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File permissions issue with python/Spyder/Anaconda after upgrading mac to Catalina

After upgrading macOS to Catalina, my Anaconda installation was helpfully reconfigured by Apple. Advice from the Anaconda website suggested a fresh install was the best way to go. Did that and all seemed good. I use spyder from the Anaconda navigator. But trying a previously running python code failed due to apparent file permission problems. For example,
file='/Users/stingay/Documents/Coaching/WAIS/2019:20/041019/Race Walk Test-2019-10-04T16.29.13.774-C5612E80FB1D-Accelerometer.csv'
with open(file,'rt') as f:
data = csv.reader(f)
next(data)
results in:
PermissionError: [Errno 1] Operation not permitted: '/Users/stingay/Documents/Coaching/WAIS/2019:20/041019/Race Walk Test-2019-10-04T16.29.13.774-C5612E80FB1D-Accelerometer.csv'
I can't see an issue with the permissions on the file or the directory structure in which the file sits. If I move the file to~/.spyder-py3 (the working directory), it works.
Looks like there is some extra python/spyder/anaconda permissions issue with the file/directory I can't spot. Any ideas?

I guess you have solved this by now, but for future reference, I still post my answer.
TLDR: I opened a file (from the folder causing the problem) directly in
the spyder editor (File | open). As a consequence, the editor should have triggered the pop-up dialog question whether you want to allow access or not. In my case, the mac silently granted python/spyder access to the folder. Now I can run the code in spyder without more problems than I have caused myself.
Longer version:
The source of your problem is described here:
https://www.howtogeek.com/443611/how-macos-catalinas-new-security-features-work/
Knowing that links are something frown upon, here's a summary:
The problem is that the folders "Documents" and "Downloads" folders nowadays are protected and you would need to go to the security & privacy settings and "Files and Folder,s" and allow the applications to access these. Unfortunately, spyder does not show up here. So, if you want to run your python program from the terminal, you should probably grant the terminal access to the folders.

Total noob here, but I might have stumbled upon a solution for people that have problems reading in their data in spyder after the Catalina update. I had the same problems you describe and got the same file permission errors.
I couldn't resolve the issue, reinstalled several times but didn't work for me. I couldn't use my Utorrent either, and while attempting to solve that problem I came across https://discuss.pixls.us/t/problems-with-darktable-and-mac-osx-catalina-solved-with-dt-2-6-3-1/14400/19 this forum.
Long story short, in the forum people couldn't really resolve the issue, but someone pointed out that if you just run the application from the terminal, it somehow works. I tried to do this with Spyder, and I seem to be able to use the read_csv('file') function again. So try opening the terminal, then type 'spyder' (without '') and press enter. Somehow all issues seem to be resolved. Hope this helps someone.

Same problem here. I re-installed Anaconda based on this link and Python is able to access folders where Catalina has added newly restricted security:
Install Anaconda following instructions below:
https://www.anaconda.com/how-to-restore-anaconda-after-macos-catalina-update/
For Anaconda-Jupyter user, you are good to go
For Commandline (Terminal) Python user, you are good to go
For Anaconda-Spyder user, two options as a workaround after installation above:
Avoid Mac default setup-folders and relocate files to /Users/[user_name]/..
OR
Launch Spyder through Terminal (execute "sudo spyder") under root user
Lastly, changing or reseting folder/file permission does not resolve permission issue. Despite of the security issue under the more restricted security folders, somehow Spyder-Python is able to open .py files in these folders.
Since Jupyter and commandline Python can access these folders, I assume there will be a fix in the future for Anaconda-Spyder.

