I have a .yml file that I would like to create a python environment with called icesattest.yml It is in my downloads folder. When I run the following command in the Anaconda Prompt:
conda env create -f icesattest.yml
I get the following error:
EnvironmentFileNotFound: 'C:\Users\scox4\icesattest.yml' file not found
How do I tell the Anaconda prompt to look for the .yml at C:\Users\scox4\downloads\icesattest.yml? Or, how do I move the .yml file to this path so it is read? I tried to drag and drop icesattest.yml to the My PC sidebar on file explorer but it wouldn't let me move it there. I know this is a really silly mistake but I am a complete novice so any simply advice would help!
I searched and found the command that is used to create environments from .yml files so I copy pasted it as so but it failed. I changed the command to match the icesattest.yml file and it still did not work.
The way I typically handle this is via the env update command. I've found it to be a bit more robust when it comes to working with environment files.
conda env update -n <name of virtual environment> -f environment.yml
This command works both with existing environments and with new environments.
I should mention that I typically work with Linux and not Windows, so I can only guarantee that this will work well with unix systems. I'd recommend you check out something like WSL if you can, as working with Linux is typically a lot easier than Windows once you get the hang of it.
If you want to read more about conda environments: https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#updating-an-environment
Related
I'm trying to build a dashboard app via Plotly.Dash.
Therefore, I'm transitioning from using Jupyter to Atom.ide.
It seems I have managed to set up a virtual environment and activated it with no errors; in that virtual environment dash_reqlibs.yml i'm trying to install Plotly lib, which also loads with no errors according to terminal:
After the installation i'm trying to run my simple test code and it tells me it doesn't see module plotly:
Now, please note, that according to my research I'm not even supposed to do that since in my dash_reqlibs.yml I have specified all need - doesn't work either way though:
UPDATE:
Removed bad venv
Created new one successfully
Changed to app.py directory and activated the venv
cannot select venv as it doesnt show up
Try creating environment from the beginning again, using these steps:
Create “dash_reqlibs.yml” file with required libraries
Save it inside your Environments folder (or whatever name you call that folder)
Open Windows Command Prompt (or Atom terminal) and ‘cd’ into your Environments folder
Crate new virtual environment by typing: conda env create -f dash_reqlibs.yml
Activate your new environment:
a. On Windows, type: conda activate env_dash (name value inside the .yml file)
Let me know how it goes.
I previously had Conda running smoothly on Mojave, but I've found that the upgrade to Catalina moves the "anaconda3" folder to your Desktop > Relocated Items > Security > anaconda3. It seems Catalina's security settings may not allow applications to install directly under the user directory anymore.
I tried the suggestion here, written below:
Hi, I might have a solution
Copy the folder anaconda3 located in Relocated Items to /Users/myname/
Open Terminal
Enter: export PATH=''/Users/myname/anaconda3/bin:$PATH"
Enter: conda init zsh
It worked! Good luck!
But this doesn't work for me. After conda init zsh I get:
-bash: /Users/USER/anaconda3/bin/conda: /anaconda3/bin/python: bad interpreter: No such file or directory
How can I get Conda up and running again without losing all my virtual environments? Thanks!
Update
I got Conda to work following #Ted Shaowang's suggestion. This means that conda env list shows all the virtual environments created via Conda.
However I am still experiencing an issue with virtualenv as since I changed the default anaconda3 file locations, python cannot be found.
The python executable located at .virtualenvs/env/bin/python cannot be found. Do I need to make further changes in order for python to work from virtualenv too?
I have the exact same problem and this works for me:
After you move anaconda from "Relocated Items" to ~/anaconda3, edit the first line of ~/anaconda3/bin/conda file from #!/anaconda3/bin/python to #!/Users/USERNAME/anaconda3/bin/python to reflect the change.
I would probably abstain from using the above solution. That ~/anaconda3/bin directory has lots of runnables (not just the conda one) that would need to be altered in this manual way. For example, unless you make the same change you cannot run jupyter notebook either, neither from base nor from other envs you might have.
My tip: Try getting a requirements file for your virtual envs, and do a fresh installation. You could use pipreqs to get the requirements used for individual projects: https://www.idiotinside.com/2015/05/10/python-auto-generate-requirements-txt/
No solution will be completely working without fixing the baked-in hard-coded prefix entries in files. There's a longer description and a recommended fix at https://www.anaconda.com/how-to-restore-anaconda-after-macos-catalina-update/
Technically this is reinstalling anaconda, however, I restored all my conda envs so, hopefully this is an acceptable solution!
