output dir
+    if os.path.exists(os.path.join(plugin_input_dir, 'images')):
+        shutil.copytree(os.path.join(plugin_input_dir, 'images'), os.path.join(plugin_output_dir, 'images'), dirs_exist_ok=True)
+
+    index_file = os.path.join(plugin_output_dir, 'index.md')
+    if plugin_type == 'wiki':
+        shutil.copyfile(os.path.join(plugin_input_dir, 'Home.md'), index_file)
+        with open(index_file) as f:
+            text = f.read()
+            append_text = '''---
+layout: default
+title: {plugin_name}
+long_title: {plugin_name}
+parent: Plugins
+categories: plugins
+has_children: true
+---
+'''.format(plugin_name=plugin_name)
+            text = append_text + text
+            with open(index_file, 'w') as out:
+                out.write(text)
+
+        for root, dirs, files in os.walk(plugin_input_dir):
+            for file in files:
+                if file.endswith('.md') and not file.startswith('index') and not file.startswith('Home'):
+                    append_to_file(os.path.join(plugin_input_dir, file), file.strip('.md'), plugin_name, os.path.join(plugin_output_dir, file))
+    else:
+        shutil.copyfile(os.path.join(plugin_input_dir, 'README.md'), index_file)
+        with open(index_file) as f:
+            text = f.read()
+            append_text = '''---
+layout: default
+title: {plugin_name}
+long_title: {plugin_name}
+parent: Plugins
+---
+'''.format(plugin_name=plugin_name)
+            text = append_text + text
+            with open(index_file, 'w') as out:
+                out.write(text)
+
+# main
+def main():
+    if len(sys.argv) != 4:
+        print('Usage: python test.py <plugin_dir_path> <plugin_name> <plugin_type>')
+        sys.exit(1)
+    dirpath = sys.argv[1]
+    plugin_name = sys.argv[2]
+    plugin_type = sys.argv[3]
+    reformat_plugin_dir(dirpath, plugin_name, plugin_type)
+
+if __name__ == "__main__":
+    main()

code/plugins/update_plugins.py

@@ -7,7 +7,7 @@ def run_command(command):
         print(f"Command failed: {command}\nError: {result.stderr}")
     return result
 
-def update_repo(repo, script, type='readme'):
+def update_repo(repo, script, plugin_type='readme'):
     print(f"Updating {repo}...")
     current_dir = os.getcwd()
     repo_path = os.path.join(current_dir, 'github', repo)
@@ -16,22 +16,22 @@ def update_repo(repo, script, type='readme'):
         os.chdir(repo_path)
         run_command('git pull')
     else:
-        if type == "wiki":
+        if plugin_type == "wiki":
             run_command(f'git clone https://github.com/sccn/{repo}.wiki.git {repo_path}')
         else:
             run_command(f'git clone https://github.com/sccn/{repo}.git {repo_path}')
 
     os.chdir(current_dir)
-    run_command(f'python {script} {repo_path} {repo}')
+    run_command(f'python {script} {repo_path} {repo} {plugin_type}')
 
 if __name__ == "__main__":
     # if 'github' not in current directory, create it
     if not os.path.exists('github'):
         os.makedirs('github')
 
-    wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'PACT', 'nsgportal', 'clean_rawdata']
-    for plugin in wiki_plugins:
-        update_repo(plugin, "Wiki_plugin.py", 'wiki')
-    readme_plugins = ['roiconnect', 'EEG-BIDS', 'trimOutlier', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'amica', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline', 'ARfitStudio ', 'NIMA', 'firfilt']
+    # wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'PACT', 'nsgportal', 'clean_rawdata']
+    # for plugin in wiki_plugins:
+    #     update_repo(plugin, "reformat_plugin.py", 'wiki')
+    readme_plugins = ['ARfitStudio'] #, 'roiconnect', 'EEG-BIDS', 'trimOutlier', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'amica', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline','NIMA', 'firfilt']
     for plugin in readme_plugins:
-        update_repo(plugin, "README_plugin.py")
+        update_repo(plugin, "reformat_plugin.py", "readme")

plugins/SIFT/Chapter-1.-Downloads.md

@@ -9,8 +9,7 @@ grand_parent: Plugins
 
 SIFT releases can be downloaded below
 
-| You can install SIFT using the [EEGLAB Extension Manager](https://eeglab.org/others/EEGLAB_Extensions.html) (see also section 5.1). |                                                                                                                                                                                                                                                                                           
-|------------------------------------------------------------------------------------------------------------------------|
+You can install SIFT using the [EEGLAB Extension Manager](https://eeglab.org/others/EEGLAB_Extensions.html) (see also section 5.1).                                                                                                                                                                                                                                                                                           
 
