make guid compatible with python 3

4i0n · Mar 25, 2017 · ad9835d · ad9835d
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Showing 3 changed files with 20 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -104,8 +104,7 @@ If you don't have root access, remove the `sudo` part and instead  use  `--user`
 **Common Problems:**
 
  * `Could not find SATe tools bundle directory:`: this means you don't have the right tools directory at the right location. Maybe you downloaded MAC instead of Linux? Or, maybe you didn't put the directory in the parent directory of where pasta code is? Most likely, you used the zip files and forgot to remove teh `-master` from the directory name. Run `mv sate-tools-mac-master sate-tools-mac` on MAC or `mv sate-tools-linux-master sate-tools-linux` to fix this issue. 
- * The `setup.py` script is supposed to install setuptools for you if you don't have it. This sometimes works and sometimes doesn't. If you get and error with a message like ` invalid command 'develop'`, it means that setuptools is not installed. To solve this issue, you can manually install [setup tools](https://pypi.python.org/pypi/setuptools#installation-instructions). For example, on Linux, you can run: 
-     * `curl https://bootstrap.pypa.io/ez_setup.py -o - | sudo python` 
+ * The `setup.py` script is supposed to install setuptools for you if you don't have it. This sometimes works and sometimes doesn't. If you get and error with a message like ` invalid command 'develop'`, it means that setuptools is not installed. To solve this issue, you can manually install [setup tools](https://pypi.python.org/pypi/setuptools#installation-instructions). For example, on Linux, you can run `curl https://bootstrap.pypa.io/ez_setup.py -o - | sudo python` 
 (but note there are other ways of installing setuptools as well).
 
 
@@ -141,7 +140,9 @@ To run the GUI version,
 
 ```
     python run_pasta_gui.py
-```    
+```
+
+on some machines you may need to use `pythonw run_pasta_gui.py` instead. 
 
 Options
 ------

diff --git a/pasta-doc/pasta-tutorial.md b/pasta-doc/pasta-tutorial.md
@@ -124,11 +124,24 @@ PASTA can be run using command-line or GUI.
 ### From GUI:
 1. If you have installed PASTA from the .dmg file, to run the PASTA GUI you just click on the application you copied on your machine. 
 2. If you have installed PASTA from the code, you need to open a terminal (sorry!) and run: 
-3. On the VM, on the left hand side, there is a PASTA icon. Click that to open PASTA. 
 
 ```
 run_pasta_gui.py
 ``` 
+on some machines, this may not work, saying
+
+```
+This program needs access to the screen. Please run with a Framework build of python, and only when you are logged in on the main display of your Mac.
+```
+
+you may be able to fix this by running:
+
+```
+pythonw {PATH to pasta}/run_pasta_gui.py
+```
+note the use of `pythonw` instead of `python`
+
+3. On the VM, on the left hand side, there is a PASTA icon. Click that to open PASTA. 
 
 This will open up the PASTA GUI. To provide then input file, click on ``Sequence File`` button and select the input fasta file. 
 

diff --git a/pasta/__init__.py b/pasta/__init__.py
@@ -12,8 +12,8 @@
 PROGRAM_NAME = "PASTA"
 PROGRAM_AUTHOR = ["Siavash Mirarab","Nam Nguyen","Jiaye Yu", "Mark T. Holder", "Jeet Sukumaran", "Jamie Oaks"]
 PROGRAM_LICENSE = "GNU General Public License, version 3"
-PROGRAM_VERSION = "1.7.0"
-PROGRAM_YEAR = "2013-2016"
+PROGRAM_VERSION = "1.7.1"
+PROGRAM_YEAR = "2013-2017"
 PROGRAM_DESCRIPTION = "Practical Alignment using SATe and TrAnsitivity"
 PROGRAM_WEBSITE = "http://www.cs.utexas.edu/~phylo/software/pasta/"
 PROGRAM_INSTITUTE = "Department of Computer Science, University of Texas at Austin"