My code didn't work at all after Catalina update. The simplest partial solution that I found was to copy all files containing the scripts in a new folder. That works at least to run the codes, but I still dealing with annoying message to allow access to my files.

conda update --all in terminal worked for me. It updated everything. I did have to go through the annoying messages for access to my files as well. but after clicking yes a hundred times it was ab

svn: E155007: '/home/k/python/myproject_env/django-myproject/myproject' is not a working copy

I have been building django project and I want to use Subversion for version control on Ubuntu.
As you know, I need to keep most of the projects in the repository, however, some files and directories should only stay locally and not be tracked.
So I went to my project directory and typed the following command.
svn propedit svn:ignore myproject
But exception has occurred like this.
svn: E155007: '/home/k/python/myproject_env/django-myproject/myproject' is not a working copy
The path is ture that my app is located at /home/k/python/myproject_env/django-myproject/myproject
The guide says that when I type the command above, this will open a temporary file in the editor, where I need to put the following file and directory patterns for Subversion to ignore. But it doesn't work.
I already found the solution, but there is no answer anywhere.
I would like to know the solution. Thanks for your time.

Spyder: [Errno 2] No such file or directory

I want to run this code in Github : https://github.com/llazzaro/lsa_python
but I don't know how to execute it with nosetests. I have python 2.7.11 and anaconda 4.0.0, I have to run it with Spyder because I need scientific packages so when I put this link: https://github.com/llazzaro/lsa_python on Spyder I get this:
[C:\Anaconda2\python.exe: can't open file 'C:\Users\CLIENT\Desktop\lsa_python-master\sanstitre0.py': [Errno 2] No such file or directory]

Maybe you need to set your working directory correctly. It probably looks for the path from the current working directory.
You can change it here:

Little late to answer these questions But still if anyone facing the same issue this answer might help
I was facing the same issue. I even reinstall the anaconda. But it's still doing the same issue. Then I figure out something very silly.
First of all, you have to set your working directory
After that, you have to hit the Run button.
I was pressing ctrl + enter
But after setting the working directory for the first time you have to hit the run button then it will work
Hope it will help.

Error when running tests with nose-gae

I've been using nose-gae for awhile, and I just updated to release 0.3.0, which is only 3 days old. I'm running GAE SDK 1.9.17 on Mac OS X Yosemite.
When I run my tests, I get the following error:
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python:
can't open file
'/Library/Frameworks/Python.framework/Versions/2.7/bin/_python_runtime.py':
[Errno 2] No such file or directory
Sure enough, that file doesn't exist. My tests appear to run successfully however (test output below). I don't see any such errors when running the dev_appserver.
I don't know what _python_runtime.py is and what is causing the error. Any help figuring out what is going on would be appreciated.
====
$ nosetests -x tests/functional_tests.py
................/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '/Library/Frameworks/Python.framework/Versions/2.7/bin/_python_runtime.py': [Errno 2] No such file or directory
...
----------------------------------------------------------------------
Ran 19 tests in 11.032s
OK

This module _python_runtime.py should be in the SDK root folder. (confirmation here https://code.google.com/p/googleappengine/source/browse/trunk/python/)
Are you sure that it is included in your PATH? If yes -- it is best to fill an issue here, such nose-gae still buggy after update.
UPDATE this issue is solved with latest NoseGAE update, which is currently in dev branch here. Just clone it and use sudo python setup.py install to update it.

I think the problem is that nose-gae uses the old devappserver rather than the newer one. The old devappserver was removed from the SDK in 1.9.17.

Why does gitpython on windows always get file not found errors?

When looking at the tutorial located here for gitpython, and following step by step there are some issues on my machine. The environment is Windows 7, and git version 1.7.11.msysgit.1 along with Python 2.7. Everything installed fine with easy_install. Repo object successfully gets created, and commands like repo.tree() and repo.branches work. If I do a repo.is_dirty() there are non-specific file not found errors. WindowsError: [Error 2] The system cannot find the file specified. Any ideas?
path = "c:\\path_to_repo"
repo = Repo(path)
assert repo.bare == False
print repo.tree()
repo.branches
print dir(repo)
#these always crash...
repo.is_dirty()
TIA for any help.

You might not have git.ext in your PATH, but that can easily be tested by executing it yourself. If you see an error, you can either add it to the PATH, or set the GIT_PYTHON_GIT_EXECUTABLE to the executable that git-python should execute for git command line services.
The reason it works for .tree() and related object queries is that gitpython uses a pure-python backend for these operations. More complex operations like .is_dirty() still require the git executable to be in your PATH by default.