Here is how I got it working on Catalina as of a few minutes ago (now using z-shell):
- Verified the existence of "Relocated Items" directory on my desktop and the "anaconda3" directory and its contents inside
- Navigated into the envs directory under "anaconda3" and left the finder window open (see screenshot)
THEN:
opened new Terminal (z-shell)
ran (this installed to /usr/local/anaconda3):
brew cask install anaconda
after installation was successful I opened my ~/.zshrc file (for my z-shell aliases) and added the following line:
export PATH="/usr/local/anaconda3/bin:$PATH"
saved my ~/.zshrc file, then reloaded with:
source ~/.zshrc
to verify conda command works now, I ran:
conda env list
for me, this showed a base env and that was it
then open Finder to the new envs location:
open /usr/local/anaconda3/envs/.
I dragged (moved) all my old envs into the new envs folder, and then ran:
conda env list
And all my old envs are back! :)
updated my PyCharm interpreter / env paths to reflect the new locations of these envs (had to restart PyCharm after, but now it works!)
DONE
Unsure whether this is considered a comment or at least a temporary answer, but I would refrain from attempting to fix any Catalina compatibility issues with Anaconda for now. See this GitHub issue.
I have the same problem, and this work for me :
My solution:
Copy your anaconda3 from Relocated Items folder
Paste in User/YourUserName
Open conda file in anaconda3/bin with the editor and edit the first line #!/anaconda3/bin/python to #!/Users/YourUserName/anaconda3/bin/python
Save it and run conda file
Open Terminal
Run this : export PATH=''/Users/YourUserName/anaconda3/bin:$PATH"
Run conda init zsh
I had incurred the same issue, and the following solution worked for me, and this is the easiest solution:
Instead of messing around copying the anaconda3 file from relocated items into User/USERNAME directory, better would be just to reinstall anaconda navigator's latest version from its official website : https://www.anaconda.com/distribution/#macos
While installation, it will ask you some permissions which are a result of new Apple Security Policies, just grant them, and it works just the way it should after this fresh installation!
This is what worked for me.
These are my header files (Catalina 10.15):
/Library/Developer/CommandLineTools/usr/include/c++/v1/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Kernel.framework/Versions/A/Headers/sys/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Kernel.framework/Versions/A/Headers/sys/stdio.h
Run sudo find /Library -name stdio.h to see where yours are located.
Mojave 10.14 header files:
$ sudo find /Library -name stdio.h
/Library/Developer/CommandLineTools/usr/include/c++/v1/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/Kernel.framework/Versions/A/Headers/sys/stdio.h
As can be seen the SDKs are now split into MACOSX10.14 and 10.15 unlike in Mojave.
TLDR
So, these were my SDK folders on Catalina:
Rename MacOSX.sdk to MacOSX_orig.sdk
Right click on MacOSX10.14.sdk
Duplicate
Rename duplicate folder to MacOSX.sdk
Your folder structure should now look like this:
Like this we are basically using the previous version's OSX sdk as sysroot. Hope this helps.
I'm pretty new to programming, so maybe there's something painfully obvious that I've missed, but I've searched a lot around for solutions to this issue without finding any.
I just got a new computer and installed Anaconda and PyCharm for Anaconda. I got it to work fine on my old computer, but when I try to open PyCharm now and create a project, it gets stuck on the creation of the conda environment. Apparently there's a new conda update, so I tried to update to this one in Spyder, which seemed to work fine, but when PyCharm tries creating a new environment, it gets stuck and only displays
"Creating Conda environment"
"$ conda update -n base -c defaults conda"
Does anybody know what's happening? I've tried just waiting it out, but it doesn't seem to be moving forward at all from that point. I've also uninstalled both Anaconda and PyCharm with all their plugins and reinstalling them, but to no avail.
Thanks for any help or input!
Sincerely, confused first year student
It appears that Sophie was able to get the conda environment up and running.
However, other newcomers might come across a similar problem with regards to setting up Anaconda for use within PyCharm. Therefore, I provide a guide below that I recently (today) used in order to accomplish this on a fresh install on a new computer. For this I decided to use PyCharm Community Edition 2018.3 and Anaconda3 version 2019.07. I performed this on Windows 10 Enterprise version 1903. I have also performed this procedure on Windows 7 Home Premium edition (some time ago).
This will enable you to use PyCharm and Anaconda together, so that you can:
Know the prerequisite steps leading up to creating a conda environment, and become familiar with the steps following this action with using Anaconda with PyCharm.
Use the Terminal window in PyCharm with packages that are installed with Anaconda's version of Python. You can then use both regular python and conda commands to view, update or install packages. For instance, depending on your preference, you could use 'pip list' (python command) or 'conda list' to list installed packages.
Use the Anaconda python interpreter as the default Python Console in PyCharm
To accomplish this, please follow these steps:
Install PyCharm, and import any settings file you may have from previous PyCharm installation on other computer (optional). Assuming you are starting fresh, create a new project and set the (default) project folder location.
