From af6a1eb1cba68a9775c99b31456c0df7929c46f9 Mon Sep 17 00:00:00 2001
From: Jessie <jessieyr@outlook.com>
Date: Tue, 9 Aug 2022 16:55:58 -0400
Subject: [PATCH 01/11] changed docs/source/getting_started.rst, brew install
 openjdk

---
 docs/source/getting_started.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
index 2f166a09..5d8125ca 100644
--- a/docs/source/getting_started.rst
+++ b/docs/source/getting_started.rst
@@ -58,7 +58,7 @@ Mac
 ```
 
 #. Ensure Java 11 is installed inside Anaconda distribution (``conda install -c anaconda openjdk``) if using Anaconda, or
-   via Homebrew otherwise (``brew cask install java``)
+   via Homebrew otherwise (``brew install openjdk``)
 #. Check Java version is 11 via ``java --version``
 #. Once PolyglotDB is installed, run :code:`pgdb install /path/to/where/you/want/data/to/be/stored`, or
    :code:`pgdb install` to save data in the default directory.

From bf10089e2b5c2dad5faf8117be525acd0644e2d8 Mon Sep 17 00:00:00 2001
From: Jessie <jessieyr@outlook.com>
Date: Tue, 9 Aug 2022 17:21:44 -0400
Subject: [PATCH 02/11] add docs/source/tshoot_install.rst, pgdb setup on Mac

---
 docs/source/tshoot_install.rst | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 docs/source/tshoot_install.rst

diff --git a/docs/source/tshoot_install.rst b/docs/source/tshoot_install.rst
new file mode 100644
index 00000000..a47e6fe0
--- /dev/null
+++ b/docs/source/tshoot_install.rst
@@ -0,0 +1,12 @@
+************
+Installation (for Mac users) 
+************
+
+If the ``pgdb`` command does not work, you may try the following steps:
+
+1. Uninstall Java
+2. Make sure Anaconda is installed on your Mac. If you are using Miniconda, run ``miniconda install anaconda`` to install Anaconda. 
+3. Reinstall Java by ``conda install -anaconda openjdk``. Note that you should not use Homebrew to install Java, since Anaconda helps to manage the Java version appropriate for PolyGlot installation. 
+4. ``pgdb install``, ``pgdb start``, and ``pgdb stop`` should work now. 
+
+

From 756120d000429ad6bf370e7d64658ff9cdd61186 Mon Sep 17 00:00:00 2001
From: Jessie <jessieyr@outlook.com>
Date: Tue, 9 Aug 2022 17:32:19 -0400
Subject: [PATCH 03/11] added troubleshooting.rst

---
 docs/source/troubleshoot.rst   | 17 +++++++++++++++++
 docs/source/tshoot_install.rst |  2 ++
 2 files changed, 19 insertions(+)
 create mode 100644 docs/source/troubleshoot.rst

diff --git a/docs/source/troubleshoot.rst b/docs/source/troubleshoot.rst
new file mode 100644
index 00000000..dec54d35
--- /dev/null
+++ b/docs/source/troubleshoot.rst
@@ -0,0 +1,17 @@
+.. _troubleshooting:
+
+***************
+Troubleshooting
+***************
+
+This section contains several troubleshooting tips on installation, tutorials, etc. 
+
+
+Contents:
+
+..  toctree::
+    :maxdepth: 2
+
+    tshoot_install.rst 
+
+
diff --git a/docs/source/tshoot_install.rst b/docs/source/tshoot_install.rst
index a47e6fe0..079a9412 100644
--- a/docs/source/tshoot_install.rst
+++ b/docs/source/tshoot_install.rst
@@ -1,3 +1,5 @@
+.. _tshoot_install:
+
 ************
 Installation (for Mac users) 
 ************

From 477bacd76671de092419865b66d5b115d54f8cf0 Mon Sep 17 00:00:00 2001
From: Jessie <jessieyr@outlook.com>
Date: Tue, 9 Aug 2022 17:34:17 -0400
Subject: [PATCH 04/11] changed docs/source/index.rst

---
 docs/source/index.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index bb6c2818..d7e6ba09 100755
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -18,6 +18,7 @@ Contents:
    queries.rst
    developer.rst
    changelog.rst
+   troubleshooting.rst
 
 See `the PolyglotDB wiki`_ for the changelog.