 <table>
 <tbody>
@@ -20,7 +19,7 @@ SIFT releases can be downloaded below
 </tr>
 <tr class="odd">
 <td><p><img src="images/Dlpdf.jpeg"></p></td>
-<td><p>70-page <a href="https://sccn.ucsd.edu/githubwiki/files/sift_manual_0.1a.pdf" title="wikilink">SIFT manual</a>. It gives both SIFT methods theory and a practical guide to using SIFT using downloadable sample data (some of the content in the PDF document is outdated, and this wiki is more up-to-date).
+<td><p>70-page <a href="https://sccn.ucsd.edu/githubwiki/files/sift_manual_0.1a.pdf" title="wikilink">SIFT manual</a>. It gives both SIFT methods theory and a practical guide to using SIFT using downloadable sample data (some of the content in the PDF document is outdated, and this wiki is more up-to-date).</p></td>
 </tr>
 <tr class="even">
 <td><p><img src="images/Dlpdf.jpeg"></p></td>
@@ -29,7 +28,7 @@ SIFT releases can be downloaded below
 <tr class="even">
 <td><p><img src="images/Dlpdf.jpeg"></p></td>
 <td><p>A short video lecture on the (very) basic theory and application of SIFT to modeling distributed brain dynamics in EEG is available
-<a href="https://www.youtube.com/watch?v=6_WW6EMHmWo&list=PLXc9qfVbMMN2xFa3w5ceJB52Dx-3Sgg2Z&index=12l">here</a>. A longer video is available <a href="https://youtu.be/NO3hbYlqNF0">here</a>. </td>
+<a href="https://www.youtube.com/watch?v=6_WW6EMHmWo&list=PLXc9qfVbMMN2xFa3w5ceJB52Dx-3Sgg2Z&index=12l">here</a>. A longer video is available <a href="https://youtu.be/NO3hbYlqNF0">here</a>.</p></td>
 </tr>
 </tbody>
 </table>

plugins/SIFT/Chapter-5.1.-SIFT-install.md

@@ -25,8 +25,8 @@ Folder**)
 model-fitting algorithm.  You must manually install
 as follows: Download the free ARfit package from
 <https://climate-dynamics.org/software/#arfit>. After downloading and
-unzipping the ARfit package, place the **`/arfit/`** folder in
-**<SIFT-path>`/external/`** where **<SIFT-path>** is the full path to
+unzipping the ARfit package, place the **/arfit/** folder in
+**SIFT-path/external/** where **SIFT-path** is the full path to
 the SIFT root directory.
 
 6\) Once the EEGLAB main GUI is visible, you are good to go! You will

plugins/SIFT/Chapter-5.2.-Loading-and-preparing-the-data.md

@@ -25,7 +25,7 @@ options set. From the EEGLAB menu select **File > Memory and other options**. Ma
 
 Now let’s load our sample datasets in EEGLAB. We will first load the
 *RespWrong.set* file and then *RespCorr.set* located in the
-**<SIFT-path>`/Data/`** folder (click on [Chapter 1. Downloads](Chapter-1.-Downloads) to download the data).
+**SIFT-path/Data/** folder (click on [Chapter 1. Downloads](Chapter-1.-Downloads) to download the data).
 
 ![Image:images/SIFTfig5.jpg](images/SIFTfig5.jpg )
 

plugins/dipfit.md → plugins/dipfit/index.md

@@ -12,7 +12,7 @@ A major obstacle to using EEG data to visualize macroscopic brain dynamics is th
 
 Documentation
 ====
-For documentation see https://eeglab.org/tutorials/09_source/DIPFIT.html
+For documentation see [https://eeglab.org/tutorials/09_source/DIPFIT.html](https://eeglab.org/tutorials/09_source/DIPFIT.html)
 
 Version history
 =====