Install Anaconda. My install location was set to C:\ProgramData\Anaconda3. Note that 'ProgramData' folder is hidden by default. You should enable viewing of hidden folders in windows explorer, if you need to manually browse for it. Upon installation, I decided to have the options Add Anaconda to my PATH environment variable and Register Anaconda as my default Python 3.7 set as deselected.
Open Windows Explorer and paste in C:\ProgramData\Anaconda3 (or your install directory) in the address bar. This should take you to that directory. Navigate to the environments folder named envs. Select the address bar and copy that address. I got C:\ProgramData\Anaconda3\envs. You will need this later.
Open program named Anaconda Navigator (Anaconda3). You should see this from the list of newly installed programs. Alternatively, search for it and open it. This will initialize some stuff (unknown to me) that I have found necessary to be able to complete this guide. For the next steps we dont need this program running. You could close it if you want.
Decide on a name for the (ana)conda environment that we will create. I used py37 for simplicity. You only need to do this once for the python projects you will make. It is possible to make more environments if you should need that for some python projects in the future.
Open program named Anaconda Prompt (Anaconda3), preferentially as administrator. Opening as administrator may prevent complications that could occur on some systems. To do so, search for the program and then right-click it, and choose Run as administrator.
Enter this command: conda create -n py37 python=3.7 anaconda. It should prompt you to install some packages. Enter y to accept and proceed with the setup. This step may take some time to finish. Once finished, it may show you the needed command to activate the environment. Don't activate it just yet, ie. ignore that message for now.
Assuming environment path C:\ProgramData\Anaconda3\envs and environment name py37, run the following command (alter as needed to match your environment path and name): set PATH=C:\ProgramData\Anaconda\envs\py37\Scripts;C:\ProgramData\Anaconda\envs\py37;%PATH%
Run this command: conda activate py37. This will activate your environment.
Navigate to a folder you can easily access, such as the Documents folder on your machine. To do so, execute this command: cd "C:\Users\YourUsername\Documents".
Execute the following command: echo %PATH% > path_value.txt. This will export "PATH" values to a text file that can be found in the Documents folder as path_value.txt. Open this file and copy the content within. This will be needed in the following steps with setting up PyCharm for use with the Anaconda environment.
In PyCharm, navigate to Settings - Tools - Terminal. Check that Start directory field contains the path of your project folder, ie. such as C:/Users/YourUsername/Documents/YourProjectFolderName. Then, select the folder icon for the Environment variables field. Click the plus symbol, and add a new entry with PATH and your path value (as found from the path_value.txt file) in the Name and Value fields, respectively.
In PyCharm, navigate to Settings - Project Interpreter - Add Python Interpreter - Conda Environment - Existing environment. Browse for C:\ProgramData\Anaconda3 (or your install directory). Select the file named python.exe. I chose to edit the Name field of this Anaconda python interpreter as Python 3.7 Anaconda.
In PyCharm, navigate to Settings - Build, Execution, Deployment - Console - Python Console. Check that the Python interpreter field contains Project Default (Python 3.7 Anaconda) or similar entry. The Environment variables input may be empty. Select the folder button next to it and add a new entry with PATH and your path value (as found from the path_value.txt file) in the Name and Value fields, respectively. Exactly the same entries as was inputted in step 12.
[Optional] In PyCharm, navigate to Settings and search for the Run context configuration option. Right click it and select a desired shortcut method. Personally I use a keyboard shortcut which is set to Ctrl+Shift+Less. Once the rest of these steps are followed, this will allow you to run the current python .py file you have open, without having to manually set up configuration options for it (through Add Configuration option, next to green play button, as seen if you have no configurations set up from before). It will force PyCharm to use the default project interpreter (which now is the desired Anaconda-delivered Python 3.7 installation) for whatever project you have open. To use it, just open a .py python file with some code inside, click anywhere inside of it, and then use your shortcut option.
[Note: If you skipped step 15, go to step 17] Run your python file with the method from step 15. This should automatically set up a run configuration option for that file. You may get an error of missing packages. Ignore that for now.
Select Edit Configuration or Add Configuration in the dropdown box next to the green play / run button. Open the Templates tree, then select Python. Check that the Python interpreter option contains Python 3.7 Anaconda or similar. The Environment variables field may contain PYTHONUNBUFFERED=1. Regardless, select the related folder button and add a new entry with PATH and your path value (as found from the path_value.txt file) in the Name and Value fields, respectively. Exactly the same as we did in steps 12 and 14.
Restart PyCharm to re-initialize the Terminal and Python Console windows. Or manually close and reopen those windows.