 

From a04c86d00dd5aea37f48dd89313bb324c2ec8741 Mon Sep 17 00:00:00 2001
From: Jessie <jessieyr@outlook.com>
Date: Tue, 9 Aug 2022 17:39:06 -0400
Subject: [PATCH 05/11] modified index.rst

---
 docs/source/{troubleshoot.rst => troubleshooting.rst} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename docs/source/{troubleshoot.rst => troubleshooting.rst} (100%)

diff --git a/docs/source/troubleshoot.rst b/docs/source/troubleshooting.rst
similarity index 100%
rename from docs/source/troubleshoot.rst
rename to docs/source/troubleshooting.rst

From 6d1426e8a9354d9882e4f7b80d54a1c4c88a0fa9 Mon Sep 17 00:00:00 2001
From: Jessie <jessieyr@outlook.com>
Date: Tue, 9 Aug 2022 17:46:00 -0400
Subject: [PATCH 06/11] modified index.rst

---
 docs/source/troubleshooting.rst | 6 +++---
 docs/source/tshoot_install.rst  | 5 ++++-
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index dec54d35..252a6f51 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -9,9 +9,9 @@ This section contains several troubleshooting tips on installation, tutorials, e
 
 Contents:
 
-..  toctree::
-    :maxdepth: 2
+.. toctree::
+   :maxdepth: 2
 
-    tshoot_install.rst 
+   tshoot_install.rst 
 
 
diff --git a/docs/source/tshoot_install.rst b/docs/source/tshoot_install.rst
index 079a9412..f1130fad 100644
--- a/docs/source/tshoot_install.rst
+++ b/docs/source/tshoot_install.rst
@@ -1,9 +1,12 @@
 .. _tshoot_install:
 
 ************
-Installation (for Mac users) 
+Installation 
 ************
 
+For Mac users 
+=============
+
 If the ``pgdb`` command does not work, you may try the following steps:
 
 1. Uninstall Java

From 44bc40b8f4564ed53774874abb846415516b9729 Mon Sep 17 00:00:00 2001
From: Jessie <jessieyr@outlook.com>
Date: Tue, 9 Aug 2022 19:28:58 -0400
Subject: [PATCH 07/11] add tshoot_other.rst and tshoot_tut.rst

---
 docs/source/troubleshooting.rst |  3 +--
 docs/source/tshoot_install.rst  |  2 +-
 docs/source/tshoot_other.rst    | 32 +++++++++++++++++++++++++++
 docs/source/tshoot_tut.rst      | 39 +++++++++++++++++++++++++++++++++
 4 files changed, 73 insertions(+), 3 deletions(-)
 create mode 100644 docs/source/tshoot_other.rst
 create mode 100644 docs/source/tshoot_tut.rst

diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index 252a6f51..cc131493 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -1,7 +1,7 @@
 .. _troubleshooting:
 
 ***************
-Troubleshooting
+Troubleshooting Tips
 ***************
 
 This section contains several troubleshooting tips on installation, tutorials, etc. 
@@ -14,4 +14,3 @@ Contents:
 
    tshoot_install.rst 
 
-
diff --git a/docs/source/tshoot_install.rst b/docs/source/tshoot_install.rst
index f1130fad..24c70fc6 100644
--- a/docs/source/tshoot_install.rst
+++ b/docs/source/tshoot_install.rst
@@ -4,7 +4,7 @@
 Installation 
 ************
 
-For Mac users 
+On Mac
 =============
 
 If the ``pgdb`` command does not work, you may try the following steps:
diff --git a/docs/source/tshoot_other.rst b/docs/source/tshoot_other.rst
new file mode 100644
index 00000000..1169d8b9
--- /dev/null
+++ b/docs/source/tshoot_other.rst
@@ -0,0 +1,32 @@
+.. _tshoot_other:
+
+************
+Others
+************
+
+Run time error 
+===============
+
+If this error occurs: 
+
+.. code::
+    RuntimeError: 
+        An attempt has been made to start a new process before the
+        current process has finished its bootstrapping phase.
+
+        This probably means that you are not using fork to start your
+        child processes and you have forgotten to use the proper idiom
+        in the main module:
+
+            if __name__ == '__main__':
+                freeze_support()
+                ...
+
+        The "freeze_support()" line can be omitted if the program
+        is not going to be frozen to produce an executable.
+
+
+You need to add ``if __name__ == '__main__'`` at the beginning of your vowel-formant.py file.
+
+
+
diff --git a/docs/source/tshoot_tut.rst b/docs/source/tshoot_tut.rst
new file mode 100644
index 00000000..aa0789b1
--- /dev/null
+++ b/docs/source/tshoot_tut.rst
@@ -0,0 +1,39 @@
+.. _tshoot_tut:
+
+************
+Tutorials
+************
+
+Corpus Structure
+===============
+
+* Your corpus should be arranged by speaker. 
+* Each speaker directory contains TextGrid files and the corresponding wav files. If some corresponding wav files are missing, the ``KeyError: 'vowel_file_path'`` may appear. 
+* If the KeyError still exists, you may reset the corpus as below. 
+
+.. code-block::
+    with CorpusContext(corpus_name) as c:
+        c.reset()
+
+
+Defining Vowel Set (Tutorial 4)
+===============
+
+**In vowel formant analysis, make sure to check the output of the phone set, and accordingly define your own vowel set.** This is because, in Tutorial 4, the regex used to define the vowel set may not work for the language you are working on. 
+
+In other words, instead of using:
+
+.. code-block::
+    vowel_set = [re.search(vowel_regex, p).string for p in phone_set
+            if re.search(vowel_regex, p) != None and p not in non_speech_set]
+
+
+Use (e.g., for Cantonese): 
+
+.. code-block::
+    vowel_set = ['6', '6j', '6w', '9', '9y', 'E:', 'O:', 'O:j', 'a:', 'a:j', 'a:w', 'ej', 'i:', 'ow', 'u:', 'y:']
+
+
+You can either use your own regex or type the vowels manually based the output of the phone set. 
+
+

From 180b33aa44eec857c107aa12bc1fd8ad103814f9 Mon Sep 17 00:00:00 2001
From: Jessie <jessieyr@outlook.com>
Date: Tue, 9 Aug 2022 19:31:03 -0400
Subject: [PATCH 08/11] change troubleshooting.rst

---
 docs/source/troubleshooting.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index cc131493..2a8a32c5 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -13,4 +13,7 @@ Contents:
    :maxdepth: 2
 
    tshoot_install.rst 
+   tshoot_tut.rst
+   tshoot_other.rst
+
 

From fa4a2e19b6c1ce4e7d8e08d157ba93356814bba3 Mon Sep 17 00:00:00 2001
From: Jessie <jessieyr@outlook.com>
Date: Tue, 9 Aug 2022 19:35:09 -0400
Subject: [PATCH 09/11] edit code block

---
 docs/source/tshoot_other.rst | 2 +-
 docs/source/tshoot_tut.rst   | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/source/tshoot_other.rst b/docs/source/tshoot_other.rst
index 1169d8b9..a2ce236c 100644
--- a/docs/source/tshoot_other.rst
+++ b/docs/source/tshoot_other.rst
@@ -9,7 +9,7 @@ Run time error
 
 If this error occurs: 
 
-.. code::
+.. code-block:: python 
     RuntimeError: 
         An attempt has been made to start a new process before the
         current process has finished its bootstrapping phase.
diff --git a/docs/source/tshoot_tut.rst b/docs/source/tshoot_tut.rst
index aa0789b1..4f57aa1e 100644
--- a/docs/source/tshoot_tut.rst
+++ b/docs/source/tshoot_tut.rst
@@ -11,7 +11,7 @@ Corpus Structure
 * Each speaker directory contains TextGrid files and the corresponding wav files. If some corresponding wav files are missing, the ``KeyError: 'vowel_file_path'`` may appear. 