You have now created and activated an (ana)conda environment, and enabled it's use from within PyCharm. You should also now be able to ie. copy your code over to a fresh new file, and then hit ie. Ctrl+Shift+Less to run the file without having to manually set a configuration file for it.
Hope this helped!
Sources: source1, source2, source3
In my Experience I just opened PyCharm as administrator and the error was gone!
If you use PyCharm to create conda environment, you can choose conda environment not virtualenv.
When you get the error like "can't get the /path/to/", you can open PyCharm with administrator.
If you use "anaconda prompt" to create conda environment, you can use command line like conda create -n py36 python=3.6. Then you can activate environment using conda activate py36.
conda env create -f python3.6-environment.yml
This is the code I used to try to create an environment on conda, using a .yml file.
Fetching package metadata ...............
Solving package specifications: .
After running the first code, I get stuck at this.
However, I noticed that I can copy the contents in the .yml file & create a .py file with it.
conda env create -f python3.6-environment.py
Can I then run this code instead & have all the same files installed as with the .yml?
The contents of the .yml file are from github:
https://github.com/enigmampc/catalyst/blob/master/etc/python3.6-environment.yml
I think conceptually this works but for the sake of factoring I would suggest you write the activation as a bash script that also instantiates your python code. Just a thought.
I successfully created two separate Python environments in Anaconda, yet seem to be unable to activate either one of them. I have tried to read up on this topic as much as possible here on Stackoverflow, yet no solution did resolve my issue. I added information asked for by comments in this question (Anaconda Environment Doesnt activate).
When trying to activate an environment, the console output is -bash: activate: No such file or directory.
The output of which conda is /Users/username/anaconda3/bin/conda.
The output of type source is source is a shell builtin.
When trying which activate, the shell returns nothing.
In my bin folder, I also seem not to have an activate executable, but only one which is called activate-global-python-argcomplete.
Why do I lack the standard activate file and how I could resolve this issue best?
I experience a similar problem. In my case, the problem is related to the use of the tcsh, but activate only supports bash and zsh.
You can check your current used shell with the command
echo $0.
You have to use a compatible shell in order to use the source activate command.
I think you happened to install a buggy version of anaconda which was quickly patched.
conda update conda
should get you back up and running.
Start a new terminal and try again. Alternatively, type hash -r and see if it helps.
Do not do this!!!, this broke my dnf
First I tried to point source to a activate file,
source /usr/lib64/python3.6/venv/scripts/common/activate environment
That appeared to work, but no actual values got updated. I tried the answer by mattexx, but it complained conda wasn't installed, so I used.
conda install conda
I had to have root permission since it was being installed to the root environment, but after that everything appears to work.
That is what broke my fedora installation
tcsh was the problem for me. Changed to bash and all is ok.
In this case, the problem might be that the virtual environment was created in /Users/username/anaconda3/envs/ and hence the activate will be in:
/Users/username/anaconda3/envs/NAME_OF_YOUR_VIRTUAL_ENV/bin/activate
Hence to activate the environment you could run:
source /Users/username/anaconda3/envs/NAME_OF_YOUR_VIRTUAL_ENV/bin/activate
My problem was that file /opt/pycharm/plugins/terminal/.zshrc (using ZSH) contained line source $JEDITERM_SOURCE. That variable contained correct paths as two parameters <path-to-anaconda-activate>/activate <path-to-anaconda>, but apparently they got interpreted as a single parameter: <path-to-anaconda-activate>/activate <path-to-anaconda>.
I solved that prepending eval to that line, making it eval source $JEDITERM_SOURCE. Now, the variable expands correctly.
If you're using bash then make the same change to /opt/pycharm/plugins/terminal/jediterm-bash.in.
I'm using the bash shell inside pycharm and fixed the problem by making this change:
[~/opt/pycharm-community/plugins/terminal]$ diff jediterm-bash.in.old jediterm-bash.in
65c65
< source "$JEDITERM_SOURCE"
---
> eval source "$JEDITERM_SOURCE"
Essentially making the same change recommended above by https://stackoverflow.com/users/1564931/netchkin, but to ~/opt/pycharm-community/plugins/terminal/jediterm-bash.in.
This fixed my existing projects. But any new projects don't seem to try and activate the conda environment at all. It seems as if new projects created in Pycharm 2017.1.2 don't set the JEDITERM_SOURCE variable when starting a session in the terminal plugin.
There is an open issue on this at https://youtrack.jetbrains.com/issue/PY-23417
Looks like there was a big change to the conda activate script in version 4.4.0. See https://conda.io/docs/release-notes.html. If I downgrade conda to 4.3.34 then I can get conda virtual environments to work in the pycharm terminal again.