 * If the KeyError still exists, you may reset the corpus as below. 
 
-.. code-block::
+.. code-block:: python 
     with CorpusContext(corpus_name) as c:
         c.reset()
 
@@ -23,14 +23,14 @@ Defining Vowel Set (Tutorial 4)
 
 In other words, instead of using:
 
-.. code-block::
+.. code-block:: python
     vowel_set = [re.search(vowel_regex, p).string for p in phone_set
             if re.search(vowel_regex, p) != None and p not in non_speech_set]
 
 
 Use (e.g., for Cantonese): 
 
-.. code-block::
+.. code-block:: python 
     vowel_set = ['6', '6j', '6w', '9', '9y', 'E:', 'O:', 'O:j', 'a:', 'a:j', 'a:w', 'ej', 'i:', 'ow', 'u:', 'y:']
 
 

From 2e9f848b432475cf4a9074d5d80b0a7a63cbd56c Mon Sep 17 00:00:00 2001
From: Jessie <jessieyr@outlook.com>
Date: Tue, 9 Aug 2022 19:37:14 -0400
Subject: [PATCH 10/11] edit code block again

---
 docs/source/tshoot_other.rst | 1 +
 docs/source/tshoot_tut.rst   | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/docs/source/tshoot_other.rst b/docs/source/tshoot_other.rst
index a2ce236c..44e77eed 100644
--- a/docs/source/tshoot_other.rst
+++ b/docs/source/tshoot_other.rst
@@ -10,6 +10,7 @@ Run time error
 If this error occurs: 
 
 .. code-block:: python 
+    
     RuntimeError: 
         An attempt has been made to start a new process before the
         current process has finished its bootstrapping phase.
diff --git a/docs/source/tshoot_tut.rst b/docs/source/tshoot_tut.rst
index 4f57aa1e..9d7bc20f 100644
--- a/docs/source/tshoot_tut.rst
+++ b/docs/source/tshoot_tut.rst
@@ -12,6 +12,7 @@ Corpus Structure
 * If the KeyError still exists, you may reset the corpus as below. 
 
 .. code-block:: python 
+
     with CorpusContext(corpus_name) as c:
         c.reset()
 
@@ -24,6 +25,7 @@ Defining Vowel Set (Tutorial 4)
 In other words, instead of using:
 
 .. code-block:: python
+
     vowel_set = [re.search(vowel_regex, p).string for p in phone_set
             if re.search(vowel_regex, p) != None and p not in non_speech_set]
 
@@ -31,6 +33,7 @@ In other words, instead of using:
 Use (e.g., for Cantonese): 
 
 .. code-block:: python 
+    
     vowel_set = ['6', '6j', '6w', '9', '9y', 'E:', 'O:', 'O:j', 'a:', 'a:j', 'a:w', 'ej', 'i:', 'ow', 'u:', 'y:']
 
 

From a3d2df631b6cc1fb0d5084aad51d710ecb608972 Mon Sep 17 00:00:00 2001
From: Jessie <jessieyr@outlook.com>
Date: Tue, 9 Aug 2022 19:53:48 -0400
Subject: [PATCH 11/11] update rtd_requirements.txt, sphinx_rtd_theme>=0.3.1

---
 rtd_requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rtd_requirements.txt b/rtd_requirements.txt
index 7d202d79..599f0e86 100755
--- a/rtd_requirements.txt
+++ b/rtd_requirements.txt
@@ -1,4 +1,4 @@
 sphinx
 numpydoc
 mock
-sphinx_rtd_theme
+sphinx_rtd_theme>=0.3.1